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Huang Q, Li X, Li Q, Zhong S, Li X, Yang J, Tan F, Ren T, Li Z, Suizhuang Y. Three novel QTLs for FHB resistance identified and mapped in spring wheat PI672538 by bulked segregant analysis of the recombinant inbred line. FRONTIERS IN PLANT SCIENCE 2024; 15:1409095. [PMID: 39135653 PMCID: PMC11317384 DOI: 10.3389/fpls.2024.1409095] [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: 04/02/2024] [Accepted: 07/04/2024] [Indexed: 08/15/2024]
Abstract
Introduction Fusarium head blight (FHB) has a large influence on both the yield and quality of wheat grain worldwide. Host resistance is the most effective method for controlling FHB, but unfortunately, very few genetic resources on FHB resistance are available; therefore, identifying novel resistance genes or quantitative trait loci (QTLs) is valuable. Methods Here, a recombinant inbred line (RIL) population containing 451 lines derived from the cross L661/PI672538 was sown in four different environments (2019CZa, 2019CZb, 2021QL and 2021WJ). Results Five QTLs, consisting of two previously reported QTLs (FhbL693a and FhbL693b) and three new QTLs (FhbL693c, FhbL693d and FhbL693e), were identified. Further investigation revealed that FhbL693b, FhbL693c and FhbL693d could be detected in all four environments, and FhbL693a and FhbL693e were detected only in 2019CZb and 2021WJ, respectively. Among the QTLs, the greatest contribution (10.5%) to the phenotypic variation effect (PVE) was FhbL693d in 2021WJ, while the smallest (1.2%) was FhbL693e and FhbL693a in 2019CZb. The selection of 5Dindel-4 for FhbL693d, 4Aindel-7 for FhbL693c and 3Bindel-24 for FhbL693b decreased the number of damaged spikelets by 2.1, and a new line resistant to FHB named H140-2 was developed by marker-assisted selection (MAS). Discussion These results could help to further improve FHB resistance in the future.
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Affiliation(s)
- Qianglan Huang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Provincial Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xin Li
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Qing Li
- Provincial Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
- Department of Biology and Chemistry, Chongqing Industry and Trade Polytechnic, Fuling, Chongqing, China
| | - Shengfu Zhong
- Provincial Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiuying Li
- Provincial Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiezhi Yang
- Wheat Research Institute, Neijiang Academy of Agricultural Sciences, Neijiang, Sichuan, China
| | - Feiquan Tan
- Provincial Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tianheng Ren
- Provincial Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhi Li
- Provincial Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yang Suizhuang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
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Li X, Dong Y, Yu H, Zhao J, Yang F, Song W, Wang C, Liu J, Liang Q, Wang Y, Yang KQ, Fang H. A dual RNA-seq analyses revealed dynamic arms race during the invasion of walnut by Colletotrichum gloeosporioides. BMC PLANT BIOLOGY 2024; 24:653. [PMID: 38987678 PMCID: PMC11234561 DOI: 10.1186/s12870-024-05368-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 07/01/2024] [Indexed: 07/12/2024]
Abstract
BACKGROUND Walnut anthracnose caused by Colletotrichum gloeosporioides seriously endangers the yield and quality of walnut, and has now become a catastrophic disease in the walnut industry. Therefore, understanding both pathogen invasion mechanisms and host response processes is crucial to defense against C. gloeosporioides infection. RESULTS Here, we investigated the mechanisms of interaction between walnut fruits (anthracnose-resistant F26 fruit bracts and anthracnose-susceptible F423 fruit bracts) and C. gloeosporioides at three infection time points (24hpi, 48hpi, and 72hpi) using a high-resolution time series dual transcriptomic analysis, characterizing the arms race between walnut and C. gloeosporioides. A total of 20,780 and 6670 differentially expressed genes (DEGs) were identified in walnut and C. gloeosporioides against 24hpi, respectively. Generous DEGs in walnut exhibited opposite expression patterns between F26 and F423, which indicated that different resistant materials exhibited different transcriptional responses to C. gloeosporioides during the infection process. KEGG functional enrichment analysis indicated that F26 displayed a broader response to C. gloeosporioides than F423. Meanwhile, the functional analysis of the C. gloeosporioides transcriptome was conducted and found that PHI, SignalP, CAZy, TCDB genes, the Fungal Zn (2)-Cys (6) binuclear cluster domain (PF00172.19) and the Cytochrome P450 (PF00067.23) were largely prominent in F26 fruit. These results suggested that C. gloeosporioides secreted some type of effector proteins in walnut fruit and appeared a different behavior based on the developmental stage of the walnut. CONCLUSIONS Our present results shed light on the arms race process by which C. gloeosporioides attacked host and walnut against pathogen infection, laying the foundation for the green prevention of walnut anthracnose.
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Affiliation(s)
- Xichen Li
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, Shandong, 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream, Areas of the Yellow River, Taian, Shandong, 271018, China
| | - Haiyi Yu
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Jing Zhao
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Fei Yang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Weichen Song
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Changxi Wang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Jianning Liu
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Qiang Liang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, Shandong, 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream, Areas of the Yellow River, Taian, Shandong, 271018, China
| | - Yicheng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China.
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, Shandong, 271018, China.
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream, Areas of the Yellow River, Taian, Shandong, 271018, China.
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China.
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, Shandong, 271018, China.
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream, Areas of the Yellow River, Taian, Shandong, 271018, China.
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Mu Y, Dong Y, Li X, Gong A, Yu H, Wang C, Liu J, Liang Q, Yang K, Fang H. JrPHL8-JrWRKY4-JrSTH2L module regulates resistance to Colletotrichum gloeosporioides in walnut. HORTICULTURE RESEARCH 2024; 11:uhae148. [PMID: 38988616 PMCID: PMC11233879 DOI: 10.1093/hr/uhae148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/21/2024] [Indexed: 07/12/2024]
Abstract
Walnut anthracnose (Colletotrichum gloeosporioides) reduces walnut yield and quality and seriously threatens the healthy development of the walnut industry. WRKY transcription factors (TFs) are crucial regulatory factors involved in plant-pathogen interactions. Our previous transcriptome analysis results indicate that JrWRKY4 responds to infection by C. gloeosporioides, but its specific regulatory network and disease resistance mechanism are still unclear. Herein, the characteristics of JrWRKY4 as a transcription activator located in the nucleus were first identified. Gain-of-function and loss-of-function analyses showed that JrWRKY4 could enhance walnut resistance against C. gloeosporioides. A series of molecular experiments showed that JrWRKY4 directly interacted with the promoter region of JrSTH2L and positively regulated its expression. In addition, JrWRKY4 interacted with JrVQ4 to form the protein complex, which inhibited JrWRKY4 for the activation of JrSTH2L. Notably, a MYB TF JrPHL8 interacting with the JrWRKY4 promoter has also been identified, which directly bound to the MBS element in the promoter of JrWRKY4 and induced its activity. Our study elucidated a novel mechanism of the JrPHL8-JrWRKY4-JrSTH2L in regulating walnut resistance to anthracnose. This mechanism improves our understanding of the molecular mechanism of WRKY TF mediated resistance to anthracnose in walnut, which provides new insights for molecular breeding of disease-resistant walnuts in the future.
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Affiliation(s)
- Yutian Mu
- College of Forestry, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Taian 271018, Shandong, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian 271018, Shandong, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian 271018, Shandong, China
| | - Xichen Li
- College of Forestry, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Andi Gong
- College of Forestry, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Haiyi Yu
- College of Forestry, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Changxi Wang
- College of Forestry, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Jianning Liu
- College of Forestry, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Qiang Liang
- College of Forestry, Shandong Agricultural University, Taian 271018, Shandong, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian 271018, Shandong, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian 271018, Shandong, China
| | - Keqiang Yang
- College of Forestry, Shandong Agricultural University, Taian 271018, Shandong, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian 271018, Shandong, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian 271018, Shandong, China
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Taian 271018, Shandong, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian 271018, Shandong, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian 271018, Shandong, China
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Yang C, Ban X, Zhou M, Zhou Y, Luo K, Yang X, Li Z, Liu F, Li Q, Luo Y, Zhou X, Lei J, Long P, Wang J, Guo J. Construction of a high-density genetic map based on large-scale marker development in Coix lacryma-jobi L. using specific-locus amplified fragment sequencing (slaf-seq). Sci Rep 2024; 14:9606. [PMID: 38670987 PMCID: PMC11053130 DOI: 10.1038/s41598-024-58167-8] [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: 07/03/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Coix lacryma-jobi L. is one of the most economically and medicinally important corns. This study constructed a high-density genetic linkage map of C. lacryma-jobi based on a cross between the parents 'Qianyi No. 2' × 'Wenyi No. 2' and their F2 progeny through high-throughput sequencing and the construction of a specific-locus amplified fragment (SLAF) library. After pre-processing, 325.49 GB of raw data containing 1628 M reads were obtained. A total of 22,944 high-quality SLAFs were identified, among which 3952 SLAFs and 3646 polymorphic markers met the requirements for the construction of a genetic linkage map. The integrated map contained 3605 high-quality SLAFs, which were grouped into ten genetic linkage groups. The total length of the map was 1620.39 cM, with an average distance of 0.45 cM and an average of 360.5 markers per linkage group. This report presents the first high-density genetic map of C. lacryma-jobi. This map was constructed using an F2 population and SLAF-seq approach, which allows the development of a large number of polymorphic markers in a short period. These results provide a platform for precise gene/quantitative trait locus (QTL) mapping, map-based gene separation, and molecular breeding in C. lacryma-jobi. They also help identify a target gene for tracking, splitting quantitative traits, and estimating the phenotypic effects of each QTL for QTL mapping. They are of great significance for improving the efficiency of discovering and utilizing excellent gene resources of C. lacryma-jobi.
