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Liu D, Ye Y, Tang R, Gong Y, Chen S, Zhang C, Mei P, Chen J, Chen L, Ma C. High-density genetic map construction and QTL mapping of a zigzag-shaped stem trait in tea plant (Camellia sinensis). BMC PLANT BIOLOGY 2024; 24:382. [PMID: 38724900 PMCID: PMC11080114 DOI: 10.1186/s12870-024-05082-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
The highly unique zigzag-shaped stem phenotype in tea plants boasts significant ornamental value and is exceptionally rare. To investigate the genetic mechanism behind this trait, we developed BC1 artificial hybrid populations. Our genetic analysis revealed the zigzag-shaped trait as a qualitative trait. Utilizing whole-genome resequencing, we constructed a high-density genetic map from the BC1 population, incorporating 5,250 SNP markers across 15 linkage groups, covering 3,328.51 cM with an average marker interval distance of 0.68 cM. A quantitative trait locus (QTL) for the zigzag-shaped trait was identified on chromosome 4, within a 61.2 to 97.2 Mb range, accounting for a phenotypic variation explained (PVE) value of 13.62%. Within this QTL, six candidate genes were pinpointed. To better understand their roles, we analyzed gene expression in various tissues and individuals with erect and zigzag-shaped stems. The results implicated CsXTH (CSS0035625) and CsCIPK14 (CSS0044366) as potential key contributors to the zigzag-shaped stem formation. These discoveries lay a robust foundation for future functional genetic mapping and tea plant genetic enhancement.
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Affiliation(s)
- Dingding Liu
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Yuanyuan Ye
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Rongjin Tang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Yang Gong
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Si Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Chenyu Zhang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Piao Mei
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Jiedan Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.
| | - Liang Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.
| | - Chunlei Ma
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.
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2
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He Q, Zhang H, Li T, Zhang X, Li X, Dong C. NIR Spectral Inversion of Soil Physicochemical Properties in Tea Plantations under Different Particle Size States. SENSORS (BASEL, SWITZERLAND) 2023; 23:9107. [PMID: 38005495 PMCID: PMC10675699 DOI: 10.3390/s23229107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/05/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023]
Abstract
Soil fertility is vital for the growth of tea plants. The physicochemical properties of soil play a key role in the evaluation of soil fertility. Thus, realizing the rapid and accurate detection of soil physicochemical properties is of great significance for promoting the development of precision agriculture in tea plantations. In recent years, spectral data have become an important tool for the non-destructive testing of soil physicochemical properties. In this study, a support vector regression (SVR) model was constructed to model the hydrolyzed nitrogen, available potassium, and effective phosphorus in tea plantation soils of different grain sizes. Then, the successful projections algorithm (SPA) and least-angle regression (LAR) and bootstrapping soft shrinkage (BOSS) variable importance screening methods were used to optimize the variables in the soil physicochemical properties. The findings demonstrated that soil particle sizes of 0.25-0.5 mm produced the best predictions for all three physicochemical properties. After further using the dimensionality reduction approach, the LAR algorithm (R2C = 0.979, R2P = 0.976, RPD = 6.613) performed optimally in the prediction model for hydrolytic nitrogen at a soil particle size of 0.25~0.5. The models using data dimensionality reduction and those that used the BOSS method to estimate available potassium (R2C = 0.977, R2P = 0.981, RPD = 7.222) and effective phosphorus (R2C = 0.969, R2P = 0.964, RPD = 5.163) had the best accuracy. In order to offer a reference for the accurate detection of soil physicochemical properties in tea plantations, this study investigated the modeling effect of each physicochemical property under various soil particle sizes and integrated the regression model with various downscaling strategies.
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Affiliation(s)
- Qinghai He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310008, China; (Q.H.); (X.L.)
- Shandong Academy of Agricultural Machinery Science, Jinan 250100, China;
| | - Haowen Zhang
- Shandong Academy of Agricultural Machinery Science, Jinan 250100, China;
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China;
- College of Mechanical and Electrical Engineering, Shandong Agricultural University, Tai’an 271000, China;
| | - Tianhua Li
- College of Mechanical and Electrical Engineering, Shandong Agricultural University, Tai’an 271000, China;
| | - Xiaojia Zhang
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China;
| | - Xiaoli Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310008, China; (Q.H.); (X.L.)
| | - Chunwang Dong
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China;
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Abstract
Specific length amplified fragment sequencing (SLAF-seq) technology is a simplified genome sequencing technology based on next-generation sequencing. SLAF-seq technology has several distinguishing characteristics: 1. Deep sequencing to ensure accuracy of genotyping; 2. Effectively reduce sequencing costs; 3. Pre-designed simplified representation scheme to optimize marker efficiency; 4. Doubled barcode system for large populations. The advantages and technical process of SLAF-seq are described briefly with summarized results for the application of SLAF-seq in development of molecular markers, construction of high-density genetic map and gene mapping in ornamental plants. Finally, the difficulties and prospects of this method are discussed in application.
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Affiliation(s)
- Yang Zhou
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China.
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Chen T, Hu L, Wang S, Wang L, Cheng X, Chen H. Construction of High-Density Genetic Map and Identification of a Bruchid Resistance Locus in Mung Bean (Vigna radiata L.). Front Genet 2022; 13:903267. [PMID: 35873485 PMCID: PMC9305327 DOI: 10.3389/fgene.2022.903267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Mung bean (Vigna radiata L.) is an economically important grain legume cultivated in Asian countries. High-density genetic linkage is a valuable and effective tool for mapping quantitative trait loci (QTL). In the current study, a high-resolution genetic map containing 4,180 single-nucleotide polymorphisms (SNPs) was assigned to 11 linkage groups (LGs) and spanning 1,751.39 cM in length was constructed for mung bean, and the average distance between adjacent markers was 0.42 cM. Bruchids (Callosobruchus spp.) cause significant damage to and loss of legume seeds. A locus for bruchid resistance was detected. The gene Vradi05g03810, encoding a probable resistance-specific protein, was found to be the most likely key candidate gene in mung beans. A 69-bp sequence deletion was identified in the coding region by comparing the cDNA sequences of bruchid-resistant and bruchid-susceptible lines. This SNP-based high-density linkage map is one of the first to be constructed across the mung bean genome. This map will not only facilitate the genetic mapping of genes or complex loci that control important agronomic traits but also offer a tool for promoting future genetics and comparative genomic studies in Vigna.
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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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Zhang Q, Liu J, Liu W, Liu N, Zhang Y, Xu M, Liu S, Ma X, Zhang Y. Construction of a High-Density Genetic Map and Identification of Quantitative Trait Loci Linked to Fruit Quality Traits in Apricots Using Specific-Locus Amplified Fragment Sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:798700. [PMID: 35237282 PMCID: PMC8882730 DOI: 10.3389/fpls.2022.798700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/10/2022] [Indexed: 05/17/2023]
Abstract
Improving fruit quality is one of the main tasks in modern commercial apricot breeding. Because of the lack of high-density linkage maps and fine mapping, it is difficult to obtain molecular markers that can assist in breeding for quantitative inheritance of fruit quality traits. In this study, specific-locus amplified fragment sequencing was used to genotype 169 seedlings of F1 apricot (Prunus armeniaca L.) progenies derived from crossing "Chuanzhihong" (H) with "Saimaiti" (S). After aligning to the Prunus armeniaca reference genome and filtering out low-quality variants, 6,012 high-quality single nucleotide polymorphisms were obtained and employed to construct a genetic map for each parent. The genetic linkage maps showed eight linkage groups of apricot, covering a distance of 809.6 cM in "H" and 1076.4 cM in "S". The average distance between markers in "H" and "S" was 0.62 and 0.95 cM, respectively. To map quantitative trait loci (QTLs) for fruit quality, we investigated fruit quality traits, including fruit weight (FW), fruit height (FH), fruit lateral width (FL), fruit ventral width (FV), soluble solids content (SSC), and fruit firmness (FF) for all seedlings genotyped in 2018 and 2019. Eleven and nine QTLs linked to fruit quality traits were anchored on the "H" and "S" maps, respectively, and 1,138 putative candidate genes for 16 most significant regions on the corresponding chromosome were identified based on gene annotation. Among them, fruit size contained 648 genes in 11 intervals on the reference genome, SSC contained 372 genes in 3 intervals, and FF contained 117 genes in 2 intervals. Our findings uncovered the genetic basis of apricot fruit quality, and provided candidate genes for further molecular genetic studies on fruit quality and QTL targets for future marker-assisted selection of apricot quality improvement breeding.
