1
|
Zhao D, Xiao S, Zhang A, Zhao L, Dai X, Yuan R, Wang J, Wang Y, Li Q, Zhou Z. Construction of high-density genetic map based on SLAF-seq and QTL analysis of major traits in sweetpotato [Ipomoea batatas (L.) Lam.]. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108647. [PMID: 38703497 DOI: 10.1016/j.plaphy.2024.108647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
Sweetpotato, Ipomoea batatas (L.) Lam., is an important worldwide crop used as feed, food, and fuel. However, its polyploidy, high heterozygosity and self-incompatibility makes it difficult to study its genetics and genomics. Longest vine length (LVL), yield per plant (YPP), dry matter content (DMC), starch content (SC), soluble sugar content (SSC), and carotenoid content (CC) are some of the major agronomic traits being used to evaluate sweetpotato. However limited research has actually examined how these traits are inherited. Therefore, after selecting 212 F1 from a Xin24 × Yushu10 crossing as the mapping population, this study applied specific-locus amplified fragment sequencing (SLAF-seq), at an average sequencing depth of 26.73 × (parents) and 52.25 × (progeny), to detect single nucleotide polymorphisms (SNPs). This approach generated an integrated genetic map of length 2441.56 cM and a mean distance of 0.51 cM between adjacent markers, encompassing 15 linkage groups (LGs). Based on the linkage map, 26 quantitative trait loci (QTLs), comprising six QTLs for LVL, six QTLs for YPP, ten QTLs for DMC, one QTL for SC, one QTL for SSC, and two QTLs for CC, were identified. Each of these QTLs explained 6.3-10% of the phenotypic variation. It is expected that the findings will be of benefit for marker-assisted breeding and gene cloning of sweetpotato.
Collapse
Affiliation(s)
- Donglan Zhao
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, China
| | - Shizhuo Xiao
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, China
| | - An Zhang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, China
| | - Lingxiao Zhao
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, China
| | - Xibin Dai
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, China
| | - Rui Yuan
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, China
| | - Jie Wang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, China
| | - Yao Wang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, China
| | - Qinglian Li
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, China
| | - Zhilin Zhou
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, China.
| |
Collapse
|
2
|
Hu Z, Fan Z, Li S, Wang M, Huang M, Ma X, Liu W, Wang Y, Yu Y, Li Y, Sun Y, Li X, Li J, Yin H. Genomics insights into flowering and floral pattern formation: regional duplication and seasonal pattern of gene expression in Camellia. BMC Biol 2024; 22:50. [PMID: 38414012 PMCID: PMC10900828 DOI: 10.1186/s12915-024-01851-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/20/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND The formation and domestication of ornamental traits are influenced by various aspects, such as the recognition of esthetic values and cultural traditions. Camellia japonica is widely appreciated and domesticated around the world mainly due to its rich variations in ornamental traits. Ornamental camellias have a diverse range of resources, including different bud variations from Camellia spp. as well as inter- and intra- specific hybridization. Despite research on the formation of ornamental traits, a basic understanding of their genetics and genomics is still lacking. RESULTS Here, we report the chromosomal-level reference genome of C. japonica through combining multiple DNA-sequencing technologies and obtain a high-density genetic linkage map of 4255 markers by sequencing 98 interspecific F1 hybrids between C. japonica and C. chekiangoleosa. We identify two whole-genome duplication events in C. japonica: one is a shared ancient γ event, and the other is revealed to be specific to genus Camellia. Based on the micro-collinearity analysis, we find large-scale segmental duplication of chromosome 8, resulting to two copies of the AGAMOUS loci, which may play a key role in the domestication of floral shapes. To explore the regulatory mechanisms of seasonal flowering, we have analyzed year-round gene expression patterns of C. japonica and C. azalea-a sister plant of continuous flowering that has been widely used for cross breeding. Through comparative analyses of gene co-expression networks and annual gene expression patterns, we show that annual expression rhythms of some important regulators of seasonal growth and development, including GIGANTEA and CONSTANS of the photoperiod pathway, have been disrupted in C. azalea. Furthermore, we reveal that the distinctive expression patterns of FLOWERING LOCUS T can be correlated with the seasonal activities of flowering and flushing. We demonstrate that the regulatory module involved in GIGANTEA, CONSTANS, and FLOWERING LOCUS T is central to achieve seasonality. CONCLUSIONS Through the genomic and comparative genomics characterizations of ornamental Camellia spp., we propose that duplication of chromosomal segments as well as the establishment of gene expression patterns has played a key role in the formation of ornamental traits (e.g., flower shape, flowering time). This work provides a valuable genomic platform for understanding the molecular basis of ornamental traits.
Collapse
Affiliation(s)
- Zhikang Hu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Zhengqi Fan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Sijia Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Minyan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Mingchuan Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xianjin Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Weixin Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Yupeng Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
| | - Yifan Yu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Yaxuan Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Yingkun Sun
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xinlei Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Jiyuan Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China.
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China.
| |
Collapse
|
3
|
Wen T, Zhang X, Zhu J, Zhang S, Rhaman MS, Zeng W. A SLAF-based high-density genetic map construction and genetic architecture of thermotolerant traits in maize ( Zea mays L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1338086. [PMID: 38384753 PMCID: PMC10880447 DOI: 10.3389/fpls.2024.1338086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
The leaf scorching trait at flowering is a crucial thermosensitive phenotype in maize under high temperature stress (HS), yet the genetic basis of this trait remains poorly understood. In this study, we genotyped a 254 RIL-F2:8 population, derived from the leaf scorch-free parental inbred line Abe2 and the leaf scorching maternal inbred line B73, using the specific-locus amplified fragment sequencing (SLAF-seq) method. A total of 10,112 polymorphic SLAF markers were developed, and a high-density genetic map with a total length of 1,475.88 cM was constructed. The average sequencing depth of the parents was 55.23X, and that of the progeny was 12.53X. Then, we identified a total of 16 QTLs associated with thermotolerant traits at flowering, of which four QTLs of leaf scorching damage (LS) were distributed on chromosomes 1 (qLS1), 2 (qLS2.1, qLS2.2) and 3 (qLS3), which could explain 19.73% of phenotypic variation. Combining one qLS1 locus with QTL-seq results led to the identification of 6 candidate genes. Expression experiments and sequence variation indicated that Zm00001d033328, encoding N-acetyl-gamma-glutamyl-phosphate reductase, was the most likely candidate gene controlling thermotolerant traits at flowering. In summary, the high-density genetic map and genetic basis of thermotolerant traits lay a critical foundation for mapping other complex traits and identifying the genes associated with thermotolerant traits in maize.
Collapse
Affiliation(s)
- Tingting Wen
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
- Seed Administration Station of Shandong Province, Jinan, China
| | - Xuefei Zhang
- Taian Daiyue District Bureau of Agriculture and Rural Affairs, Taian, China
| | - Jiaojiao Zhu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Susu Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Mohammad Saidur Rhaman
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Wei Zeng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| |
Collapse
|
4
|
Partap M, Verma V, Thakur M, Bhargava B. Designing of future ornamental crops: a biotechnological driven perspective. HORTICULTURE RESEARCH 2023; 10:uhad192. [PMID: 38023473 PMCID: PMC10681008 DOI: 10.1093/hr/uhad192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/14/2023] [Indexed: 12/01/2023]
Abstract
With a basis in human appreciation of beauty and aesthetic values, the new era of ornamental crops is based on implementing innovative technologies and transforming symbols into tangible assets. Recent advances in plant biotechnology have attracted considerable scientific and industrial interest, particularly in terms of modifying desired plant traits and developing future ornamental crops. By utilizing omics approaches, genomic data, genetic engineering, and gene editing tools, scientists have successively explored the underlying molecular mechanism and potential gene(s) behind trait regulation such as floral induction, plant architecture, stress resistance, plasticity, adaptation, and phytoremediation in ornamental crop species. These signs of progress lay a theoretical and practical foundation for designing and enhancing the efficiency of ornamental plants for a wide range of applications. In this review, we briefly summarized the existing literature and advances in biotechnological approaches for the improvement of vital traits in ornamental plants. The future ornamental plants, such as light-emitting plants, biotic/abiotic stress detectors, and pollution abatement, and the introduction of new ornamental varieties via domestication of wild species are also discussed.
Collapse
Affiliation(s)
- Mahinder Partap
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR), Institute of Himalayan Bioresource Technology (IHBT), Post Box No. 6, 176 061 (HP) Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Vipasha Verma
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR), Institute of Himalayan Bioresource Technology (IHBT), Post Box No. 6, 176 061 (HP) Palampur, India
| | - Meenakshi Thakur
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR), Institute of Himalayan Bioresource Technology (IHBT), Post Box No. 6, 176 061 (HP) Palampur, India
| | - Bhavya Bhargava
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR), Institute of Himalayan Bioresource Technology (IHBT), Post Box No. 6, 176 061 (HP) Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| |
Collapse
|
5
|
Che Y, Yang Y, Yang Y, Wei L, Guo J, Yang X, Li X, Liu W, Li L. Construction of a high-density genetic map and mapping of a spike length locus for rye. PLoS One 2023; 18:e0293604. [PMID: 37903124 PMCID: PMC10615298 DOI: 10.1371/journal.pone.0293604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
Genetic maps provide the foundation for QTL mapping of important traits of crops. As a valuable food and forage crop, rye (Secale cereale L., RR) is also one of the tertiary gene sources of wheat, especially wild rye, Secale cereale subsp. segetale, possessing remarkable stress tolerance, tillering capacity and numerous valuable traits. In this study, based on the technique of specific-locus amplified fragment sequencing (SLAF-seq), a high-density single nucleotide polymorphism (SNP) linkage map of the cross-pollinated (CP) hybrid population crossed by S. cereale L (female parent) and S. cereale subsp. segetale (male parent) was successfully constructed. Following preprocessing, the number of 1035.11 M reads were collected and 2425800 SNP were obtained, of which 409134 SNP were polymorphic. According to the screening process, 9811 SNP markers suitable for constructing linkage groups (LGs) were selected. Subsequently, all of the markers with MLOD values lower than 3 were filtered out. Finally, an integrated map was constructed with 4443 markers, including 1931 female mapping markers and 3006 male mapping markers. A major quantitative trait locus (QTL) linked with spike length (SL) was discovered at 73.882 cM on LG4, which explained 25.29% of phenotypic variation. Meanwhile two candidate genes for SL, ScWN4R01G329300 and ScWN4R01G329600, were detected. This research presents the first high-quality genetic map of rye, providing a substantial number of SNP marker loci that can be applied to marker-assisted breeding. Additionally, the finding could help to use SLAF marker mapping to identify certain QTL contributing to important agronomic traits. The QTL and the candidate genes identified through the high-density genetic map above may provide diverse potential gene resources for the genetic improvement of rye.
Collapse
Affiliation(s)
- Yonghe Che
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Yunjie Yang
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Yanping Yang
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Lai Wei
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Juan Guo
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Xinming Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuquan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
6
|
Feng Y, Yang C, Zhang J, Qiao J, Wang B, Zhao Y. Construction of a High-Density Paulownia Genetic Map and QTL Mapping of Important Phenotypic Traits Based on Genome Assembly and Whole-Genome Resequencing. Int J Mol Sci 2023; 24:15647. [PMID: 37958630 PMCID: PMC10647314 DOI: 10.3390/ijms242115647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Quantitative trait locus (QTL) mapping based on a genetic map is a very effective method of marker-assisted selection in breeding, and whole-genome resequencing is one of the useful methods to obtain high-density genetic maps. In this study, the hybrid assembly of Illumina, PacBio, and chromatin interaction mapping data was used to construct high-quality chromosomal genome sequences of Paulownia fortunei, with a size of 476.82 Mb, a heterozygosity of 0.52%, and a contig and scaffold N50s of 7.81 Mb and 21.81 Mb, respectively. Twenty scaffolds with a total length of 437.72 Mb were assembled into 20 pseudochromosomes. Repeat sequences with a total length of 243.96 Mb accounted for 51.16% of the entire genome. In all, 26,903 protein-coding gene loci were identified, and 26,008 (96.67%) genes had conserved functional motifs. Further comparative genomics analysis preliminarily showed that the split of P. fortunei with Tectona grandis likely occurred 38.8 (33.3-45.1) million years ago. Whole-genome resequencing was used to construct a merged genetic map of 20 linkage groups, with 2993 bin markers (3,312,780 SNPs), a total length of 1675.14 cm, and an average marker interval of 0.56 cm. In total, 73 QTLs for important phenotypic traits were identified (19 major QTLs with phenotypic variation explained ≥ 10%), including 10 for the diameter at breast height, 7 for the main trunk height, and 56 for branch-related traits. These results not only enrich P. fortunei genomic data but also form a solid foundation for fine QTL mapping and key marker/gene mining of Paulownia, which is of great significance for the directed genetic improvement of these species.
