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Wang W, Li Y, Le M, Tian L, Sun X, Liu R, Guo X, Wu Y, Li Y, Zhao J, Liu D, Zhang Z. QTL Mapping of Fiber- and Seed-Related Traits in Chromosome Segment Substitution Lines Derived from Gossypium hirsutum × Gossypium darwinii. Int J Mol Sci 2024; 25:9639. [PMID: 39273586 DOI: 10.3390/ijms25179639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/30/2024] [Accepted: 09/03/2024] [Indexed: 09/15/2024] Open
Abstract
A narrow genetic basis limits further the improvement of modern Gossypium hirsutum cultivar. The abundant genetic diversity of wild species provides available resources to solve this dilemma. In the present study, a chromosome segment substitution line (CSSL) population including 553 individuals was established using G. darwinii accession 5-7 as the donor parent and G. hirsutum cultivar CCRI35 as the recipient parent. After constructing a high-density genetic map with the BC1 population, the genotype and phenotype of the CSSL population were investigated. A total of 235 QTLs, including 104 QTLs for fiber-related traits and 132 QTLs for seed-related traits, were identified from four environments. Among these QTLs, twenty-seven QTLs were identified in two or more environments, and twenty-five QTL clusters consisted of 114 QTLs. Moreover, we identified three candidate genes for three stable QTLs, including GH_A01G1096 (ARF5) and GH_A10G0141 (PDF2) for lint percentage, and GH_D01G0047 (KCS4) for seed index or oil content. These results pave way for understanding the molecular regulatory mechanism of fiber and seed development and would provide valuable information for marker-assisted genetic improvement in cotton.
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Affiliation(s)
- Wenwen Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing 400715, China
| | - Yan Li
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing 400715, China
| | - Mingmei Le
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing 400715, China
| | - Lixia Tian
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing 400715, China
| | - Xujing Sun
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing 400715, China
| | - Rui Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing 400715, China
| | - Xin Guo
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing 400715, China
| | - Yan Wu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing 400715, China
| | - Yibing Li
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing 400715, China
| | - Jiaoyun Zhao
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing 400715, China
| | - Dajun Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing 400715, China
| | - Zhengsheng Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing 400715, China
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Yang P, Sun X, Liu X, Wang W, Hao Y, Chen L, Liu J, He H, Zhang T, Bao W, Tang Y, He X, Ji M, Guo K, Liu D, Teng Z, Liu D, Zhang J, Zhang Z. Identification of Candidate Genes for Lint Percentage and Fiber Quality Through QTL Mapping and Transcriptome Analysis in an Allotetraploid Interspecific Cotton CSSLs Population. FRONTIERS IN PLANT SCIENCE 2022; 13:882051. [PMID: 35574150 PMCID: PMC9100888 DOI: 10.3389/fpls.2022.882051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Upland cotton (Gossypium hirsutum) has long been an important fiber crop, but the narrow genetic diversity of modern G. hirsutum limits the potential for simultaneous improvement of yield and fiber quality. It is an effective approach to broaden the genetic base of G. hirsutum through introgression of novel alleles from G. barbadense with excellent fiber quality. In the present study, an interspecific chromosome segment substitution lines (CSSLs) population was established using G. barbadense cultivar Pima S-7 as the donor parent and G. hirsutum cultivar CCRI35 as the recipient parent. A total of 105 quantitative trait loci (QTL), including 85 QTL for fiber quality and 20 QTL for lint percentage (LP), were identified based on phenotypic data collected from four environments. Among these QTL, 25 stable QTL were detected in two or more environments, including four for LP, eleven for fiber length (FL), three for fiber strength (FS), six for fiber micronaire (FM), and one for fiber elongation (FE). Eleven QTL clusters were observed on nine chromosomes, of which seven QTL clusters harbored stable QTL. Moreover, eleven major QTL for fiber quality were verified through analysis of introgressed segments of the eight superior lines with the best comprehensive phenotypes. A total of 586 putative candidate genes were identified for 25 stable QTL associated with lint percentage and fiber quality through transcriptome analysis. Furthermore, three candidate genes for FL, GH_A08G1681 (GhSCPL40), GH_A12G2328 (GhPBL19), and GH_D02G0370 (GhHSP22.7), and one candidate gene for FM, GH_D05G1346 (GhAPG), were identified through RNA-Seq and qRT-PCR analysis. These results lay the foundation for understanding the molecular regulatory mechanism of fiber development and provide valuable information for marker-assisted selection (MAS) in cotton breeding.
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Zwyrtková J, Blavet N, Doležalová A, Cápal P, Said M, Molnár I, Vrána J, Doležel J, Hřibová E. Draft Sequencing Crested Wheatgrass Chromosomes Identified Evolutionary Structural Changes and Genes and Facilitated the Development of SSR Markers. Int J Mol Sci 2022; 23:ijms23063191. [PMID: 35328613 PMCID: PMC8948999 DOI: 10.3390/ijms23063191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 02/01/2023] Open
Abstract
Crested wheatgrass (Agropyron cristatum), a wild relative of wheat, is an attractive source of genes and alleles for their improvement. Its wider use is hampered by limited knowledge of its complex genome. In this work, individual chromosomes were purified by flow sorting, and DNA shotgun sequencing was performed. The annotation of chromosome-specific sequences characterized the DNA-repeat content and led to the identification of genic sequences. Among them, genic sequences homologous to genes conferring plant disease resistance and involved in plant tolerance to biotic and abiotic stress were identified. Genes belonging to the important groups for breeders involved in different functional categories were found. The analysis of the DNA-repeat content identified a new LTR element, Agrocen, which is enriched in centromeric regions. The colocalization of the element with the centromeric histone H3 variant CENH3 suggested its functional role in the grass centromere. Finally, 159 polymorphic simple-sequence-repeat (SSR) markers were identified, with 72 of them being chromosome- or chromosome-arm-specific, 16 mapping to more than one chromosome, and 71 mapping to all the Agropyron chromosomes. The markers were used to characterize orthologous relationships between A. cristatum and common wheat that will facilitate the introgression breeding of wheat using A. cristatum.