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An Y, Chen L, Tao L, Liu S, Wei C. QTL Mapping for Leaf Area of Tea Plants ( Camellia sinensis) Based on a High-Quality Genetic Map Constructed by Whole Genome Resequencing. FRONTIERS IN PLANT SCIENCE 2021; 12:705285. [PMID: 34394160 PMCID: PMC8358608 DOI: 10.3389/fpls.2021.705285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/07/2021] [Indexed: 05/08/2023]
Abstract
High-quality genetic maps play important roles in QTL mapping and molecular marker-assisted breeding. Tea leaves are not only important vegetative organs but are also the organ for harvest with important economic value. However, the key genes and genetic mechanism of regulating leaf area have not been clarified. In this study, we performed whole-genome resequencing on "Jinxuan," "Yuncha 1" and their 96 F1 hybrid offspring. From the 1.84 Tb of original sequencing data, abundant genetic variation loci were identified, including 28,144,625 SNPs and 2,780,380 indels. By integrating the markers of a previously reported genetic map, a high-density genetic map consisting of 15 linkage groups including 8,956 high-quality SNPs was constructed. The total length of the genetic map is 1,490.81 cM, which shows good collinearity with the genome. A total of 25 representative markers (potential QTLs) related to leaf area were identified, and there were genes differentially expressed in large and small leaf samples near these markers. GWAS analysis further verified the reliability of QTL mapping. Thirty-one pairs of newly developed indel markers located near these potential QTLs showed high polymorphism and had good discrimination between large and small leaf tea plant samples. Our research will provide necessary support and new insights for tea plant genetic breeding, quantitative trait mapping and yield improvement.
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Affiliation(s)
- Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Linbo Chen
- Yunnan Provincial Key Laboratory of Tea Science, Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, China
| | - Lingling Tao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- *Correspondence: Chaoling Wei,
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Wang L, Conteh B, Fang L, Xia Q, Nian H. QTL mapping for soybean (Glycine max L.) leaf chlorophyll-content traits in a genotyped RIL population by using RAD-seq based high-density linkage map. BMC Genomics 2020; 21:739. [PMID: 33096992 PMCID: PMC7585201 DOI: 10.1186/s12864-020-07150-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/13/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Different soybean (Glycine max L.) leaf chlorophyll-content traits are considered to be significantly linked to soybean yield. To map the quantitative trait loci (QTLs) of soybean leaf chlorophyll-content traits, an advanced recombinant inbred line (RIL, ZH, Zhonghuang 24 × Huaxia 3) population was adopted to phenotypic data acquisitions for the target traits across six distinct environments (seasons and soybean growth stages). Moreover, the restriction site-associated DNA sequencing (RAD-seq) based high-density genetic linkage map of the RIL population was utilized for QTL mapping by carrying out the composite interval mapping (CIM) approach. RESULTS Correlation analyses showed that most traits were correlated with each other under specific chlorophyll assessing method and were regulated both by hereditary and environmental factors. In this study, 78 QTLs for soybean leaf chlorophyll-content traits were identified. Furthermore, 13 major QTLs and five important QTL hotspots were classified and highlighted from the detected QTLs. Finally, Glyma01g15506, Glyma02g08910, Glyma02g11110, Glyma07g15960, Glyma15g19670 and Glyma15g19810 were predicted from the genetic intervals of the major QTLs and important QTL hotspots. CONCLUSIONS The detected QTLs and candidate genes may facilitate to gain a better understanding of the hereditary basis of soybean leaf chlorophyll-content traits and may be valuable to pave the way for the marker-assisted selection (MAS) breeding of the target traits.
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Affiliation(s)
- Liang Wang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Brima Conteh
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Linzhi Fang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Qiuju Xia
- Beijing Genomics Institute (BGI) Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083 Guangdong People’s Republic of China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
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Huang J, Ma Q, Cai Z, Xia Q, Li S, Jia J, Chu L, Lian T, Nian H, Cheng Y. Identification and Mapping of Stable QTLs for Seed Oil and Protein Content in Soybean [ Glycine max (L.) Merr.]. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6448-6460. [PMID: 32401505 DOI: 10.1021/acs.jafc.0c01271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This research aimed to identify stable quantitative trait loci (QTL) associated with oil and protein content in soybean. A population of 196 recombinant inbred lines (RILs) derived from Huachun 2 × Wayao was used to evaluate these target traits. A high-density genetic linkage map was constructed by using high-throughput genome-wide sequencing technology, which contained 3413 recombination bin markers and spanned 5400.4 cM with an average distance of 1.58 cM between markers. Eighteen stable QTLs controlling oil and protein content were detected. Among them, qOil-11-1 was identified for the first time as a novel QTL, while qOil-5-1, qPro-10-1, and qPro-14-1 were strong and stable QTLs with high log-likelihood (LOD) values. Sixteen differentially expressed genes (DEGs) within these four QTLs were shown to be highly expressed during seed development based on RNA sequencing (RNA-seq) data analysis. Our results may contribute toward gene mining and marker-assisted selection (MAS) for breeding a high-quality soybean in the future.
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Affiliation(s)
- Jinghua Huang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Qiuju Xia
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, People's Republic of China
| | - Shuxian Li
- United States Department of Agriculture, Agricultural Research Service, Crop Genetics Research Unit, 141 Experiment Station Road, P.O. Box 345, Stoneville, Mississippi 38776, United States
| | - Jia Jia
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Li Chu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
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Chen JD, Zheng C, Ma JQ, Jiang CK, Ercisli S, Yao MZ, Chen L. The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant. HORTICULTURE RESEARCH 2020; 7:63. [PMID: 32377354 PMCID: PMC7192901 DOI: 10.1038/s41438-020-0288-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/02/2020] [Accepted: 03/08/2020] [Indexed: 05/07/2023]
Abstract
Tea is one of the most popular nonalcoholic beverages due to its characteristic secondary metabolites with numerous health benefits. Although two draft genomes of tea plant (Camellia sinensis) have been published recently, the lack of chromosome-scale assembly hampers the understanding of the fundamental genomic architecture of tea plant and potential improvement. Here, we performed a genome-wide chromosome conformation capture technique (Hi-C) to obtain a chromosome-scale assembly based on the draft genome of C. sinensis var. sinensis and successfully ordered 2984.7 Mb (94.7%) scaffolds into 15 chromosomes. The scaffold N50 of the improved genome was 218.1 Mb, ~157-fold higher than that of the draft genome. Collinearity comparison of genome sequences and two genetic maps validated the high contiguity and accuracy of the chromosome-scale assembly. We clarified that only one Camellia recent tetraploidization event (CRT, 58.9-61.7 million years ago (Mya)) occurred after the core-eudicot common hexaploidization event (146.6-152.7 Mya). Meanwhile, 9243 genes (28.6%) occurred in tandem duplication, and most of these expanded after the CRT event. These gene duplicates increased functionally divergent genes that play important roles in tea-specific biosynthesis or stress response. Sixty-four catechin- and caffeine-related quantitative trait loci (QTLs) were anchored to chromosome assembly. Of these, two catechin-related QTL hotspots were derived from the CRT event, which illustrated that polyploidy has played a dramatic role in the diversification of tea germplasms. The availability of a chromosome-scale genome of tea plant holds great promise for the understanding of genome evolution and the discovery of novel genes contributing to agronomically beneficial traits in future breeding programs.