Collapse
Affiliation(s)
- Yanzhi Feng
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Chaowei Yang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Jiajia Zhang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Jie Qiao
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Baoping Wang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Yang Zhao
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| |
Collapse
|
7
|
Zhan Y, Hu W, He H, Dang X, Chen S, Bie Z. A major QTL identification and candidate gene analysis of watermelon fruit cracking using QTL-seq and RNA-seq. FRONTIERS IN PLANT SCIENCE 2023; 14:1166008. [PMID: 37255568 PMCID: PMC10225605 DOI: 10.3389/fpls.2023.1166008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/11/2023] [Indexed: 06/01/2023]
Abstract
Fruit cracking decreases the total production and the commercial value of watermelon. The molecular mechanisms of fruit cracking are unknown. In this study, 164 recombinant inbred lines (RILs) of watermelon, derived from the crossing of the WQ1 (cracking-sensitive) and WQ2 (cracking-tolerant) lines, were sequenced using specific length amplified fragment sequencing (SLAF-seq). A high-density genetic linkage map was constructed with 3,335 markers spanning 1,322.74 cM, at an average 0.40 cM across whole-genome flanking markers. The cracking tolerance capacity (CTC), depth of fruit cracking (DFC), rind thickness (RT), and rind hardness (RH) were measured for quantitative trait locus (QTL) analysis. Of the four traits analyzed, one major QTL with high phenotypic variation (41.04%-61.37%) was detected at 76.613-76.919 cM on chromosome 2, which contained 104 annotated genes. Differential gene expression analysis with RNA sequencing (RNA-seq) data between the two parents identified 4,508 differentially expressed genes (DEGs). Comparison of the genes between the QTL region and the DEGs obtained eight coexisting genes. Quantitative real-time PCR (qRT-PCR) analysis revealed that these genes were significant differentially expressed between the two parents. These results provide new insights into the identification of QTLs or genes and marker-assisted breeding in watermelon.
Collapse
Affiliation(s)
- Yuanfeng Zhan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wei Hu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Huang He
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xuanmin Dang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Songbi Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zhilong Bie
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
8
|
Peng T, Guo C, Yang J, Wan X, Wang W, Zhang J, Bao M, Zhang J. Transcriptome analysis revealed molecular basis of cold response in Prunus mume. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:34. [PMID: 37312744 PMCID: PMC10248647 DOI: 10.1007/s11032-023-01376-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/29/2023] [Indexed: 06/15/2023]
Abstract
Japanese apricot (Prunus mume Sieb. et Zucc.) is a traditional woody flower and fruit tree restrictedly cultivated in northern area due to its inability to survive harsh winters and early springs. In the current study, RNA-seq and physiological assay were used to study the cold response of P. mume 'Xuemei'. A total of 4705 genes were identified as differentially expressed genes (DEGs) in the 21 pairwise comparisons among seven time points under 0 °C cold treatment, and 3678 of them showed differential levels compared with control at normal temperature. The gene expression profiles indicated that the number of upregulated genes increased with prolongation of treatment time throughout the whole 48 h. Hierarchical clustering suggested three obvious phases of the gene expression profiles. Gene ontology (GO) analysis of the 4705 DEGs resulted in 102 significantly enriched GO items in which the transcription activity was dominant. 225 DEGs were predicted to encode transcription factor (TF) genes. Some important TFs (ERF, CBF, WRKY, NAC, MYB, bHLH) were strongly induced during the whole cold treatment. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that plant signal transduction pathways such as plant hormone and calcium (Ca2+) were notable. Metabolic pathways such as sugar metabolism, especially RFOs (raffinose family oligosaccharides) were activated, which was accompanied by the accumulation of soluble sugars. SOD and POD enzyme activities coupled with reactive oxygen species (ROS)-related gene expression profile implied a gradually induced ROS scavenging system under cold treatment. These results might shed light on the sensitivity to cold stress in Japanese apricot and provide new insights into hardiness studies in P. mume and its related species. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01376-2.
Collapse
Affiliation(s)
- Ting Peng
- College of Agriculture, Guizhou University, Guiyang, 550000 People’s Republic of China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Cong Guo
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430070 People’s Republic of China
| | - Jie Yang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- School of Nuclear Technology and Chemistry and Biology, Hubei University of Science and Technology, Xianning, 437100 People’s Republic of China
| | - Xueli Wan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- College of Landscape and Forestry, Qingdao Agricultural University, Qingdao, 266109 People’s Republic of China
| | - Wenwu Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Junwei Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| |
Collapse
|
9
|
Abstract
Specific length amplified fragment sequencing (SLAF-seq) technology is a simplified genome sequencing technology based on next-generation sequencing. SLAF-seq technology has several distinguishing characteristics: 1. Deep sequencing to ensure accuracy of genotyping; 2. Effectively reduce sequencing costs; 3. Pre-designed simplified representation scheme to optimize marker efficiency; 4. Doubled barcode system for large populations. The advantages and technical process of SLAF-seq are described briefly with summarized results for the application of SLAF-seq in development of molecular markers, construction of high-density genetic map and gene mapping in ornamental plants. Finally, the difficulties and prospects of this method are discussed in application.
Collapse
Affiliation(s)
- Yang Zhou
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China.
| |
Collapse
|
10
|
Hongyan Z, Xianming L, Fuchen Y, Junfan T, Li Y, Tao W, Zhongqi Q, Dazhao Y. SNP-based high-density linkage map construction and QTL mapping of black spot disease resistance in Chinese sand pear. J Appl Genet 2023; 64:23-36. [PMID: 36261770 DOI: 10.1007/s13353-022-00726-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 01/22/2023]
Abstract
Black spot disease (PBS) caused by Alternaria alternata is an economic disease of pear (Pyrus pyrifolia Nakai). Developing cultivars with durable PBS resistance traits is an important research objective for improving pear germplasm. The Deshengxiang is a popular pear variety in China and resistant to PBS. This study aimed to detect quantitative trait loci (QTL) associated with PBS resistance trait in pear and determine closely linked molecular markers by specific locus amplified fragment sequencing (SLAF-seq). F1 population resulting from a cross between "Deshengxiang" (female) and "Guiguan," a susceptible (male) variety, was developed and evaluated in 2016 and 2017. SLAF technology was used to discover SNPs in the F1 individuals and subsequently a high-density genetic linkage map for PBS resistance was constructed which contained 17,604 SNP markers. Based on the linkage map, the markers were distributed into 17 linkage groups, spanning 1548.48 cM, with a mean marker distance of 0.09 cM, representing the densest genetic map of the genus Pyrus. QTL analysis of PBS resistance identified a locus strongly related to PBS resistance at 77.68 ~ 112.99 cM on linkage group 15, which was further narrowed down to 93.79 ~ 112.99 cM. Two markers, Marker94293 and Marker94206, located at 97.47 and 102.93 cM, were closely associated with PBS resistance, with a Δ (SNP index) value of 0.46. Co-localization of QTL interval, bioinformatics analysis, and functional annotation revealed PBS putative candidate genes. Overall, the high-density pear linkage map is a suitable reference for mapping PBS resistance trait, QTL, and genes identified in this study contribute information that could be useful for PBS improvement in pear.
Collapse
Affiliation(s)
- Zhu Hongyan
- Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, 430064, People's Republic of China.,College of Life Science, Wuhan University, Wuhan, Hubei, 430072, People's Republic of China.,Ministry of Agriculture Key Laboratory of Integrated Pest Management On Crop in Central China, Wuhan, 430064, People's Republic of China
| | - Li Xianming
- Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, 430064, People's Republic of China
| | - Yang Fuchen
- Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, 430064, People's Republic of China
| | - Tu Junfan
- Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, 430064, People's Republic of China
| | - Yang Li
- Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, 430064, People's Republic of China
| | - Wu Tao
- Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, 430064, People's Republic of China
| | - Qin Zhongqi
- Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, 430064, People's Republic of China.
| | - Yu Dazhao
- College of Life Science, Wuhan University, Wuhan, Hubei, 430072, People's Republic of China. .,Ministry of Agriculture Key Laboratory of Integrated Pest Management On Crop in Central China, Wuhan, 430064, People's Republic of China.
| |
Collapse
|
11
|
Li Y, Huo Y, Yang Y, Wang Z, Sun Y, Liu B, Wu X. Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion. FRONTIERS IN PLANT SCIENCE 2023; 14:1100691. [PMID: 36818885 PMCID: PMC9928573 DOI: 10.3389/fpls.2023.1100691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Onion (Allium cepa L., 2n=16) is an economically and nutritionally important vegetable crop worldwide. Construction of a high-resolution genetic map and map-based gene mining in onion have lagged behind other vegetable crops such as tomato and pepper. METHODS In this study, we constructed a high-resolution genetic map of onion using 321 F2 individuals from a cross between two double haploid lines DH-1×DH-17 and employing specific length amplified fragment (SLAF)-seq technology. The genetic map containing 10,584 polymorphic SLAFs with 21,250 single nucleotide polymorphism (SNP) markers and 8 linkage groups was developed for onion, which spanned 928.32 cM, with an average distance of 0.09 cM between adjacent markers. RESULTS Using this map, we carried out QTL mapping of Ms locus related to the male-fertile trait and reproduced previous mapping results, which proved that this map was of good quality. Then, four QTLs (located on LG2, LG5, and LG8) were detected for flower stalk height, explaining 26.60% of the phenotypic variance. Among them, we proposed that 20 SLAF markers (in three QTLs) of flower stalk height trait were effective favorable allelic variant markers associated with heterosis. DISCUSSION Overall, the genetic map was structured using SLAF-seq based on DH lines, and it is the highest-quality and highest-resolution linkage map of onion to date. It lays a foundation for the fine mapping and candidate gene identification of flower stalk height, and provides new insights into the developmental genetic mechanisms in onion breeding.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Xiong Wu
- *Correspondence: Bingjiang Liu, ; Xiong Wu,
| |
Collapse
|
12
|
Bhattarai K, Sharma S, Verma S, Peres NA, Xiao S, Clark DG, Deng Z. Construction of a genome-wide genetic linkage map and identification of quantitative trait loci for powdery mildew resistance in Gerbera daisy. FRONTIERS IN PLANT SCIENCE 2023; 13:1072717. [PMID: 36684731 PMCID: PMC9853552 DOI: 10.3389/fpls.2022.1072717] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Powdery mildew (PM) is a common fungal disease in many important crops. The PM caused by Podosphaera xanthii has been the most challenging problem in commercial Gerbera (Gerbera hybrida) production globally, often leading to severe losses of crop yield and quality. A small number of PM-resistant breeding lines and cultivars have been reported in Gerbera, but the underlying genetics for PM resistance in Gerbera is largely unknown. Scarcity of genomic resources such as genetic linkage maps and molecular markers has severely hindered the effort to understand the genetic basis and locate loci controlling PM resistance in Gerbera. This study aimed to construct a genome-wide genetic linkage map, identify quantitative trait loci (QTL), and molecular markers for PM resistance in Gerbera. A segregating mapping population was developed by crossing PM-resistant and -susceptible Gerbera breeding lines, genotyped by sequencing, and phenotyped for PM resistance. A genome-wide genetic linkage map constructed with 791 single polymorphic site (SNP) markers spans 1912.30 cM across 27 linkage groups (LG) and reaches a density of 1 marker per 2.42 cM. One major consistent QTL was discovered in LG16, explaining more than 16.6% of the phenotypic variance for PM resistance. The QTL was tagged with two flanking SNP markers. The availability of this genetic linkage map will be very useful for locating and tagging QTLs for other important traits in Gerbera, and the newly discovered QTL and SNP markers will enable development of molecular markers for improving Gerbera for resistance to PM.
Collapse
Affiliation(s)
- Krishna Bhattarai
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences (IFAS), Wimauma, FL, United States
| | - Sadikshya Sharma
- Department of Horticultural Science, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Sujeet Verma
- Department of Horticultural Science, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Natalia A. Peres
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma, FL, United States
| | - Shunyuan Xiao
- University of Maryland, Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD, United States
| | - David G. Clark
- Department of Environmental Horticulture, University of Florida, IFAS, Gainesville, FL, United States
| | - Zhanao Deng
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences (IFAS), Wimauma, FL, United States
| |
Collapse
|
13
|
Liu X, Wang Y, Zhu H, Mei G, Liao Y, Rao S, Li S, Chen A, Liu H, Zeng L, Xiao Y, Li X, Yang Z, Hou X. Natural allelic variation confers high resistance to sweet potato weevils in sweet potato. NATURE PLANTS 2022; 8:1233-1244. [PMID: 36376755 DOI: 10.1038/s41477-022-01272-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/10/2022] [Indexed: 06/16/2023]
Abstract
Sweet potato (Ipomoea batatas L.) is a major root crop worldwide. Sweet potato weevils (SPWs) pose one of the most significant challenges to sweet potato production in tropical and subtropical regions, causing deleterious economic and environmental effects. Characterizing the mechanisms underlying natural resistance to SPWs is therefore crucial; however, the genetic basis of host SPW resistance (SPWR) remains unclear. Here we obtained two sweet potato germplasm with high SPWR and, by map-based cloning, revealed two major SPW-resistant genes-SPWR1 and SPWR2-that are important regulators of natural defence against SPWs. The SPW-induced WRKY transcriptional factor SPWR1 directly activates the expression of SPWR2, and SPWR2, the conserved dehydroquinate synthase, promotes the accumulation of quinate derivative metabolites that confer SPWR in sweet potato. Generally, our results provide new insights into the molecular mechanism underlying sweet potato-SPW interactions and will aid future efforts to achieve eco-friendly SPW management.