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Affiliation(s)
- Chenglong Yang
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, 542600, Guizhou, People's Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Innovation in Karst Plateau Mountains, Guiyang, 550025, Guizhou, People's Republic of China
| | - Xiuwen Ban
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, 542600, Guizhou, People's Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Innovation in Karst Plateau Mountains, Guiyang, 550025, Guizhou, People's Republic of China
| | - Mingqiang Zhou
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, 542600, Guizhou, People's Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Innovation in Karst Plateau Mountains, Guiyang, 550025, Guizhou, People's Republic of China
| | - Yu Zhou
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, 542600, Guizhou, People's Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Innovation in Karst Plateau Mountains, Guiyang, 550025, Guizhou, People's Republic of China
| | - Kai Luo
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, 542600, Guizhou, People's Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Innovation in Karst Plateau Mountains, Guiyang, 550025, Guizhou, People's Republic of China
| | - Xiaoyu Yang
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, 542600, Guizhou, People's Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Innovation in Karst Plateau Mountains, Guiyang, 550025, Guizhou, People's Republic of China
| | - Zhifang Li
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, 542600, Guizhou, People's Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Innovation in Karst Plateau Mountains, Guiyang, 550025, Guizhou, People's Republic of China
| | - Fanzhi Liu
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, 542600, Guizhou, People's Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Innovation in Karst Plateau Mountains, Guiyang, 550025, Guizhou, People's Republic of China
| | - Qing Li
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, 542600, Guizhou, People's Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Innovation in Karst Plateau Mountains, Guiyang, 550025, Guizhou, People's Republic of China
| | - Yahong Luo
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, 542600, Guizhou, People's Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Innovation in Karst Plateau Mountains, Guiyang, 550025, Guizhou, People's Republic of China
| | - Xiang Zhou
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, 542600, Guizhou, People's Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Innovation in Karst Plateau Mountains, Guiyang, 550025, Guizhou, People's Republic of China
| | - Jing Lei
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, 542600, Guizhou, People's Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Innovation in Karst Plateau Mountains, Guiyang, 550025, Guizhou, People's Republic of China
| | - Peilin Long
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, 542600, Guizhou, People's Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Innovation in Karst Plateau Mountains, Guiyang, 550025, Guizhou, People's Republic of China
| | - Jian Wang
- The Key Laboratory of Agricultural Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, People's Republic of China.
| | - Jianchun Guo
- Hainan Institute for Tropical Agricultural Resources & Institute of Tropical Bioscience and Biotechnology, CATAS, Haikou, 571101, People's Republic of China.
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Han L, Luo X, Zhao Y, Li N, Xu Y, Ma K. A haplotype-resolved genome provides insight into allele-specific expression in wild walnut (Juglans regia L.). Sci Data 2024; 11:278. [PMID: 38459062 PMCID: PMC10923786 DOI: 10.1038/s41597-024-03096-4] [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: 10/11/2023] [Accepted: 02/27/2024] [Indexed: 03/10/2024] Open
Abstract
Wild germplasm resources are crucial for gene mining and molecular breeding because of their special trait performance. Haplotype-resolved genome is an ideal solution for fully understanding the biology of subgenomes in highly heterozygous species. Here, we surveyed the genome of a wild walnut tree from Gongliu County, Xinjiang, China, and generated a haplotype-resolved reference genome of 562.99 Mb (contig N50 = 34.10 Mb) for one haplotype (hap1) and 561.07 Mb (contig N50 = 33.91 Mb) for another haplotype (hap2) using PacBio high-fidelity (HiFi) reads and Hi-C technology. Approximately 527.20 Mb (93.64%) of hap1 and 526.40 Mb (93.82%) of hap2 were assigned to 16 pseudochromosomes. A total of 41039 and 39744 protein-coding gene models were predicted for hap1 and hap2, respectively. Moreover, 123 structural variations (SVs) were identified between the two haplotype genomes. Allele-specific expression genes (ASEGs) that respond to cold stress were ultimately identified. These datasets can be used to study subgenome evolution, for functional elite gene mining and to discover the transcriptional basis of specific traits related to environmental adaptation in wild walnut.
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Affiliation(s)
- Liqun Han
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China
| | - Xiang Luo
- College of Agriculture, Henan University, Zhengzhou, China
| | - Yu Zhao
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China
| | - Yuhui Xu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China.
| | - Kai Ma
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China.
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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.
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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
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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.
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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
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Wang L, Zhu T. Strong Opponent of Walnut Anthracnose- Bacillus velezensis and Its Transcriptome Analysis. Microorganisms 2023; 11:1885. [PMID: 37630445 PMCID: PMC10456653 DOI: 10.3390/microorganisms11081885] [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: 06/21/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Walnut is a significant economic tree species worldwide. Walnut anthracnose, caused by the pathogen Colletotrichum gloeosporioides, greatly reduces walnut production and economic benefits. Our study showed that Bacillus velezensis effectively halted the growth of C. gloeosporioides, inducing noticeable abnormalities such as hyphal breakage and distortion, thereby curtailing the pathogen's virulence. A 50-100 times dilution of B. velezensis fermentation broth, applied every two to three days, served as an efficient protective layer for walnut leaves and fruits against C. gloeosporioides infection. Transcriptomic analysis of B. velezensis unveiled its dynamic response against C. gloeosporioides. On the second day, B. velezensis upregulated a significant number of differentially expressed genes related to the synthesis of metabolic products, amino acid biosynthesis, and motility. On the fourth day, continuous synthesis of metabolic products and amino acids, along with differential expression of spore-related genes, was observed. By the sixth day, the focus shifted towards environmental adaptation and carbon source utilization. Throughout the process, B. velezensis likely employed strategies such as the release of metabolic products, increased chemotaxis, and nutrient competition to exert its antagonistic effect on C. gloeosporioides. Fluorescence quantitative results showed that 15 primer pairs were up-regulated and 15 were down-regulated, with a 100% similarity rate to transcriptome sequencing results, confirming their authenticity. These findings provided a foundation for the widespread application of B. velezensis as a biocontrol agent in agriculture and forestry.
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Affiliation(s)
| | - Tianhui Zhu
- College of Forestry, Sichuan Agricultural University, Yaan 625000, China
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Zhou R, Dong Y, Wang C, Liu J, Liang Q, Meng X, Lang X, Xu S, Liu W, Zhang S, Wang N, Yang KQ, Fang H. LncRNA109897-JrCCR4-JrTLP1b forms a positive feedback loop to regulate walnut resistance against anthracnose caused by Colletotrichum gloeosporioides. HORTICULTURE RESEARCH 2023; 10:uhad086. [PMID: 37786525 PMCID: PMC10541558 DOI: 10.1093/hr/uhad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/20/2023] [Indexed: 10/04/2023]
Abstract
Walnut anthracnose induced by Colletotrichum gloeosporioides is a disastrous disease that severely restricts the development of the walnut industry in China. Long non-coding RNAs (lncRNAs) are involved in adaptive responses to disease, but their roles in the regulation of walnut anthracnose resistance response are not well defined. In this study, transcriptome analysis demonstrated that a C. gloeosporioides-induced lncRNA, lncRNA109897, located upstream from the target gene JrCCR4, upregulated the expression of JrCCR4. JrCCR4 interacted with JrTLP1b and promoted its transcriptional activity. In turn, JrTLP1b induced the transcription of lncRNA109897 to promote its expression. Meanwhile, transient expression in walnut leaves and stable transformation of Arabidopsis thaliana further proved that lncRNA, JrCCR4, and JrTLP1b improve the resistance of C. gloeosporioides. Collectively, these findings provide insights into the mechanism by which the lncRNA109897-JrCCR4-JrTLP1b transcriptional cascade regulates the resistance of walnut to anthracnose.
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Affiliation(s)
- Rui Zhou
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Yuhui Dong
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Changxi Wang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Jianning Liu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Qiang Liang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Xiaoye Meng
- Department of Natural Resources Of Shandong Province, Forestry Protection and Development Service Center, Jinan, Shandong, China, 250000
| | - Xinya Lang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Shengyi Xu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Wenjun Liu
- State Key Laboratory of Crop Biology, College of Horticulture Sciences and Engineering, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Shuhui Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Sciences and Engineering, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Nan Wang
- State Key Laboratory of Crop Biology, College of Horticulture Sciences and Engineering, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Ke Qiang Yang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Hongcheng Fang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
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10
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Itoo H, Shah RA, Qurat S, Jeelani A, Khursheed S, Bhat ZA, Mir MA, Rather GH, Zargar SM, Shah MD, Padder BA. Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut ( Juglans regia L.). 3 Biotech 2023; 13:136. [PMID: 37124992 PMCID: PMC10130282 DOI: 10.1007/s13205-023-03563-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/15/2023] [Indexed: 05/02/2023] Open
Abstract
In the present study, we designed and validated genome-wide polymorphic SSR markers (110 SSRs) by mining the walnut genome. A total of 198,924 SSR loci were identified. Among these, successful primers were designed for 162,594 (81.73%) SSR loci. Dinucleotides were the most predominant accounting for 88.40% (175,075) of total SSRs. The SSR frequency was 377.312 SSR/Mb and it showed a decreasing trend from dinucleotide to octanucleotide motifs. We identified 20 highly polymorphic SSR markers and used them to genotype 72 walnut accessions. Over all, we obtained 118 alleles that ranged from 2 to 12 with an average value of 5.9. The higher SSR PIC values indicate their robustness in discriminating walnut genotypes. Heat map, PCA, and population structure categorized 72 walnut genotypes into 2 distinct clusters. The genetic variation within population was higher than among population as inferred by analysis of molecular variance (AMOVA). For walnut improvement, it is necessary to have a large repository of SSRs with high discriminative power. The present study reports 150,000 SSRs, which is the largest SSR repository for this important nut crop. Scientific communities may use this repository for walnut improvement such as QTL mapping, genetic studies, linkage map construction, and marker-assisted selection. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03563-6.
