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Li Z, Zhu QH, Moncuquet P, Wilson I, Llewellyn D, Stiller W, Liu S. Quantitative genomics-enabled selection for simultaneous improvement of lint yield and seed traits in cotton (Gossypium hirsutum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:142. [PMID: 38796822 PMCID: PMC11128407 DOI: 10.1007/s00122-024-04645-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 05/04/2024] [Indexed: 05/29/2024]
Abstract
KEY MESSAGE A Bayesian linkage disequilibrium-based multiple-locus mixed model identified QTLs for fibre, seed and oil traits and predicted breeding worthiness of test lines, enabling their simultaneous improvement in cotton. Improving cotton seed and oil yields has become increasingly important while continuing to breed for higher lint yield. In this study, a novel Bayesian linkage disequilibrium-based multiple-locus mixed model was developed for QTL identification and genomic prediction (GP). A multi-parent population consisting of 256 recombinant inbred lines, derived from four elite cultivars with distinct combinations of traits, was used in the analysis of QTLs for lint percentage, seed index, lint index and seed oil content and their interrelations. All four traits were moderately heritable and correlated but with no large influence of genotype × environment interactions across multiple seasons. Seven to ten major QTLs were identified for each trait with many being adjacent or overlapping for different trait pairs. A fivefold cross-validation of the model indicated prediction accuracies of 0.46-0.62. GP results based on any two-season phenotypes were strongly correlated with phenotypic means of a pooled analysis of three-season experiments (r = 0.83-0.92). When used for selection of improvement in lint, seed and oil yields, GP captured 40-100% of individuals with comparable lint yields of those selected based on the three-season phenotypic results. Thus, this quantitative genomics-enabled approach can not only decipher the genomic variation underlying lint, seed and seed oil traits and their interrelations, but can provide predictions for their simultaneous improvement. We discuss future breeding strategies in cotton that will enhance the entire value of the crop, not just its fibre.
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Affiliation(s)
- Zitong Li
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | | | - Iain Wilson
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | | | | | - Shiming Liu
- CSIRO Agriculture and Food, Narrabri, NSW, 2390, Australia.
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Khidirov MT, Ernazarova DK, Rafieva FU, Ernazarova ZA, Toshpulatov AK, Umarov RF, Kholova MD, Oripova BB, Kudratova MK, Gapparov BM, Khidirova MM, Komilov DJ, Turaev OS, Udall JA, Yu JZ, Kushanov FN. Genomic and Cytogenetic Analysis of Synthetic Polyploids between Diploid and Tetraploid Cotton ( Gossypium) Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:4184. [PMID: 38140511 PMCID: PMC10748080 DOI: 10.3390/plants12244184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
Cotton (Gossypium spp.) is the most important natural fiber source in the world. The genetic potential of cotton can be successfully and efficiently exploited by identifying and solving the complex fundamental problems of systematics, evolution, and phylogeny, based on interspecific hybridization of cotton. This study describes the results of interspecific hybridization of G. herbaceum L. (A1-genome) and G. mustelinum Miers ex Watt (AD4-genome) species, obtaining fertile hybrids through synthetic polyploidization of otherwise sterile triploid forms with colchicine (C22H25NO6) treatment. The fertile F1C hybrids were produced from five different cross combinations: (1) G. herbaceum subsp. frutescens × G. mustelinum; (2) G. herbaceum subsp. pseudoarboreum × G. mustelinum; (3) G. herbaceum subsp. pseudoarboreum f. harga × G. mustelinum; (4) G. herbaceum subsp. africanum × G. mustelinum; (5) G. herbaceum subsp. euherbaceum (variety A-833) × G. mustelinum. Cytogenetic analysis discovered normal conjugation of bivalent chromosomes in addition to univalent, open, and closed ring-shaped quadrivalent chromosomes at the stage of metaphase I in the F1C and F2C hybrids. The setting of hybrid bolls obtained as a result of these crosses ranged from 13.8-92.2%, the fertility of seeds in hybrid bolls from 9.7-16.3%, and the pollen viability rates from 36.6-63.8%. Two transgressive plants with long fiber of 35.1-37.0 mm and one plant with extra-long fiber of 39.1-41.0 mm were identified in the F2C progeny of G. herbaceum subsp. frutescens × G. mustelinum cross. Phylogenetic analysis with 72 SSR markers that detect genomic changes showed that tetraploid hybrids derived from the G. herbaceum × G. mustelinum were closer to the species G. mustelinum. The G. herbaceum subsp. frutescens was closer to the cultivated form, and its subsp. africanum was closer to the wild form. New knowledge of the interspecific hybridization and synthetic polyploidization was developed for understanding the genetic mechanisms of the evolution of tetraploid cotton during speciation. The synthetic polyploids of cotton obtained in this study would provide beneficial genes for developing new cotton varieties of the G. hirsutum species, with high-quality cotton fiber and strong tolerance to biotic or abiotic stress. In particular, the introduction of these polyploids to conventional and molecular breeding can serve as a bridge of transferring valuable genes related to high-quality fiber and stress tolerance from different cotton species to the new cultivars.
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Affiliation(s)
- Mukhammad T. Khidirov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
- Department of Genetics, National University of Uzbekistan, Tashkent 100174, Uzbekistan;
| | - Feruza U. Rafieva
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Ziraatkhan A. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Abdulqahhor Kh. Toshpulatov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Ramziddin F. Umarov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Madina D. Kholova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Barno B. Oripova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Mukhlisa K. Kudratova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | | | - Doniyor J. Komilov
- Department of Biology, Namangan State University, Uychi Street-316, Namangan 160100, Uzbekistan;
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
- Department of Genetics, National University of Uzbekistan, Tashkent 100174, Uzbekistan;
| | - Joshua A. Udall
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA;
| | - John Z. Yu
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA;
| | - Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
- Department of Genetics, National University of Uzbekistan, Tashkent 100174, Uzbekistan;
- Department of Biology, Namangan State University, Uychi Street-316, Namangan 160100, Uzbekistan;
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Wang Y, Guo X, Xu Y, Sun R, Cai X, Zhou Z, Qin T, Tao Y, Li B, Hou Y, Wang Q, Liu F. Genome-wide association study for boll weight in Gossypium hirsutum races. Funct Integr Genomics 2023; 23:331. [PMID: 37940771 DOI: 10.1007/s10142-023-01261-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023]
Abstract
High yield has always been an essential target in almost all of the cotton breeding programs. Boll weight (BW) is a key component of cotton yield. Numerous linkage mapping and genome-wide association studies (GWAS) have been performed to understand the genetic mechanism of BW, but information on the markers/genes controlling BW remains limited. In this study, we conducted a GWAS for BW using 51,268 high-quality single-nucleotide polymorphisms (SNPs) and 189 Gossypium hirsutum accessions across five different environments. A total of 55 SNPs significantly associated with BW were detected, of which 29 and 26 were distributed in the A and D subgenomes, respectively. Five SNPs were simultaneously detected in two environments. For TM5655, TM8662, TM36371, and TM50258, the BW grouped by alleles of each SNP was significantly different. The ± 550 kb regions around these four key SNPs contained 262 genes. Of them, Gh_A02G1473, Gh_A10G1765, and Gh_A02G1442 were expressed highly at 0 to 1 days post-anthesis (dpa), - 3 to 0 dpa, and - 3 to 0 dpa in ovule of TM-1, respectively. They were presumed as the candidate genes for fiber cell differentiation, initiation, or elongation based on gene annotation of their homologs. Overall, these results supplemented valuable information for dissecting the genetic architecture of BW and might help to improve cotton yield through molecular marker-assisted selection breeding and molecular design breeding.