Collapse
Affiliation(s)
- Xu Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yaru Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongbo Zhu
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Guoguo Mei
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yinyin Liao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
| | - Shunfa Rao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
| | - Shuquan Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ao Chen
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongjie Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lanting Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yangyang Xiao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziyin Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xingliang Hou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
14
|
Dong B, Zheng Z, Zhong S, Ye Y, Wang Y, Yang L, Xiao Z, Fang Q, Zhao H. Integrated Transcriptome and Metabolome Analysis of Color Change and Low-Temperature Response during Flowering of Prunus mume. Int J Mol Sci 2022; 23:12831. [PMID: 36361622 PMCID: PMC9658476 DOI: 10.3390/ijms232112831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 10/07/2023] Open
Abstract
In China, Prunus mume is a famous flowering tree that has been cultivated for 3000 years. P. mume grows in tropical and subtropical regions, and most varieties lack cold resistance; thus, it is necessary to study the low-temperature response mechanism of P. mume to expand the scope of its cultivation. We used the integrated transcriptomic and metabolomic analysis of a cold-resistant variety of P. mume 'Meiren', to identify key genes and metabolites associated with low temperatures during flowering. The 'Meiren' cultivar responded in a timely manner to temperature by way of a low-temperature signal transduction pathway. After experiencing low temperatures, the petals fade and wilt, resulting in low ornamental value. At the same time, in the cold response pathway, the activities of related transcription factors up- or downregulate genes and metabolites related to low temperature-induced proteins, osmotic regulators, protective enzyme systems, and biosynthesis and metabolism of sugars and acids. Our findings promote research on the adaptation of P. mume to low temperatures during wintering and early flowering for domestication and breeding.
Collapse
Affiliation(s)
- Bin Dong
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Hangzhou 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou 311300, China
| | - Zifei Zheng
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Shiwei Zhong
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Hangzhou 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou 311300, China
| | - Yong Ye
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Yiguang Wang
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Hangzhou 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou 311300, China
| | - Liyuan Yang
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Hangzhou 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou 311300, China
| | - Zheng Xiao
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Hangzhou 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou 311300, China
| | - Qiu Fang
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Hangzhou 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou 311300, China
| | - Hongbo Zhao
- School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Hangzhou 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou 311300, China
| |
Collapse
|
15
|
Rong H, Huang B, Han X, Wu K, Xu M, Zhang W, Yang F, Xu LA. Pedigree reconstruction and genetic analysis of major ornamental characters of ornamental crabapple (Malus spp.) based on paternity analysis. Sci Rep 2022; 12:14093. [PMID: 35982151 PMCID: PMC9388634 DOI: 10.1038/s41598-022-18352-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 08/10/2022] [Indexed: 11/09/2022] Open
Abstract
Ornamental crabapple is an important woody ornamental plant in the Northern Hemisphere. Its flowers, fruits, leaves and tree habit are all important ornamental characters. As there has been no research on the selection of superior parents and phenotypic variation, new varieties of ornamental crabapple are mainly selected from open-pollination progeny. In order to explore the transmission rule of ornamental traits between parents and offspring of crabapple, and to provide a basis for the selection of hybrid parents for directional breeding, 14 pairs of SSR markers were used in this study for paternity analysis of 384 offspring from 4 female parents crossed with 91 candidate male parents. And 273 offspring (71.1%) were matched with only the father at a 95% strict confidence level. We reconstructed 7 full-sib families (number of progeny ≥ 10) on the basis of the paternity analysis results. Genetic analysis of characters in the full-sib families revealed that green leaves and white flowers were dominant traits. All the hybrid offspring from the white flower (♀) × non-white flower (♂) cross produced white flowers, while 7.04% produced non-white flowers when both parents had white flowers. The results showed that white flowers might be a dominant qualitative trait in crabapple, while the depth of red was a quantitative trait. The genetic characteristics of green and non-green leaves and the depth of red of the peel were similar to flower color. Compared with the upright and spreading traits, the weeping trait was recessive. Some progeny showed an earlier blooming period, indicating the possibility of breeding for blooming period. Our findings are important for parent screening and improving the breeding efficiency of new varieties in ornamental crabapple hybridization.
Collapse
Affiliation(s)
- Hao Rong
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Bin Huang
- Jiangxi Provincial Key Laboratory of Camellia Germplasm Conservation and Utilization, Jiangxi Academy of Forestry, Nanchang, China
| | - Xin Han
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Kai Wu
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Meng Xu
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wangxiang Zhang
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Feng Yang
- Qingdao Municipal Supervision Consulting CO., LTD, Qingdao, China
| | - Li-An Xu
- College of Forestry, Nanjing Forestry University, Nanjing, China. .,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
| |
Collapse
|
16
|
Chen T, Hu L, Wang S, Wang L, Cheng X, Chen H. Construction of High-Density Genetic Map and Identification of a Bruchid Resistance Locus in Mung Bean (Vigna radiata L.). Front Genet 2022; 13:903267. [PMID: 35873485 PMCID: PMC9305327 DOI: 10.3389/fgene.2022.903267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Mung bean (Vigna radiata L.) is an economically important grain legume cultivated in Asian countries. High-density genetic linkage is a valuable and effective tool for mapping quantitative trait loci (QTL). In the current study, a high-resolution genetic map containing 4,180 single-nucleotide polymorphisms (SNPs) was assigned to 11 linkage groups (LGs) and spanning 1,751.39 cM in length was constructed for mung bean, and the average distance between adjacent markers was 0.42 cM. Bruchids (Callosobruchus spp.) cause significant damage to and loss of legume seeds. A locus for bruchid resistance was detected. The gene Vradi05g03810, encoding a probable resistance-specific protein, was found to be the most likely key candidate gene in mung beans. A 69-bp sequence deletion was identified in the coding region by comparing the cDNA sequences of bruchid-resistant and bruchid-susceptible lines. This SNP-based high-density linkage map is one of the first to be constructed across the mung bean genome. This map will not only facilitate the genetic mapping of genes or complex loci that control important agronomic traits but also offer a tool for promoting future genetics and comparative genomic studies in Vigna.
Collapse
|
17
|
Boopathi NM, Tiwari GJ, Jena SN, Nandhini K, Sri Subalakhshmi VKI, Shyamala P, Joshi B, Premalatha N, Rajeswari S. Identification of Stable and Multiple Environment Interaction QTLs and Candidate Genes for Fiber Productive Traits Under Irrigated and Water Stress Conditions Using Intraspecific RILs of Gossypium hirsutum var. MCU5 X TCH1218. FRONTIERS IN PLANT SCIENCE 2022; 13:851504. [PMID: 35519814 PMCID: PMC9062235 DOI: 10.3389/fpls.2022.851504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Cotton productivity under water-stressed conditions is controlled by multiple quantitative trait loci (QTL). Enhancement of these productivity traits under water deficit stress is crucial for the genetic improvement of upland cotton, Gossypium hirsutum. In the present study, we constructed a genetic map with 504 single nucleotide polymorphisms (SNPs) covering a total span length of 4,416 cM with an average inter-marker distance of 8.76 cM. A total of 181 intra-specific recombinant inbred lines (RILs) were derived from a cross between G. hirsutum var. MCU5 and TCH1218 were used. Although 2,457 polymorphic SNPs were detected between the parents using the CottonSNP50K assay, only 504 SNPs were found to be useful for the construction of the genetic map. In the SNP genotyping, a large number of SNPs showed either >20% missing data, duplication, or segregation distortion. However, the mapped SNPs of this study showed collinearity with the physical map of the reference genome (G. hirsutum var.TM-1), indicating that there was no chromosomal rearrangement within the studied mapping population. RILs were evaluated under multi-environments and seasons for which the phenotypic data were acquired. A total of 53 QTL controlling plant height (PH), number of sympodial branches, boll number (BN), and boll weight (BW) were dissected by QTL analysis under irrigated and water stress conditions. Additionally, it was found that nine QTL hot spots not only co-localized for more than one investigated trait but were also stable with major QTL, i.e., with > 10% of phenotypic variation. One QTL hotspot on chromosome 22 flanked by AX-182254626-AX-182264770 with a span length of 89.4 cM co-localized with seven major and stable QTL linked to a number of sympodial branches both under irrigated and water stress conditions. In addition, putative candidate genes associated with water stress in the QTL hotspots were identified. Besides, few QTL from the hotspots were previously reported across various genetic architects in cotton validating the potential applications of these identified QTL for cotton breeding and improvement. Thus, the major and stable QTL identified in the present study would improve the cotton productivity under water-limited environments through marker-assisted selection.
Collapse
Affiliation(s)
| | - Gopal Ji Tiwari
- Plant Molecular Genetics Laboratory, CSIR-National Botanical Research Institute, Lucknow, India
| | - Satya Narayan Jena
- Plant Molecular Genetics Laboratory, CSIR-National Botanical Research Institute, Lucknow, India
| | - Kemparaj Nandhini
- Department of Cotton, CPBG, Tamil Nadu Agricultural University, Coimbatore, India
| | | | - Pilla Shyamala
- Department of Plant Biotechnology, CPMB&B, Tamil Nadu Agricultural University, Coimbatore, India
| | - Babita Joshi
- Plant Molecular Genetics Laboratory, CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | - S. Rajeswari
- Department of Cotton, CPBG, Tamil Nadu Agricultural University, Coimbatore, India
| |
Collapse
|
18
|
Wang J, Li Y, Xu F, Xu H, Han Z, Liu L, Song Y. Candidate powdery mildew resistance gene in wheat landrace cultivar Hongyoumai discovered using SLAF and BSR-seq. BMC PLANT BIOLOGY 2022; 22:83. [PMID: 35196978 PMCID: PMC8864798 DOI: 10.1186/s12870-022-03448-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is an important disease affecting wheat production. Planting resistant cultivars is an effective, safe, and economical method to control the disease. Map construction using next-generation sequencing facilitates gene cloning based on genetic maps and high-throughput gene expression studies. In this study, specific-locus amplified fragment sequencing (SLAF) was used to analyze Huixianhong (female parent), Hongyoumai (male parent) and two bulks (50 homozygous resistant and 50 susceptible F2:3 segregating population derived from Huixianhong × Hongyoumai to determine a candidate gene region for resistance to powdery mildew on the long arm of chromosome 7B in wheat landrace Hongyoumai. Gene expressions of candidate regions were obtained using bulked segregant RNA-seq in 10 homozygous resistant and 10 susceptible progeny inoculated by Bgt.. Candidate genes were obtained using homology-based cloning in two parents. RESULTS A 12.95 Mb long candidate region in chromosome 7BL was identified, and five blocks in SLAF matched the scaffold of the existing co-segregation marker Xmp1207. In the candidate region, 39 differentially expressed genes were identified using RNA-seq, including RGA4 (Wheat_Chr_Trans_newGene_16173)-a disease resistance protein whose expression was upregulated in the resistant pool at 16 h post inoculation with Bgt. Quantitative reverse transcription (qRT)-PCR was used to further verify the expression patterns in Wheat_Chr_Trans_newGene_16173 that were significantly different in the two parents Hongyoumai and Huixianhong. Two RGA4 genes were cloned based on the sequence of Wheat_Chr_Trans_newGene_16173, respectively from two parent and there was one amino acid mutation: S to G in Huixianhong on 510 loci. CONCLUSION The combination of SLAF and BSR-seq methods identified a candidate region of pmHYM in the chromosome 7BL of wheat landrace cultivar Hongyoumai. Comparative analysis between the scaffold of co-segregating marker Xmp1207 and SLAF-seq showed five matching blocks. qRT-PCR showed that only the resistant gene Wheat_Chr_Trans_newGene_16173 was significantly upregulated in the resistant parent Hongyoumai after inoculation with Bgt, and gene cloning revealed a difference in one amino acid between the two parent genes, indicating it was involved in the resistance response and may be the candidate resistance gene pmHYM.
Collapse
Affiliation(s)
- Junmei Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences; Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People's Republic of China, Zhengzhou, 450002, China
| | - Yahong Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences; Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People's Republic of China, Zhengzhou, 450002, China
| | - Fei Xu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences; Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People's Republic of China, Zhengzhou, 450002, China
| | - Hongxing Xu
- School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Zihang Han
- Institute of Plant Protection, Henan Academy of Agricultural Sciences; Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People's Republic of China, Zhengzhou, 450002, China
| | - Lulu Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences; Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People's Republic of China, Zhengzhou, 450002, China
| | - Yuli Song
- Institute of Plant Protection, Henan Academy of Agricultural Sciences; Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People's Republic of China, Zhengzhou, 450002, China.
| |
Collapse
|
19
|
Gong H, Rehman F, Ma Y, A B, Zeng S, Yang T, Huang J, Li Z, Wu D, Wang Y. Germplasm Resources and Strategy for Genetic Breeding of Lycium Species: A Review. FRONTIERS IN PLANT SCIENCE 2022; 13:802936. [PMID: 35222468 PMCID: PMC8874141 DOI: 10.3389/fpls.2022.802936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/07/2022] [Indexed: 06/01/2023]
Abstract
Lycium species (goji), belonging to Solanaceae, are widely spread in the arid to semiarid environments of Eurasia, Africa, North and South America, among which most species have affinal drug and diet functions, resulting in their potential to be a superior healthy food. However, compared with other crop species, scientific research on breeding Lycium species lags behind. This review systematically introduces the present germplasm resources, cytological examination and molecular-assisted breeding progress in Lycium species. Introduction of the distribution of Lycium species around the world could facilitate germplasm collection for breeding. Karyotypes of different species could provide a feasibility analysis of fertility between species. The introduction of mapping technology has discussed strategies for quantitative trait locus (QTL) mapping in Lycium species according to different kinds of traits. Moreover, to extend the number of traits and standardize the protocols of trait detection, we also provide 1,145 potential traits (275 agronomic and 870 metabolic) in different organs based on different reference studies on Lycium, tomato and other Solanaceae species. Finally, perspectives on goji breeding research are discussed and concluded. This review will provide breeders with new insights into breeding Lycium species.
