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Li C, Dong C, Zhao H, Wang J, Du L, Ai N. Identification of superior parents with high fiber quality using molecular markers and phenotypes based on a core collection of upland cotton ( Gossypium hirsutum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:30. [PMID: 37312963 PMCID: PMC10248707 DOI: 10.1007/s11032-022-01300-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
The combination of molecular markers and phenotypes to select superior parents has become the goal of modern breeders. In this study, 491 upland cotton (Gossypium hirsutum L.) accessions were genotyped using the CottonSNP80K array and then a core collection (CC) was constructed. Superior parents with high fiber quality were identified using molecular markers and phenotypes based on the CC. The Nei diversity index, Shannon's diversity index, and polymorphism information content among chromosomes for 491 accessions ranged from 0.307 to 0.402, 0.467 to 0.587, and 0.246 to 0.316, with mean values of 0.365, 0.542, and 0.291, respectively. A CC containing 122 accessions was established and was categorized into eight clusters based on the K2P genetic distances. From the CC, 36 superior parents (including duplicates) were selected, which contained the elite alleles of markers and ranked in the top 10% of phenotypic values for each fiber quality trait. Among the 36 materials, eight were for fiber length, four were for fiber strength, nine were for fiber micronaire, five were for fiber uniformity, and ten were for fiber elongation. In particular, the nine materials, 348 (Xinluzhong34), 319 (Xinluzhong3), 325 (Xinluzhong9), 397 (L1-14), 205 (XianIII9704), 258 (9D208), 464 (DP201), 467 (DP150), and 465 (DP208), possessed the elite alleles of markers for at least two traits and could be given priority in breeding applications for a more synchronous improvement of fiber quality. The work provides an efficient method for superior parent selection and will facilitate the application of molecular design breeding to cotton fiber quality. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01300-0.
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Affiliation(s)
- Chengqi Li
- Life Science College, Yuncheng University, Yuncheng, 044000 China
| | - Chengguang Dong
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture, Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000 China
| | - Haihong Zhao
- Life Science College, Yuncheng University, Yuncheng, 044000 China
| | - Juan Wang
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture, Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000 China
| | - Lei Du
- Life Science College, Yuncheng University, Yuncheng, 044000 China
| | - Nijiang Ai
- Shihezi Agricultural Science Research Institute, Shihezi, 832000 China
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Kumar P, Nimbal S, Budhlakoti N, Singh V, Sangwan RS. Genetic diversity and population structure analysis for morphological traits in upland cotton (Gossypium hirsutum L.). J Appl Genet 2021; 63:87-101. [PMID: 34718944 DOI: 10.1007/s13353-021-00667-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 11/27/2022]
Abstract
A total of 96 different genotypes of upland cotton (Gossypium hirsutum) were selected from the breeding material and germplasm available at CCS HAU, India, to find the novel marker-trait associations for morphological traits used for registration of variety in upland cotton. Twenty-three morphological traits of the selected genotypes were recorded in field trials conducted in two replication of randomized block design during Kharif 2018 and 2019. A total of 11 traits showed sufficient variations in the screened germplasm and the same were further used for association mapping. A total of 168 SSRs were used for genotyping, of which 97 SSRs showed polymorphism amplifying 293 different alleles with an average of 3.02 alleles per SSR. Clustering, principal component analysis, and population structure analysis advocated that the current germplasm panel has enough diversity to be considered for association mapping. A total of 20 significant marker-trait associations were identified by the mixed linear model (MLM) and compressed mixed linear model (CMLM), of which 15 were common to both models, hence considered as promising associations. To the best of our knowledge, it is a first attempt to identify the linked markers in relation to morphological traits for the cotton crop. Results of the present study will be highly useful in speeding up variety registration programmes of upland cotton complementing to Distinctiveness, Uniformity, and Stability (DUS) testing.
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Affiliation(s)
- Pawan Kumar
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Somveer Nimbal
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, 125004, India.
| | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Varsha Singh
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, 125004, Hisar, India
| | - Rajvir Singh Sangwan
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, 125004, India
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Kumar P, Nimbal S, Sangwan RS, Budhlakoti N, Singh V, Mishra DC, Sagar, Choudhary RR. Identification of Novel Marker-Trait Associations for Lint Yield Contributing Traits in Upland Cotton ( Gossypium hirsutum L.) Using SSRs. FRONTIERS IN PLANT SCIENCE 2021; 12:653270. [PMID: 34122477 PMCID: PMC8187916 DOI: 10.3389/fpls.2021.653270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/16/2021] [Indexed: 11/10/2023]
Abstract
Improving the yield of lint is the main objective for most of the cotton crop improvement programs throughout the world as it meets the demand of fiber for textile industries. In the current study, 96 genotypes of Gossypium hirsutum were used to find novel simple sequence repeat marker-based associations for lint yield contributing traits by linkage disequilibrium. Extensive phenotyping of 96 genotypes for various agronomic traits was done for two consecutive years (2018 and 2019) in early, normal, and late sown environments. Out of 168 SSR markers screened over the 96 genotypes, a total of 97 polymorphic markers containing 293 alleles were used for analysis. Three different models, i.e., mixed linear model (MLM), compressed mixed linear model (CMLM), and multiple locus mixed linear model (MLMM), were used to detect the significant marker-trait associations for six different environments separately. A total of 38 significant marker-trait associations that were common to at least two environments were considered as promising associations and detailed annotation of the significant markers has been carried out. Twenty-two marker-trait associations were found to be novel in the current study. These results will be very useful for crop improvement programs using marker-assisted cotton breeding.
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Affiliation(s)
- Pawan Kumar
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, India
| | - Somveer Nimbal
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, India
| | - Rajvir Singh Sangwan
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, India
| | - Neeraj Budhlakoti
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Varsha Singh
- Department of Molecular Biology and Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Dwijesh Chandra Mishra
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sagar
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, India
| | - Raju Ram Choudhary
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, India
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Donde R, Mohapatra S, Baksh SKY, Padhy B, Mukherjee M, Roy S, Chattopadhyay K, Anandan A, Swain P, Sahoo KK, Singh ON, Behera L, Dash SK. Identification of QTLs for high grain yield and component traits in new plant types of rice. PLoS One 2020; 15:e0227785. [PMID: 32673318 PMCID: PMC7365460 DOI: 10.1371/journal.pone.0227785] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 06/11/2020] [Indexed: 11/18/2022] Open
Abstract
A panel of 60 genotypes comprising New Plant Types (NPTs) along with indica, tropical and temperate japonica genotypes was phenotypically evaluated for four seasons in irrigated situation for grain yield per se and component traits. Twenty NPT genotypes were found promising with an average grain yield varying from 5.45 to 8.8 t/ha. A total of 85 SSR markers were used in the study to identify QTLs associated with grain yield per se and related traits. Sixty-six (77.65%) markers were found to be polymorphic. The PIC values varied from 0.516 to 0.92 with an average of 0.704. A moderate level of genetic diversity (0.39) was detected among genotypes. Variation to the tune of 8% within genotypes, 68% among the genotypes within the population and 24% among the populations were observed (AMOVA). This information may help in identification of potential parents for development of transgressive segregants with very high yield. The association analysis using GLM and MLM models led to the identification of 30 and 10 SSR markers associated with 70 and 16 QTLs, respectively. Thirty novel QTLs linked with 16 SSRs were identified to be associated with eleven traits, namely tiller number (qTL-6.1, qTL-11.1, qTL-4.1), panicle length (qPL-1.1, qPL-5.1, qPL-7.1, qPL-8.1), flag leaf length (qFLL-8.1, qFLL-9.1), flag leaf width (qFLW-6.2, qFLW-5.1, qFLW-8.1, qFLW-7.1), total no. of grains (qTG-2.2, qTG-a7.1), thousand-grain weight (qTGW-a1.1, qTGW-a9.2, qTGW-5.1, qTGW-8.1), fertile grains (qFG-7.1), seed length-breadth ratio (qSlb-3.1), plant height (qPHT-6.1, qPHT-9.1), days to 50% flowering (qFD-1.1) and grain yield per se (qYLD-5.1, qYLD-6.1a, qYLD-11.1).Some of the SSRs were co-localized with more than two traits. The highest co-localization was identified with RM5709 linked to nine traits, followed by RM297 with five traits. Similarly, RM5575, RM204, RM168, RM112, RM26499 and RM22899 were also recorded to be co-localized with more than one trait and could be rated as important for marker-assisted backcross breeding programs, for pyramiding of these QTLs for important yield traits, to produce new-generation rice for prospective increment in yield potentiality and breaking yield ceiling.