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Affiliation(s)
- Yuanyuan Wang
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xinlei Guo
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Runrun Sun
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Hainan Yazhou Bay Seed Laboratory / National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Tengfei Qin
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ye Tao
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Baihui Li
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Qinglian Wang
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China.
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Hainan Yazhou Bay Seed Laboratory / National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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Joshi B, Singh S, Tiwari GJ, Kumar H, Boopathi NM, Jaiswal S, Adhikari D, Kumar D, Sawant SV, Iquebal MA, Jena SN. Genome-wide association study of fiber yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1252746. [PMID: 37941674 PMCID: PMC10630025 DOI: 10.3389/fpls.2023.1252746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/11/2023] [Indexed: 11/10/2023]
Abstract
Upland cotton (Gossypium hirsutum L.) is a major fiber crop that is cultivated worldwide and has significant economic importance. India harbors the largest area for cotton cultivation, but its fiber yield is still compromised and ranks 22nd in terms of productivity. Genetic improvement of cotton fiber yield traits is one of the major goals of cotton breeding, but the understanding of the genetic architecture underlying cotton fiber yield traits remains limited and unclear. To better decipher the genetic variation associated with fiber yield traits, we conducted a comprehensive genome-wide association mapping study using 117 Indian cotton germplasm for six yield-related traits. To accomplish this, we generated 2,41,086 high-quality single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS) methods. Population structure, PCA, kinship, and phylogenetic analyses divided the germplasm into two sub-populations, showing weak relatedness among the germplasms. Through association analysis, 205 SNPs and 134 QTLs were identified to be significantly associated with the six fiber yield traits. In total, 39 novel QTLs were identified in the current study, whereas 95 QTLs overlapped with existing public domain data in a comparative analysis. Eight QTLs, qGhBN_SCY_D6-1, qGhBN_SCY_D6-2, qGhBN_SCY_D6-3, qGhSI_LI_A5, qGhLI_SI_A13, qGhLI_SI_D9, qGhBW_SCY_A10, and qGhLP_BN_A8 were identified. Gene annotation of these fiber yield QTLs revealed 2,509 unique genes. These genes were predominantly enriched for different biological processes, such as plant cell wall synthesis, nutrient metabolism, and vegetative growth development in the gene ontology (GO) enrichment study. Furthermore, gene expression analysis using RNAseq data from 12 diverse cotton tissues identified 40 candidate genes (23 stable and 17 novel genes) to be transcriptionally active in different stages of fiber, ovule, and seed development. These findings have revealed a rich tapestry of genetic elements, including SNPs, QTLs, and candidate genes, and may have a high potential for improving fiber yield in future breeding programs for Indian cotton.
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Affiliation(s)
- Babita Joshi
- Plant Genetic Resources and Improvement, CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sanjay Singh
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Gopal Ji Tiwari
- Plant Genetic Resources and Improvement, CSIR-National Botanical Research Institute, Lucknow, India
| | - Harish Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Regional Research Station, Faridkot, Punjab, India
| | - Narayanan Manikanda Boopathi
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dibyendu Adhikari
- Plant Ecology and Climate Change Science, CSIR-National Botanical Research Institute, Lucknow, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Samir V. Sawant
- Molecular Biology & Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Satya Narayan Jena
- Plant Genetic Resources and Improvement, CSIR-National Botanical Research Institute, Lucknow, India
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Niu H, Kuang M, Huang L, Shang H, Yuan Y, Ge Q. Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60. BMC PLANT BIOLOGY 2023; 23:179. [PMID: 37020180 PMCID: PMC10074700 DOI: 10.1186/s12870-023-04147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Upland cotton (Gossypium hirsutum L.) is the most economically important species in the cotton genus (Gossypium spp.). Enhancing the cotton yield is a major goal in cotton breeding programs. Lint percentage (LP) and boll weight (BW) are the two most important components of cotton lint yield. The identification of stable and effective quantitative trait loci (QTLs) will aid the molecular breeding of cotton cultivars with high yield. RESULTS Genotyping by target sequencing (GBTS) and genome-wide association study (GWAS) with 3VmrMLM were used to identify LP and BW related QTLs from two recombinant inbred line (RIL) populations derived from high lint yield and fiber quality lines (ZR014121, CCRI60 and EZ60). The average call rate of a single locus was 94.35%, and the average call rate of an individual was 92.10% in GBTS. A total of 100 QTLs were identified; 22 of them were overlapping with the reported QTLs, and 78 were novel QTLs. Of the 100 QTLs, 51 QTLs were for LP, and they explained 0.29-9.96% of the phenotypic variation; 49 QTLs were for BW, and they explained 0.41-6.31% of the phenotypic variation. One QTL (qBW-E-A10-1, qBW-C-A10-1) was identified in both populations. Six key QTLs were identified in multiple-environments; three were for LP, and three were for BW. A total of 108 candidate genes were identified in the regions of the six key QTLs. Several candidate genes were positively related to the developments of LP and BW, such as genes involved in gene transcription, protein synthesis, calcium signaling, carbon metabolism, and biosynthesis of secondary metabolites. Seven major candidate genes were predicted to form a co-expression network. Six significantly highly expressed candidate genes of the six QTLs after anthesis were the key genes regulating LP and BW and affecting cotton yield formation. CONCLUSIONS A total of 100 stable QTLs for LP and BW in upland cotton were identified in this study; these QTLs could be used in cotton molecular breeding programs. Putative candidate genes of the six key QTLs were identified; this result provided clues for future studies on the mechanisms of LP and BW developments.