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Affiliation(s)
- Jie-Dan Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Chao Zheng
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Jian-Qiang Ma
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Chen-Kai Jiang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Ming-Zhe Yao
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Liang Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
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11
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Akhmetshina AO, Strygina KV, Khlestkina EK, Porokhovinova EA, Brutch NB. High-throughput sequencing techniques to flax genetics and breeding. ECOLOGICAL GENETICS 2020. [PMID: 0 DOI: 10.17816/ecogen16126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Flax (Linum usitatissimum L.) is an important oil and fiber crop. Using modern methods for flax breeding allows accelerating the introduction of some desired genes into the genotypes of future varieties. Today, an important condition for their creation is the development of research, that is based on next-generation sequencing (NGS). This review summarizes the results obtained using NGS in flax research. To date, a linkage map with a high marker density has been obtained for L. usitatissimum, which is already being used for a more efficient search for quantitative traits loci. Comparative studies of transcriptomes and miRNomes of flax under stress and in control conditions elucidated molecular-genetic mechanisms of abiotic and biotic stress responses. The very accurate model for genomic selection of flax resistant to pasmo was constructed. Based on NGS-sequencing also some details of the genus Linum evolution were clarified. The knowledge systematized in the review can be useful for researchers working in flax breeding and whereas fundamental interest for understanding the phylogenetic relationships within the genus Linum, the ontogenesis, and the mechanisms of the response of flax plants to various stress factors.
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12
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Jiang CK, Ma JQ, Liu YF, Chen JD, Ni DJ, Chen L. Identification and distribution of a single nucleotide polymorphism responsible for the catechin content in tea plants. HORTICULTURE RESEARCH 2020; 7:24. [PMID: 32140233 PMCID: PMC7049304 DOI: 10.1038/s41438-020-0247-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/23/2019] [Accepted: 01/04/2020] [Indexed: 05/15/2023]
Abstract
Catechins are the predominant products in tea plants and have essential functions for both plants and humans. Several genes encoding the enzymes regulating catechin biosynthesis have been identified, and the identification of single nucleotide polymorphisms (SNPs) resulting in nonsynonymous mutations within these genes can be used to establish a functional link to catechin content. Therefore, the transcriptomes of two parents and four filial offspring were sequenced using next-generation sequencing technology and aligned to the reference genome to enable SNP mining. Subsequently, 176 tea plant accessions were genotyped based on candidate SNPs using kompetitive allele-specific polymerase chain reaction (KASP). The catechin contents of these samples were characterized by high-performance liquid chromatography (HPLC), and analysis of variance (ANOVA) was subsequently performed to determine the relationship between genotypes and catechin content. As a result of these efforts, a SNP within the chalcone synthase (CHS) gene was shown to be functionally associated with catechin content. Furthermore, the geographical and interspecific distribution of this SNP was investigated. Collectively, these results will contribute to the early evaluation of tea plants and serve as a rapid tool for accelerating targeted efforts in tea breeding.
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Affiliation(s)
- Chen-Kai Jiang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, 9 South Meiling Road, Hangzhou, Zhejiang 310008 China
- College of Horticulture and Forestry Science, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, Hubei 430070 China
| | - Jian-Qiang Ma
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, 9 South Meiling Road, Hangzhou, Zhejiang 310008 China
| | - Yu-Fei Liu
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, 9 South Meiling Road, Hangzhou, Zhejiang 310008 China
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, Yunnan 666201 China
| | - Jie-Dan Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, 9 South Meiling Road, Hangzhou, Zhejiang 310008 China
| | - De-Jiang Ni
- College of Horticulture and Forestry Science, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, Hubei 430070 China
| | - Liang Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, 9 South Meiling Road, Hangzhou, Zhejiang 310008 China
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13
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Dubey H, Rawal HC, Rohilla M, Lama U, Kumar PM, Bandyopadhyay T, Gogoi M, Singh NK, Mondal TK. TeaMiD: a comprehensive database of simple sequence repeat markers of tea. Database (Oxford) 2020; 2020:baaa013. [PMID: 32159215 PMCID: PMC7065459 DOI: 10.1093/database/baaa013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/05/2020] [Accepted: 01/25/2020] [Indexed: 12/05/2022]
Abstract
Tea is a highly cross-pollinated, woody, perennial tree. High heterozygosity combined with a long gestational period makes conventional breeding a cumbersome process. Therefore, marker-assisted breeding is a better alternative approach when compared with conventional breeding. Considering the large genome size of tea (~3 Gb), information about simple sequence repeat (SSR) is scanty. Thus, we have taken advantage of the recently published tea genomes to identify large numbers of SSR markers in the tea. Besides the genomic sequences, we identified SSRs from the other publicly available sequences such as RNA-seq, GSS, ESTs and organelle genomes (chloroplasts and mitochondrial) and also searched published literature to catalog validated set of tea SSR markers. The complete exercise yielded a total of 935 547 SSRs. Out of the total, 82 SSRs were selected for validation among a diverse set of tea genotypes. Six primers (each with four to six alleles, an average of five alleles per locus) out of the total 27 polymorphic primers were used for a diversity analysis in 36 tea genotypes with mean polymorphic information content of 0.61-0.76. Finally, using all the information generated in this study, we have developed a user-friendly database (TeaMiD; http://indianteagenome.in:8080/teamid/) that hosts SSR from all the six resources including three nuclear genomes of tea and transcriptome sequences of 17 Camellia wild species. Database URL: http://indianteagenome.in:8080/teamid/.
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Affiliation(s)
- Himanshu Dubey
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Hukam C Rawal
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Megha Rohilla
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Urvashi Lama
- Darjeeling Tea Research and Development Centre, Tea Board, Ministry of Commerce, B.T.M. Sarani (Brabourne Road), Kolkata, West Bengal 700001, India
| | - P Mohan Kumar
- Darjeeling Tea Research and Development Centre, Tea Board, Ministry of Commerce, B.T.M. Sarani (Brabourne Road), Kolkata, West Bengal 700001, India
| | - Tanoy Bandyopadhyay
- Department of Biotechnology, Tocklai Experimental Station, Tea Research Association, Jorhat, Assam, India
| | - Madhurjya Gogoi
- Department of Biotechnology, Tocklai Experimental Station, Tea Research Association, Jorhat, Assam, India
| | - Nagendra Kumar Singh
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Tapan Kumar Mondal
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
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Xia EH, Tong W, Wu Q, Wei S, Zhao J, Zhang ZZ, Wei CL, Wan XC. Tea plant genomics: achievements, challenges and perspectives. HORTICULTURE RESEARCH 2020; 7:7. [PMID: 31908810 PMCID: PMC6938499 DOI: 10.1038/s41438-019-0225-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/17/2019] [Accepted: 11/03/2019] [Indexed: 05/18/2023]
Abstract
Tea is among the world's most widely consumed non-alcoholic beverages and possesses enormous economic, health, and cultural values. It is produced from the cured leaves of tea plants, which are important evergreen crops globally cultivated in over 50 countries. Along with recent innovations and advances in biotechnologies, great progress in tea plant genomics and genetics has been achieved, which has facilitated our understanding of the molecular mechanisms of tea quality and the evolution of the tea plant genome. In this review, we briefly summarize the achievements of the past two decades, which primarily include diverse genome and transcriptome sequencing projects, gene discovery and regulation studies, investigation of the epigenetics and noncoding RNAs, origin and domestication, phylogenetics and germplasm utilization of tea plant as well as newly developed tools/platforms. We also present perspectives and possible challenges for future functional genomic studies that will contribute to the acceleration of breeding programs in tea plants.