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Affiliation(s)
- Ravindra Donde
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Shibani Mohapatra
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - S. K. Yasin Baksh
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Barada Padhy
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Mitadru Mukherjee
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Somnath Roy
- ICAR-NRRI, Regional Research Station (CRURRS), Hazaribagh, Jharkhand
| | | | - A. Anandan
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Padmini Swain
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | | | - Onkar Nath Singh
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Lambodar Behera
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
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Ditta A, Zhou Z, Cai X, Wang X, Okubazghi KW, Shehzad M, Xu Y, Hou Y, Sajid Iqbal M, Khan MKR, Wang K, Liu F. Assessment of Genetic Diversity, Population Structure, and Evolutionary Relationship of Uncharacterized Genes in a Novel Germplasm Collection of Diploid and Allotetraploid Gossypium Accessions Using EST and Genomic SSR Markers. Int J Mol Sci 2018; 19:E2401. [PMID: 30110970 PMCID: PMC6121227 DOI: 10.3390/ijms19082401] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/08/2018] [Accepted: 08/13/2018] [Indexed: 11/17/2022] Open
Abstract
This study evaluated the genetic diversity and population structures in a novel cotton germplasm collection comprising 132 diploids, including Glossypium klotzschianum and allotetraploid cotton accessions, including Glossypium barbadense, Glossypium darwinii, Glossypium tomentosum, Glossypium ekmanianum, and Glossypium stephensii, from Santa Cruz, Isabella, San Cristobal, Hawaiian, Dominican Republic, and Wake Atoll islands. A total of 111 expressed sequence tag (EST) and genomic simple sequence repeat (gSSR) markers produced 382 polymorphic loci with an average of 3.44 polymorphic alleles per SSR marker. Polymorphism information content values counted 0.08 to 0.82 with an average of 0.56. Analysis of a genetic distance matrix revealed values of 0.003 to 0.53 with an average of 0.33 in the wild cotton collection. Phylogenetic analysis supported the subgroups identified by STRUCTURE and corresponds well with the results of principal coordinate analysis with a cumulative variation of 45.65%. A total of 123 unique alleles were observed among all accessions and 31 identified only in G. ekmanianum. Analysis of molecular variance revealed highly significant variation between the six groups identified by structure analysis with 49% of the total variation and 51% of the variation was due to diversity within the groups. The highest genetic differentiation among tetraploid populations was observed between accessions from the Hawaiian and Santa Cruz regions with a pairwise FST of 0.752 (p < 0.001). DUF819 containing an uncharacterized gene named yjcL linked to genomic markers has been found to be highly related to tryptophan-aspartic acid (W-D) repeats in a superfamily of genes. The RNA sequence expression data of the yjcL-linked gene Gh_A09G2500 was found to be upregulated under drought and salt stress conditions. The existence of genetic diversity, characterization of genes and variation in novel germplasm collection will be a landmark addition to the genetic study of cotton germplasm.
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Affiliation(s)
- Allah Ditta
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
- Nuclear Institute for Agriculture and Biology (NIAB), Jhang Road, Faisalabad 38000, Punjab, Pakistan.
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Kiflom Weldu Okubazghi
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
- Hamelmalo Agricultural College, P.O. Box 397, Keren, Eritrea.
| | - Muhammad Shehzad
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Muhammad Sajid Iqbal
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Muhammad Kashif Riaz Khan
- Nuclear Institute for Agriculture and Biology (NIAB), Jhang Road, Faisalabad 38000, Punjab, Pakistan.
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
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Li C, Fu Y, Sun R, Wang Y, Wang Q. Single-Locus and Multi-Locus Genome-Wide Association Studies in the Genetic Dissection of Fiber Quality Traits in Upland Cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1083. [PMID: 30177935 PMCID: PMC6109694 DOI: 10.3389/fpls.2018.01083] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/04/2018] [Indexed: 05/04/2023]
Abstract
A major breeding target in Upland cotton (Gossypium hirsutum L.) is to improve the fiber quality. To address this issue, 169 diverse accessions, genotyped by 53,848 high-quality single-nucleotide polymorphisms (SNPs) and phenotyped in four environments, were used to conduct genome-wide association studies (GWASs) for fiber quality traits using three single-locus and three multi-locus models. As a result, 342 quantitative trait nucleotides (QTNs) controlling fiber quality traits were detected. Of the 342 QTNs, 84 were simultaneously detected in at least two environments or by at least two models, which include 29 for fiber length, 22 for fiber strength, 11 for fiber micronaire, 12 for fiber uniformity, and 10 for fiber elongation. Meanwhile, nine QTNs with 10% greater sizes (R2) were simultaneously detected in at least two environments and between single- and multi-locus models, which include TM80185 (D13) for fiber length, TM1386 (A1) and TM14462 (A6) for fiber strength, TM18616 (A7), TM54735 (D3), and TM79518 (D12) for fiber micronaire, TM77489 (D12) and TM81448 (D13) for fiber uniformity, and TM47772 (D1) for fiber elongation. This indicates the possibility of marker-assisted selection in future breeding programs. Among 455 genes within the linkage disequilibrium regions of the nine QTNs, 113 are potential candidate genes and four are promising candidate genes. These findings reveal the genetic control underlying fiber quality traits and provide insights into possible genetic improvements in Upland cotton fiber quality.