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Affiliation(s)
- Hao Niu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Meng Kuang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Longyu Huang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, 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, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, 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, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Niu H, Ge Q, Shang H, Yuan Y. Inheritance, QTLs, and Candidate Genes of Lint Percentage in Upland Cotton. Front Genet 2022; 13:855574. [PMID: 35450216 PMCID: PMC9016478 DOI: 10.3389/fgene.2022.855574] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cotton (Gossypium spp.) is an important natural fiber plant. Lint percentage (LP) is one of the most important determinants of cotton yield and is a typical quantitative trait with high variation and heritability. Many cotton LP genetic linkages and association maps have been reported. This work summarizes the inheritance, quantitative trait loci (QTLs), and candidate genes of LP to facilitate LP genetic study and molecular breeding. More than 1439 QTLs controlling LP have been reported. Excluding replicate QTLs, 417 unique QTLs have been identified on 26 chromosomes, including 243 QTLs identified at LOD >3. More than 60 are stable, major effective QTLs that can be used in marker-assisted selection (MAS). More than 90 candidate genes for LP have been reported. These genes encode MYB, HOX, NET, and other proteins, and most are preferentially expressed during fiber initiation and elongation. A putative molecular regulatory model of LP was constructed and provides the foundation for the genetic study and molecular breeding of LP.
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Affiliation(s)
- Hao Niu
- 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, 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, 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, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Haihong Shang, ; Youlu Yuan,
| | - 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, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Haihong Shang, ; Youlu Yuan,
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7
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Kushanov FN, Turaev OS, Ernazarova DK, Gapparov BM, Oripova BB, Kudratova MK, Rafieva FU, Khalikov KK, Erjigitov DS, Khidirov MT, Kholova MD, Khusenov NN, Amanboyeva RS, Saha S, Yu JZ, Abdurakhmonov IY. Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton ( Gossypium spp.). FRONTIERS IN PLANT SCIENCE 2021; 12:779386. [PMID: 34975965 PMCID: PMC8716771 DOI: 10.3389/fpls.2021.779386] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/23/2021] [Indexed: 02/05/2023]
Abstract
Cotton genetic resources contain diverse economically important traits that can be used widely in breeding approaches to create of high-yielding elite cultivars with superior fiber quality and adapted to biotic and abiotic stresses. Nevertheless, the creation of new cultivars using conventional breeding methods is limited by the cost and proved to be time consuming process, also requires a space to make field observations and measurements. Decoding genomes of cotton species greatly facilitated generating large-scale high-throughput DNA markers and identification of QTLs that allows confirmation of candidate genes, and use them in marker-assisted selection (MAS)-based breeding programs. With the advances of quantitative trait loci (QTL) mapping and genome-wide-association study approaches, DNA markers associated with valuable traits significantly accelerate breeding processes by replacing the selection with a phenotype to the selection at the DNA or gene level. In this review, we discuss the evolution and genetic diversity of cotton Gossypium genus, molecular markers and their types, genetic mapping and QTL analysis, application, and perspectives of MAS-based approaches in cotton breeding.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
- *Correspondence: Fakhriddin N. Kushanov, ;
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Barno B. Oripova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhlisa K. Kudratova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Feruza U. Rafieva
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Kuvandik K. Khalikov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Doston Sh. Erjigitov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhammad T. Khidirov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Madina D. Kholova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Naim N. Khusenov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Roza S. Amanboyeva
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Sukumar Saha
- Crop Science Research Laboratory, USDA-ARS, Washington, DC, United States
| | - John Z. Yu
- Southern Plains Agricultural Research Center, USDA-ARS, Washington, DC, United States
| | - Ibrokhim Y. Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
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8
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Gupta A, Jaiswal V, Sawant SV, Yadav HK. Mapping QTLs for 15 morpho-metric traits in Arabidopsis thaliana using Col-0 × Don-0 population. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1021-1034. [PMID: 32377050 PMCID: PMC7196571 DOI: 10.1007/s12298-020-00800-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 01/24/2020] [Accepted: 03/17/2020] [Indexed: 05/13/2023]
Abstract
Genome wide quantitative trait loci (QTL) mapping was conducted in Arabidopsis thaliana using F2 mapping population (Col-0 × Don-0) and SNPs markers. A total of five linkage groups were obtained with number of SNPs varying from 45 to 59 per linkage group. The composite interval mapping detected a total of 36 QTLs for 15 traits and the number of QTLs ranged from one (root length, root dry biomass, cauline leaf width, number of internodes and internode distance) to seven (for bolting days). The range of phenotypic variance explained (PVE) and logarithm of the odds ratio of these 36 QTLs was found be 0.19-38.17% and 3.0-6.26 respectively. Further, the epistatic interaction detected one main effect QTL and four epistatic QTLs. Five major QTLs viz. Qbd.nbri.4.3, Qfd.nbri.4.2, Qrdm.nbri.5.1, Qncl.nbri.2.2, Qtd.nbri.4.1 with PVE > 15.0% might be useful for fine mapping to identify genes associated with respective traits, and also for development of specialized population through marker assisted selection. The identification of additive and dominant effect QTLs and desirable alleles of each of above mentioned traits would also be important for future research.
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Affiliation(s)
- Astha Gupta
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025 India
- Department of Botany, University of Delhi, New Delhi, 110 007 India
| | - Vandana Jaiswal
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
| | - Samir V. Sawant
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025 India
| | - Hemant Kumar Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025 India
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9
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Liu C, Zhang TZ. Functional diversifications of GhERF1 duplicate genes after the formation of allotetraploid cotton. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:60-74. [PMID: 30578593 DOI: 10.1111/jipb.12764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
Whole genome duplication, a prevalent force of evolution in plants, results in massive genome restructuring in different organisms. Roles of the resultant duplicated genes are poorly understood, both functionally and evolutionarily. In the present study, differentially expressed ethylene responsive factors (GhERF1s), anchored on Chr-A07 and Chr-D07, were isolated from a high-yielding cotton hybrid (XZM2) and its parents. The GhERF1 was located in the B3 subgroup of the ethylene responsive factors subfamily involved in conferring tolerance to abiotic stress. Nucleotide sequence analysis of 524 diverse accessions, together with quantitative real-time polymerase chain reaction analysis, elucidated that de-functionalization of GhERF1-7A occurred due to one base insertion following formation of the allotetraploid cotton. Our quantitative trait loci and association mapping analyses highlighted a role for GhERF1-7A in conferring high boll number per plant in modern cotton cultivars. Overexpression of GhERF1-7A in transgenic Arabidopsis resulted in a substantial increase in the number of siliques and total seed yield. Neo-functionalization of GhERF1-7A was also observed in modern cultivars rather than in races and/or landraces, further supporting its role in the development of high-yielding cotton cultivars. Both de- and neo-functionalization occurred in one of the duplicate genes, thus providing new genomic insight into the evolution of allotetraploid cotton species.