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Affiliation(s)
- En-Hua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Shu Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Zheng-Zhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Chao-Ling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Xiao-Chun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
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15
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Sudan J, Singh R, Sharma S, Salgotra RK, Sharma V, Singh G, Sharma I, Sharma S, Gupta SK, Zargar SM. ddRAD sequencing-based identification of inter-genepool SNPs and association analysis in Brassica juncea. BMC PLANT BIOLOGY 2019; 19:594. [PMID: 31888485 PMCID: PMC6937933 DOI: 10.1186/s12870-019-2188-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/05/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Narrow genetic base, complex allo-tetraploid genome and presence of repetitive elements have led the discovery of single nucleotide polymorphisms (SNPs) in Brassica juncea (AABB; 2n = 4x = 36) at a slower pace. Double digest RAD (ddRAD) - a genome complexity reduction technique followed by NGS was used to generate a total of 23 million paired-end reads from three genotypes each of Indian (Pusa Tarak, RSPR-01 and Urvashi) and Exotic (Donskaja IV, Zem 1 and EC287711) genepools. RESULTS Sequence data analysis led to the identification of 10,399 SNPs in six genotypes at a read depth of 10x coverage among the genotypes of two genepools. A total of 44 hyper-variable regions (nucleotide variation hotspots) were also found in the genome, of which 93% were found to be a part of coding genes/regions. The functionality of the identified SNPs was estimated by genotyping a subset of SNPs on MassARRAY® platform among a diverse set of B. juncea genotypes. SNP genotyping-based genetic diversity and population studies placed the genotypes into two distinct clusters based mostly on the place of origin. The genotypes were also characterized for six morphological traits, analysis of which revealed a significant difference in the mean values between Indian and Exotic genepools for six traits. The association analysis for six traits identified a total of 45 significant marker-trait associations on 11 chromosomes of A- and B- group of progenitor genomes. CONCLUSIONS Despite narrow diversity, the ddRAD sequencing was able to identify large number of nucleotide polymorphisms between the two genepools. Association analysis led to the identification of common SNPs/genomic regions associated between flowering and maturity traits, thereby underscoring the possible role of common chromosomal regions-harboring genes controlling flowering and maturity in Brassica juncea.
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Affiliation(s)
- Jebi Sudan
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, J&K, India
- JECRC University- Jaipur, Jaipur, Rajasthan, India
| | - Ravinder Singh
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, J&K, India.
| | - Susheel Sharma
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, J&K, India
| | - Romesh K Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, J&K, India
| | - Varun Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K, India
| | - Gurvinder Singh
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K, India
| | - Indu Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K, India
| | - Swarkar Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K, India
| | - Surinder K Gupta
- Division of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jaipur, J&K, India
| | - Sajad Majeed Zargar
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu, J&K, India
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Liu S, An Y, Tong W, Qin X, Samarina L, Guo R, Xia X, Wei C. Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research. BMC Genomics 2019; 20:935. [PMID: 31805860 PMCID: PMC6896268 DOI: 10.1186/s12864-019-6347-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 11/28/2019] [Indexed: 12/11/2022] Open
Abstract
Background Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations have been conducted in the long-lived perennial tea plant. Results In this study, we investigated the genome-wide genetic variations between Camellia sinensis var. sinensis ‘Shuchazao’ and Camellia sinensis var. assamica ‘Yunkang 10’, identified 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and we subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on 46 tea cultivars for transferability and genetic diversity analysis, exhibiting information with an average 4.02 of the number of alleles (Na) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the catechin/caffeine contents between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes. Conclusion The identified genome-wide genetic variations and newly-developed InDel markers will provide a valuable resource for tea plant genetic and genomic studies, especially the SNPs/InDels within catechin/caffeine biosynthesis-related genes, which may serve as pivotal candidates for elucidating the molecular mechanism governing catechin/caffeine biosynthesis.
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Affiliation(s)
- Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Xiuju Qin
- Guangxi LuYI Institute of Tea Tree Species, 17 Jinji Road, Guilin, China
| | - Lidia Samarina
- Department of Biotechnology, Russian Research Institute of Floriculture and Subtropical Crops, Sochi, Russia
| | - Rui Guo
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Xiaobo Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China.
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Wang RJ, Gao XF, Yang J, Kong XR. Genome-Wide Association Study to Identify Favorable SNP Allelic Variations and Candidate Genes That Control the Timing of Spring Bud Flush of Tea ( Camellia sinensis) Using SLAF-seq. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10380-10391. [PMID: 31464444 DOI: 10.1021/acs.jafc.9b03330] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The timing of spring bud flush (TBF) is of economic importance for tea plant (Camellia sinensis) breeding. We employed a genome-wide association study (GWAS) to identify favorable single nucleotide polymorphism (SNP) allelic variations as well as candidate genes that control TBF of C. sinensis using specific-locus-amplified fragment sequencing (SLAF-seq) in a diversity panel comprising 151 tea plant germplasm resources. GWAS analysis revealed 26 SNPs associated with TBF in three years, and we eventually identified a final significant SNP for TBF. To identify candidate genes possibly related to TBF, we screened seven candidate genes within 100 kb regions surrounding the trait-related SNP loci. Furthermore, the favorable allelic variation, the "TT" genotype in the SNP loci, was discovered, and a derived cleaved amplified polymorphism (dCAPS) marker was designed that cosegregated with TBF, which could be used for marker-assisted selection (MAS) breeding in C. sinensis. The results obtained from this study can provide a theoretical and applied basis for the MAS of early breeding in tea plants in the future.
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Affiliation(s)
- Rang Jian Wang
- Institute of Tea , Fujian Academy of Agricultural Sciences , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
- Fujian Branch , National Center for Tea Improvement , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
| | - Xiang Feng Gao
- Institute of Tea , Fujian Academy of Agricultural Sciences , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
- Fujian Branch , National Center for Tea Improvement , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
| | - Jun Yang
- Institute of Tea , Fujian Academy of Agricultural Sciences , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
- Fujian Branch , National Center for Tea Improvement , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
| | - Xiang Rui Kong
- Institute of Tea , Fujian Academy of Agricultural Sciences , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
- Fujian Branch , National Center for Tea Improvement , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
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Dong M, He Q, Zhao J, Zhang Y, Yuan D, Zhang AJ. Genetic Mapping of Prince Rupprecht's Larch ( Larix principis-rupprechtii Mayr) by Specific-Locus Amplified Fragment Sequencing. Genes (Basel) 2019; 10:genes10080583. [PMID: 31370324 PMCID: PMC6723236 DOI: 10.3390/genes10080583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 07/12/2019] [Accepted: 07/29/2019] [Indexed: 11/24/2022] Open
Abstract
A high-density genetic linkage map is essential for plant genetics and genomics research. However, due to the deficiency of genomic data and high-quality molecular markers, no genetic map has been published for Prince Rupprecht’s larch (Larix principis-rupprechtii Mayr), a conifer species with high ecological and commercial value in northern China. In this study, 145 F1 progeny individuals from an intraspecific cross between two elite clones of L. principis-rupprechtii and their parents were employed to construct the first genetic map in this important tree species using specific-locus amplified fragment sequencing (SLAF-seq). After preprocessing, the procedure yielded 300.20 Gb of raw data containing 1501.22 M pair-end reads. A total of 324,352 SNP markers were detected and 122,785 of them were polymorphic, with a polymorphism rate of 37.86%. Ultimately, 6099 SNPs were organized into a genetic map containing 12 linkage groups, consistent with the haploid chromosome number of larch and most other species in the Pinaceae family. The linkage map spanned 2415.58 cM and covered 99.6% of the L. principis-rupprechtii genome with an average of 0.4 cM between adjacent markers. To the best of our knowledge, this map is the first reference map for L. principis-rupprechtii, as well as the densest one obtained in larch species thus far. The genome-wide SNPs and the high-resolution genetic map will provide a foundation for future quantitative trait loci mapping, map-based cloning, marker-assisted selection, comparative genomics, and genome sequence assembly for larch trees.