Collapse
Affiliation(s)
- Haiguang Gong
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Fazal Rehman
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yun Ma
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Biao A
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shaohua Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Tianshun Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jianguo Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zhong Li
- Agricultural Comprehensive Development Center in Ningxia Hui Autonomous Region, Yinchuan, China
| | | | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, Gannan Normal University, Ganzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
20
|
Li M, Sang M, Wen Z, Meng J, Cheng T, Zhang Q, Sun L. Mapping Floral Genetic Architecture in Prunus mume, an Ornamental Woody Plant. FRONTIERS IN PLANT SCIENCE 2022; 13:828579. [PMID: 35211141 PMCID: PMC8860970 DOI: 10.3389/fpls.2022.828579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Floral traits are both evolutionarily and economically relevant for ornamental plants. However, their underlying genetic architecture, especially in woody ornamental plants, is still poorly understood. We perform mapping experiments aimed at identifying specific quantitative trait loci (QTLs) that control the size, shape, architecture, color, and timing of flowers in mei (Prunus mume). We find that the narrow region of chromosome 1 (5-15 Mb) contains a number of floral QTLs. Most QTLs detected from this mapping study are annotated to candidate genes that regulate various biological functions toward the floral formation. We identify strong pleiotropic control on different aspects of flower morphology (including shape, petal number, pistil number, petal color, and calyx color) and flower timing, but find different genetic systems that mediate whether a flower produces pistils and how many pistils a flower produces. We find that many floral QTLs display pleiotropic effects on shoot length growth but shoot radial growth, implicating a possible association of floral display with light capture. We conduct a transcriptomic study to characterize the genomic signature of floral QTLs expressed in mei. Our mapping results about the genetic control of floral features make it promising to select superior varieties for mei carrying flowers of ornamental value.
Collapse
Affiliation(s)
- Mingyu Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Mengmeng Sang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- School Medicine, Institute of Reproductive Medicine, Nantong University, Nantong, China
| | - Zhenying Wen
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Juan Meng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| |
Collapse
|
21
|
Wang D, Yang L, Shi C, Li S, Tang H, He C, Cai N, Duan A, Gong H. QTL mapping for growth-related traits by constructing the first genetic linkage map in Simao pine. BMC PLANT BIOLOGY 2022; 22:48. [PMID: 35065611 PMCID: PMC8783431 DOI: 10.1186/s12870-022-03425-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 01/04/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND Simao pine is one of the primary economic tree species for resin and timber production in southwest China. The exploitation and utilization of Simao pine are constrained by the relatively lacking of genetic information. Construction a fine genetic linkage map and detecting quantitative trait locis (QTLs) for growth-related traits is a prerequisite section of Simao Pine's molecular breeding program. RESULTS In our study, a high-resolution Simao pine genetic map employed specific locus amplified fragment sequencing (SLAF-seq) technology and based on an F1 pseudo-testcross population has been constructed. There were 11,544 SNPs assigned to 12 linkage groups (LGs), and the total length of the map was 2,062.85 cM with a mean distance of 0.37 cM between markers. According to the phenotypic variation analysis for three consecutive years, a total of seventeen QTLs for four traits were detected. Among 17 QTLs, there were six for plant height (Dh.16.1, Dh16.2, Dh17.1, Dh18.1-3), five for basal diameter (Dbd.17.1-5), four for needle length (Dnl17.1-3, Dnl18.1) and two for needle diameter (Dnd17.1 and Dnd18.1) respectively. These QTLs individually explained phenotypic variance from 11.0-16.3%, and the logarithm of odds (LOD) value ranged from 2.52 to 3.87. CONCLUSIONS In our study, a fine genetic map of Simao pine applied the technology of SLAF-seq has been constructed for the first time. Based on the map, a total of 17 QTLs for four growth-related traits were identified. It provides helpful information for genomic studies and marker-assisted selection (MAS) in Simao pine.
Collapse
Affiliation(s)
- Dawei Wang
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Lin Yang
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Chen Shi
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Siguang Li
- Yunnan Academy of Forestry, Kunming, China
| | - Hongyan Tang
- Puer City Institute of Forestry Sciences, Puer, China
| | - Chengzhong He
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Nianhui Cai
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Anan Duan
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Hede Gong
- School of Geography, Southwest Forestry University, Kunming, China.
| |
Collapse
|
22
|
Yan H, Ma M, Ahmad MQ, Arisha MH, Tang W, Li C, Zhang Y, Kou M, Wang X, Gao R, Song W, Li Z, Li Q. High-Density Single Nucleotide Polymorphisms Genetic Map Construction and Quantitative Trait Locus Mapping of Color-Related Traits of Purple Sweet Potato [ Ipomoea batatas (L.) Lam.]. FRONTIERS IN PLANT SCIENCE 2022; 12:797041. [PMID: 35069654 PMCID: PMC8770336 DOI: 10.3389/fpls.2021.797041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Flesh color (FC), skin color (SC), and anthocyanin content (AC) are three important traits being used for commodity evaluation in purple-fleshed sweet potato. However, to date, only a few reports are available on the inheritance of these traits. In this study, we used a biparental mapping population of 274 F1 progeny generated from a cross between a dark purple-fleshed (Xuzishu8) and white-fleshed (Meiguohong) sweet potato variety for genetic analyses. Correlation analysis showed a significant positive correlation among AC, SC, and FC. Medium-to-high heritability was observed for these traits. We detected single nucleotide polymorphisms (SNPs) by specific length amplified fragment sequencing (SLAF-seq) with the average sequencing depth of 51.72 and 25.76 for parents and progeny, respectively. Then we constructed an integrated genetic map consisting of 15 linkage groups (LGS) of sweet potato spanning on 2,233.66 cm with an average map distance of 0.71 cm between adjacent markers. Based on the linkage map, ten major quantitative trait loci (QTLs) associated to FC, SC, and AC were identified on LG12 between 0 and 64.97 cm distance, such as one QTL for SC and FC, respectively, which explained 36.3 and 45.9% of phenotypic variation; eight QTLs for AC, which explained 10.5-28.5% of the variation. These major QTLs were highly consistent and co-localized on LG12. Positive correlation, high heritability, and co-localization of QTLs on the same LG group confirm the significance of this study to establish a marker-assisted breeding program for sweet potato improvement.
Collapse
Affiliation(s)
- Hui Yan
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Meng Ma
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Muhammad Qadir Ahmad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Mohamed Hamed Arisha
- Department of Horticulture, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Wei Tang
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Chen Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yungang Zhang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Meng Kou
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Xin Wang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Runfei Gao
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Weihan Song
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Zongyun Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Qiang Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| |
Collapse
|
23
|
Sun C, Liu Y, Li Q, Wang B, Chen S, Deng J, Ma D, Yang Y. Rapid Identification of a Stripe Rust Resistance Gene YrXK in Chinese Wheat Line Xike01015 Using Specific Locus Amplified Fragment (SLAF) Sequencing. PLANT DISEASE 2022; 106:282-288. [PMID: 34253044 DOI: 10.1094/pdis-12-20-2648-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Wheat stripe rust, an airborne fungal disease caused by Puccinia striiformis Westend. f. sp. tritici, is one of the most devastating diseases of wheat. Chinese wheat cultivar Xike01015 displays high levels of all-stage resistance (ASR) to the current predominant P. striiformis f. sp. tritici race CYR33. In this study, a single dominant gene, designated YrXk, was identified in Xike01015 conferring resistance to CYR33 with genetic analysis of F2 and BC1 populations from a cross of Mingxian169 (susceptible) and Xike01015. The specific length amplified fragment sequencing (SLAF-seq) strategy was used to construct a linkage map in the F2 population. Quantitative trait loci (QTL) analysis mapped YrXk to a 12.4-Mb segment on chromosome1 BS, explaining >86.96% of the phenotypic variance. Gene annotation in the QTL region identified three differential expressed candidate genes, TraesCS1B02G168600.1, TraesCS1B02G170200.1, and TraesCS1B02G172400.1. The qRT-PCR results showed that TraesCS1B02G172400.1 and TraesCS1B02G168600.1 are upregulated and that TraesCS1B02G170200.1 is slightly downregulated after inoculation with CYR33 in the seedling stage, which indicates that these genes may function in wheat resistance to stripe rust. The results of this study can be used in wheat breeding for improving resistance to stripe rust.
Collapse
Affiliation(s)
- Cai Sun
- Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, P.R. China
- College of Plant Protection, Southwest University, Beibei 400700, P.R. China
| | - Yike Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430064, Hubei, P.R. China
| | - Qiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling 712100, Shaanxi, P.R. China
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling 712100, Shaanxi, P.R. China
| | - Shuhui Chen
- Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, P.R. China
| | - Jianxin Deng
- Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, P.R. China
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430064, Hubei, P.R. China
| | - Dongfang Ma
- Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, P.R. China
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430064, Hubei, P.R. China
| | - Yuheng Yang
- College of Plant Protection, Southwest University, Beibei 400700, P.R. China
| |
Collapse
|
24
|
Jiang X, Gong J, Zhang J, Zhang Z, Shi Y, Li J, Liu A, Gong W, Ge Q, Deng X, Fan S, Chen H, Kuang Z, Pan J, Che J, Zhang S, Jia T, Wei R, Chen Q, Wei S, Shang H, Yuan Y. Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum. FRONTIERS IN PLANT SCIENCE 2021; 12:753755. [PMID: 34975939 PMCID: PMC8716697 DOI: 10.3389/fpls.2021.753755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
Upland cotton (Gossypium hirsutum) is widely planted around the world for its natural fiber, and producing high-quality fiber is essential for the textile industry. CCRI70 is a hybrid cotton plant harboring superior yield and fiber quality, whose recombinant inbred line (RIL) population was developed from two upland cotton varieties (sGK156 and 901-001) and were used here to investigate the source of high-quality related alleles. Based on the material of the whole population, a high-density genetic map was constructed using specific locus-amplified fragment sequencing (SLAF-seq). It contained 24,425 single nucleotide polymorphism (SNP) markers, spanning a distance of 4,850.47 centimorgans (cM) over 26 chromosomes with an average marker interval of 0.20 cM. In evaluating three fiber quality traits in nine environments to detect multiple environments stable quantitative trait loci (QTLs), we found 289 QTLs, of which 36 of them were stable QTLs and 18 were novel. Based on the transcriptome analysis for two parents and two RILs, 24,941 unique differentially expressed genes (DEGs) were identified, 473 of which were promising genes. For the fiber strength (FS) QTLs, 320 DEGs were identified, suggesting that pectin synthesis, phenylpropanoid biosynthesis, and plant hormone signaling pathways could influence FS, and several transcription factors may regulate fiber development, such as GAE6, C4H, OMT1, AFR18, EIN3, bZIP44, and GAI. Notably, the marker D13_56413025 in qFS-chr18-4 provides a potential basis for enhancing fiber quality of upland cotton via marker-assisted breeding and gene cloning of important fiber quality traits.
Collapse
Affiliation(s)
- Xiao Jiang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Ürümqi, China
| | - Jianhong Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Haodong Chen
- Cotton Sciences Research Institute of Hunan, National Hybrid Cotton Research Promotion Center, Changde, China
| | - Zhengcheng Kuang
- Cotton Sciences Research Institute of Hunan, National Hybrid Cotton Research Promotion Center, Changde, China
| | - Jingtao Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jincan Che
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Shuya Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Tingting Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Renhui Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Quanjia Chen
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Ürümqi, China
| | - Shoujun Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Ürümqi, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
25
|
Cai H, Wang Q, Gao J, Li C, Du X, Ding B, Yang T. Construction of a high-density genetic linkage map and QTL analysis of morphological traits in an F1 Malusdomestica × Malus baccata hybrid. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1997-2007. [PMID: 34629774 PMCID: PMC8484404 DOI: 10.1007/s12298-021-01069-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/02/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Apple is considered the most commonly grown fruit crop in temperate regions that brings great economic profits to fruit growers. Dwarfing rootstocks have been extensively used in apple breeding as well as commercial orchards, but the molecular and genetic basis of scion dwarfing and other morphological traits induced by them is still unclear. At present, we report a genetic map of Malusdomestica × Malus baccata with high density. The F1 population was sequenced by a specific length amplified fragment (SLAF). In the genetic map, 5064 SLAF markers spanning 17 linkage groups (LG) were included. Dwarf-related and other phenotypic traits of the scion were evaluated over a 3-year growth period. Based on quantitative trait loci (QTL) evaluation of plant height and trunk diameter, two QTL clusters were found on LG 11, which exhibited remarkable influences on dwarfing of the scion. In this analysis, QTL DW2, which was previously reported as a locus that controls dwarfing, was confirmed. Moreover, three novel QTLs for total flower number and branching flower number were detected on LG2 and LG4, exhibited the phenotypic variation that has been explained by QTL ranging from 8.80% to 34.80%. The findings of the present study are helpful to find scion dwarfing and other phenotypes induced by rootstock in the apple. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01069-0.