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Affiliation(s)
- Chunxiao Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Tian Zhen Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
- Crop Science Institute, Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China
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10
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Detection of favorable alleles for yield and yield components by association mapping in upland cotton. Genes Genomics 2018; 40:725-734. [PMID: 29934807 DOI: 10.1007/s13258-018-0678-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/28/2018] [Indexed: 10/17/2022]
Abstract
Association mapping based on linkage disequilibrium provides a promising tool for dissecting the genetic basis underlying complex traits. To reveal the genetic variations of yield and yield components traits in upland cotton, 403 upland cotton accessions were collected and analyzed by 560 genome-wide simple sequence repeats (SSRs). A diverse panel consisting of 403 upland cotton accessions was grown in six different environments, and the yield and yield component traits were measured, and 560 SSR markers covering the whole genome were mapped. Association studies were performed to uncover the genotypic and phenotypic variations using a mixed linear model. Favorable alleles and typical accessions for yield traits were identified. A total of 201 markers were polymorphic, revealing 394 alleles. The average gene diversity and polymorphism information content were 0.556 and 0.483, respectively. Based on a population structure analysis, 403 accessions were divided into two subgroups. A mixed linear model analysis of the association mapping detected 43 marker loci according to the best linear unbiased prediction and in at least three of the six environments(- lgP > 1.30, P < 0.05). Among the 43 associated markers, five were associated with more than two traits simultaneously and nine were coincident with those identified previously. Based on phenotypic effects, favorable alleles and typical accessions that contained the elite allele loci related to yield traits were identified and are widely used in practical breeding. This study detected favorable quantitative trait loci's alleles and typical accessions for yield traits, these are excellent genetic resources for future high-yield breeding by marker-assisted selection in upland cotton in China.
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11
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Man W, Zhang L, Li X, Xie X, Pei W, Yu J, Yu S, Zhang J. A comparative transcriptome analysis of two sets of backcross inbred lines differing in lint-yield derived from a Gossypium hirsutum × Gossypium barbadense population. Mol Genet Genomics 2016; 291:1749-67. [PMID: 27256327 DOI: 10.1007/s00438-016-1216-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 05/13/2016] [Indexed: 01/23/2023]
Abstract
Upland cotton (Gossypium hirsutum L.) is the most important fiber crop, and its lint-yield improvement is impeded due to its narrow genetic base and the lack of understanding of the genetic basis of yield. Backcross inbred lines (BILs) or near-isogenic lines (NILs) in the same genetic background differing in lint yield, developed through advanced backcrossing, provide an important genomic resource to study the molecular genetic basis of lint yield. In the present study, a high-yield (HY) group and a low-yield (LY) group each with three BILs were selected from a BIL population between G. hirsutum and G. barbadense. Using a microarray-based comparative transcriptome analysis on developing fibers at 10 days post-anthesis (DPA) between the two groups, 1486 differentially expressed genes (DEGs) were identified. A total of 212 DEGs were further mapped in the regions of 24 yield QTL and 11 yield trait QTL hotspots as reported previously, and 81 DEGs mapped with the 7 lint-yield QTL identified in the BIL population from which the two sets of BILs were selected. Gene Ontology annotations and Blast-Mapping-Annotation-KEGG analysis via Blast2GO revealed that more DEGs were associated with catalytic activity and binding, followed by transporters, nucleic acid binding transcription factors, structural molecules and molecular transducer activities. Six DEGs were chosen for a quantitative RT-PCR assay, and the results were consistent with the microarray analysis. The development of DEGs-based markers revealed that 7 single strand conformation polymorphism-based single nucleotide polymorphic (SSCP-SNP) markers were associated with yield traits, and 3 markers with lint yield. In the present study, we identified a number of yield and yield component QTL-co-localizing DEGs and developed several DEG-based SSCP-SNP markers for the traits, thereby providing a set of candidate genes for molecular breeding and genetic manipulation of lint yield in cotton.
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Affiliation(s)
- Wu Man
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Liyuan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Xihua Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Xiaobing Xie
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China.,Wuyang A & F Bureau, Luohe, Henan, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China.
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
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12
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Liang Q, Shang L, Wang Y, Hua J. Partial Dominance, Overdominance and Epistasis as the Genetic Basis of Heterosis in Upland Cotton (Gossypium hirsutum L.). PLoS One 2015; 10:e0143548. [PMID: 26618635 PMCID: PMC4664285 DOI: 10.1371/journal.pone.0143548] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 11/05/2015] [Indexed: 11/19/2022] Open
Abstract
Determination of genetic basis of heterosis may promote hybrid production in Upland cotton (Gossypium hirsutum L.). This study was designed to explore the genetic mechanism of heterosis for yield and yield components in F2: 3 and F2: 4 populations derived from a hybrid 'Xinza No. 1'. Replicated yield field trials of the progenies were conducted in 2008 and 2009. Phenotypic data analyses indicated overdominance in F1 for yield and yield components. Additive and dominance effects at single-locus level and digenic epistatic interactions at two-locus level were analyzed by 421 marker loci spanning 3814 cM of the genome. A total of 38 and 49 QTLs controlling yield and yield components were identified in F2: 3 and F2: 4 populations, respectively. Analyses of these QTLs indicated that the effects of partial dominance and overdominance contributed to heterosis in Upland cotton simultaneously. Most of the QTLs showed partial dominance whereas 13 QTLs showing overdominance in F2:3 population, and 19 QTLs showed overdominance in F2:4. Among them, 21 QTLs were common in both F2: 3 and F2: 4 populations. A large number of two-locus interactions for yield and yield components were detected in both generations. AA (additive × additive) epistasis accounted for majority portion of epistatic effects. Thirty three complementary two-locus homozygotes (11/22 and 22/11) were the best genotypes for AA interactions in terms of bolls per plant. Genotypes of double homozygotes, 11/22, 22/11 and 22/22, performed best for AD/DA interactions, while genotype of 11/12 performed best for DD interactions. These results indicated that (1) partial dominance and overdominance effects at single-locus level and (2) epistasis at two-locus level elucidated the genetic basis of heterosis in Upland cotton.