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Affiliation(s)
- Mingliang Dong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Qingwei He
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jian Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yan Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Deshui Yuan
- National Key Seed Base of Larch, Weichang, Chengde 068450, China
| | - And Jinfeng Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
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Xu LY, Wang LY, Wei K, Tan LQ, Su JJ, Cheng H. High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing. BMC Genomics 2018; 19:955. [PMID: 30577813 PMCID: PMC6304016 DOI: 10.1186/s12864-018-5291-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 11/20/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Flavonoids are important components that confer upon tea plants a unique flavour and health functions. However, the traditional breeding method for selecting a cultivar with a high or unique flavonoid content is time consuming and labour intensive. High-density genetic map construction associated with quantitative trait locus (QTL) mapping provides an effective way to facilitate trait improvement in plant breeding. In this study, an F1 population (LJ43×BHZ) was genotyped using 2b-restriction site-associated DNA (2b-RAD) sequencing to obtain massive single nucleotide polymorphism (SNP) markers to construct a high-density genetic map for a tea plant. Furthermore, QTLs related to flavonoids were identified using our new genetic map. RESULTS A total of 13,446 polymorphic SNP markers were developed using 2b-RAD sequencing, and 4,463 of these markers were available for constructing the genetic linkage map. A 1,678.52-cM high-density map at an average interval of 0.40 cM with 4,217 markers, including 427 frameset simple sequence repeats (SSRs) and 3,800 novel SNPs, mapped into 15 linkage groups was successfully constructed. After QTL analysis, a total of 27 QTLs related to flavonoids or caffeine content (CAF) were mapped to 8 different linkage groups, LG01, LG03, LG06, LG08, LG10, LG11, LG12, and LG13, with an LOD from 3.14 to 39.54, constituting 7.5% to 42.8% of the phenotypic variation. CONCLUSIONS To our knowledge, the highest density genetic map ever reported was constructed since the largest mapping population of tea plants was adopted in present study. Moreover, novel QTLs related to flavonoids and CAF were identified based on the new high-density genetic map. In addition, two markers were located in candidate genes that may be involved in flavonoid metabolism. The present study provides valuable information for gene discovery, marker-assisted selection breeding and map-based cloning for functional genes that are related to flavonoid content in tea plants.
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Affiliation(s)
- Li-Yi Xu
- National Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 China
| | - Li-Yuan Wang
- National Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
| | - Kang Wei
- National Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
| | - Li-Qiang Tan
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jing-Jing Su
- National Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
| | - Hao Cheng
- National Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
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Ma JQ, Jin JQ, Yao MZ, Ma CL, Xu YX, Hao WJ, Chen L. Quantitative Trait Loci Mapping for Theobromine and Caffeine Contents in Tea Plant ( Camellia sinensis). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:13321-13327. [PMID: 30486648 DOI: 10.1021/acs.jafc.8b05355] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Understanding the genetic basis of theobromine and caffeine accumulation in the tea plant is important due to their contribution to tea flavor. Quantitative trait loci (QTL) analyses were carried out to identify genetic variants associated with theobromine and caffeine contents and ratio using a pseudo-testcross population derived from an intervarietal cross between two varieties of Camellia sinensis. A total of 10 QTL controlling caffeine content (CAF), theobromine content (TBR), sum of caffeine and theobromine (SCT), and caffeine-to-theobromine ratio (CTR) were identified over four measurement years. The major QTL controlling CAF, qCAF1, was mapped onto LG01 and validated across years, explaining an average of 20.1% of the phenotypic variance. The other QTL were detected in 1 or 2 years, and of them there were four, two, and three for TBR, SCT, and CTR, respectively. The present results provide valuable information for further fine mapping and cloning functional genes and for genetic improvement in tea plant.
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Affiliation(s)
- Jian-Qiang Ma
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture , Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS) , 9 South Meiling Road , Hangzhou 310008 , China
| | - Ji-Qiang Jin
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture , Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS) , 9 South Meiling Road , Hangzhou 310008 , China
| | - Ming-Zhe Yao
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture , Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS) , 9 South Meiling Road , Hangzhou 310008 , China
| | - Chun-Lei Ma
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture , Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS) , 9 South Meiling Road , Hangzhou 310008 , China
| | - Yan-Xia Xu
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture , Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS) , 9 South Meiling Road , Hangzhou 310008 , China
| | - Wan-Jun Hao
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture , Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS) , 9 South Meiling Road , Hangzhou 310008 , China
| | - Liang Chen
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture , Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS) , 9 South Meiling Road , Hangzhou 310008 , China
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21
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Carrasco B, González M, Gebauer M, García-González R, Maldonado J, Silva H. Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling. PLoS One 2018; 13:e0208032. [PMID: 30507961 PMCID: PMC6277071 DOI: 10.1371/journal.pone.0208032] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/09/2018] [Indexed: 11/19/2022] Open
Abstract
This study reports the construction of high density linkage maps of Japanese plum (Prunus salicina Lindl.) using single nucleotide polymorphism markers (SNPs), obtained with a GBS strategy. The mapping population (An x Au) was obtained by crossing cv. "Angeleno" (An) as maternal line and cv. "Aurora" (Au) as the pollen donor. A total of 49,826 SNPs were identified using the peach genome V2.1 as a reference. Then a stringent filtering was carried out, which revealed 1,441 high quality SNPs in 137 An x Au offspring, which were mapped in eight linkage groups. Finally, the consensus map was built using 732 SNPs which spanned 617 cM with an average of 0.96 cM between adjacent markers. The majority of the SNPs were distributed in the intragenic region in all the linkage groups. Considering all linkage groups together, 85.6% of the SNPs were located in intragenic regions and only 14.4% were located in intergenic regions. The genetic linkage analysis was able to co-localize two to three SNPs over 37 putative orthologous genes in eight linkage groups in the Japanese plum map. These results indicate a high level of synteny and collinearity between Japanese plum and peach genomes.