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Affiliation(s)
- H. Itoo
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Rafiq Ahmad Shah
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - S. Qurat
- Division of Fruit Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - Afnan Jeelani
- Division of Fruit Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - Sheikh Khursheed
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Zahoor A. Bhat
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - M. A. Mir
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - G. H. Rather
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - M. D. Shah
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Kashmir, 190 025 Srinagar, J&K India
| | - Bilal A. Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Kashmir, 190 025 Srinagar, J&K India
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Ma J, Zuo D, Ye H, Yan Y, Li M, Zhao P. Genome-wide identification, characterization, and expression pattern of the late embryogenesis abundant (LEA) gene family in Juglans regia and its wild relatives J. mandshurica. BMC PLANT BIOLOGY 2023; 23:80. [PMID: 36740678 PMCID: PMC9901102 DOI: 10.1186/s12870-023-04096-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Late Embryogenesis Abundant (LEA) proteins are a class of proteins associated with plant stress resistance. Two Juglans species, Juglans regia and J. mandshurica, are both diploid (2n = 32), monoecious perennial economic tree species with high edible, pharmaceutical, and timber value. The identification, characterization, and expression patterns of LEA proteins in J. regia and its wild relative, J. mandshurica, would not only provide the genetic basis of this gene family, but it would also supply clues for further studies of the evolution and regulating mechanisms of LEA proteins in other tree species. RESULTS In this study, we identified 25 and 20 members of the LEA gene family in Juglans regia and its wild relative, Juglans mandshurica, respectively. The results of phylogenetic analysis showed that the LEA members were divided into eight main subgroups. Predictions of their physicochemical properties showed the variable characteristics of LEA proteins, and the subcellular localization analysis indicated that most LEA proteins are localized in the nucleus. Chromosomal localization analysis and gene replication pattern prediction indicated that WGD is the predominant duplication mode of LEA genes. The results of the comparative analysis indicated a high level of collinearity between the two Juglans species. Analysis of cis-acting elements indicated that LEA genes had a relatively wide range of responses to abiotic stresses and phytohormonal processes, particularly in two phytohormones, methyl jasmonate and abscisic acid. Transcriptome profiling and qRT-PCR experiments showed that JrLEAs are commonly expressed in leaves, green husks, and male and female flowers, and most JmLEAs are more highly expressed in male flowers. We also hypothesized that JrLEAs are involved in the process of anthracnose resistance. Anthracnose-resistant varieties of JrLEAs presented relatively high expression levels at later stages. CONCLUSION In this study, we provide a theoretical basis for the functional study of LEA genes in J. regia and J. mandshurica. Analysis of cis-acting elements and gene expression indicated that JrLEAs and JmLEAs play important roles in resistance to biotic stresses in these species.
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Affiliation(s)
- Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, 710069 Shaanxi China
| | - Dongjun Zuo
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, 710069 Shaanxi China
- College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, 710069 Shaanxi China
| | - Yujie Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, 710069 Shaanxi China
| | - Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, 710069 Shaanxi China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, 710069 Shaanxi China
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Manzoor I, Samantara K, Bhat MS, Farooq I, Bhat KM, Mir MA, Wani SH. Advances in genomics for diversity studies and trait improvement in temperate fruit and nut crops under changing climatic scenarios. FRONTIERS IN PLANT SCIENCE 2023; 13:1048217. [PMID: 36743560 PMCID: PMC9893892 DOI: 10.3389/fpls.2022.1048217] [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: 09/19/2022] [Accepted: 11/09/2022] [Indexed: 06/18/2023]
Abstract
Genetic improvement of temperate fruit and nut crops through conventional breeding methods is not sufficient alone due to its extreme time-consuming, cost-intensive, and hard-to-handle approach. Again, few other constraints that are associated with these species, viz., their long juvenile period, high heterozygosity, sterility, presence of sexual incompatibility, polyploidy, etc., make their selection and improvement process more complicated. Therefore, to promote precise and accurate selection of plants based on their genotypes, supplement of advanced biotechnological tools, viz., molecular marker approaches along with traditional breeding methods, is highly required in these species. Different markers, especially the molecular ones, enable direct selection of genomic regions governing the trait of interest such as high quality, yield, and resistance to abiotic and biotic stresses instead of the trait itself, thus saving the overall time and space and helping screen fruit quality and other related desired traits at early stages. The availability of molecular markers like SNP (single-nucleotide polymorphism), DArT (Diversity Arrays Technology) markers, and dense molecular genetic maps in crop plants, including fruit and nut crops, led to a revelation of facts from genetic markers, thus assisting in precise line selection. This review highlighted several aspects of the molecular marker approach that opens up tremendous possibilities to reveal valuable information about genetic diversity and phylogeny to boost the efficacy of selection in temperate fruit crops through genome sequencing and thus cultivar improvement with respect to adaptability and biotic and abiotic stress resistance in temperate fruit and nut species.
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Affiliation(s)
- Ikra Manzoor
- Division of Fruit Science, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Kajal Samantara
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Momin Showkat Bhat
- Division of Floriculture and Landscape Architecture, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Iqra Farooq
- Field Station Bonera, Pulwama, Council of Industrial and Scientific Research (CSIR) Indian Institute of Integrative Medicine, J&K, Jammu, India
| | - Khalid Mushtaq Bhat
- Division of Fruit Science, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Mohammad Amin Mir
- Ambri Apple Research Centre, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shopian, India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu and Kashmir, Anantnag, India
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13
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Wang J, Ye H, Zhou H, Chen P, Liu H, Xi R, Wang G, Hou N, Zhao P. Genome-wide association analysis of 101 accessions dissects the genetic basis of shell thickness for genetic improvement in Persian walnut (Juglans regia L.). BMC PLANT BIOLOGY 2022; 22:436. [PMID: 36096735 PMCID: PMC9469530 DOI: 10.1186/s12870-022-03824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Understanding the underlying genetic mechanisms that drive phenotypic variations is essential for enhancing the efficacy of crop improvement. Persian walnut (Juglans regia L.), which is grown extensively worldwide, is an important economic tree fruit due to its horticultural, medicinal, and material value. The quality of the walnut fruit is related to the selection of traits such as thinner shells, larger filling rates, and better taste, which is very important for breeding in China. The complex quantitative fruit-related traits are influenced by a variety of physiological and environmental factors, which can vary widely between walnut genotypes. RESULTS For this study, a set of 101 Persian walnut accessions were re-sequenced, which generated a total of 906.2 Gb of Illumina sequence data with an average read depth of 13.8× for each accession. We performed the genome-wide association study (GWAS) using 10.9 Mb of high-quality single-nucleotide polymorphisms (SNPs) and 10 agronomic traits to explore the underlying genetic basis of the walnut fruit. Several candidate genes are proposed to be involved in walnut characteristics, including JrPXC1, JrWAKL8, JrGAMYB, and JrFRK1. Specifically, the JrPXC1 gene was confirmed to participate in the regulation of secondary wall cellulose thickening in the walnut shell. CONCLUSION In addition to providing considerable available genetic resources for walnut trees, this study revealed the underlying genetic basis involved in important walnut agronomic traits, particularly shell thickness, as well as providing clues for the improvement of genetic breeding and domestication in other perennial economic crops.
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Affiliation(s)
- Jiangtao Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Huijuan Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
- College of Forestry, Northwest A&F University, Yangling, 712100, China
| | - Pengpeng Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Ruimin Xi
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Gang Wang
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
| | - Na Hou
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China.
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
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Zhou R, Dong Y, Liu X, Feng S, Wang C, Ma X, Liu J, Liang Q, Bao Y, Xu S, Lang X, Gai S, Yang KQ, Fang H. JrWRKY21 interacts with JrPTI5L to activate the expression of JrPR5L for resistance to Colletotrichum gloeosporioides in walnut. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1152-1166. [PMID: 35765867 DOI: 10.1111/tpj.15883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Walnut (Juglans regia L.) anthracnose, induced by Colletotrichum gloeosporioides, is a catastrophic disease impacting the walnut industry in China. Although WRKY transcription factors play a key role in plant immunity, the function of the WRKY gene family in walnut resistance to C. gloeosporioides is not clear. Here, through transcriptome sequencing and quantitative real-time polymerase chain reaction (qRT-PCR), we identified a differentially expressed gene, JrWRKY21, that was significantly upregulated upon C. gloeosporioides infection in walnut. JrWRKY21 positively regulated walnut resistance to C. gloeosporioides, as demonstrated by virus-induced gene silencing and transient gene overexpression. Additionally, JrWRKY21 directly interacted with the transcriptional activator of the pathogenesis-related (PR) gene JrPTI5L in vitro and in vivo, and could bind to the W-box in the JrPTI5L promoter for transcriptional activation. Moreover, JrPTI5L could induce the expression of the PR gene JrPR5L through binding to the GCCGAC motif in the promoter. Our data support that JrWRKY21 can indirectly activate the expression of the JrPR5L gene via the WRKY21-PTI5L protein complex to promote resistance against C. gloeosporioides in walnut. The results will enhance our understanding of the mechanism behind walnut disease resistance and facilitate the genetic improvement of walnut by molecular breeding for anthracnose-resistant varieties.
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Affiliation(s)
- Rui Zhou
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian, Shandong Province, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian, Shandong Province, China
| | - Xia Liu
- Department of Science and Technology, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Shan Feng
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Changxi Wang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Xinmei Ma
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Jianning Liu
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Qiang Liang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian, Shandong Province, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian, Shandong Province, China
| | - Yan Bao
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Shengyi Xu
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Xinya Lang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Shasha Gai
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian, Shandong Province, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian, Shandong Province, China
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian, Shandong Province, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian, Shandong Province, China
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15
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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.