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Affiliation(s)
- Qingzhi Liang
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, China Agricultural University, Beijing, 100193, P. R. China
| | - Lianguang Shang
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, China Agricultural University, Beijing, 100193, P. R. China
| | - Yumei Wang
- Research Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
| | - Jinping Hua
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, China Agricultural University, Beijing, 100193, P. R. China
- * E-mail:
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13
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Construction of a high-density genetic map and lint percentage and cottonseed nutrient trait QTL identification in upland cotton (Gossypium hirsutum L.). Mol Genet Genomics 2015; 290:1683-700. [PMID: 25796191 DOI: 10.1007/s00438-015-1027-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 03/03/2015] [Indexed: 12/19/2022]
Abstract
Upland cotton plays a critical role not only in the textile industry, but also in the production of important secondary metabolites, such as oil and proteins. Construction of a high-density linkage map and identifying yield and seed trait quantitative trail loci (QTL) are prerequisites for molecular marker-assisted selective breeding projects. Here, we update a high-density upland cotton genetic map from recombinant inbred lines. A total of 25,313 SSR primer pairs were screened for polymorphism between Yumian 1 and T586, and 1712 SSR primer pairs were used to genotype the mapping population and construct a map. An additional 1166 loci have been added to our previously published map with 509 SSR markers. The updated genetic map spans a total recombinant length of 3338.2 cM and contains 1675 SSR loci and nine morphological markers, with an average interval of 1.98 cM between adjacent markers. Green lint (Lg) mapped on chromosome 15 in a previous report is mapped in an interval of 2.6 cM on chromosome 21. Based on the map and phenotypic data from multiple environments, 79 lint percentage and seed nutrient trait QTL are detected. These include 8 lint percentage, 13 crude protein, 15 crude oil, 8 linoleic, 10 oleic, 13 palmitic, and 12 stearic acid content QTL. They explain 3.5-62.7 % of the phenotypic variation observed. Four morphological markers identified have a major impact on lint percentage and cottonseed nutrients traits. In this study, our genetic map provides new sights into the tetraploid cotton genome. Furthermore, the stable QTL and morphological markers could be used for fine-mapping and map-based cloning.
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14
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Chen W, Yao J, Chu L, Yuan Z, Li Y, Zhang Y. Genetic mapping of the nulliplex-branch gene (gb_nb1) in cotton using next-generation sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:539-47. [PMID: 25575840 DOI: 10.1007/s00122-014-2452-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 12/24/2014] [Indexed: 05/21/2023]
Abstract
Using bulked segregant analysis based on next-generation sequencing, the recessive nulliplex-branch gene was mapped between two SNP markers ~600 kb apart. In a "nulliplex-branch" cotton mutant, most of the flowers arise directly from leaf axils on the main shoot, which usually does not have a fruiting branch. A nulliplex-branch is a useful trait by which to study cotton architecture; however, the genetic basis of this mutant has remained elusive. In this study, bulked segregant analysis combined with next-generation sequencing technology was used to finely map the underlying genes that result in a nulliplex-branch plant. The nulliplex-branch Pima cotton variety, Xinhai-18, was crossed with the normal branch upland cotton line, TM-1, resulting in an F2 population. The nulliplex-branch trait was found to be controlled by the recessive gene gb_nb1. Allelic single-nucleotide polymorphisms (SNPs) were discovered by reduced-representation sequencing between the parents, and their profiles were also characterized in the nulliplex-branch and normal branch bulks constructed using the F2 plants. A candidate ~9.0 Mb-long region comprising 42 SNP markers was found to be associated with gb_nb1, which helped localize it at the ~600-kb interval on Chr 16 by segregation analysis in the F2 population. The closely linked markers with gb_nb1 developed in this study will facilitate the marker-assisted selection of the nulliplex-branch trait, and the fine map constructed will accelerate map-based cloning of gb_nb1.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, The Chinese Academy of Agricultural Sciences, Anyang, 455004, China
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15
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Fang DD, Jenkins JN, Deng DD, McCarty JC, Li P, Wu J. Quantitative trait loci analysis of fiber quality traits using a random-mated recombinant inbred population in Upland cotton (Gossypium hirsutum L.). BMC Genomics 2014; 15:397. [PMID: 24886099 PMCID: PMC4055785 DOI: 10.1186/1471-2164-15-397] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Upland cotton (Gossypium hirsutum L.) accounts for about 95% of world cotton production. Improving Upland cotton cultivars has been the focus of world-wide cotton breeding programs. Negative correlation between yield and fiber quality is an obstacle for cotton improvement. Random-mating provides a potential methodology to break this correlation. The suite of fiber quality traits that affect the yarn quality includes the length, strength, maturity, fineness, elongation, uniformity and color. Identification of stable fiber quantitative trait loci (QTL) in Upland cotton is essential in order to improve cotton cultivars with superior quality using marker-assisted selection (MAS) strategy. RESULTS Using 11 diverse Upland cotton cultivars as parents, a random-mated recombinant inbred (RI) population consisting of 550 RI lines was developed after 6 cycles of random-mating and 6 generations of self-pollination. The 550 RILs were planted in triplicates for two years in Mississippi State, MS, USA to obtain fiber quality data. After screening 15538 simple sequence repeat (SSR) markers, 2132 were polymorphic among the 11 parents. One thousand five hundred eighty-two markers covering 83% of cotton genome were used to genotype 275 RILs (Set 1). The marker-trait associations were analyzed using the software program TASSEL. At p < 0.01, 131 fiber QTLs and 37 QTL clusters were identified. These QTLs were responsible for the combined phenotypic variance ranging from 62.3% for short fiber content to 82.8% for elongation. The other 275 RILs (Set 2) were analyzed using a subset of 270 SSR markers, and the QTLs were confirmed. Two major QTL clusters were observed on chromosomes 7 and 16. Comparison of these 131 QTLs with the previously published QTLs indicated that 77 were identified before, and 54 appeared novel. CONCLUSIONS The 11 parents used in this study represent a diverse genetic pool of the US cultivated cotton, and 10 of them were elite commercial cultivars. The fiber QTLs, especially QTL clusters reported herein can be readily implemented in a cotton breeding program to improve fiber quality via MAS strategy. The consensus QTL regions warrant further investigation to better understand the genetics and molecular mechanisms underlying fiber development.
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Affiliation(s)
- David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA 70124, USA.