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Affiliation(s)
- Basilio Carrasco
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ciencias Vegetales, Macul, Santiago, Chile
| | - Máximo González
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ciencias Vegetales, Macul, Santiago, Chile
| | - Marlene Gebauer
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ciencias Vegetales, Macul, Santiago, Chile
| | - Rolando García-González
- Sociedad BioTECNOS Ltda, R&D Department Camino a Pangal Km 2 1/2, San Javier, Región del Maule, Chile
- Facultad de Ciencias Agrarias y Forestales, Centro de Biotecnología de los Recursos Naturales (CENBio), Universidad Católica del Maule, Talca, Chile
| | - Jonathan Maldonado
- Universidad de Chile, Facultad de Ciencias Agronómicas, Departamento de Producción Agrícola, Laboratorio de Genómica Funcional & Bioinformática, La Pintana, Santiago, Chile
| | - Herman Silva
- Universidad de Chile, Facultad de Ciencias Agronómicas, Departamento de Producción Agrícola, Laboratorio de Genómica Funcional & Bioinformática, La Pintana, Santiago, Chile
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22
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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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Unraveling the Roles of Regulatory Genes during Domestication of Cultivated Camellia: Evidence and Insights from Comparative and Evolutionary Genomics. Genes (Basel) 2018; 9:genes9100488. [PMID: 30308953 PMCID: PMC6211025 DOI: 10.3390/genes9100488] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 09/29/2018] [Accepted: 10/05/2018] [Indexed: 01/01/2023] Open
Abstract
With the increasing power of DNA sequencing, the genomics-based approach is becoming a promising resolution to dissect the molecular mechanism of domestication of complex traits in trees. Genus Camellia possesses rich resources with a substantial value for producing beverage, ornaments, edible oil and more. Currently, a vast number of genetic and genomic research studies in Camellia plants have emerged and provided an unprecedented opportunity to expedite the molecular breeding program. In this paper, we summarize the recent advances of gene expression and genomic resources in Camellia species and focus on identifying genes related to key economic traits such as flower and fruit development and stress tolerances. We investigate the genetic alterations and genomic impacts under different selection programs in closely related species. We discuss future directions of integrating large-scale population and quantitative genetics and multiple omics to identify key candidates to accelerate the breeding process. We propose that future work of exploiting the genomic data can provide insights related to the targets of domestication during breeding and the evolution of natural trait adaptations in genus Camellia.
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24
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Huang H, Tan H, Xu D, Tang Y, Niu Y, Lai Y, Tie M, Li H. High-density genetic map construction and comparative genome analysis in asparagus bean. Sci Rep 2018; 8:4836. [PMID: 29555986 PMCID: PMC5859152 DOI: 10.1038/s41598-018-23173-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/07/2018] [Indexed: 12/30/2022] Open
Abstract
Genetic maps are a prerequisite for quantitative trait locus (QTL) analysis, marker-assisted selection (MAS), fine gene mapping, and assembly of genome sequences. So far, several asparagus bean linkage maps have been established using various kinds of molecular markers. However, these maps were all constructed by gel- or array-based markers. No maps based on sequencing method have been reported. In this study, an NGS-based strategy, SLAF-seq, was applied to create a high-density genetic map for asparagus bean. Through SLAF library construction and Illumina sequencing of two parents and 100 F2 individuals, a total of 55,437 polymorphic SLAF markers were developed and mined for SNP markers. The map consisted of 5,225 SNP markers in 11 LGs, spanning a total distance of 1,850.81 cM, with an average distance between markers of 0.35 cM. Comparative genome analysis with four other legume species, soybean, common bean, mung bean and adzuki bean showed that asparagus bean is genetically more related to adzuki bean. The results will provide a foundation for future genomic research, such as QTL fine mapping, comparative mapping in pulses, and offer support for assembling asparagus bean genome sequence.
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Affiliation(s)
- Haitao Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.,Mianyang Academy of Agricultural Sciences, Mianyang, 621023, China
| | - Huaqiang Tan
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dongmei Xu
- Mianyang Academy of Agricultural Sciences, Mianyang, 621023, China
| | - Yi Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yisong Niu
- Mianyang Academy of Agricultural Sciences, Mianyang, 621023, China
| | - Yunsong Lai
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Manman Tie
- Dazhou Academy of Agricultural Sciences, Dazhou, 635000, China
| | - Huanxiu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.
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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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Yi L, Gao F, Siqin B, Zhou Y, Li Q, Zhao X, Jia X, Zhang H. Construction of an SNP-based high-density linkage map for flax (Linum usitatissimum L.) using specific length amplified fragment sequencing (SLAF-seq) technology. PLoS One 2017; 12:e0189785. [PMID: 29267332 PMCID: PMC5739455 DOI: 10.1371/journal.pone.0189785] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/03/2017] [Indexed: 12/30/2022] Open
Abstract
Flax is an important crop for oil and fiber, however, no high-density genetic maps have been reported for this species. Specific length amplified fragment sequencing (SLAF-seq) is a high-resolution strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms. In this study, SLAF-seq was employed to develop SNP markers in an F2 population to construct a high-density genetic map for flax. In total, 196.29 million paired-end reads were obtained. The average sequencing depth was 25.08 in male parent, 32.17 in the female parent, and 9.64 in each F2 progeny. In total, 389,288 polymorphic SLAFs were detected, from which 260,380 polymorphic SNPs were developed. After filtering, 4,638 SNPs were found suitable for genetic map construction. The final genetic map included 4,145 SNP markers on 15 linkage groups and was 2,632.94 cM in length, with an average distance of 0.64 cM between adjacent markers. To our knowledge, this map is the densest SNP-based genetic map for flax. The SNP markers and genetic map reported in here will serve as a foundation for the fine mapping of quantitative trait loci (QTLs), map-based gene cloning and marker assisted selection (MAS) for flax.
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Affiliation(s)
- Liuxi Yi
- Biotechnology Research Center, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| | - Fengyun Gao
- Special Crops Institute, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| | - Bateer Siqin
- Biotechnology Research Center, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| | - Yu Zhou
- Special Crops Institute, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| | - Qiang Li
- Corn Institute, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| | - Xiaoqing Zhao
- Biotechnology Research Center, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| | - Xiaoyun Jia
- Special Crops Institute, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| | - Hui Zhang
- Special Crops Institute, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
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Molecular Markers in Whole Genome Evolution of Brachypodium. Methods Mol Biol 2017. [PMID: 29039008 DOI: 10.1007/978-1-4939-7278-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Molecular markers play more and more important role in population genetic and phylogenetic studies; choice of marker systems for a particular study has become a serious problem. These marker systems have different advantages and disadvantages, so it is imperative to keep in mind all the pros and cons of the technique while selecting one for the problem to be addressed.Here, we concisely introduced three molecular marker techniques, namely SSR, ISSR, and RFLP. We elaborated their properties such as reliability, simplicity, cost-effectiveness, and speed, in addition to data analysis of genetic diversity. We have outlined here the whole methodology of these techniques.
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Qin H, Yang G, Provan J, Liu J, Gao L. Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species. PLANT DIVERSITY 2017; 39:294-299. [PMID: 30159522 PMCID: PMC6112293 DOI: 10.1016/j.pld.2017.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/26/2017] [Accepted: 05/27/2017] [Indexed: 05/31/2023]
Abstract
Microsatellites are highly polymorphic markers which have been used in a wide range of genetic studies. In recent years, various sources of next-generation sequencing data have been used to develop new microsatellite loci, but compared with the more common shotgun genomic sequencing or transcriptome data, the potential utility of RAD-seq data for microsatellite ascertainment is comparatively under-used. In this study, we employed MiddRAD-seq data to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. Of 8,823,053 clean reads generated for ten individuals of a population, 94,851 (∼1%) contained microsatellite motifs. These corresponded to 2993 unique loci, of which 526 (∼18%) exhibited polymorphism. Of which, 237 were suitable for designing microsatellite primer pairs, and 128 loci were randomly selected for PCR validation and microsatellite screening. Out of the 128 primer pairs, 16 loci gave clear, reproducible patterns, and were then screened and characterized in 24 individuals from two populations. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
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Affiliation(s)
- Hantao Qin
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoqian Yang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jim Provan
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3DA, UK
| | - Jie Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Lianming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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29
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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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Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney RK, He Z. Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives. MOLECULAR PLANT 2017; 10:1047-1064. [PMID: 28669791 DOI: 10.1016/j.molp.2017.06.008] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/29/2017] [Accepted: 06/19/2017] [Indexed: 05/18/2023]
Abstract
There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype-phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.