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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
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16
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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.
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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.
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17
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Jinnan W, Ruyue W, Jihong L, Yanting T, Haoping G, Lili H, Dongyue W, Xueling W. Construction of a high-density genetic map using specific-length amplified fragment markers and identification of QTLs for branching angle in poplar. Mol Genet Genomics 2022; 297:345-356. [PMID: 35015131 DOI: 10.1007/s00438-021-01850-6] [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: 07/26/2021] [Accepted: 12/18/2021] [Indexed: 11/28/2022]
Abstract
Branching angle is a critical factor that determines the morphological establishment and is a typical quantitative trait controlled by multiple genes. In this study, we used SLAF-seq to construct a high-density genetic map, to investigate the genetic architecture of branching angle in poplar (Populus leucopyramidalis). A total of 240,672 SLAF tags were obtained, including 103,691 polymorphic SLAF tags. After filtering, 53,407 polymorphic markers were sorted into eight segregation types, and 11,162 of them were used to construct the genetic map. 8447 were on the female parent map, 8532 were on the male parent map, and 11,162 were on the integrated map. The marker coverage was 4820.84 and 5044.80 cM for the female and male maps, and 3142.61 cM for the integrated map. The average intervals between two adjacent mapped markers were 0.55, 0.59, and 0.28 cM for the three maps, respectively. Two quantitative trait loci (QTLs) were detected. Seven markers that exceeded the threshold in these two regions were considered as being associated with branching angle and the phenotypic variance explained by each of these marker was 10.64-11.66%. After functional annotation, we identified 15 candidate genes and analyzed the expression of candidate genes in narrow and wide crown progenies by qRT-PCR. These results show that the combination of QTL and SLAF-seq will contribute to future breeding plans in poplar breeding, especially in narrow crown poplar breeding.
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Affiliation(s)
- Wang Jinnan
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Wang Ruyue
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Li Jihong
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China. .,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China. .,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China.
| | - Tian Yanting
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Guo Haoping
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Hou Lili
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Wang Dongyue
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Wang Xueling
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
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18
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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.
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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
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19
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Fang H, Liu X, Dong Y, Feng S, Zhou R, Wang C, Ma X, Liu J, Yang KQ. Transcriptome and proteome analysis of walnut (Juglans regia L.) fruit in response to infection by Colletotrichum gloeosporioides. BMC PLANT BIOLOGY 2021; 21:249. [PMID: 34059002 PMCID: PMC8166054 DOI: 10.1186/s12870-021-03042-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/13/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Walnut anthracnose induced by Colletotrichum gloeosporioides is a disastrous disease affecting walnut production. The resistance of walnut fruit to C. gloeosporioides is a highly complicated and genetically programmed process. However, the underlying mechanisms have not yet been elucidated. RESULTS To understand the molecular mechanism underlying the defense of walnut to C. gloeosporioides, we used RNA sequencing and label-free quantitation technologies to generate transcriptomic and proteomic profiles of tissues at various lifestyle transitions of C. gloeosporioides, including 0 hpi, pathological tissues at 24 hpi, 48 hpi, and 72 hpi, and distal uninoculated tissues at 120 hpi, in anthracnose-resistant F26 fruit bracts and anthracnose-susceptible F423 fruit bracts, which were defined through scanning electron microscopy. A total of 21,798 differentially expressed genes (DEGs) and 1929 differentially expressed proteins (DEPs) were identified in F26 vs. F423 at five time points, and the numbers of DEGs and DEPs were significantly higher in the early infection stage. Using pairwise comparisons and weighted gene co-expression network analysis of the transcriptome, we identified two modules significantly related to disease resistance and nine hub genes in the transcription expression gene networks. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis of the DEGs and DEPs revealed that many genes were mainly related to immune response, plant hormone signal transduction, and secondary metabolites, and many DEPs were involved in carbon metabolism and photosynthesis. Correlation analysis between the transcriptome data and proteome data also showed that the consistency of the differential expression of the mRNA and corresponding proteins was relatively higher in the early stage of infection. CONCLUSIONS Collectively, these results help elucidate the molecular response of walnut fruit to C. gloeosporioides and provide a basis for the genetic improvement of walnut disease resistance.
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Affiliation(s)
- Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Tai'an, Shandong Province, China
- State Forestry and Grassland Administr, ation Key Laboratory of Silviculture inthe Downstream Areas of the Yellow River, Shandong Agricultural University, Tai'an, Shandong Province, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Tai'an, Shandong Province, China
| | - Xia Liu
- Department of Science and Technology, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Tai'an, Shandong Province, China
- State Forestry and Grassland Administr, ation Key Laboratory of Silviculture inthe Downstream Areas of the Yellow River, Shandong Agricultural University, Tai'an, Shandong Province, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Tai'an, Shandong Province, China
| | - Shan Feng
- College of Forestry, Shandong Agricultural University, Tai'an, Shandong Province, China
| | - Rui Zhou
- College of Forestry, Shandong Agricultural University, Tai'an, Shandong Province, China
| | - Changxi Wang
- College of Forestry, Shandong Agricultural University, Tai'an, Shandong Province, China
| | - Xinmei Ma
- College of Forestry, Shandong Agricultural University, Tai'an, Shandong Province, China
| | - Jianning Liu
- College of Forestry, Shandong Agricultural University, Tai'an, Shandong Province, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Tai'an, Shandong Province, China.
- State Forestry and Grassland Administr, ation Key Laboratory of Silviculture inthe Downstream Areas of the Yellow River, Shandong Agricultural University, Tai'an, Shandong Province, China.
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Tai'an, Shandong Province, China.
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20
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Feng S, Fang H, Liu X, Dong Y, Wang Q, Yang KQ. Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia). BMC Genomics 2021; 22:15. [PMID: 33407106 PMCID: PMC7789297 DOI: 10.1186/s12864-020-07310-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/07/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is an important walnut production problem in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease resistance, the molecular mechanisms underlying resistance to C. gloeosporioides in walnut remain poorly understood. RESULTS The anthracnose-resistant F26 fruits from the B26 clone and the anthracnose-susceptible F423 fruits from the 4-23 clone of walnut were used as the test materials. Specifically, we performed a comparative transcriptome analysis of F26 and F423 fruit bracts to identify differentially expressed LncRNAs (DELs) at five time-points (tissues at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi). Compared with F423, a total of 14,525 DELs were identified, including 10,645 upregulated lncRNAs and 3846 downregulated lncRNAs in F26. The number of upregulated lncRNAs in F26 compared to in F423 was significantly higher at the early stages of C. gloeosporioides infection. A total of 5 modules related to disease resistance were screened by WGCNA and the target genes of lncRNAs were obtained. Bioinformatic analysis showed that the target genes of upregulated lncRNAs were enriched in immune-related processes during the infection of C. gloeosporioides, such as activation of innate immune response, defense response to bacterium, incompatible interaction and immune system process, and enriched in plant hormone signal transduction, phenylpropanoid biosynthesis and other pathways. And 124 known target genes for 96 hub lncRNAs were predicted, including 10 known resistance genes. The expression of 5 lncRNAs and 5 target genes was confirmed by qPCR, which was consistent with the RNA-seq data. CONCLUSIONS The results of this study provide the basis for future functional characterizations of lncRNAs regarding the C. gloeosporioides resistance of walnut fruit bracts.
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Affiliation(s)
- Shan Feng
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Tai'an, 271018, Shandong Province, China
- Shandong Taishan Forest Ecosystem Research Station, Tai'an, 271018, Shandong Province, China
| | - Xia Liu
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
- Department of Science and Technology, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Qingpeng Wang
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China.
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Tai'an, 271018, Shandong Province, China.
- Shandong Taishan Forest Ecosystem Research Station, Tai'an, 271018, Shandong Province, China.
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21
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Zeng D, Yang C, Li Q, Zhu W, Chen X, Peng M, Chen X, Lin Y, Wang H, Liu H, Liang J, Liu Q, Zhao Y. Identification of a quantitative trait loci (QTL) associated with ammonia tolerance in the Pacific white shrimp (Litopenaeus vannamei). BMC Genomics 2020; 21:857. [PMID: 33267780 PMCID: PMC7709431 DOI: 10.1186/s12864-020-07254-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 11/18/2020] [Indexed: 12/18/2022] Open
Abstract
Background Ammonia is one of the most common toxicological environment factors affecting shrimp health. Although ammonia tolerance in shrimp is closely related to successful industrial production, few genetic studies of this trait are available. Results In this study, we constructed a high-density genetic map of the Pacific white shrimp (Litopenaeus vannamei) using specific length amplified fragment sequencing (SLAF-seq). The constructed genetic map contained 17,338 polymorphic markers spanning 44 linkage groups, with a total distance of 6360.12 centimorgans (cM) and an average distance of 0.37 cM. Using this genetic map, we identified a quantitative trait locus (QTL) that explained 7.41–8.46% of the phenotypic variance in L. vannamei survival time under acute ammonia stress. We then sequenced the transcriptomes of the most ammonia-tolerant and the most ammonia-sensitive individuals from each of four genetically distinct L. vannamei families. We found that 7546 genes were differentially expressed between the ammonia-tolerant and ammonia-sensitive individuals. Using QTL analysis and the transcriptomes, we identified one candidate gene (annotated as an ATP synthase g subunit) associated with ammonia tolerance. Conclusions In this study, we constructed a high-density genetic map of L. vannamei and identified a QTL for ammonia tolerance. By combining QTL and transcriptome analyses, we identified a candidate gene associated with ammonia tolerance. Our work provides the basis for future genetic studies focused on molecular marker-assisted selective breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07254-x.