Collapse
Affiliation(s)
- Huacheng Cai
- Pomology Institute, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, 030031 Shanxi China
| | - Qian Wang
- Pomology Institute, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, 030031 Shanxi China
| | - Jingdong Gao
- Pomology Institute, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, 030031 Shanxi China
| | - Chunyan Li
- Pomology Institute, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, 030031 Shanxi China
| | - Xuemei Du
- Pomology Institute, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, 030031 Shanxi China
| | - Baopeng Ding
- Pomology Institute, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- College of Forestry, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Tingzhen Yang
- Pomology Institute, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, 030031 Shanxi China
| |
Collapse
|
26
|
Zhuo X, Zheng T, Li S, Zhang Z, Zhang M, Zhang Y, Ahmad S, Sun L, Wang J, Cheng T, Zhang Q. Identification of the PmWEEP locus controlling weeping traits in Prunus mume through an integrated genome-wide association study and quantitative trait locus mapping. HORTICULTURE RESEARCH 2021; 8:131. [PMID: 34059642 PMCID: PMC8167129 DOI: 10.1038/s41438-021-00573-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/20/2021] [Accepted: 04/07/2021] [Indexed: 05/20/2023]
Abstract
Weeping Prunus mume (mei) has long been cultivated in East Asia for its specific ornamental value. However, little is known about the regulatory mechanism of the weeping trait in mei, which limits molecular breeding for the improvement of weeping-type cultivars. Here, we quantified the weeping trait in mei using nested phenotyping of 214 accessions and 342 F1 hybrids. Two major associated loci were identified from the genome-wide association study (GWAS), which was conducted using 3,014,409 single nucleotide polymorphisms (SNPs) derived from resequencing, and 8 QTLs and 55 epistatic loci were identified from QTL mapping using 7,545 specific lengths amplified fragment (SLAF) markers. Notably, an overlapping PmWEEP major QTL was fine mapped within a 0.29 Mb region on chromosome 7 (Pa7), and a core SNP locus closely associated with the weeping trait was screened and validated. Furthermore, a total of 22 genes in the PmWEEP QTL region were expressed in weeping or upright mei based on RNA-seq analysis. Among them, only a novel gene (Pm024213) containing a thioredoxin (Trx) domain was found to be close to the core SNP and specifically expressed in buds and branches of weeping mei. Co-expression analysis of Pm024213 showed that most of the related genes were involved in auxin and lignin biosynthesis. These findings provide insights into the regulatory mechanism of the weeping trait and effective molecular markers for molecular-assisted breeding in Prunus mume.
Collapse
Affiliation(s)
- Xiaokang Zhuo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Tangchun Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China.
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China.
| | - Suzhen Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Zhiyong Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Man Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Yichi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Sagheer Ahmad
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Lidan Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China.
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China.
| |
Collapse
|
27
|
Xu YY, Liu SR, Gan ZM, Zeng RF, Zhang JZ, Hu CG. High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata. Int J Mol Sci 2021; 22:ijms22115723. [PMID: 34072027 PMCID: PMC8198561 DOI: 10.3390/ijms22115723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/06/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding.
Collapse
Affiliation(s)
| | | | | | | | - Jin-Zhi Zhang
- Correspondence: (J.-Z.Z.); (C.-G.H.); Tel.: +86-27-8728-2010 (J.-Z.Z. & C.-G.H.)
| | - Chun-Gen Hu
- Correspondence: (J.-Z.Z.); (C.-G.H.); Tel.: +86-27-8728-2010 (J.-Z.Z. & C.-G.H.)
| |
Collapse
|
28
|
Zheng T, Li P, Li L, Zhang Q. Research advances in and prospects of ornamental plant genomics. HORTICULTURE RESEARCH 2021; 8:65. [PMID: 33790259 PMCID: PMC8012582 DOI: 10.1038/s41438-021-00499-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 05/14/2023]
Abstract
The term 'ornamental plant' refers to all plants with ornamental value, which generally have beautiful flowers or special plant architectures. China is rich in ornamental plant resources and known as the "mother of gardens". Genomics is the science of studying genomes and is useful for carrying out research on genome evolution, genomic variations, gene regulation, and important biological mechanisms based on detailed genome sequence information. Due to the diversity of ornamental plants and high sequencing costs, the progress of genome research on ornamental plants has been slow for a long time. With the emergence of new sequencing technologies and a reduction in costs since the whole-genome sequencing of the first ornamental plant (Prunus mume) was completed in 2012, whole-genome sequencing of more than 69 ornamental plants has been completed in <10 years. In this review, whole-genome sequencing and resequencing of ornamental plants will be discussed. We provide analysis with regard to basic data from whole-genome studies of important ornamental plants, the regulation of important ornamental traits, and application prospects.
Collapse
Affiliation(s)
- Tangchun Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Ping Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Lulu Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
29
|
A Genetic Linkage Map of BC2 Population Reveals QTL Associated with Plant Architecture Traits in Lagerstroemia. FORESTS 2021. [DOI: 10.3390/f12030322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Plant architecture improvement is of great significance in influencing crop yield, harvesting efficiency and ornamental value, by changing the spatial structure of the canopy. However, the mechanism on plant architecture in woody plants is still unclear. In order to study the genetic control of plant architecture traits and promote marker-assisted selection (MAS), a genetic linkage map was constructed, and QTL mapping was performed. In this study, using 188 BC2 progenies as materials, a genetic map of Lagerstroemia was constructed using amplification fragment length polymorphisms (AFLP) and simple sequence repeats (SSR) markers, and the QTLs of four key plant architecture traits (plant height, crown width, primary lateral branch height and internode length) were analyzed. The genetic map contains 22 linkage groups, including 198 AFLP markers and 36 SSR markers. The total length of the genome covered by the map is 1272 cM, and the average distance between markers is 6.8 cM. Three QTLs related to plant height were located in LG1, LG4 and LG17 linkage groups, and the phenotypic variation rates were 32.36, 16.18 and 12.73%, respectively. A QTL related to crown width was located in LG1 linkage group, and the phenotypic variation rate was 18.07%. Two QTLs related to primary lateral branch height were located in the LG1 and LG7 linkage groups, and the phenotypic variation rates were 20.59 and 15.34%, respectively. Two QTLs related to internode length were located in the LG1 and LG20 linkage groups, and the phenotypic variation rates were 14.86 and 9.87%. The results provide a scientific basis for finely mapping genes of plant architecture traits and marker-assisted breeding in Lagerstroemia.
Collapse
|
30
|
Li L, Zhang Y, Zheng T, Zhuo X, Li P, Qiu L, Liu W, Wang J, Cheng T, Zhang Q. Comparative gene expression analysis reveals that multiple mechanisms regulate the weeping trait in Prunus mume. Sci Rep 2021; 11:2675. [PMID: 33514804 PMCID: PMC7846751 DOI: 10.1038/s41598-021-81892-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 01/13/2021] [Indexed: 11/23/2022] Open
Abstract
Prunus mume (also known as Mei) is an important ornamental plant that is popular with Asians. The weeping trait in P. mume has attracted the attention of researchers for its high ornamental value. However, the formation of the weeping trait of woody plants is a complex process and the molecular basis of weeping stem development is unclear. Here, the morphological and histochemical characteristics and transcriptome profiles of upright and weeping stems from P. mume were studied. Significant alterations in the histochemical characteristics of upright and weeping stems were observed, and the absence of phloem fibres and less xylem in weeping stems might be responsible for their inability to resist gravity and to grow downward. Transcriptome analysis showed that differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis and phytohormone signal transduction pathways. To investigate the differential responses to hormones, upright and weeping stems were treated with IAA (auxin) and GA3 (gibberellin A3), respectively, and the results revealed that weeping stems had a weaker IAA response ability and reduced upward bending angles than upright stems. On the contrary, weeping stems had increased upward bending angles than upright stems with GA3 treatment. Compared to upright stems, interestingly, DEGs associated with diterpenoid biosynthesis and phenylpropanoid biosynthesis were significantly enriched after being treated with IAA, and expression levels of genes associated with phenylpropanoid biosynthesis, ABC transporters, glycosylphosphatidylinositol (GPI)—anchor biosynthesis were altered after being treated with GA3 in weeping stems. Those results reveal that multiple molecular mechanisms regulate the formation of weeping trait in P. mume, which lays a theoretical foundation for the cultivation of new varieties.
Collapse
Affiliation(s)
- Lulu Li
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Yichi Zhang
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tangchun Zheng
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
| | - Xiaokang Zhuo
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Ping Li
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Like Qiu
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Weichao Liu
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Jia Wang
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tangren Cheng
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
31
|
Mao T, Zhu H, Liu Y, Bao M, Zhang J, Fu Q, Xiong C, Zhang J. Weeping candidate genes screened using comparative transcriptomic analysis of weeping and upright progeny in an F1 population of Prunus mume. PHYSIOLOGIA PLANTARUM 2020; 170:318-334. [PMID: 32754906 PMCID: PMC7693177 DOI: 10.1111/ppl.13179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/07/2020] [Accepted: 08/02/2020] [Indexed: 05/15/2023]
Abstract
Weeping is a specific plant architecture with high ornamental value. Despite the considerable importance of the weeping habit to landscaping applications and knowledge of plant architecture biology, little is known regarding the underlying molecular mechanisms. In this study, growth and phytohormone content were analyzed among the progeny of different branch types in an F1 mapping population of Prunus mume with varying plant architecture. Bulked segregant RNA sequencing was conducted to compare differences among progeny at a transcriptional level. The weeping habit appears to be a complex process regulated by a series of metabolic pathways, with photosynthesis and flavonoid biosynthesis highly enriched in differentially expressed genes between weeping and upright progeny. Based on functional annotation and homologous analyses, we identified 30 candidate genes related to weeping that merit further analysis, including 10 genes related to IAA and GA3 biosynthesis, together with 6 genes related to secondary branch growth. The results of this study will facilitate further studies of the molecular mechanisms underlying the weeping habit in P. mume.
Collapse
Affiliation(s)
- Tian‐Yu Mao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry ScienceHuazhong Agricultural UniversityWuhan430070China
| | - Huan‐Huan Zhu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry ScienceHuazhong Agricultural UniversityWuhan430070China
| | - Yao‐Yao Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry ScienceHuazhong Agricultural UniversityWuhan430070China
| | - Man‐Zhu Bao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry ScienceHuazhong Agricultural UniversityWuhan430070China
| | - Jun‐Wei Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry ScienceHuazhong Agricultural UniversityWuhan430070China
| | - Qiang Fu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry ScienceHuazhong Agricultural UniversityWuhan430070China
| | - Cai‐Feng Xiong
- Moshan Administrative OfficeWuhan East Lake Eco‐tourism Scenic SpotWuhanChina
| | - Jie Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry ScienceHuazhong Agricultural UniversityWuhan430070China
| |
Collapse
|
32
|
Rehman F, Gong H, Li Z, Zeng S, Yang T, Ai P, Pan L, Huang H, Wang Y. Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.). BMC PLANT BIOLOGY 2020; 20:474. [PMID: 33059596 PMCID: PMC7565837 DOI: 10.1186/s12870-020-02567-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/22/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Goji (Lycium spp., 2n = 24) is a fruit bearing woody plant popular as a superfood for extensive medicinal and nutritional advantages. Fruit size associated attributes are important for evaluating small-fruited goji berry and plant architecture. The domestication traits are regulated quantitatively in crop plants but few studies have attempted on genomic regions corresponding to fruit traits. RESULTS In this study, we established high-resolution map using specific locus amplified fragment (SLAF) sequencing for de novo SNPs detection based on 305 F1 individuals derived from L. chinense and L. barbarum and performed quantitative trait loci (QTL) analysis of fruit size related traits in goji berry. The genetic map contained 3495 SLAF markers on 12 LGs, spanning 1649.03 cM with 0.47 cM average interval. Female and male parents and F1 individuals` sequencing depth was 111.85-fold and 168.72-fold and 35.80-fold, respectively. The phenotype data were collected for 2 successive years (2018-2019); however, two-year mean data were combined in an extra year (1819). Total 117 QTLs were detected corresponding to multiple traits, of which 78 QTLs in 2 individual years and 36 QTLs in extra year. Six Promising QTLs (qFW10-6.1, qFL10-2.1, qLL10-2.1, qLD10-2.1, qLD12-4.1, qLA10-2.1) were discovered influencing fruit weight, fruit length and leaf related attributes covering an interval ranged from 27.32-71.59 cM on LG10 with peak LOD of 10.48 and 14.6% PVE. Three QTLs targeting fruit sweetness (qFS3-1, qFS5-2) and fruit firmness (qFF10-1) were also identified. Strikingly, various traits QTLs were overlapped on LG10, in particular, qFL10-2.1 was co-located with qLL10-2.1, qLD10-2.1 and qLA10-2.1 among stable QTLs, harbored tightly linked markers, while qLL10-1 was one major QTL with 14.21 highest LOD and 19.3% variance. As LG10 harbored important traits QTLs, we might speculate that it could be hotspot region regulating fruit size and plant architectures. CONCLUSIONS This report highlights the extremely saturated linkage map using SLAF-seq and novel loci contributing fruit size-related attributes in goji berry. Our results will shed light on domestication traits and further strengthen molecular and genetic underpinnings of goji berry; moreover, these findings would better facilitate to assemble the reference genome, determining potential candidate genes and marker-assisted breeding.