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Affiliation(s)
- Awais Rasheed
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Awais Khan
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY, USA
| | - Yunbi Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China.
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Liu H, Cao F, Yin T, Chen Y. A Highly Dense Genetic Map for Ginkgo biloba Constructed Using Sequence-Based Markers. FRONTIERS IN PLANT SCIENCE 2017; 8:1041. [PMID: 28663754 PMCID: PMC5471298 DOI: 10.3389/fpls.2017.01041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/30/2017] [Indexed: 05/19/2023]
Abstract
Ginkgo biloba L. is a well-known living gymnosperm fossil that has medicinal and ornamental value. In this study, a high density genetic map was constructed with megagametophytes of 94 seeds from a single Ginkgo tree by employing the specific-locus amplified fragment (SLAF) sequencing technique. The average sequencing depth was 11.20×, which yielded 538,031 high-quality SLAFs. Among these SLAFs, 204,361 were heterozygous in the maternal tree and segregated in the progeny. The established map contained 12,263 SLAFs that were assigned to 12 linkage groups (LGs). The number of LGs on this map equaled the number of chromosomes in Ginkgo. The total map length was 1,671.77 cM, with an average distance of 0.89 cM between adjacent marker bins. Map evaluation based on the haplotype map and the heat map validated the high quality of the established map. Because Ginkgo is an economically and biologically important tree, strenuous efforts have been exerted to sequence its genome. This new map, built using sequence-based markers, will serve in the future as a fundamental platform for anchoring sequence assemblies along Ginkgo chromosomes. This map also provides a desirable platform for various genetic studies of Ginkgo, including gene/quantitative trait locus mapping and marker-aided selection.
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Bai ZY, Han XK, Liu XJ, Li QQ, Li JL. Construction of a high-density genetic map and QTL mapping for pearl quality-related traits in Hyriopsis cumingii. Sci Rep 2016; 6:32608. [PMID: 27587236 PMCID: PMC5009340 DOI: 10.1038/srep32608] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/11/2016] [Indexed: 11/22/2022] Open
Abstract
A high-density genetic map is essential for quantitative trait locus (QTL) fine mapping. In this study, 4,508 effective single nucleotide polymorphism markers (detected using specific-locus amplified fragment sequencing) and 475 microsatellites were mapped to 19 linkage groups (LGs) using a family with 157 individuals. The map spanned 2,713 cM, with an average of 259 markers and 79 loci per LG and an average inter-marker distance of 1.81 cM. To identify QTLs for pearl quality traits, 26 putatively significant QTLs were detected for 10 traits, including, three for shell width, seven for body weight, two for shell weight, two for margin mantle weight, five for inner mantle weight, and seven for shell nacre colour. Among them, five QTLs associated with shell nacre colour were mapped to LG17 and explained 19.7% to 22.8% of the trait variation; this suggests that some important genes or loci determine shell nacre colour in LG17. The linkage map and mapped QTLs for shell nacre colour would be useful for improving the quality of Hyriopsis cumingii via marker-assisted selection.
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Affiliation(s)
- Zhi-Yi Bai
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, China
- Shanghai Engineering Research Centre of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Xue-Kai Han
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, China
| | - Xiao-Jun Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, China
| | - Qing-Qing Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, China
| | - Jia-Le Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, China
- Shanghai Engineering Research Centre of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
- Aquaculture Division, E-Institute of Shanghai Universities, Shanghai Ocean University, Shanghai 201306, China
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Wang RJ, Gao XF, Kong XR, Yang J. An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers. SPRINGERPLUS 2016; 5:1152. [PMID: 27504250 PMCID: PMC4958088 DOI: 10.1186/s40064-016-2835-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 07/14/2016] [Indexed: 02/02/2023]
Abstract
Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait 'cultivar processing-property'. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(-5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property.
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Affiliation(s)
- Rang Jian Wang
- Institute of Tea, Fu Jian Academy of Agricultural Sciences, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China ; Fu Jian Branch, National Center for Tea Improvement, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China
| | - Xiang Feng Gao
- Institute of Tea, Fu Jian Academy of Agricultural Sciences, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China ; Fu Jian Branch, National Center for Tea Improvement, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China
| | - Xiang Rui Kong
- Institute of Tea, Fu Jian Academy of Agricultural Sciences, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China ; Fu Jian Branch, National Center for Tea Improvement, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China
| | - Jun Yang
- Institute of Tea, Fu Jian Academy of Agricultural Sciences, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China ; Fu Jian Branch, National Center for Tea Improvement, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China
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Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s40011-016-0770-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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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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Zhang J, Yuan H, Li M, Li Y, Wang Y, Ma X, Zhang Y, Tan F, Wu R. A High-Density Genetic Map of Tetraploid Salix matsudana Using Specific Length Amplified Fragment Sequencing (SLAF-seq). PLoS One 2016; 11:e0157777. [PMID: 27327501 PMCID: PMC4915623 DOI: 10.1371/journal.pone.0157777] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/03/2016] [Indexed: 01/20/2023] Open
Abstract
As a salt-tolerant arbor tree species, Salix matsudana plays an important role in afforestation and greening in the coastal areas of China. To select superior Salix varieties that adapt to wide saline areas, it is of paramount importance to understand and identify the mechanisms of salt-tolerance at the level of the whole genome. Here, we describe a high-density genetic linkage map of S. matsudana that represents a good coverage of the Salix genome. An intraspecific F1 hybrid population was established by crossing the salt-sensitive “Yanjiang” variety as the female parent with the salt-tolerant “9901” variety as the male parent. This population, along with its parents, was genotyped by specific length amplified fragment sequencing (SLAF-seq), leading to 277,333 high-quality SLAF markers. By marker analysis, we found that both the parents and offspring were tetraploid. The mean sequencing depth was 53.20-fold for “Yanjiang”, 47.41-fold for “9901”, and 11.02-fold for the offspring. Of the SLAF markers detected, 42,321 are polymorphic with sufficient quality for map construction. The final genetic map was constructed using 6,737 SLAF markers, covering 38 linkage groups (LGs). The genetic map spanned 5,497.45 cM in length, with an average distance of 0.82 cM. As a first high-density genetic map of S. matsudana constructed from salt tolerance-varying varieties, this study will provide a foundation for mapping quantitative trait loci that modulate salt tolerance and resistance in Salix and provide important references for molecular breeding of this important forest tree.
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Affiliation(s)
- Jian Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Jiangsu Riverine Institute of Agricultural Sciences, Rugao, Jiangsu, China
| | - Huwei Yuan
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Min Li
- Jiangsu Riverine Institute of Agricultural Sciences, Rugao, Jiangsu, China
| | - Yujuan Li
- Jiangsu Riverine Institute of Agricultural Sciences, Rugao, Jiangsu, China
| | - Ying Wang
- Jiangsu Riverine Institute of Agricultural Sciences, Rugao, Jiangsu, China
| | - Xiangjian Ma
- Jiangsu Riverine Institute of Agricultural Sciences, Rugao, Jiangsu, China
| | - Yuan Zhang
- Jiangsu Riverine Institute of Agricultural Sciences, Rugao, Jiangsu, China
| | - Feng Tan
- Jiangsu Riverine Institute of Agricultural Sciences, Rugao, Jiangsu, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Center for Statistical Genetics, Pennsylvania State University, Hershey, United States of America
- * E-mail: ;
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Zhang Z, Shang H, Shi Y, Huang L, Li J, Ge Q, Gong J, Liu A, Chen T, Wang D, Wang Y, Palanga KK, Muhammad J, Li W, Lu Q, Deng X, Tan Y, Song W, Cai J, Li P, Rashid HO, Gong W, Yuan Y. Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.). BMC PLANT BIOLOGY 2016; 16:79. [PMID: 27067834 PMCID: PMC4827241 DOI: 10.1186/s12870-016-0741-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/17/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. RESULTS In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0-153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15-16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. CONCLUSIONS This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection.