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Affiliation(s)
- Digang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Chunling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Qiangyong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Weilin Zhu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Xiaohan Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Yong Lin
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Huanling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agriculture University, Wuhan, 430070, China
| | - Hong Liu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agriculture University, Wuhan, 430070, China
| | - Jingzhen Liang
- Life Science Research Institute, Guangxi University, Nanning, 530004, China
| | - Qingyun Liu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
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22
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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.
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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.
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Schwarzkopf EJ, Motamayor JC, Cornejo OE. Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations. BMC Genomics 2020; 21:332. [PMID: 32349675 PMCID: PMC7191684 DOI: 10.1186/s12864-020-6746-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/21/2020] [Indexed: 12/16/2022] Open
Abstract
Background Recombination plays an important evolutionary role by breaking up haplotypes and shuffling genetic variation. This process impacts the ability of selection to eliminate deleterious mutations or increase the frequency of beneficial mutations in a population. To understand the role of recombination generating and maintaining haplotypic variation in a population, we can construct fine-scale recombination maps. Such maps have been used to study a variety of model organisms and proven to be informative of how selection and demographics shape species-wide variation. Here we present a fine-scale recombination map for ten populations of Theobroma cacao – a non-model, long-lived, woody crop. We use this map to elucidate the dynamics of recombination rates in distinct populations of the same species, one of which is domesticated. Results Mean recombination rates in range between 2.5 and 8.6 cM/Mb for most populations of T. cacao with the exception of the domesticated Criollo (525 cM/Mb) and Guianna, a more recently established population (46.5 cM/Mb). We found little overlap in the location of hotspots of recombination across populations. We also found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. We find mutations in FIGL-1, a protein shown to downregulate cross-over frequency in Arabidopsis, statistically associated to higher recombination rates in domesticated Criollo. Conclusions We generated fine-scale recombination maps for ten populations of Theobroma cacao and used them to understand what processes are associated with population-level variation in this species. Our results provide support to the hypothesis of increased recombination rates in domesticated plants (Criollo population). We propose a testable mechanistic hypothesis for the change in recombination rate in domesticated populations in the form of mutations to a previously identified recombination-suppressing protein. Finally, we establish a number of possible correlates of recombination hotspots that help explain general patterns of recombination in this species.
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Affiliation(s)
| | | | - Omar E Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA, USA.
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Luo X, Chen J. Distinguishing Sichuan Walnut Cultivars and Examining Their Relationships with Juglans regia and J. sigillata by FISH, Early-Fruiting Gene Analysis, and SSR Analysis. FRONTIERS IN PLANT SCIENCE 2020; 11:27. [PMID: 32161605 PMCID: PMC7052499 DOI: 10.3389/fpls.2020.00027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 06/02/2023]
Abstract
Walnuts are economically important tree species in Sichuan Province (China) that provide heathy nuts. Fluorescence in situ hybridization (FISH) and analyses of an early-fruiting gene fragment and simple sequence repeats (SSRs) were used to distinguish Sichuan walnut cultivars and examine their relationships with Juglans regia L. and Juglans sigillata Dode. Thirty-four small chromosomes were counted in four Sichuan walnut cultivars. In the four cultivars, 5S rDNA was located in the proximal regions of two chromosomes (5 and 6), while (AG3T3)3 was located at both ends of each chromosome. The existence of the signal at both chromosome ends ensured accurate chromosome counts. 5S rDNA and (AG3T3)3 were not effective in identifying Sichuan walnut cultivars. Evolutionary analysis involving 32 early-fruiting nucleotide sequences from Sichuan walnut materials were performed with the maximum likelihood method. There were a total of 602 positions. All positions with gaps and missing data were eliminated, resulting in a final dataset of 562 positions. The ML tree with the highest log likelihood (-1607.82) revealed two obvious groups: one including materials of J. regia, which fruits 1 year after grafting, and another including materials of J. sigillata, which fruits >3 years after grafting. The early-fruiting gene fragment divided 22 walnut materials (10 walnut cultivars and 12 walnut accessions) into two groups, indicating that it was somewhat effective for distinguishing Sichuan walnut cultivars. Furthermore, 22 SSR loci were revealed to identify nine walnut cultivars. Eight cultivars were exclusively discerned by one SSR locus each: Chuanzao 1 [CUJRB307 (116) or CUJRA206a (182)], Chuanzao 2 [JSI-73 (154)], Shuangzao [CUJRB103a (123), CUJRB218 (144), JSI-71 (146), or CUJRA206a (176)], Shimianju [ZMZ11 (138)], Meigupao [CUJRB218 (149), CUJRB103a (151), or CUJRA206a (190)], Muzhilinhe [CUJRB220 (136), ZMZ11 (147), CUJRC310 (156), or JSI-73 (166)], Maerkang [CUJRA124 (154), CUJRB218 (159), or CUJRA123 (182)], Yanyuanzao [CUJRA124 (150) or CUJRA206a (192)]. The Shuling cultivar was identified by the combination of ZMZ11 (148) and other SSR loci, which distinguished and excluded the Chuanzao 1 and Yanyuanzao cultivars. Our results will guide the identification and breeding of Sichuan walnut cultivars.
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Lu N, Zhang M, Xiao Y, Han D, Liu Y, Zhang Y, Yi F, Zhu T, Ma W, Fan E, Qu G, Wang J. Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F 1 population of Catalpa bungei × Catalpa duclouxii Dode. BMC PLANT BIOLOGY 2019; 19:596. [PMID: 31888555 PMCID: PMC6937828 DOI: 10.1186/s12870-019-2207-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/17/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Catalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for identifying key quantitative trait loci (QTLs) that affect important traits, such as plant growth and leaf traits, but also for other genetic studies. RESULTS Restriction site-associated DNA sequencing (RAD-seq) was used to identify molecular markers and construct a genetic map. Approximately 280.77 Gb of clean data were obtained after sequencing, and in total, 25,614,295 single nucleotide polymorphisms (SNPs) and 2,871,647 insertions-deletions (InDels) were initially identified in the genomes of 200 individuals of a C. bungei (7080) × Catalpa duclouxii (16-PJ-3) F1 population and their parents. Finally, 9072 SNP and 521 InDel markers that satisfied the requirements for constructing a genetic map were obtained. The integrated genetic map contained 9593 pleomorphic markers in 20 linkage groups and spanned 3151.63 cM, with an average distance between adjacent markers of 0.32 cM. Twenty QTLs for seven leaf traits and 13 QTLs for plant height at five successive time points were identified using our genetic map by inclusive composite interval mapping (ICIM). Q16-60 was identified as a QTL for five leaf traits, and three significant QTLs (Q9-1, Q18-66 and Q18-73) associated with plant growth were detected at least twice. Genome annotation suggested that a cyclin gene participates in leaf trait development, while the growth of C. bungei may be influenced by CDC48C and genes associated with phytohormone synthesis. CONCLUSIONS This is the first genetic map constructed in C. bungei and will be a useful tool for further genetic study, molecular marker-assisted breeding and genome assembly.
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Affiliation(s)
- Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Miaomiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Yao Xiao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Donghua Han
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037 Jiangsu People’s Republic of China
| | - Ying Liu
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Yu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Fei Yi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Tianqing Zhu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Erqin Fan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, People’s Republic of China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, People’s Republic of China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
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Zhao J, Xu Y, Li H, Yin Y, An W, Li Y, Wang Y, Fan Y, Wan R, Guo X, Cao Y. A SNP-Based High-Density Genetic Map of Leaf and Fruit Related Quantitative Trait Loci in Wolfberry ( Lycium Linn.). FRONTIERS IN PLANT SCIENCE 2019; 10:977. [PMID: 31440266 PMCID: PMC6693522 DOI: 10.3389/fpls.2019.00977] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 07/11/2019] [Indexed: 05/26/2023]
Abstract
Wolfberry (Lycium Linn. 2n = 24) fruit, Gouqizi, is a perennial shrub, traditional food and medicinal plant resource in China. Leaf and fruit related characteristics are economically important traits that are the focus for genetic improvement, but few studies into the molecular genetics of this crop have been reported to date. Here, an F1 population (302 individuals) derived from a cross between "NO.1 Ningqi" (Lycium barbarum L.) and "Chinese gouqi" (Lycium chinese Mill.) was constructed. We recorded fruit weight, longitude, diameter and index along with leaf length, width and index for three consecutive years from 2015 to 2017. Based on this population and these phenotypic data, we constructed the first high-density genetic map of Lycium using specific length amplified fragment sequencing (SLAF-seq) and analyzed quantitative trait loci (QTLs). The map contains 6733 single nucleotide polymorphisms and 12 linkage groups (LG) with a total map distance of 1702.45 cM and an average map distance of 0.253 cM. A total of 55 QTLs were mapped for more than 2 years, of which 18 stable QTLs for fruit index on LG 11, spanning an interval of 73.492-90.945 cM, were detected. qFI11-15 for fruit index was an impressive QTL with logarithm of odds (LOD) and proportion of variance explained (PEV) values reaching 11.07 and 19.7%, respectively. The QTLs on LG 11 were gathered tightly, having an average interval of less than 1 cM per QTL, suggesting that there might be a cluster region controlling fruit index. Remarkably, qLI10-2 and qLI11-2 for leaf index were detectable for 3 years. These results give novel insight into the genetic control of leaf and fruit related traits in Lycium and provide robust support for undertaking further positional cloning studies and implementing marker-assisted selection in seedlings.