Collapse
Affiliation(s)
- Fazal Rehman
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiguang Gong
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhong Li
- Bairuiyuan Company, Yinchuan, 750000, Ningxia, China
| | - Shaohua Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
- GNNU-SCBG Joint Laboratory of Modern Agricultural Technology, College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Tianshun Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Peiyan Ai
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lizhu Pan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hongwen Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
- GNNU-SCBG Joint Laboratory of Modern Agricultural Technology, College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China.
| |
Collapse
|
33
|
Shi P, Xu Z, Zhang S, Wang X, Ma X, Zheng J, Xing L, Zhang D, Ma J, Han M, Zhao C. Construction of a high-density SNP-based genetic map and identification of fruit-related QTLs and candidate genes in peach [Prunus persica (L.) Batsch]. BMC PLANT BIOLOGY 2020; 20:438. [PMID: 32967617 PMCID: PMC7510285 DOI: 10.1186/s12870-020-02557-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/19/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND High-density genetic mapping is a valuable tool for mapping loci that control specific traits for perennial fruit trees. Peach is an economically important fruit tree and a model Rosaceae species for genomic and genetic research. In peach, even though many molecular markers, genetic maps and QTL mappings have been reported, further research on the improvement of marker numbers, map densities, QTL accuracy and candidate gene identification is still warranted. RESULTS A high-density single nucleotide polymorphism (SNP)-based peach linkage map was constructed using specific locus amplified fragment sequencing (SLAF-seq). This genetic map consisted of 7998 SLAF markers, spanning 1098.79 cM with an average distance of 0.17 cM between adjacent markers. A total of 40 QTLs and 885 annotated candidate genes were detected for 10 fruit-related traits, including fruit weight (FW), fruit diameter (FD), percentage of red skin colour (PSC), eating quality (EQ), fruit flavour (FV), red in flesh (RF), red around pit (RP), adherence to pit (AP), fruit development period (FDP) and fruit fibre content (FFC). Eighteen QTLs for soluble solid content (SSC) were identified along LGs 1, 4, 5, and 6 in 2015 and 2016, and 540 genes were annotated in QTL intervals. Thirty-two QTLs for fruit acidity content (FA) were detected on LG1, and 2, 4, 5, 6, and 1232 candidate genes were identified. The expression profiles of 2 candidate genes for SSC and 4 for FA were analysed in parents and their offspring. CONCLUSIONS We constructed a high-density genetic map in peach based on SLAF-seq, which may contribute to the identification of important agronomic trait loci. Ninety QTLs for 12 fruit-related traits were identified, most of which overlapped with previous reports, and some new QTLs were obtained. A large number of candidate genes for fruit-related traits were screened and identified. These results may improve our understanding of the genetic control of fruit quality traits and provide useful information in marker-assisted selection for fruit quality in peach breeding programmes.
Collapse
Affiliation(s)
- Pei Shi
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ze Xu
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Shaoyu Zhang
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xianju Wang
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xiaofei Ma
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jicheng Zheng
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Libo Xing
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Dong Zhang
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Juanjuan Ma
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Mingyu Han
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Caiping Zhao
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| |
Collapse
|
34
|
Li LF, Cushman SA, He YX, Li Y. Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping forsythia. HORTICULTURE RESEARCH 2020; 7:130. [PMID: 32821413 PMCID: PMC7395120 DOI: 10.1038/s41438-020-00352-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/24/2020] [Accepted: 05/24/2020] [Indexed: 05/06/2023]
Abstract
Understanding the genetic basis underlying the local adaptation of nonmodel species is a fundamental goal in evolutionary biology. In this study, we explored the genetic mechanisms of the local adaptation of Forsythia suspensa using genome sequence and population genomics data obtained from specific-locus amplified fragment sequencing. We assembled a high-quality reference genome of weeping forsythia (Scaffold N50 = 7.3 Mb) using ultralong Nanopore reads. Then, genome-wide comparative analysis was performed for 15 natural populations of weeping forsythia across its current distribution range. Our results revealed that candidate genes associated with local adaptation are functionally correlated with solar radiation, temperature and water variables across heterogeneous environmental scenarios. In particular, solar radiation during the period of fruit development and seed drying after ripening, cold, and drought significantly contributed to the adaptive differentiation of F. suspensa. Natural selection exerted by environmental factors contributed substantially to the population genetic structure of F. suspensa. Our results supported the hypothesis that adaptive differentiation should be highly pronounced in the genes involved in signal crosstalk between different environmental variables. Our population genomics study of F. suspensa provides insights into the fundamental genetic mechanisms of the local adaptation of plant species to climatic gradients.
Collapse
Affiliation(s)
- Lin-Feng Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Samuel A. Cushman
- U.S. Forest Service, Rocky Mountain Research Station, 2500 S. Pine Knoll Dr., Flagstaff, Arizona USA
| | - Yan-Xia He
- School of Life Sciences, Henan University, Kaifeng, China
| | - Yong Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
| |
Collapse
|
35
|
Lou L, Su X, Liu X, Liu Z. Construction of a high-density genetic linkage map and identification of gene controlling resistance to cucumber mosaic virus in Luffa cylindrica (L.) Roem. based on specific length amplified fragment sequencing. Mol Biol Rep 2020; 47:5831-5841. [PMID: 32700128 DOI: 10.1007/s11033-020-05652-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/08/2020] [Indexed: 10/23/2022]
Abstract
Luffa cylindrica L. is a cash crop which has important health, medicinal and industrial value, but no high saturation genetic map has been constructed owing to a lack of efficient markers. Furthermore, no genes were reportedly responsible for CMV resistance in Luffa spp. Specific length amplified fragment sequencing (SLAF-seq) is a valuable tool for large-scale discovery of markers and genetic mapping. The present study reported the construction of a high-density genetic map and the mapping of CMV resistant genes by using an F2 population of 130 individuals and their two inbred line parents. A total of 271.01 Mb pair-end reads were generated. 100,077 high-quality SLAFs were detected, and 7404 of them were polymorphic. Finally, 3701 of the polymorphic markers were selected for genetic map construction, and 13 linkage groups were generated. The map spanned 1518.56 cM with an average distance of 0.41 cM between adjacent markers. Based on the newly constructed high-density map, one gene located on chromosome 1 (100.072-100.457 cM) was identified to regulate CMV resistance in L. cylindrica. A gag-polypeptide of LTR copia-type retrotransposon was predicted as the candidate gene responsible for CMV resistance in L. cylindrica. The high-density genetic map and the CMV resistant gene mapped and predicted in this study will be useful in future research.
Collapse
Affiliation(s)
- Lina Lou
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Zhongling Street 50, Nanjing, 210014, Jiangsu Province, China.
| | - Xiaojun Su
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Zhongling Street 50, Nanjing, 210014, Jiangsu Province, China
| | - Xiaohong Liu
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Zhongling Street 50, Nanjing, 210014, Jiangsu Province, China
| | - Zhe Liu
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Zhongling Street 50, Nanjing, 210014, Jiangsu Province, China
| |
Collapse
|
36
|
Song X, Xu Y, Gao K, Fan G, Zhang F, Deng C, Dai S, Huang H, Xin H, Li Y. High-density genetic map construction and identification of loci controlling flower-type traits in Chrysanthemum ( Chrysanthemum × morifolium Ramat.). HORTICULTURE RESEARCH 2020; 7:108. [PMID: 32637136 PMCID: PMC7326996 DOI: 10.1038/s41438-020-0333-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/16/2020] [Accepted: 05/01/2020] [Indexed: 05/31/2023]
Abstract
Flower type is an important and extremely complicated trait of chrysanthemum. The corolla tube merged degree (CTMD) and the relative number of ray florets (RNRF) are the two key factors affecting chrysanthemum flower type. However, few reports have clarified the inheritance of these two complex traits, which limits directed breeding for flower-type improvement. In this study, 305 F1 hybrids were obtained from two parents with obvious differences in CTMD and RNRF performance. Using specific-locus amplified fragment sequencing (SLAF-seq) technology, we constructed a high-density genetic linkage map with an average map distance of 0.76 cM. Three major QTLs controlling CTMD and four major QTLs underlying RNRF were repeatedly detected in the 2 years. Moreover, the synteny between the genetic map and other Compositae species was investigated, and weak collinearity was observed. In QTL regions with a high degree of genomic collinearity, eight annotated genes were probed in the Helianthus annuus L. and Lactuca sativa L. var. ramosa Hort. genomes. Furthermore, 20 and 11 unigenes were identified via BLAST searches between the SNP markers of the QTL regions and the C. vestitum and C. lavandulifolium transcriptomes, respectively. These results lay a foundation for molecular marker-assisted breeding and candidate gene exploration in chrysanthemum without a reference assembly.
Collapse
Affiliation(s)
- Xuebin Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083 China
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266109 Shandong China
| | - Yuhui Xu
- Biomarker Technologies Co., LTD, Beijing, 101300 China
- LC Science Co., LTD., Hangzhou, 310018 China
| | - Kang Gao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083 China
| | - Guangxun Fan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083 China
| | - Fan Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083 China
| | - Chengyan Deng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083 China
| | - Silan Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083 China
| | - He Huang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083 China
| | - Huaigen Xin
- Biomarker Technologies Co., LTD, Beijing, 101300 China
| | - Yingying Li
- Biomarker Technologies Co., LTD, Beijing, 101300 China
| |
Collapse
|
37
|
Khan SA, Chen H, Deng Y, Chen Y, Zhang C, Cai T, Ali N, Mamadou G, Xie D, Guo B, Varshney RK, Zhuang W. High-density SNP map facilitates fine mapping of QTLs and candidate genes discovery for Aspergillus flavus resistance in peanut (Arachis hypogaea). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2239-2257. [PMID: 32285164 DOI: 10.1007/s00122-020-03594-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
Two novel resistant QTLs mapped and candidate genes identified for Aspergillus flavus resistance in cultivated peanut using SLAF-seq. Aflatoxin contamination in peanuts caused by Aspergillus flavus is a serious food safety issue for human health around the world. Host plant resistance to fungal infection and reduction in aflatoxin are crucial for mitigating this problem. Identification of the resistance-linked markers can be used in marker-assisted breeding for varietal development. Here we report construction of two high-density genetic linkage maps with 1975 SNP loci and 5022 SNP loci, respectively. Two consistent quantitative trait loci (QTL) were identified as qRAF-3-1 and qRAF-14-1, which located on chromosomes A03 and B04, respectively. QTL qRAF-3-1 was mapped within 1.67 cM and had more than 19% phenotypic variance explained (PVE), while qRAF-14-1 was located within 1.34 cM with 5.15% PVE. While comparing with the reference genome, the mapped QTLs, qRAF-3-1 and qRAF-14-1, were located within a physical distance of 1.44 Megabase pair (Mbp) and 2.22 Mbp, harboring 67 and 137 genes, respectively. Among the identified candidate genes, six genes with the same function were found within both QTLs regions. In addition, putative disease resistance RPP13-like protein 1 (RPP13), lipoxygenase (Lox), WRKY transcription factor (WRKY) and cytochrome P450 71B34 genes were also identified. Using microarray analysis, genes responded to A. flavus infection included coding for RPP13, pentatricopeptide repeat-containing-like protein, and Lox which may be possible candidate genes for resistance to A. flavus. The QTLs and candidate genes will further facilitate marker development and validation of genes for deployment in the molecular breeding programs against A. flavus in peanuts.
Collapse
Affiliation(s)
- Shahid Ali Khan
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Hua Chen
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ye Deng
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yuhua Chen
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chong Zhang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Tiecheng Cai
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Niaz Ali
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Gandeka Mamadou
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Dongyang Xie
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, GA, 31793, USA
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, 502324, India
| | - Weijian Zhuang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| |
Collapse
|
38
|
Luo X, Li H, Wu Z, Yao W, Zhao P, Cao D, Yu H, Li K, Poudel K, Zhao D, Zhang F, Xia X, Chen L, Wang Q, Jing D, Cao S. The pomegranate (Punica granatum L.) draft genome dissects genetic divergence between soft- and hard-seeded cultivars. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:955-968. [PMID: 31549477 PMCID: PMC7061868 DOI: 10.1111/pbi.13260] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 09/03/2019] [Accepted: 09/09/2019] [Indexed: 05/18/2023]
Abstract
Complete and highly accurate reference genomes and gene annotations are indispensable for basic biological research and trait improvement of woody tree species. In this study, we integrated single-molecule sequencing and high-throughput chromosome conformation capture techniques to produce a high-quality and long-range contiguity chromosome-scale genome assembly of the soft-seeded pomegranate cultivar 'Tunisia'. The genome covers 320.31 Mb (scaffold N50 = 39.96 Mb; contig N50 = 4.49 Mb) and includes 33 594 protein-coding genes. We also resequenced 26 pomegranate varieties that varied regarding seed hardness. Comparative genomic analyses revealed many genetic differences between soft- and hard-seeded pomegranate varieties. A set of selective loci containing SUC8-like, SUC6, FoxO and MAPK were identified by the selective sweep analysis between hard- and soft-seeded populations. An exceptionally large selective region (26.2 Mb) was identified on chromosome 1. Our assembled pomegranate genome is more complete than other currently available genome assemblies. Our results indicate that genomic variations and selective genes may have contributed to the genetic divergence between soft- and hard-seeded pomegranate varieties.