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16
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Fang DD, Jenkins JN, Deng DD, McCarty JC, Li P, Wu J. Quantitative trait loci analysis of fiber quality traits using a random-mated recombinant inbred population in Upland cotton (Gossypium hirsutum L.). BMC Genomics 2014. [PMID: 24886099 DOI: 10.1186/1471‐2164‐15‐397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Upland cotton (Gossypium hirsutum L.) accounts for about 95% of world cotton production. Improving Upland cotton cultivars has been the focus of world-wide cotton breeding programs. Negative correlation between yield and fiber quality is an obstacle for cotton improvement. Random-mating provides a potential methodology to break this correlation. The suite of fiber quality traits that affect the yarn quality includes the length, strength, maturity, fineness, elongation, uniformity and color. Identification of stable fiber quantitative trait loci (QTL) in Upland cotton is essential in order to improve cotton cultivars with superior quality using marker-assisted selection (MAS) strategy. RESULTS Using 11 diverse Upland cotton cultivars as parents, a random-mated recombinant inbred (RI) population consisting of 550 RI lines was developed after 6 cycles of random-mating and 6 generations of self-pollination. The 550 RILs were planted in triplicates for two years in Mississippi State, MS, USA to obtain fiber quality data. After screening 15538 simple sequence repeat (SSR) markers, 2132 were polymorphic among the 11 parents. One thousand five hundred eighty-two markers covering 83% of cotton genome were used to genotype 275 RILs (Set 1). The marker-trait associations were analyzed using the software program TASSEL. At p < 0.01, 131 fiber QTLs and 37 QTL clusters were identified. These QTLs were responsible for the combined phenotypic variance ranging from 62.3% for short fiber content to 82.8% for elongation. The other 275 RILs (Set 2) were analyzed using a subset of 270 SSR markers, and the QTLs were confirmed. Two major QTL clusters were observed on chromosomes 7 and 16. Comparison of these 131 QTLs with the previously published QTLs indicated that 77 were identified before, and 54 appeared novel. CONCLUSIONS The 11 parents used in this study represent a diverse genetic pool of the US cultivated cotton, and 10 of them were elite commercial cultivars. The fiber QTLs, especially QTL clusters reported herein can be readily implemented in a cotton breeding program to improve fiber quality via MAS strategy. The consensus QTL regions warrant further investigation to better understand the genetics and molecular mechanisms underlying fiber development.
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Affiliation(s)
- David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA 70124, USA.
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17
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Fang DD, Jenkins JN, Deng DD, McCarty JC, Li P, Wu J. Quantitative trait loci analysis of fiber quality traits using a random-mated recombinant inbred population in Upland cotton (Gossypium hirsutum L.). BMC Genomics 2014. [PMID: 24886099 DOI: 10.1186/14712164-15-397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Upland cotton (Gossypium hirsutum L.) accounts for about 95% of world cotton production. Improving Upland cotton cultivars has been the focus of world-wide cotton breeding programs. Negative correlation between yield and fiber quality is an obstacle for cotton improvement. Random-mating provides a potential methodology to break this correlation. The suite of fiber quality traits that affect the yarn quality includes the length, strength, maturity, fineness, elongation, uniformity and color. Identification of stable fiber quantitative trait loci (QTL) in Upland cotton is essential in order to improve cotton cultivars with superior quality using marker-assisted selection (MAS) strategy. RESULTS Using 11 diverse Upland cotton cultivars as parents, a random-mated recombinant inbred (RI) population consisting of 550 RI lines was developed after 6 cycles of random-mating and 6 generations of self-pollination. The 550 RILs were planted in triplicates for two years in Mississippi State, MS, USA to obtain fiber quality data. After screening 15538 simple sequence repeat (SSR) markers, 2132 were polymorphic among the 11 parents. One thousand five hundred eighty-two markers covering 83% of cotton genome were used to genotype 275 RILs (Set 1). The marker-trait associations were analyzed using the software program TASSEL. At p < 0.01, 131 fiber QTLs and 37 QTL clusters were identified. These QTLs were responsible for the combined phenotypic variance ranging from 62.3% for short fiber content to 82.8% for elongation. The other 275 RILs (Set 2) were analyzed using a subset of 270 SSR markers, and the QTLs were confirmed. Two major QTL clusters were observed on chromosomes 7 and 16. Comparison of these 131 QTLs with the previously published QTLs indicated that 77 were identified before, and 54 appeared novel. CONCLUSIONS The 11 parents used in this study represent a diverse genetic pool of the US cultivated cotton, and 10 of them were elite commercial cultivars. The fiber QTLs, especially QTL clusters reported herein can be readily implemented in a cotton breeding program to improve fiber quality via MAS strategy. The consensus QTL regions warrant further investigation to better understand the genetics and molecular mechanisms underlying fiber development.
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Affiliation(s)
- David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA 70124, USA.
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18
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Zhao Y, Wang H, Chen W, Li Y. Genetic structure, linkage disequilibrium and association mapping of Verticillium wilt resistance in elite cotton (Gossypium hirsutum L.) germplasm population. PLoS One 2014; 9:e86308. [PMID: 24466016 PMCID: PMC3900507 DOI: 10.1371/journal.pone.0086308] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 12/07/2013] [Indexed: 11/25/2022] Open
Abstract
Understanding the population structure and linkage disequilibrium in an association panel can effectively avoid spurious associations and improve the accuracy in association mapping. In this study, one hundred and fifty eight elite cotton (Gossypium hirsutum L.) germplasm from all over the world, which were genotyped with 212 whole genome-wide marker loci and phenotyped with an disease nursery and greenhouse screening method, were assayed for population structure, linkage disequilibrium, and association mapping of Verticillium wilt resistance. A total of 480 alleles ranging from 2 to 4 per locus were identified from all collections. Model-based analysis identified two groups (G1 and G2) and seven subgroups (G1a–c, G2a–d), and differentiation analysis showed that subgroup having a single origin or pedigree was apt to differentiate with those having a mixed origin. Only 8.12% linked marker pairs showed significant LD (P<0.001) in this association panel. The LD level for linked markers is significantly higher than that for unlinked markers, suggesting that physical linkage strongly influences LD in this panel, and LD level was elevated when the panel was classified into groups and subgroups. The LD decay analysis for several chromosomes showed that different chromosomes showed a notable change in LD decay distances for the same gene pool. Based on the disease nursery and greenhouse environment, 42 marker loci associated with Verticillium wilt resistance were identified through association mapping, which widely were distributed among 15 chromosomes. Among which 10 marker loci were found to be consistent with previously identified QTLs and 32 were new unreported marker loci, and QTL clusters for Verticillium wilt resistanc on Chr.16 were also proved in our study, which was consistent with the strong linkage in this chromosome. Our results would contribute to association mapping and supply the marker candidates for marker-assisted selection of Verticillium wilt resistance in cotton.