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Affiliation(s)
- Zhen Zhang
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Haihong Shang
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Yuzhen Shi
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Long Huang
- />Biomarker Technologies Corporation, Beijing, 103100 China
| | - Junwen Li
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Qun Ge
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Juwu Gong
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Aiying Liu
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Tingting Chen
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Dan Wang
- />Biomarker Technologies Corporation, Beijing, 103100 China
| | - Yanling Wang
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Koffi Kibalou Palanga
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Jamshed Muhammad
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Weijie Li
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Quanwei Lu
- />Anyang Institute of Technology, Anyang, 455000 Henan China
| | - Xiaoying Deng
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Yunna Tan
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Weiwu Song
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Juan Cai
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Pengtao Li
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Harun or Rashid
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Wankui Gong
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Youlu Yuan
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
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Zhao Z, Gu H, Sheng X, Yu H, Wang J, Huang L, Wang D. Genome-Wide Single-Nucleotide Polymorphisms Discovery and High-Density Genetic Map Construction in Cauliflower Using Specific-Locus Amplified Fragment Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:334. [PMID: 27047515 PMCID: PMC4800193 DOI: 10.3389/fpls.2016.00334] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 03/04/2016] [Indexed: 05/19/2023]
Abstract
Molecular markers and genetic maps play an important role in plant genomics and breeding studies. Cauliflower is an important and distinctive vegetable; however, very few molecular resources have been reported for this species. In this study, a novel, specific-locus amplified fragment (SLAF) sequencing strategy was employed for large-scale single nucleotide polymorphism (SNP) discovery and high-density genetic map construction in a double-haploid, segregating population of cauliflower. A total of 12.47 Gb raw data containing 77.92 M pair-end reads were obtained after processing and 6815 polymorphic SLAFs between the two parents were detected. The average sequencing depths reached 52.66-fold for the female parent and 49.35-fold for the male parent. Subsequently, these polymorphic SLAFs were used to genotype the population and further filtered based on several criteria to construct a genetic linkage map of cauliflower. Finally, 1776 high-quality SLAF markers, including 2741 SNPs, constituted the linkage map with average data integrity of 95.68%. The final map spanned a total genetic length of 890.01 cM with an average marker interval of 0.50 cM, and covered 364.9 Mb of the reference genome. The markers and genetic map developed in this study could provide an important foundation not only for comparative genomics studies within Brassica oleracea species but also for quantitative trait loci identification and molecular breeding of cauliflower.
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Affiliation(s)
- Zhenqing Zhao
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Xiaoguang Sheng
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Huifang Yu
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Jiansheng Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Long Huang
- Biomarker Technologies CorporationBeijing, China
| | - Dan Wang
- Biomarker Technologies CorporationBeijing, China
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Yang H, Wei CL, Liu HW, Wu JL, Li ZG, Zhang L, Jian JB, Li YY, Tai YL, Zhang J, Zhang ZZ, Jiang CJ, Xia T, Wan XC. Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing. PLoS One 2016; 11:e0151424. [PMID: 26962860 PMCID: PMC4786323 DOI: 10.1371/journal.pone.0151424] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 02/28/2016] [Indexed: 12/19/2022] Open
Abstract
Tea is one of the most popular beverages across the world and is made exclusively from cultivars of Camellia sinensis. Many wild relatives of the genus Camellia that are closely related to C. sinensis are native to Southwest China. In this study, we first identified the distinct genetic divergence between C. sinensis and its wild relatives and provided a glimpse into the artificial selection of tea plants at a genome-wide level by analyzing 15,444 genomic SNPs that were identified from 18 cultivated and wild tea accessions using a high-throughput genome-wide restriction site-associated DNA sequencing (RAD-Seq) approach. Six distinct clusters were detected by phylogeny inferrence and principal component and genetic structural analyses, and these clusters corresponded to six Camellia species/varieties. Genetic divergence apparently indicated that C. taliensis var. bangwei is a semi-wild or transient landrace occupying a phylogenetic position between those wild and cultivated tea plants. Cultivated accessions exhibited greater heterozygosity than wild accessions, with the exception of C. taliensis var. bangwei. Thirteen genes with non-synonymous SNPs exhibited strong selective signals that were suggestive of putative artificial selective footprints for tea plants during domestication. The genome-wide SNPs provide a fundamental data resource for assessing genetic relationships, characterizing complex traits, comparing heterozygosity and analyzing putatitve artificial selection in tea plants.
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Affiliation(s)
- Hua Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- Department of Applied Chemistry, School of Science, Anhui Agricultural University, Hefei, 230036, China
| | - Chao-Ling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Hong-Wei Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jun-Lan Wu
- School of Information & Computer, Anhui Agricultural University, Hefei, 230036, China
| | - Zheng-Guo Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Liang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | | | - Ye-Yun Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yu-Ling Tai
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jing Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Zheng-Zhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Chang-Jun Jiang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Xiao-Chun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- * E-mail:
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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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Characterization and fine mapping of a novel barley Stage Green-Revertible Albino Gene (HvSGRA) by Bulked Segregant Analysis based on SSR assay and Specific Length Amplified Fragment Sequencing. BMC Genomics 2015; 16:838. [PMID: 26494145 PMCID: PMC4619012 DOI: 10.1186/s12864-015-2015-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 10/06/2015] [Indexed: 11/28/2022] Open
Abstract
Background Leaf color variations are common in plants. Herein we describe a natural mutant of barley cultivar Edamai No.6, whs18, whose leaf color showed stable and inheritable stage-green-revertible-albino under field condition. Methods Bulked Segregant Analysis (BSA) based on SSR assay and Specific Length Amplified Fragment Sequencing (SLAF-seq) was used to map the candidate gene for this trait. Results We found that leaf color of whs18 was green at seedling stage, while the seventh or eighth leaf began to show etiolation, and albino leaves emerged after a short period. The newly emerged leaves began to show stripe white before jointing stage, and normal green leaves emerged gradually. The duration of whs18 with abnormal leaf color lasted for about 3 months, which had some negative impacts on yield-related-traits. Further investigations showed that the variation was associated with changes in chlorophyII content and chloroplast development. Genetic analysis revealed that the trait was controlled by a single recessive nuclear gene, and was designed as HvSGRA in this study. Based on the F2 population derived from Edamai No.9706 and whs18, we initially mapped the HvSGRA gene on the short arm of chromosome 2H using SSR and BSA. GBMS247 on 2HS showed co-segregation with HvSGRA. The genetic distance between the other marker GBM1187 and HvSGRA was 1.2 cM. Further analysis using BSA with SLAF-seq also identified this region as candidate region. Finally, HvSGRA interval was narrowed to 0.4 cM between morex_contig_160447 and morex_contig_92239, which were anchored to two adjacent FP contigs, contig_34437 and contig_46434, respectively. Furthermore, six putative genes with high-confidence in this interval were identified by POPSEQ. Further analysis showed that the substitution from C to A in the third exon of fructokinase-1-like gene generated a premature stop codon in whs18, which may lead to loss function of this gene. Conclusions Using SSR and SLAF-seq in conjunction with BSA, we mapped HvSGRA within two adjacent FP contigs of barley. The mutation of fructokinase-1-like gene in whs18 may cause the stage green-revertible albino of barley. The current study lays foundation for hierarchical map-based cloning of HvSGRA and utilizing the gene/trait as a visualized maker in molecular breeding in future. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2015-1) contains supplementary material, which is available to authorized users.
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