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Feng L, Chen Y, Xu M, Yang Y, Yue H, Su Q, Zhou C, Feng G, Ai N, Wang N, Zhou B. Genome-Wide Introgression and Quantitative Trait Locus Mapping Reveals the Potential of Asian Cotton ( Gossypium arboreum) in Improving Upland Cotton ( Gossypium hirsutum). FRONTIERS IN PLANT SCIENCE 2021; 12:719371. [PMID: 34408767 PMCID: PMC8365338 DOI: 10.3389/fpls.2021.719371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Gossypium arboreum (2n=2x=26, A2), the putative progenitor of the At-subgenome of Gossypium hirsutum (2n=4x=52, AD), is a repository of genes of interesting that have been eliminated during evolution/domestication of G. hirsutum. However, its valuable genes remain untapped so far due to species isolation. Here, using a synthetic amphiploid (AADDA2A2) previously reported, we developed a set of 289 G. arboreum chromosome segment introgression lines (ILs) in G. hirsutum by expanding the backcrossing population and through precise marker-assisted selection (MAS) although complex chromosomal structural variations existed between parents which severely hindered introgression. Our results showed the total coverage length of introgressed segments was 1,116.29 Mb, representing 78.48% of the At-subgenome in the G. hirsutum background, with an average segment-length of 8.69 Mb. A total of 81 co- quantitative trait loci (QTLs) for yield and fiber quality were identified by both the RSTEP-ADD-based QTL mapping and the genome-wide association study (GWAS) analysis, with 1.01-24.78% of the phenotypic variance explained. Most QTLs for boll traits showed negative additive effects, but G. arboreum still has the potential to improve boll-number traits in G. hirsutum. Most QTLs for fiber quality showed negative additive effects, implying these QTLs were domesticated in G. hirsutum compared with G. arboreum and, a small quantity of fiber quality QTLs showing positive additive effects, conversely; however, indicates that G. arboreum has the underlying genes of enhancing fiber quality of G. hirsutum. This study provides new insights into the breeding genetic potential of G. arboreum, lays the foundation for further mining favorable genes of interest, and provides guidance for inter-ploidy gene transference from relatives into cultivated crops.
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Affiliation(s)
- Liuchun Feng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Yu Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Min Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Ying Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Haoran Yue
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Qiao Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Chenhui Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Guoli Feng
- Shihezi Agricultural Science Research Institute, Shihezi, China
| | - Nijiang Ai
- Shihezi Agricultural Science Research Institute, Shihezi, China
| | - Ningshan Wang
- Shihezi Agricultural Science Research Institute, Shihezi, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
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Liu D, Teng Z, Kong J, Liu X, Wang W, Zhang X, Zhai T, Deng X, Wang J, Zeng J, Xiao Y, Guo K, Zhang J, Liu D, Wang W, Zhang Z. Natural variation in a CENTRORADIALIS homolog contributed to cluster fruiting and early maturity in cotton. BMC PLANT BIOLOGY 2018; 18:286. [PMID: 30458710 PMCID: PMC6245773 DOI: 10.1186/s12870-018-1518-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/07/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plant architecture and the vegetative-reproductive transition have major impacts on the agronomic success of crop plants, but genetic mechanisms underlying these traits in cotton (Gossypium spp.) have not been identified. RESULTS We identify four natural mutations in GoCEN-Dt associated with cluster fruiting (cl) and early maturity. The situ hybridization shows that GhCEN is preferentially expressed in cotton shoot apical meristems (SAM) of the main stem and axillary buds. Constitutive GhCEN-Dt overexpression suppresses the transition of the cotton vegetative apex to a reproductive shoot. Silencing GoCEN leads to early flowering and determinate growth, and in tetraploids causes the main stem to terminate in a floral bud, a novel phenotype that exemplifies co-adaptation of polyploid subgenomes and suggests new research and/or crop improvement approaches. Natural cl variations are enriched in cottons adapted to high latitudes with short frost-free periods, indicating that mutants of GoCEN have been strongly selected for early maturity. CONCLUSION We show that the cotton gene GoCEN-Dt, a homolog of Antirrhinum CENTRORADIALIS, is responsible for determinate growth habit and cluster fruiting. Insight into the genetic control of branch and flower differentiation offers new approaches to develop early maturing cultivars of cotton and other crops with plant architecture appropriate for mechanical harvesting.
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Affiliation(s)
- Dexin Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Zhonghua Teng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, urumqi, Xinjiang 830091 People’s Republic of China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Xueying Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Wenwen Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Xiao Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Tengfei Zhai
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Xianping Deng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Jinxia Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Jianyan Zeng
- Biotechnology Research Center, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Yuehua Xiao
- Biotechnology Research Center, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Kai Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Dajun Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Weiran Wang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, urumqi, Xinjiang 830091 People’s Republic of China
| | - Zhengsheng Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
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