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Affiliation(s)
- Yunlei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang, People's Republic of China
| | - Hongmei Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang, People's Republic of China
- * E-mail:
| | - Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang, People's Republic of China
| | - Yunhai Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang, People's Republic of China
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Cai C, Ye W, Zhang T, Guo W. Association analysis of fiber quality traits and exploration of elite alleles in Upland cotton cultivars/accessions (Gossypium hirsutum L.). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:51-62. [PMID: 24428209 DOI: 10.1111/jipb.12124] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 10/28/2013] [Indexed: 05/02/2023]
Abstract
Exploring the elite alleles and germplasm accessions related to fiber quality traits will accelerate the breeding of cotton for fiber quality improvement. In this study, 99 Gossypium hirsutum L. accessions with diverse origins were used to perform association analysis of fiber quality traits using 97 polymorphic microsatellite marker primer pairs. A total of 107 significant marker-trait associations were detected for three fiber quality traits under three different environments, with 70 detected in two or three environments and 37 detected in only one environment. Among the 70 significant marker-trait associations, 52.86% were reported previously, implying that these are stable loci for target traits. Furthermore, we detected a large number of elite alleles associated simultaneously with two or three traits. These elite alleles were mainly from accessions collected in China, introduced to China from the United States, or rare alleles with a frequency of less than 5%. No one cultivar contained more than half of the elite alleles, but 10 accessions were collected from China and the two introduced from the United States did contain more than half of these alleles. Therefore, there is great potential for mining elite alleles from germplasm accessions for use in fiber quality improvement in modern cotton breeding.
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Affiliation(s)
- Caiping Cai
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
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Mei H, Zhu X, Zhang T. Favorable QTL alleles for yield and its components identified by association mapping in Chinese Upland cotton cultivars. PLoS One 2013; 8:e82193. [PMID: 24386089 PMCID: PMC3873261 DOI: 10.1371/journal.pone.0082193] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 10/21/2013] [Indexed: 11/24/2022] Open
Abstract
Linkage disequilibrium based association mapping is a powerful tool for dissecting the genetic basis underlying complex traits. In this study, an association mapping panel consisting of 356 representative Upland cotton cultivars was constructed, evaluated in three environments and genotyped using 381 SSRs to detect molecular markers associated with lint yield and its components. The results showed that abundant phenotypic and moderate genetic diversities existed within this germplasm panel. The population could be divided into two subpopulations, and weak relatedness was detected between pair-wise accessions. LD decayed to the background (r2 = 0.1182, P≤0.01), r2 = 0.1 and r2 = 0.2 level within 12–13 cM, 17–18 cM and 3–4 cM, respectively, providing the potential for association mapping of agronomically important traits in Chinese Upland cotton. A total of 55 marker-trait associations were detected between 26 SSRs and seven lint yield traits, based on a mixed linear model (MLM) and Bonferroni correction (P≤0.05/145, −log10P≥3.46). Of which 41 could be detected in more than one environment and 17 markers were simultaneously associated with two or more traits. Many associations were consistent with QTLs identified by linkage mapping in previous reports. Phenotypic values of alleles of each loci in 41 stably detected associations were compared, and 23 favorable alleles were identified. Population frequency of each favorable allele in historically released cultivar groups was also evaluated. The QTLs detected in this study will be helpful in further understanding the genetic basis of lint yield and its components, and the favorable alleles may facilitate future high-yield breeding by genomic selection in Upland cotton.
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Affiliation(s)
- Hongxian Mei
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, China
- Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiefei Zhu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, China
| | - Tianzhen Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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21
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Topdar N, Kundu A, Sinha MK, Sarkar D, Das M, Banerjee S, Kar CS, Satya P, Balyan HS, Mahapatra BS, Gupta PK. A complete genetic linkage map and QTL analyses for bast fibre quality traits, yield and yield components in jute (Corchorus olitorius L.). CYTOL GENET+ 2013. [DOI: 10.3103/s0095452713030092] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Liang Q, Hu C, Hua H, Li Z, Hua J. Construction of a linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.). ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11434-013-5807-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Zhang T, Qian N, Zhu X, Chen H, Wang S, Mei H, Zhang Y. Variations and transmission of QTL alleles for yield and fiber qualities in upland cotton cultivars developed in China. PLoS One 2013; 8:e57220. [PMID: 23468939 PMCID: PMC3584144 DOI: 10.1371/journal.pone.0057220] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 01/18/2013] [Indexed: 12/02/2022] Open
Abstract
Cotton is the world’s leading cash crop, and genetic improvement of fiber yield and quality is the primary objective of cotton breeding program. In this study, we used various approaches to identify QTLs related to fiber yield and quality. Firstly, we constructed a four-way cross (4WC) mapping population with four base core cultivars, Stoneville 2B, Foster 6, Deltapine 15 and Zhongmiansuo No.7 (CRI 7), as parents in Chinese cotton breeding history and identified 83 QTLs for 11 agronomic and fiber quality traits. Secondly, association mapping of agronomical and fiber quality traits was based on 121 simple sequence repeat (SSR) markers using a general linear model (GLM). For this, 81 Gossypium hirsutum L. accessions including the four core parents and their derived cultivars were grown in seven diverse environments. Using these approaches, we successfully identified 180 QTLs significantly associated with agronomic and fiber quality traits. Among them were 66 QTLs that were identified via linkage disequilibrium (LD) and 4WC family-based linkage (FBL) mapping and by previously published family-based linkage (FBL) mapping in modern Chinese cotton cultivars. Twenty eight and 44 consistent QTLs were identified by 4WC and LD mapping, and by FBL and LD mapping methods, respectively. Furthermore, transmission and variation of QTL-alleles mapped by LD association in the three breeding periods revealed that some could be detected in almost all Chinese cotton cultivars, suggesting their stable transmission and some identified only in the four base cultivars and not in the modern cultivars, suggesting they were missed in conventional breeding. These results will be useful to conduct genomics-assisted breeding effectively using these existing and novel QTL alleles to improve yield and fiber qualities in cotton.