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Affiliation(s)
- Jianhua Zhao
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yuhui Xu
- Biomarker Technology Corporation, Beijing, China
| | - Haoxia Li
- Desertification Control Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yue Yin
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Wei An
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yanlong Li
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yajun Wang
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yunfang Fan
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Ru Wan
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Xin Guo
- Biomarker Technology Corporation, Beijing, China
| | - Youlong Cao
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
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Zhang XF, Wang GY, Dong TT, Chen B, Du HS, Li CB, Zhang FL, Zhang HY, Xu Y, Wang Q, Geng SS. High-density genetic map construction and QTL mapping of first flower node in pepper (Capsicum annuum L.). BMC PLANT BIOLOGY 2019; 19:167. [PMID: 31035914 PMCID: PMC6489210 DOI: 10.1186/s12870-019-1753-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/31/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.). The trait is controlled by quantitative trait loci (QTL); however, studies have been limited on QTL mapping and genes contributing to the trait. RESULTS In this study, we developed a high density genetic map using specific-locus amplified fragment sequencing (SLAF-seq), a high-throughput strategy for de novo single nucleotide polymorphism discovery, based on 146 recombinant inbred lines (RILs) derived from an intraspecific cross between PM702 and FS871. The map contained 9328 SLAF markers on 12 linkage groups (LGs), and spanned a total genetic distance of 2009.69 centimorgan (cM) with an average distance of 0.22 cM. The sequencing depth for the map was 72.39-fold in the male parent, 57.04-fold in the female parent, and 15.65-fold in offspring. Using the genetic map, two major QTLs, named Ffn2.1 and Ffn2.2, identified on LG02 were strongly associated with FFN, with a phenotypic variance explanation of 28.62 and 19.56%, respectively. On the basis of the current annotation of C. annuum cv. Criollo de Morelos (CM334), 59 candidate genes were found within the Ffn2.1 and Ffn2.2 region, but only 3 of 59 genes were differentially expressed according to the RNA-seq results. Eventually we identified one gene associated with the FFN based on the function through GO, KEGG, and Swiss-prot analysis. CONCLUSIONS Our research showed that the construction of high-density genetic map using SLAF-seq is a valuable tool for fine QTL mapping. The map we constructed is by far the most saturated complete genetic map of pepper, and using it we conducted fine QTL mapping for the important trait, FFN. QTLs and candidate genes obtained in this study lay a good foundation for the further research on FFN-related genes and other genetic applications in pepper.
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Affiliation(s)
- Xiao-fen Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
- College of Horticulture, China Agricultural University, Beijing, 100097 People’s Republic of China
| | - Guo-yun Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Ting-ting Dong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Bin Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - He-shan Du
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Chang-bao Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Feng-lan Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Hai-ying Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Yong Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Qian Wang
- College of Horticulture, China Agricultural University, Beijing, 100097 People’s Republic of China
| | - San-sheng Geng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
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Mariotti R, Fornasiero A, Mousavi S, Cultrera NG, Brizioli F, Pandolfi S, Passeri V, Rossi M, Magris G, Scalabrin S, Scaglione D, Di Gaspero G, Saumitou-Laprade P, Vernet P, Alagna F, Morgante M, Baldoni L. Genetic Mapping of the Incompatibility Locus in Olive and Development of a Linked Sequence-Tagged Site Marker. FRONTIERS IN PLANT SCIENCE 2019; 10:1760. [PMID: 32117338 PMCID: PMC7025539 DOI: 10.3389/fpls.2019.01760] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/16/2019] [Indexed: 05/20/2023]
Abstract
The genetic control of self-incompatibility (SI) has been recently disclosed in olive. Inter-varietal crossing confirmed the presence of only two incompatibility groups (G1 and G2), suggesting a simple Mendelian inheritance of the trait. A double digest restriction associated DNA (ddRAD) sequencing of a biparental population segregating for incompatibility groups has been performed and high-density linkage maps were constructed in order to map the SI locus and identify gene candidates and linked markers. The progeny consisted of a full-sib family of 229 individuals derived from the cross 'Leccino' (G1) × 'Dolce Agogia' (G2) varieties, segregating 1:1 (G1:G2), in accordance with a diallelic self-incompatibility (DSI) model. A total of 16,743 single nucleotide polymorphisms was identified, 7,006 in the female parent 'Leccino' and 9,737 in the male parent 'Dolce Agogia.' Each parental map consisted of 23 linkage groups and showed an unusual large size (5,680 cM in 'Leccino' and 3,538 cM in 'Dolce Agogia'). Recombination was decreased across all linkage groups in pollen mother cells of 'Dolce Agogia,' the parent with higher heterozygosity, compared to megaspore mother cells of 'Leccino,' in a context of a species that showed exceptionally high recombination rates. A subset of 109 adult plants was assigned to either incompatibility group by a stigma test and the diallelic self-incompatibility (DSI) locus was mapped to an interval of 5.4 cM on linkage group 18. This region spanned a size of approximately 300 Kb in the olive genome assembly. We developed a sequence-tagged site marker in the DSI locus and identified five haplotypes in 57 cultivars with known incompatibility group assignment. A combination of two single-nucleotide polymorphisms (SNPs) was sufficient to predict G1 or G2 phenotypes in olive cultivars, enabling early marker-assisted selection of compatible genotypes and allowing for a rapid screening of inter-compatibility among cultivars in order to guarantee effective fertilization and increase olive production. The construction of high-density linkage maps has led to the development of the first functional marker in olive and provided positional candidate genes in the SI locus.
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Affiliation(s)
- Roberto Mariotti
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Alice Fornasiero
- Institute of Applied Genomics, Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Soraya Mousavi
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | | | - Federico Brizioli
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Saverio Pandolfi
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Valentina Passeri
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Martina Rossi
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Gabriele Magris
- Institute of Applied Genomics, Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | | | | | | | | | - Philippe Vernet
- University of Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | | | - Michele Morgante
- Institute of Applied Genomics, Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Luciana Baldoni
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
- *Correspondence: Luciana Baldoni,
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Wang Y, Wang C, Han H, Luo Y, Wang Z, Yan C, Xu W, Qu S. Construction of a High-Density Genetic Map and Analysis of Seed-Related Traits Using Specific Length Amplified Fragment Sequencing for Cucurbita maxima. FRONTIERS IN PLANT SCIENCE 2019; 10:1782. [PMID: 32153597 PMCID: PMC7046561 DOI: 10.3389/fpls.2019.01782] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/20/2019] [Indexed: 05/03/2023]
Abstract
Seed traits are agronomically important for Cucurbita breeding, but the genes controlling seed size, seed weight and seed number have not been mapped in Cucurbita maxima (C. maxima). In this study, 100 F2 individual derived from two parental lines, "2013-12" and "9-6", were applied to construct a 3,376.87-cM genetic map containing 20 linkage groups (LGs) with an average genetic distance of 0.47 cM using a total of 8,406 specific length amplified fragment (SLAF) markers in C. maxima. Ten quantitative trait loci (QTLs) of seed width (SW), seed length (SL) and hundred-seed weight (HSW) were identified using the composite interval mapping (CIM) method. The QTLs affecting SW, SL and HSW explained a maximum of 38.6%, 28.9% and 17.2% of the phenotypic variation and were detected in LG6, LG6 and LG17, respectively. To validate these results, an additional 150 F2 individuals were used for QTL mapping of SW and SL with cleaved amplified polymorphic sequence (CAPS) markers. We found that two major QTLs, SL6-1 and SW6-1, could be detected in both SLAF-seq and CAPS markers in an overlapped region. Based on gene annotation and non-synonymous single-nucleotide polymorphisms (SNPs) in the major SWand SL-associated regions, we found that two genes encoding a VQ motif and an E3 ubiquitin-protein ligase may be candidate genes influencing SL, while an F-box and leucinerich repeat (LRR) domain-containing protein is the potential regulator for SW in C. maxima. This study provides the first high-density linkage map of C. maxima using SNPs developed by SLAF-seq technology, which is a powerful tool for associated mapping of important agronomic traits, map-based gene cloning and marker-assisted selection (MAS)-based breeding in C. maxima.
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Affiliation(s)
- Yunli Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Chaojie Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Hongyu Han
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yusong Luo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Zhichao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Chundong Yan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Wenlong Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Shuping Qu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- *Correspondence: Shuping Qu,
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Yang Y, Xuan L, Yu C, Wang Z, Xu J, Fan W, Guo J, Yin Y. High-density genetic map construction and quantitative trait loci identification for growth traits in (Taxodium distichum var. distichum × T. mucronatum) × T. mucronatum. BMC PLANT BIOLOGY 2018; 18:263. [PMID: 30382825 PMCID: PMC6474422 DOI: 10.1186/s12870-018-1493-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 10/19/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND 'Zhongshanshan' is the general designation for the superior interspecific hybrid clones of Taxodium species, which is widely grown for economic and ecological purposes in southern China. Growth is the priority objective in 'Zhongshanshan' tree improvement. A high-density linkage map is vital to efficiently identify key quantitative trait loci (QTLs) that affect growth. RESULTS In total, 403.16 Gb of data, containing 2016,336 paired-end reads, was obtained after preprocessing. The average sequencing depth was 28.49 in T. distichum var. distichum, 25.18 in T. mucronatum, and 11.12 in each progeny. In total, 524,662 high-quality SLAFs were detected, of which 249,619 were polymorphic, and 6166 of the polymorphic markers met the requirements for use in constructing a genetic map. The final map harbored 6156 SLAF markers on 11 linkage groups, and was 1137.86 cM in length, with an average distance of 0.18 cM between adjacent markers. Separate QTL analyses of traits in different years by CIM detected 7 QTLs. While combining multiple-year data, 13 QTLs were detected by ICIM. 5 QTLs were repeatedly detected by the two methods, and among them, 3 significant QTLs (q6-2, q4-2 and q2-1) were detected in at least two traits. Bioinformatic analysis discoveried a gene annotated as a leucine-rich repeat receptor-like kinase gene within q4-2. CONCLUSIONS This map is the most saturated one constructed in a Taxodiaceae species to date, and would provide useful information for future comparative mapping, genome assembly, and marker-assisted selection.