Collapse
Affiliation(s)
- Xiang Luo
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Haoxian Li
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Zhikun Wu
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop ScienceCollege of Life SciencesHenan Agricultural UniversityZhengzhouChina
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Da Cao
- School of Biological SciencesUniversity of QueenslandBrisbaneQldAustralia
| | - Haiyan Yu
- Biomarker Technologies CorporationBeijingChina
| | - Kaidi Li
- Biomarker Technologies CorporationBeijingChina
| | - Krishna Poudel
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Diguang Zhao
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Fuhong Zhang
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Xiaocong Xia
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Lina Chen
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Qi Wang
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Dan Jing
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Shangyin Cao
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| |
Collapse
|
39
|
Wu X, Wang B, Xie F, Zhang L, Gong J, Zhu W, Li X, Feng F, Huang J. QTL mapping and transcriptome analysis identify candidate genes regulating pericarp thickness in sweet corn. BMC PLANT BIOLOGY 2020; 20:117. [PMID: 32171234 PMCID: PMC7071591 DOI: 10.1186/s12870-020-2295-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 02/19/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND In recent years, the planting area of sweet corn in China has expanded rapidly. Some new varieties with high yields and good adaptabilities have emerged. However, the improvement of edible quality traits, especially through the development of varieties with thin pericarp thickness, has not been achieved to date. Pericarp thickness is a complex trait that is the key factor determining the edible quality of sweet corn. Genetic mapping combined with transcriptome analysis was used to identify candidate genes controlling pericarp thickness. RESULTS To identify novel quantitative trait loci (QTLs) for pericarp thickness, a sweet corn BC4F3 population of 148 lines was developed using the two sweet corn lines M03 (recurrent parent) and M08 (donor parent). Additionally, a high-density genetic linkage map containing 3876 specific length amplified fragment (SLAF) tags was constructed and used for mapping QTLs for pericarp thickness. Interestingly, 14 QTLs for pericarp thickness were detected, and one stable QTL (qPT10-5) was detected across multiple years, which explained 7.78-35.38% of the phenotypic variation located on chromosome 10 (144,631,242-145,532,401). Forty-two candidate genes were found within the target region of qPT10-5. Moreover, of these 42 genes, five genes (GRMZM2G143402, GRMZM2G143389, GRMZM2G143352, GRMZM6G287947, and AC234202.1_FG004) were differentially expressed between the two parents, as revealed by transcriptome analysis. According to the gene annotation information, three genes might be considered candidates for pericarp thickness. GRMZM2G143352 and GRMZM2G143402 have been annotated as AUX/IAA transcription factor and ZIM transcription factor, respectively, while GRMZM2G143389 has been annotated as FATTY ACID EXPORT 2, chloroplastic. CONCLUSIONS This study identified a major QTL and candidate genes that could accelerate breeding for the thin pericarp thickness variety of sweet corn, and these results established the basis for map-based cloning and further functional research.
Collapse
Affiliation(s)
- Xiaming Wu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Bo Wang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Fugui Xie
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Liping Zhang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Jie Gong
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Wei Zhu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Xiaoqin Li
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Faqiang Feng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Jun Huang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| |
Collapse
|
40
|
Yang T, Meng W, Guo B. Population Genomic Analysis of Two Endemic Schizothoracins Reveals Their Genetic Differences and Underlying Selection Associated with Altitude and Temperature. Animals (Basel) 2020; 10:ani10030447. [PMID: 32156058 PMCID: PMC7142781 DOI: 10.3390/ani10030447] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 01/18/2023] Open
Abstract
Simple Summary Diptychus maculates and Gymnodiptychus dybowskii are two rare aboriginal fishes in the Xinjiang Uygur Autonomous Region. In recent years, due to overfishing and habitat fragmentation caused by construction of water conservancy and hydropower projects, the fishery resources have decreased sharply. Understanding the genetic background is of great significance for resource protection. In this study, we revealed the similar trends of population genetic diversities in these two species collected from the Tarim River and the Yili River. In addition, outlier SNPs associated with temperature and altitude were detected in both of them, indicating that Schizothoracinae fishes represented by D. maculates and G. dybowskii were still under the selection pressure of plateau environments. Abstract Schizothoracins are a group of cyprinid fishes distributed throughout the Qinghai–Tibet Plateau, which can be classified in three grades: primitive, specialised and highly specialised according to adaptation ability to plateau environments. As the only specialised schizothoracins in Xinjiang, China, Diptychus maculates and Gymnodiptychus dybowskii are ideal materials for adaptive evolution research. Based on single-nucleotide polymorphism (SNP) loci detected by specific-locus amplified fragment (SLAF) technology, the genome-wide genetic diversities of these two species from nine sites in Xinjiang were evaluated. D.maculates in the Muzat River (BM) and G. dybowskii in the Kaidu River (LKG) presented the lowest genetic diversity levels, whereas D. maculates in the Kumarik River (BK) and G.dybowskii in the Kashi River (LK) were just the opposite. Cluster and principal component analysis demonstrated a distant genetic affinity between D. maculates in the Tashkurgan River (BT) and other populations. Outlier SNP loci were discovered both in D. maculates and G. dybowskii. The coalescent Bayenv and latent factor mixed model (LFMM) methods showed that a total of thirteen and eighteen SNPs in D. maculates were associated with altitude and temperature gradient, respectively. No intersection was revealed in G. dybowskii. The results indicated that D. maculates was subject to much greater divergent selection pressure. A strong signal of isolation-by-distance (IBD) was detected across D. maculates (Mantel test, rs = 0.65; p = 0.05), indicating an evident geographical isolation in the Tarim River. Isolation-by-environment (IBE) analysis implied that temperature and altitude selections were more intensive in D. maculates, with greater environmental variation resulting in weak gene flow.
Collapse
Affiliation(s)
- Tianyan Yang
- College of Fishery, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Wei Meng
- Marine Fisheries Research Institute of Zhejiang, Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture, Zhoushan 316021, China
- Correspondence: (W.M.); (B.G.); Tel.: +86-580-229-9888 (W.M.); +86-10-6480-7978 (B.G.)
| | - Baocheng Guo
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (W.M.); (B.G.); Tel.: +86-580-229-9888 (W.M.); +86-10-6480-7978 (B.G.)
| |
Collapse
|
41
|
Wang F, Zhang J, Chen Y, Zhang C, Gong J, Song Z, Zhou J, Wang J, Zhao C, Jiao M, Liu A, Du Z, Yuan Y, Fan S, Zhang J. Identification of candidate genes for key fibre-related QTLs and derivation of favourable alleles in Gossypium hirsutum recombinant inbred lines with G. barbadense introgressions. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:707-720. [PMID: 31446669 PMCID: PMC7004909 DOI: 10.1111/pbi.13237] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/15/2019] [Indexed: 05/02/2023]
Abstract
Fine mapping QTLs and identifying candidate genes for cotton fibre-quality and yield traits would be beneficial to cotton breeding. Here, we constructed a high-density genetic map by specific-locus amplified fragment sequencing (SLAF-seq) to identify QTLs associated with fibre-quality and yield traits using 239 recombinant inbred lines (RILs), which was developed from LMY22 (a high-yield Gossypium hirsutumL. cultivar) × LY343 (a superior fibre-quality germplasm with G. barbadenseL. introgressions). The genetic map spanned 3426.57 cM, including 3556 SLAF-based SNPs and 199 SSR marker loci. A total of 104 QTLs, including 67 QTLs for fibre quality and 37 QTLs for yield traits, were identified with phenotypic data collected from 7 environments. Among these, 66 QTLs were co-located in 19 QTL clusters on 12 chromosomes, and 24 QTLs were detected in three or more environments and determined to be stable. We also investigated the genomic components of LY343 and their contributions to fibre-related traits by deep sequencing the whole genome of LY343, and we found that genomic components from G. hirsutum races (which entered LY343 via its G. barbadense parent) contributed more favourable alleles than those from G. barbadense. We further identified six putative candidate genes for stable QTLs, including Gh_A03G1147 (GhPEL6), Gh_D07G1598 (GhCSLC6) and Gh_D13G1921 (GhTBL5) for fibre-length QTLs and Gh_D03G0919 (GhCOBL4), Gh_D09G1659 (GhMYB4) and Gh_D09G1690 (GhMYB85) for lint-percentage QTLs. Our results provide comprehensive insight into the genetic basis of the formation of fibre-related traits and would be helpful for cloning fibre-development-related genes as well as for marker-assisted genetic improvement in cotton.
Collapse
Affiliation(s)
- Furong Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Chuanyun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Juwu Gong
- State Key Laboratory of Cotton BiologyKey Laboratory of Biological and Genetic Breeding of CottonMinistry of AgricultureInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhangqiang Song
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Juan Zhou
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Jingjing Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Chengjie Zhao
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Mengjia Jiao
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Aiying Liu
- State Key Laboratory of Cotton BiologyKey Laboratory of Biological and Genetic Breeding of CottonMinistry of AgricultureInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhaohai Du
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Youlu Yuan
- State Key Laboratory of Cotton BiologyKey Laboratory of Biological and Genetic Breeding of CottonMinistry of AgricultureInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Shoujin Fan
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
| |
Collapse
|
42
|
Wen Y, Fang Y, Hu P, Tan Y, Wang Y, Hou L, Deng X, Wu H, Zhu L, Zhu L, Chen G, Zeng D, Guo L, Zhang G, Gao Z, Dong G, Ren D, Shen L, Zhang Q, Xue D, Qian Q, Hu J. Construction of a High-Density Genetic Map Based on SLAF Markers and QTL Analysis of Leaf Size in Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:1143. [PMID: 32849702 PMCID: PMC7411225 DOI: 10.3389/fpls.2020.01143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/14/2020] [Indexed: 05/02/2023]
Abstract
Leaf shape is an important agronomic trait for constructing an ideal plant type in rice, and high-density genetic map is facilitative in improving accuracy and efficiency for quantitative trait loci (QTL) analysis of leaf trait. In this study, a high-density genetic map contained 10,760 specific length amplified fragment sequencing (SLAF) markers was established based on 149 recombinant inbred lines (RILs) derived from the cross between Rekuangeng (RKG) and Taizhong1 (TN1), which exhibited 1,613.59 cM map distance with an average interval of 0.17 cM. A total of 24 QTLs were detected and explained the phenotypic variance ranged from 9% to 33.8% related to the leaf morphology across two areas. Among them, one uncloned major QTL qTLLW1 (qTLL1 and qTLLW1) involved in regulating leaf length and leaf width with max 33.8% and 22.5% phenotypic variance respectively was located on chromosome 1, and another major locus qTLW4 affecting leaf width accounted for max 25.3% phenotypic variance was mapped on chromosome 4. Fine mapping and qRT-PCR expression analysis indicated that qTLW4 may be allelic to NAL1 (Narrow leaf 1) gene.
Collapse
Affiliation(s)
- Yi Wen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, China
| | - Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Peng Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yiqing Tan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yueying Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Linlin Hou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xuemei Deng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hao Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lixin Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guang Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qiang Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, China
- *Correspondence: Qian Qian, ; Jiang Hu,
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- *Correspondence: Qian Qian, ; Jiang Hu,
| |
Collapse
|
43
|
Zhang Z, Li J, Jamshed M, Shi Y, Liu A, Gong J, Wang S, Zhang J, Sun F, Jia F, Ge Q, Fan L, Zhang Z, Pan J, Fan S, Wang Y, Lu Q, Liu R, Deng X, Zou X, Jiang X, Liu P, Li P, Iqbal MS, Zhang C, Zou J, Chen H, Tian Q, Jia X, Wang B, Ai N, Feng G, Wang Y, Hong M, Li S, Lian W, Wu B, Hua J, Zhang C, Huang J, Xu A, Shang H, Gong W, Yuan Y. Genome-wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield-related traits in a Gossypium hirsutum recombinant inbred line population. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:239-253. [PMID: 31199554 PMCID: PMC6920336 DOI: 10.1111/pbi.13191] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 05/30/2019] [Accepted: 06/11/2019] [Indexed: 05/02/2023]
Abstract
Cotton is widely cultivated globally because it provides natural fibre for the textile industry and human use. To identify quantitative trait loci (QTLs)/genes associated with fibre quality and yield, a recombinant inbred line (RIL) population was developed in upland cotton. A consensus map covering the whole genome was constructed with three types of markers (8295 markers, 5197.17 centimorgans (cM)). Six fibre yield and quality traits were evaluated in 17 environments, and 983 QTLs were identified, 198 of which were stable and mainly distributed on chromosomes 4, 6, 7, 13, 21 and 25. Thirty-seven QTL clusters were identified, in which 92.8% of paired traits with significant medium or high positive correlations had the same QTL additive effect directions, and all of the paired traits with significant medium or high negative correlations had opposite additive effect directions. In total, 1297 genes were discovered in the QTL clusters, 414 of which were expressed in two RNA-Seq data sets. Many genes were discovered, 23 of which were promising candidates. Six important QTL clusters that included both fibre quality and yield traits were identified with opposite additive effect directions, and those on chromosome 13 (qClu-chr13-2) could increase fibre quality but reduce yield; this result was validated in a natural population using three markers. These data could provide information about the genetic basis of cotton fibre quality and yield and help cotton breeders to improve fibre quality and yield simultaneously.
Collapse
|
44
|
Wu X, Feng F, Zhu Y, Xie F, Yang J, Gong J, Liu Y, Zhu W, Gao T, Chen D, Li X, Huang J. Construction of High-Density Genetic Map and Identification of QTLs Associated with Seed Vigor after Exposure to Artificial Aging Conditions in Sweet Corn Using SLAF-seq. Genes (Basel) 2019; 11:genes11010037. [PMID: 31905667 PMCID: PMC7016829 DOI: 10.3390/genes11010037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 01/23/2023] Open
Abstract
Seed vigor is a key factor that determines the quality of seeds, which is of great significance for agricultural production, with the potential to promote growth and productivity. However, the underlying molecular mechanisms and genetic basis for seed vigor remain unknown. High-density genetic linkage mapping is an effective method for genomic study and quantitative trait loci (QTL) mapping. In this study, a high-density genetic map was constructed from a 148 BC4F3 population cross between ‘M03’ and ‘M08’ strains based on specific-locus amplified fragment (SLAF) sequencing. The constructed high-density genetic linkage map (HDGM) included 3876 SNP markers on ten chromosomes covering 2413.25 cM in length, with a mean distance between markers of 0.62 cM. QTL analysis was performed on four sweet corn germination traits that are related to seed vigor under artificial aging conditions. A total of 18 QTLs were identified in two seasons. Interestingly, a stable QTL was detected in two seasons on chromosome 10—termed qGR10—within an interval of 1.37 Mb. Within this interval, combined with gene annotation, we found four candidate genes (GRMZM2G074309, GRMZM2G117319, GRMZM2G465812, and GRMZM2G343519) which may be related to seed vigor after artificial aging.