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Affiliation(s)
- Tianzhen Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
- * E-mail:
| | - Neng Qian
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Xiefei Zhu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Hong Chen
- Cotton Research Institute, Xinjiang Academy of Agriculture and Reclamation Sciences, Xinjiang, People’s Republic of China
| | - Sen Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Hongxian Mei
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Yuanming Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
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Adawy SS, Diab AA, Atia MAM, Hussein EHA. Construction of genetic linkage map with chromosomal assigment and quantitative trait loci associated with some important agronomic traits in cotton. GM CROPS & FOOD 2013; 4:36-49. [PMID: 23333856 DOI: 10.4161/gmcr.23287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Cotton is the world's leading natural fiber and second most important oilseed crop and has been a focus of genetic, systematic and breeding research. The genetic and physiological bases of some important agronomic traits in cotton were investigated by QTL mapping through constructing of genetic map with chromosomal assignment. A segregating F2 population derived from an interspecific cross (G. barbadense x G. hirsutum) between two genotypes, cvs. "Giza 83" and "Deltapine" was used in this study. Different molecular markers including SSR, EST, EST-SSR, AFLP and RAPD were employed to identify markers that reveal differences between the parents. In total 42 new markers were merged with 140 previously mapped markers to produce a new map with 182 loci covering a total length of 2370.5 cM. Among these new markers, some of them were used to assign chromosomes to the produced 26 linkage groups. The LG2, LG3, LG11 and LG26 were assigned to chromosomes 1, 6, 5 and 20 respectively. Single point analysis was used to identify genomic regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number of bolls. In total 40 significant QTL were identified for the five traits on 11 linkage groups (1, 2, 3, 4, 5, 10, 11, 12, 18, 19 and 23). This work represents an improvement of the previously constructed genetic map in addition to chromosomal assignment and detection of new significant QTL for the five traits in Egyptian cotton. The Significant QTLs detected in this study can be employed in marker assisted selection for molecular breeding programs aiming at developing cotton cultivars with improved agronomic traits.
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Affiliation(s)
- Sami S Adawy
- Molecular Markers and Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
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Boopathi NM, Thiyagu K, Urbi B, Santhoshkumar M, Gopikrishnan A, Aravind S, Swapnashri G, Ravikesavan R. Marker-assisted breeding as next-generation strategy for genetic improvement of productivity and quality: can it be realized in cotton? INTERNATIONAL JOURNAL OF PLANT GENOMICS 2011; 2011:670104. [PMID: 21577317 PMCID: PMC3092514 DOI: 10.1155/2011/670104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 01/22/2011] [Indexed: 05/29/2023]
Abstract
The dawdling development in genetic improvement of cotton with conventional breeding program is chiefly due to lack of complete knowledge on and precise manipulation of fiber productivity and quality. Naturally available cotton continues to be a resource for the upcoming breeding program, and contemporary technologies to exploit the available natural variation are outlined in this paper for further improvement of fiber. Particularly emphasis is given to application, obstacles, and perspectives of marker-assisted breeding since it appears to be more promising in manipulating novel genes that are available in the cotton germplasm. Deployment of system quantitative genetics in marker-assisted breeding program would be essential to realize its role in cotton. At the same time, role of genetic engineering and in vitro mutagenesis cannot be ruled out in genetic improvement of cotton.
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Affiliation(s)
- N. Manikanda Boopathi
- Department of Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - K. Thiyagu
- Department of Cotton, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - B. Urbi
- Department of Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M. Santhoshkumar
- Department of Cotton, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - A. Gopikrishnan
- Department of Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - S. Aravind
- Department of Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Gat Swapnashri
- Department of Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - R. Ravikesavan
- Department of Cotton, Tamil Nadu Agricultural University, Coimbatore 641003, India
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Zhang X, Liu F, Wang W, Li S, Wang C, Zhang X, Wang Y, Wang K. Primary analysis of QTG contribution to heterosis in upland cotton. CHINESE SCIENCE BULLETIN-CHINESE 2010. [DOI: 10.1007/s11434-010-4020-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Yu J, Kohel RJ, Smith CW. The construction of a tetraploid cotton genome wide comprehensive reference map. Genomics 2010; 95:230-40. [PMID: 20171271 DOI: 10.1016/j.ygeno.2010.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 01/17/2010] [Accepted: 02/03/2010] [Indexed: 10/19/2022]
Abstract
Integration of multiple genomic maps provides a higher density of markers and greater genome coverage, which not only facilitates the identification and positioning of QTLs and candidate genes, but it also provides a basic structure for the genome sequence assembly. However, the diversity in markers and populations used in individual mapping studies limits the ability to fully integrate the available data. By concentrating on marker orders rather than marker distances, published map data could be used to produce a comprehensive reference map (CRM) that includes a majority of known markers with optimally estimated order of those markers across the genome. In this study, a tetraploid cotton genome-wide CRM was constructed from 28 public cotton genetic maps. The initial CRM contained 7,424 markers and represented over 93% of the combined mapping information from the 28 individual maps. The current output is stored and displayed through CottonDB (http://www.cottondb.org), the public cotton genome database.
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Affiliation(s)
- Jing Yu
- The Department of Soil and Crop Sciences, Texas A&M University, TX, USA.
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Ngwako S. Mapping quantitative trait loci using the marker regression and the interval mapping methods. Pak J Biol Sci 2008; 11:553-8. [PMID: 18817125 DOI: 10.3923/pjbs.2008.553.558] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The marker regression and the interval mapping methods were used for the detection of qualitative trait loci (QTL) in Arabidopsis thaliana in a cross between early flowering ecotypes Landsberg erecta and Columbia. The interval mapping method employs pairs of neighbouring markers to obtain maximum linkage information about the presence of a QTL within the enclosed segment of the chromosome, whereas the marker regression approach fits a model to all the marker means on a given chromosome simultaneously and obtains significance tests by simulation. The interval mapping method detected 22 QTL in seven traits and the marker regression method detected 22 QTL in six traits. The two methods detected sixteen QTL at similar positions of the Arabidopsis chromosomes and QTL for similar traits were localised to similar regions of the chromosomes and they showed similar mode of additive effect. This suggested that the two methods are similar in their QTL detection even though they employed different significant levels.
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Affiliation(s)
- S Ngwako
- Department of Crop Science and Production, Botswana College of Agriculture, P/Bag 0027, Gaborone, Botswana
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Mapping QTLs with epistatic effects and QTL × environment interactions for plant height using a doubled haploid population in cultivated wheat. J Genet Genomics 2008; 35:119-27. [DOI: 10.1016/s1673-8527(08)60017-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2007] [Revised: 11/20/2007] [Accepted: 11/21/2007] [Indexed: 11/18/2022]
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A brief summary of major advances in cotton functional genomics and molecular breeding studies in China. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s11434-007-0500-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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