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Affiliation(s)
- Ying Yang
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Lei Xuan
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Chaoguang Yu
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Ziyang Wang
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jianhua Xu
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Wencai Fan
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jinbo Guo
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yunlong Yin
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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Ridzuan R, Rafii MY, Ismail SI, Mohammad Yusoff M, Miah G, Usman M. Breeding for Anthracnose Disease Resistance in Chili: Progress and Prospects. Int J Mol Sci 2018; 19:E3122. [PMID: 30314374 PMCID: PMC6213496 DOI: 10.3390/ijms19103122] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/17/2018] [Accepted: 08/18/2018] [Indexed: 11/16/2022] Open
Abstract
Chili anthracnose is one of the most devastating fungal diseases affecting the quality and yield production of chili. The aim of this review is to summarize the current knowledge concerning the chili anthracnose disease, as well as to explore the use of marker-assisted breeding programs aimed at improving anthracnose disease resistance in this species. This disease is caused by the Colletotrichum species complex, and there have been ongoing screening methods of chili pepper genotypes with resistance to anthracnose in the field, as well as in laboratories. Conventional breeding involves phenotypic selection in the field, and it is more time-consuming compared to molecular breeding. The use of marker-assisted selection (MAS) on the basis of inheritance, the segregation ratio of resistance to susceptibility, and the gene-controlling resistance may contribute to the development of an improved chili variety and speed up the selection process, while also reducing genetic drag in the segregating population. More importantly, by using molecular markers, the linkage groups are determined dominantly and co-dominantly, meaning that the implementation of a reliable method to produce resistant varieties is crucial in future breeding programs. This updated information will offer a supportive direction for chili breeders to develop an anthracnose-resistant chili variety.
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Affiliation(s)
- Raihana Ridzuan
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Mohd Y Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Martini Mohammad Yusoff
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Gous Miah
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Magaji Usman
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
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Zhang Y, Li W, Lin Y, Zhang L, Wang C, Xu R. Construction of a high-density genetic map and mapping of QTLs for soybean (Glycine max) agronomic and seed quality traits by specific length amplified fragment sequencing. BMC Genomics 2018; 19:641. [PMID: 30157757 PMCID: PMC6116504 DOI: 10.1186/s12864-018-5035-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 08/23/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Soybean is not only an important oil crop, but also an important source of edible protein and industrial raw material. Yield-traits and quality-traits are increasingly attracting the attention of breeders. Therefore, fine mapping the QTLs associated with yield-traits and quality-traits of soybean would be helpful for soybean breeders. In the present study, a high-density linkage map was constructed to identify the QTLs for the yield-traits and quality-traits, using specific length amplified fragment sequencing (SLAF-seq). RESULTS SLAF-seq was performed to screen SLAF markers with 149 F8:11 individuals from a cross between a semi wild soybean, 'Huapidou', and a cultivated soybean, 'Qihuang26', which generated 400.91 M paired-end reads. In total, 53,132 polymorphic SLAF markers were obtained. The genetic linkage map was constructed by 5111 SLAF markers with segregation type of aa×bb. The final map, containing 20 linkage groups (LGs), was 2909.46 cM in length with an average distance of 0.57 cM between adjacent markers. The average coverage for each SLAF marker on the map was 81.26-fold in the male parent, 45.79-fold in the female parent, and 19.84-fold average in each F8:11 individual. According to the high-density map, 35 QTLs for plant height (PH), 100-seeds weight (SW), oil content in seeds (Oil) and protein content in seeds (Protein) were found to be distributed on 17 chromosomes, and 14 novel QTLs were identified for the first time. The physical distance of 11 QTLs was shorter than 100 Kb, suggesting a direct opportunity to find candidate genes. Furthermore, three pairs of epistatic QTLs associated with Protein involving 6 loci on 5 chromosomes were identified. Moreover, 13, 14, 7 and 9 genes, which showed tissue-specific expression patterns, might be associated with PH, SW, Oil and Protein, respectively. CONCLUSIONS With SLAF-sequencing, some novel QTLs and important QTLs for both yield-related and quality traits were identified based on a new, high-density linkage map. Moreover, 43 genes with tissue-specific expression patterns were regarded as potential genes in further study. Our findings might be beneficial to molecular marker-assisted breeding, and could provide detailed information for accurate QTL localization.
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Affiliation(s)
- Yanwei Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 China
| | - Wei Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 China
| | - Yanhui Lin
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 China
| | - Lifeng Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 China
| | - Caijie Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 China
| | - Ran Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 China
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Da Lio D, Cobo-Díaz JF, Masson C, Chalopin M, Kebe D, Giraud M, Verhaeghe A, Nodet P, Sarrocco S, Le Floch G, Baroncelli R. Combined Metabarcoding and Multi-locus approach for Genetic characterization of Colletotrichum species associated with common walnut (Juglans regia) anthracnose in France. Sci Rep 2018; 8:10765. [PMID: 30018385 PMCID: PMC6050315 DOI: 10.1038/s41598-018-29027-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/28/2018] [Indexed: 12/01/2022] Open
Abstract
Juglans regia (walnut) is a species belonging to the family Juglandaceae. Broadly spread in diverse temperate and subtropical regions, walnut is primarily cultivated for its nuts. In France, Colletotrichum sp. on walnut was detected for the first time in 2007; in 2011 the disease led to 50-70% losses in nut production. A combined approach of metabarcoding analysis and multi-locus genetic characterization of isolated strains has been used for taxonomic designation and to study the genetic variability of this pathogen in France. Evidence indicates that four Colletotrichum species are associated with walnut in France: 3 belong to the C. acutatum species complex and 1 to the C. gloeosporioides species complex. Results also show that C. godetiae is the most abundant species followed by C. fioriniae; while C. nymphaeae and another Colletotrichum sp. belonging to the C. gloeosporioides complex are found rarely. Representative isolates of detected species were also used to confirm pathogenicity on walnut fruits. The results show a high variability of lesion's dimensions among isolates tested. This study highlights the genetic and pathogenic heterogeneity of Colletotrichum species associated with walnut anthracnose in France providing useful information for targeted treatments or selection of resistant cultivars, in order to better control the disease.
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Affiliation(s)
- Daniele Da Lio
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Université de Brest, EA 3882, Technopôle Brest-Iroise, 29280, Plouzané, France
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - José F Cobo-Díaz
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Université de Brest, EA 3882, Technopôle Brest-Iroise, 29280, Plouzané, France
| | - Cyrielle Masson
- Station Expérimentale Nucicole Rhône-Alpes, 385 A Route de St Marcellin, 38160, Chatte, France
| | - Morgane Chalopin
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Université de Brest, EA 3882, Technopôle Brest-Iroise, 29280, Plouzané, France
| | - Djiby Kebe
- Station Expérimentale Nucicole Rhône-Alpes, 385 A Route de St Marcellin, 38160, Chatte, France
| | - Michel Giraud
- Centre Technique Interprofessionnel des Fruits et Légumes, Centre de Lanxade, 28 route des Nébouts, 24130, Prigonrieux, France
| | - Agnes Verhaeghe
- CTIFL/SENuRA, 385 A Route de St Marcellin, 38160, Chatte, France
| | - Patrice Nodet
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Université de Brest, EA 3882, Technopôle Brest-Iroise, 29280, Plouzané, France
| | - Sabrina Sarrocco
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Gaetan Le Floch
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Université de Brest, EA 3882, Technopôle Brest-Iroise, 29280, Plouzané, France
| | - Riccardo Baroncelli
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Université de Brest, EA 3882, Technopôle Brest-Iroise, 29280, Plouzané, France.
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Wu J, Zhao Q, Zhang L, Li S, Ma Y, Pan L, Lin H, Wu G, Yuan H, Yu Y, Wang X, Yang X, Li Z, Jiang T, Sun D. QTL Mapping of Fiber-Related Traits Based on a High-Density Genetic Map in Flax ( Linum usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2018; 9:885. [PMID: 30065730 PMCID: PMC6056681 DOI: 10.3389/fpls.2018.00885] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/07/2018] [Indexed: 05/18/2023]
Abstract
UNLABELLED A genetic map is an important and valuable tool for quantitative trait locus (QTL) mapping, marker-assisted selection (MAS)-based breeding, and reference-assisted chromosome assembly. In this study, 112 F2 plants from a cross between Linum usitatissimum L. "DIANE" and "NY17" and parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 61.64 Gb of raw data containing 253.71 Mb paired-end reads, each 101 bp in length, were obtained. A total of 192,797 SLAFs were identified, of which 23,115 were polymorphic, with a polymorphism rate of 11.99%. Finally, 2,339 SLAFs were organized into a linkage map consisting of 15 linkage groups (LGs). The total length of the genetic map was 1483.25 centimorgans (cM) and the average distance between adjacent markers was 0.63 cM. Combined with flax chromosome-scale pseudomolecules, 12 QTLs associating with 6 flax fiber-related traits were mapped on the chromosomal scaffolds. This high-density genetic map of flax should serve as a foundation for flax fine QTL mapping, draft genome assembly, and MAS-guided breeding. Ultimately, the genomic regions identified in this research could potentially be valuable for improving flax fiber cultivars, as well as for identification of candidate genes involved in flax fiber formation processes. SIGNIFICANCE STATEMENT A high-density genetic map of flax was constructed, and QTLs were identified on the sequence scaffolds to be interrelated with fiber-related traits. The results of this study will not only provide a platform for gene/QTL fine mapping, map-based gene isolation, and molecular breeding for flax, but also provide a reference to help position sequence scaffolds on the physical map and assist in the process of assembling the flax genome sequence.