Collapse
Affiliation(s)
- Xiaming Wu
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Faqiang Feng
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Yuzhong Zhu
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Fugui Xie
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Jing Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China;
| | - Jie Gong
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Yu Liu
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Wei Zhu
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Tianle Gao
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Danyi Chen
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Xiaoqin Li
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Jun Huang
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
- Correspondence: ; Tel.: +86-020-85288311
| |
Collapse
|
45
|
Du H, Zhang H, Wei L, Li C, Duan Y, Wang H. A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.). BMC PLANT BIOLOGY 2019; 19:588. [PMID: 31881840 PMCID: PMC6935206 DOI: 10.1186/s12870-019-2172-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/28/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population by using specific length amplified fragment (SLAF) technique and determined the quantitative trait loci (QTLs) of seed-related traits for sesame based on the phenotypes of F3 progeny. RESULTS The genetic map comprised 2159 SNP markers distributed on 13 linkage groups (LGs) and was 2128.51 cM in length, with an average distance of 0.99 cM between adjacent markers. QTL mapping revealed 19 major-effect QTLs with the phenotypic effect (R2) more than 10%, i.e., eight QTLs for seed coat color, nine QTLs for seed size, and two QTLs for 1000-seed weight (TSW), using composite interval mapping method. Particularly, LG04 and LG11 contained collocated QTL regions for the seed coat color and seed size traits, respectively, based on their close or identical locations. In total, 155 candidate genes for seed coat color, 22 for seed size traits, and 54 for TSW were screened and analyzed. CONCLUSIONS This report presents the first QTL mapping of seed-related traits in sesame using an F2 population. The results reveal the location of specific markers associated with seed-related traits in sesame and provide the basis for further seed quality traits research.
Collapse
Affiliation(s)
- Hua Du
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Huili Wang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| |
Collapse
|
46
|
Zhang S, Hu X, Miao H, Chu Y, Cui F, Yang W, Wang C, Shen Y, Xu T, Zhao L, Zhang J, Chen J. QTL identification for seed weight and size based on a high-density SLAF-seq genetic map in peanut (Arachis hypogaea L.). BMC PLANT BIOLOGY 2019; 19:537. [PMID: 31795931 PMCID: PMC6892246 DOI: 10.1186/s12870-019-2164-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/26/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND The cultivated peanut is an important oil and cash crop grown worldwide. To meet the growing demand for peanut production each year, genetic studies and enhanced selection efficiency are essential, including linkage mapping, genome-wide association study, bulked-segregant analysis and marker-assisted selection. Specific locus amplified fragment sequencing (SLAF-seq) is a powerful tool for high density genetic map (HDGM) construction and quantitative trait loci (QTLs) mapping. In this study, a HDGM was constructed using SLAF-seq leading to identification of QTL for seed weight and size in peanut. RESULTS A recombinant inbred line (RIL) population was advanced from a cross between a cultivar 'Huayu36' and a germplasm line '6-13' with contrasting seed weight, size and shape. Based on the cultivated peanut genome, a HDGM was constructed with 3866 loci consisting of SLAF-seq and simple sequence repeat (SSR) markers distributed on 20 linkage groups (LGs) covering a total map distance of 1266.87 cM. Phenotypic data of four seed related traits were obtained in four environments, which mostly displayed normal distribution with varied levels of correlation. A total of 27 QTLs for 100 seed weight (100SW), seed length (SL), seed width (SW) and length to width ratio (L/W) were identified on 8 chromosomes, with LOD values of 3.16-31.55 and explaining phenotypic variance (PVE) from 0.74 to 83.23%. Two stable QTL regions were identified on chromosomes 2 and 16, and gene content within these regions provided valuable information for further functional analysis of yield component traits. CONCLUSIONS This study represents a new HDGM based on the cultivated peanut genome using SLAF-seq and SSRs. QTL mapping of four seed related traits revealed two stable QTL regions on chromosomes 2 and 16, which not only facilitate fine mapping and cloning these genes, but also provide opportunity for molecular breeding of new peanut cultivars with improved seed weight and size.
Collapse
Affiliation(s)
- Shengzhong Zhang
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China
| | - Xiaohui Hu
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China
| | - Huarong Miao
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China
| | - Ye Chu
- Department of Horticulture, University of Georgia Tifton Campus, Tifton, GA, 31793, USA
| | - Fenggao Cui
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China
| | - Weiqiang Yang
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China
| | - Chunming Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yi Shen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Tingting Xu
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China
| | - Libo Zhao
- Qingdao Agricultural Radio and Television School, Qingdao, 266071, People's Republic of China
| | - Jiancheng Zhang
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China
| | - Jing Chen
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China.
| |
Collapse
|
47
|
Zhang Z, Xie W, Zhang J, Wang N, Zhao Y, Wang Y, Bai S. Construction of the first high-density genetic linkage map and identification of seed yield-related QTLs and candidate genes in Elymus sibiricus, an important forage grass in Qinghai-Tibet Plateau. BMC Genomics 2019; 20:861. [PMID: 31726988 PMCID: PMC6857239 DOI: 10.1186/s12864-019-6254-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/31/2019] [Indexed: 11/28/2022] Open
Abstract
Background Elymus sibiricus is an ecologically and economically important perennial, self-pollinated, and allotetraploid (StStHH) grass, widely used for forage production and animal husbandry in Western and Northern China. However, it has low seed yield mainly caused by seed shattering, which makes seed production difficult for this species. The goals of this study were to construct the high-density genetic linkage map, and to identify QTLs and candidate genes for seed-yield related traits. Results An F2 mapping population of 200 individuals was developed from a cross between single genotype from “Y1005” and “ZhN06”. Specific-locus amplified fragment sequencing (SLAF-seq) was applied to construct the first genetic linkage map. The final genetic map included 1971 markers on the 14 linkage groups (LGs) and was 1866.35 cM in total. The length of each linkage group varied from 87.67 cM (LG7) to 183.45 cM (LG1), with an average distance of 1.66 cM between adjacent markers. The marker sequences of E. sibiricus were compared to two grass genomes and showed 1556 (79%) markers mapped to wheat, 1380 (70%) to barley. Phenotypic data of eight seed-related traits (2016–2018) were used for QTL identification. A total of 29 QTLs were detected for eight seed-related traits on 14 linkage groups, of which 16 QTLs could be consistently detected for two or three years. A total of 6 QTLs were associated with seed shattering. Based on annotation with wheat and barley genome and transcriptome data of abscission zone in E. sibiricus, we identified 30 candidate genes for seed shattering, of which 15, 7, 6 and 2 genes were involved in plant hormone signal transcription, transcription factor, hydrolase activity and lignin biosynthetic pathway, respectively. Conclusion This study constructed the first high-density genetic linkage map and identified QTLs and candidate genes for seed-related traits in E. sibiricus. Results of this study will not only serve as genome-wide resources for gene/QTL fine mapping, but also provide a genetic framework for anchoring sequence scaffolds on chromosomes in future genome sequence assembly of E. sibiricus.
Collapse
Affiliation(s)
- Zongyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Wengang Xie
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.
| | - Junchao Zhang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Na Wang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Yongqiang Zhao
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.
| | - Shiqie Bai
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, 611731, People's Republic of China
| |
Collapse
|
48
|
Ma J, Pei W, Ma Q, Geng Y, Liu G, Liu J, Cui Y, Zhang X, Wu M, Li X, Li D, Zang X, Song J, Tang S, Zhang J, Yu S, Yu J. QTL analysis and candidate gene identification for plant height in cotton based on an interspecific backcross inbred line population of Gossypium hirsutum × Gossypium barbadense. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2663-2676. [PMID: 31236630 DOI: 10.1007/s00122-019-03380-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/14/2019] [Indexed: 05/24/2023]
Abstract
We constructed the first high-quality and high-density genetic linkage map for an interspecific BIL population in cotton by specific-locus amplified fragment sequencing for QTL mapping. A novel gene GhPIN3 for plant height was identified in cotton. Ideal plant height (PH) is important for improving lint yield and mechanized harvesting in cotton. Most published genetic studies on cotton have focused on fibre yield and quality traits rather than PH. To facilitate the understanding of the genetic basis in PH, an interspecific backcross inbred line (BIL) population of 250 lines derived from upland cotton (Gossypium hirsutum L.) CRI36 and Egyptian cotton (G. barbadense L.) Hai7124 was used to construct a high-density genetic linkage map for quantitative trait locus (QTL) mapping. The high-density genetic map harboured 7,709 genotyping-by-sequencing (GBS)-based single nucleotide polymorphism (SNP) markers that covered 3,433.24 cM with a mean marker interval of 0.67 cM. In total, ten PH QTLs were identified and each explained 4.27-14.92% of the phenotypic variation, four of which were stable as they were mapped in at least two tests or based on best linear unbiased prediction in seven field tests. Based on functional annotation of orthologues in Arabidopsis and transcriptome data for the genes within the stable QTL regions, GhPIN3 encoding for the hormone auxin efflux carrier protein was identified as a candidate gene located in the stable QTL qPH-Dt1-1 region. A qRT-PCR analysis showed that the expression level of GhPIN3 in apical tissues was significantly higher in four short-statured cotton genotypes than that in four tall-statured cotton genotypes. Virus-induced gene silencing cotton has significantly increased PH when the expression of the GhPIN3 gene was suppressed.
Collapse
Affiliation(s)
- Jianjiang Ma
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
- College of Agriculture, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Wenfeng Pei
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830001, China
| | - Qifeng Ma
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Yanhui Geng
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Guoyuan Liu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Yupeng Cui
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Xia Zhang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Man Wu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Xingli Li
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Dan Li
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - XinShan Zang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Jikun Song
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Shurong Tang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, 880033, USA.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China.
- College of Agriculture, Northwest A&F University, Yangling, 712100, Shanxi, China.
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China.
| |
Collapse
|
49
|
Dong M, He Q, Zhao J, Zhang Y, Yuan D, Zhang AJ. Genetic Mapping of Prince Rupprecht's Larch ( Larix principis-rupprechtii Mayr) by Specific-Locus Amplified Fragment Sequencing. Genes (Basel) 2019; 10:genes10080583. [PMID: 31370324 PMCID: PMC6723236 DOI: 10.3390/genes10080583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 07/12/2019] [Accepted: 07/29/2019] [Indexed: 11/24/2022] Open
Abstract
A high-density genetic linkage map is essential for plant genetics and genomics research. However, due to the deficiency of genomic data and high-quality molecular markers, no genetic map has been published for Prince Rupprecht’s larch (Larix principis-rupprechtii Mayr), a conifer species with high ecological and commercial value in northern China. In this study, 145 F1 progeny individuals from an intraspecific cross between two elite clones of L. principis-rupprechtii and their parents were employed to construct the first genetic map in this important tree species using specific-locus amplified fragment sequencing (SLAF-seq). After preprocessing, the procedure yielded 300.20 Gb of raw data containing 1501.22 M pair-end reads. A total of 324,352 SNP markers were detected and 122,785 of them were polymorphic, with a polymorphism rate of 37.86%. Ultimately, 6099 SNPs were organized into a genetic map containing 12 linkage groups, consistent with the haploid chromosome number of larch and most other species in the Pinaceae family. The linkage map spanned 2415.58 cM and covered 99.6% of the L. principis-rupprechtii genome with an average of 0.4 cM between adjacent markers. To the best of our knowledge, this map is the first reference map for L. principis-rupprechtii, as well as the densest one obtained in larch species thus far. The genome-wide SNPs and the high-resolution genetic map will provide a foundation for future quantitative trait loci mapping, map-based cloning, marker-assisted selection, comparative genomics, and genome sequence assembly for larch trees.
Collapse
Affiliation(s)
- Mingliang Dong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Qingwei He
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jian Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yan Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Deshui Yuan
- National Key Seed Base of Larch, Weichang, Chengde 068450, China
| | - And Jinfeng Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
| |
Collapse
|
50
|
Li J, Lv J, Liu P, Chen P, Wang J, Li J. Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits. BMC Genomics 2019; 20:598. [PMID: 31331278 PMCID: PMC6647322 DOI: 10.1186/s12864-019-5981-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/16/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND High-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of eastern China and western Korea. However, quite limited genomics and genetics information have been exploited for genetic improvement of economic traits in this species. RESULTS In the present study, we conducted genome survey and constructed high-resolution genetic linkage maps of the ridgetail white prawn with reciprocal-cross mapping family genotyped using next-generation sequencing approaches. The estimated genome size was 9.33 Gb with a heterozygosity of 0.26% and a repeat sequence ratio of 76.62%. 65,772 protein-coding genes were identified by genome annotation. A total of 10,384 SNPs were used to high-throughput genotyping and assigned to 45 linkage groups (LGs) from reciprocal backcross families of E. carinicauda, and the average marker distances were 0.73 cM and 0.55 cM, respectively. Based on the high-resolution linkage map, twenty-three QTLs related to five growth traits were detected. All QTLs could explain 8.8-15.7% of the total growth-traits variation. CONCLUSIONS The genome size of E. carinicauda was estimated more accurately by genome survey analysis, which revealed basic genomic architecture. The first high-resolution backcross genetic linkage map and QTLs related to growth traits will provide important information for QTL fine mapping, genome assembly and genetic improvement of E. carinicauda and other palaemon shrimps.
Collapse
Affiliation(s)
- Jitao Li
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Jianjian Lv
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Ping Liu
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Ping Chen
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Jiajia Wang
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Jian Li
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China. .,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China.
| |
Collapse
|