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Affiliation(s)
- Jianzhong Wu
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Qian Zhao
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Liyan Zhang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Suiyan Li
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yanhua Ma
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Liyan Pan
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Hong Lin
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Guangwen Wu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Hongmei Yuan
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ying Yu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xun Wang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xue Yang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zhugang Li
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
- *Correspondence: Zhugang Li
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Tingbo Jiang
| | - Dequan Sun
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Dequan Sun
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He Y, Yuan W, Dong M, Han Y, Shang F. The First Genetic Map in Sweet Osmanthus ( Osmanthus fragrans Lour.) Using Specific Locus Amplified Fragment Sequencing. FRONTIERS IN PLANT SCIENCE 2017; 8:1621. [PMID: 29018460 PMCID: PMC5614988 DOI: 10.3389/fpls.2017.01621] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/05/2017] [Indexed: 05/23/2023]
Abstract
Osmanthus fragrans is an ornamental plant of substantial commercial value, and no genetic linkage maps of this species have previously been reported. Specific-locus amplified fragment sequencing (SLAF-seq) is a recently developed technology that allows massive single nucleotide polymorphisms (SNPs) to be identified and high-resolution genotyping. In our current research, we generated the first genetic map of O. fragrans using SLAF-seq, which is composed with 206.92 M paired-end reads and 173,537 SLAF markers. Among total 90,715 polymorphic SLAF markers, 15,317 polymorphic SLAFs could be used for genetic map construction. The integrated map contained 14,189 high quality SLAFs that were grouped in 23 genetic linkage groups, with a total length of 2962.46 cM and an average distance of 0.21 cM between two adjacent markers. In addition, 23,664 SNPs were identified from the mapped markers. As far as we know, this is the first of the genetic map of O. fragrans. Our results are further demonstrate that SLAF-seq is a very effective method for developing markers and constructing high-density linkage maps. The SNP markers and the genetic map reported in this study should be valuable resource in future research.
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Affiliation(s)
- Yanxia He
- Plant Germplasm Resources and Genetic Laboratory, College of Life Sciences, Henan UniversityKaifeng, China
| | - Wangjun Yuan
- Institute of Pharmacy, Pharmaceutical College of Henan UniversityKaifeng, China
| | - Meifang Dong
- Plant Germplasm Resources and Genetic Laboratory, College of Life Sciences, Henan UniversityKaifeng, China
| | - Yuanji Han
- Plant Germplasm Resources and Genetic Laboratory, College of Life Sciences, Henan UniversityKaifeng, China
| | - Fude Shang
- Plant Germplasm Resources and Genetic Laboratory, College of Life Sciences, Henan UniversityKaifeng, China
- Woe Key Laboratory of Plant Stress Biology, Henan UniversityKaifeng, China
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Qian W, Fan G, Liu D, Zhang H, Wang X, Wu J, Xu Z. Construction of a high-density genetic map and the X/Y sex-determining gene mapping in spinach based on large-scale markers developed by specific-locus amplified fragment sequencing (SLAF-seq). BMC Genomics 2017; 18:276. [PMID: 28376721 PMCID: PMC5379770 DOI: 10.1186/s12864-017-3659-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 03/25/2017] [Indexed: 12/21/2022] Open
Abstract
Background Cultivated spinach (Spinacia oleracea L.) is one of the most widely cultivated types of leafy vegetable in the world, and it has a high nutritional value. Spinach is also an ideal plant for investigating the mechanism of sex determination because it is a dioecious species with separate male and female plants. Some reports on the sex labeling and localization of spinach in the study of molecular markers have surfaced. However, there have only been two reports completed on the genetic map of spinach. The lack of rich and reliable molecular markers and the shortage of high-density linkage maps are important constraints in spinach research work. In this study, a high-density genetic map of spinach based on the Specific-locus Amplified Fragment Sequencing (SLAF-seq) technique was constructed; the sex-determining gene was also finely mapped. Results Through bio-information analysis, 50.75 Gb of data in total was obtained, including 207.58 million paired-end reads. Finally, 145,456 high-quality SLAF markers were obtained, with 27,800 polymorphic markers and 4080 SLAF markers were finally mapped onto the genetic map after linkage analysis. The map spanned 1,125.97 cM with an average distance of 0.31 cM between the adjacent marker loci. It was divided into 6 linkage groups corresponding to the number of spinach chromosomes. Besides, the combination of Bulked Segregation Analysis (BSA) with SLAF-seq technology(super-BSA) was employed to generate the linkage markers with the sex-determining gene. Combined with the high-density genetic map of spinach, the sex-determining gene X/Y was located at the position of the linkage group (LG) 4 (66.98 cM–69.72 cM and 75.48 cM–92.96 cM), which may be the ideal region for the sex-determining gene. Conclusions A high-density genetic map of spinach based on the SLAF-seq technique was constructed with a backcross (BC1) population (which is the highest density genetic map of spinach reported at present). At the same time, the sex-determining gene X/Y was mapped to LG4 with super-BSA. This map will offer a suitable basis for further study of spinach, such as gene mapping, map-based cloning of Specific genes, quantitative trait locus (QTL) mapping and marker-assisted selection (MAS). It will also provide an efficient reference for studies on the mechanism of sex determination in other dioecious plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3659-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Qian
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guiyan Fan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dandan Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Helong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhaosheng Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis. Sci Rep 2017; 7:39826. [PMID: 28045132 PMCID: PMC5206627 DOI: 10.1038/srep39826] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 11/28/2016] [Indexed: 02/03/2023] Open
Abstract
The Chinese mitten crab Eriocheir sinensis is the most economically important cultivated crab species in China, and its genome has a high number of chromosomes (2n = 146). To obtain sufficient markers for construction of a dense genetic map for this species, we employed the recently developed specific-locus amplified fragment sequencing (SLAF-seq) method for large-scale SNPs screening and genotyping in a F1 full-sib family of 149 individuals. SLAF-seq generated 127,677 polymorphic SNP markers, of which 20,803 valid markers were assigned into five segregation types and were used together with previous SSR markers for linkage map construction. The final integrated genetic map included 17,680 SNP and 629 SSR markers on the 73 linkage groups (LG), and spanned 14,894.9 cM with an average marker interval of 0.81 cM. QTL mapping localized three significant growth-related QTL to a 1.2 cM region in LG53 as well as 146 sex-linked markers in LG48. Genome-wide QTL-association analysis further identified four growth-related QTL genes named LNX2, PAK2, FMRFamide and octopamine receptors. These genes are involved in a variety of different signaling pathways including cell proliferation and growth. The map and SNP markers described here will be a valuable resource for the E. sinensis genome project and selective breeding programs.
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Zhao X, Huang L, Zhang X, Wang J, Yan D, Li J, Tang L, Li X, Shi T. Construction of high-density genetic linkage map and identification of flowering-time QTLs in orchardgrass using SSRs and SLAF-seq. Sci Rep 2016; 6:29345. [PMID: 27389619 PMCID: PMC4937404 DOI: 10.1038/srep29345] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/17/2016] [Indexed: 11/09/2022] Open
Abstract
Orchardgrass (Dactylis glomerata L.) is one of the most economically important perennial, cool-season forage species grown and pastured worldwide. High-density genetic linkage mapping is a valuable and effective method for exploring complex quantitative traits. In this study, we developed 447,177 markers based on SLAF-seq and used them to perform a comparative genomics analysis. Perennial ryegrass sequences were the most similar (5.02%) to orchardgrass sequences. A high-density linkage map of orchardgrass was constructed using 2,467 SLAF markers and 43 SSRs, which were distributed on seven linkage groups spanning 715.77 cM. The average distance between adjacent markers was 0.37 cM. Based on phenotyping in four environments, 11 potentially significant quantitative trait loci (QTLs) for two target traits–heading date (HD) and flowering time (FT)–were identified and positioned on linkage groups LG1, LG3, and LG5. Significant QTLs explained 8.20–27.00% of the total phenotypic variation, with the LOD ranging from 3.85–12.21. Marker167780 and Marker139469 were associated with FT and HD at the same location (Ya’an) over two different years. The utility of SLAF markers for rapid generation of genetic maps and QTL analysis has been demonstrated for heading date and flowering time in a global forage grass.
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Affiliation(s)
- Xinxin Zhao
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xinquan Zhang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jianping Wang
- Agronomy Department, University of Florida, FL, 32610, USA
| | - Defei Yan
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ji Li
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lu Tang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaolong Li
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Tongwei Shi
- Biomarker Technologies Corporation, Beijing, 101300, China
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Luo C, Shu B, Yao Q, Wu H, Xu W, Wang S. Construction of a High-Density Genetic Map Based on Large-Scale Marker Development in Mango Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq). FRONTIERS IN PLANT SCIENCE 2016; 7:1310. [PMID: 27625670 PMCID: PMC5003885 DOI: 10.3389/fpls.2016.01310] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/16/2016] [Indexed: 05/22/2023]
Abstract
Genetic maps are particularly important and valuable tools for quantitative trait locus (QTL) mapping and marker assisted selection (MAS) of plant with desirable traits. In this study, 173 F1 plants from a cross between Mangifera indica L. "Jin-Hwang" and M. indica L. "Irwin" and their parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 66.02 Gb of raw data containing 330.64 M reads were obtained. A total of 318,414 SLAFs were detected, of which 156,368 were polymorphic. Finally, 6594 SLAFs were organized into a linkage map consisting of 20 linkage groups (LGs). The total length of the map was 3148.28 cM and the average distance between adjacent markers was 0.48 cM. This map could be considered, to our knowledge, the first high-density genetic map of mango, and might form the basis for fine QTL mapping and MAS of mango.
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