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Affiliation(s)
- Chengqi Li
- Collaborative Innovation Center of Modern Biological Breeding, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Yuanzhi Fu
- Collaborative Innovation Center of Modern Biological Breeding, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Runrun Sun
- Collaborative Innovation Center of Modern Biological Breeding, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Yuanyuan Wang
- Collaborative Innovation Center of Modern Biological Breeding, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Qinglian Wang
- Collaborative Innovation Center of Modern Biological Breeding, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
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Ma Q, Zhao J, Lin H, Ning X, Liu P, Deng F, Si A, Li J. Association between SSR markers and fibre traits in sea island cotton (Gossypium barbadense) germplasm resources. J Genet 2017; 96:e55-e63. [PMID: 29321342 DOI: 10.1007/s12041-017-0849-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Identification of molecular markers associated with fibre traits can accelerate cotton marker-assisted selection (MAS) programmes. In this study, Gossypium barbadense germplasm accessions with diverse origins (n = 123) were used to perform association analysis of fibre traits with 120 polymorphic simple sequence repeat (SSR) markers. In total, 120 polymorphic primer pairs amplified 258 loci with a mean of 2.15 loci per primer. Population structure analysis identified three main clusters for the accessions, which indicated agreement of genetic and predefined populations. Marker-trait associations (n = 58) were detected for 10 fibre traits with 26 SSR markers located on 15 chromosomes. The R² (phenotypic variation explained) ranged from 3.19 to 15.21%. Two markers (NAU5465 and NAU3013) were found to be stably associated with boll number per plant (BNP) and fibre uniformity (UI), respectively. Four markers (BNL252, NAU3424,NAU3324 and CGR5202) associated with fibre quality traits preferentially clustered on the D8 chromosome, which was thus identified as an important candidate region for study molecular mechanisms underlying fibre quality and for use in breeding cotton cultivars for improving fibre quality. This study generated molecular data with a potential for better understanding of the genetic basis of the fibre traits and provided new markers for MAS in G. barbadense breeding programmes.
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Affiliation(s)
- Qi Ma
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, People's Republic of China.
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Wang C, Ulloa M, Duong TT, Roberts PA. QTL Analysis of Transgressive Nematode Resistance in Tetraploid Cotton Reveals Complex Interactions in Chromosome 11 Regions. FRONTIERS IN PLANT SCIENCE 2017; 8:1979. [PMID: 29209344 PMCID: PMC5702019 DOI: 10.3389/fpls.2017.01979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/02/2017] [Indexed: 05/24/2023]
Abstract
Transgressive segregation in cotton (Gossypium spp.) provides an important approach to enhance resistance to the major pest root-knot nematode (RKN) Meloidogyne incognita. Our previous studies reported transgressive RKN resistance in an intraspecific Gossypium hirsutum resistant NemX × susceptible SJ-2 recombinant inbred line (RIL) population and early generations of interspecific cross Gossypium barbadense (susceptible Pima S-7) × G. hirsutum (NemX). However, the underlying functional mechanisms for this phenomenon are not known. In this study, the region of RKN resistance gene rkn1 on chromosome (Chr) 11 and its homoeologous Chr 21 was fine mapped with G. raimondii D5 genome reference sequence. Transgressive resistance was found in the later generation of a new RIL population F2:7 (Pima S-7 × NemX) and one interspecific F2 (susceptible Pima S-7 × susceptible SJ-2). QTL analysis revealed similar contributions to root-galling and egg-production resistance phenotypes associated with SSR marker CIR316 linked to resistance gene rkn1 in NemX on Chr 11 in all seven populations analyzed. In testcross NemX × F1 (Pima S-7 × SJ-2) marker allele CIR069-271 from Pima S-7 linked to CIR316 contributed 63% of resistance to galling phenotype in the presence of rkn1. Similarly, in RIL population F2:8 (NemX × SJ-2), SJ-2 markers closely linked to CIR316 contributed up to 82% of resistance to root-galling. These results were confirmed in BC1F1 SJ-2 × F1 (NemX × SJ-2), F2 (NemX × SJ-2), and F2 (Pima S-7 × SJ-2) populations in which up to 44, 36, and 15% contribution in resistance to galling was found, respectively. Transgressive segregation for resistance was universal in all intra- and inter-specific populations, although stronger transgressive resistance occurred in later than in early generations in the intraspecific cross compared with the interspecific cross. Transgressive effects on progeny from susceptible parents are possibly provided in the rkn1 resistance region of chromosome 11 by tandemly arrayed allele (TAA) or gene (TAG) interactions contributing to transgressive resistance. Complex TAA and TAG recombination and interactions in the rkn1 resistance region provide three genes and a model to study disease and transgressive resistance in polyploid plants, and novel genotypes for plant breeding.
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Affiliation(s)
- Congli Wang
- Department of Nematology, University of California, Riverside, Riverside, CA, United States
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Mauricio Ulloa
- Plant Stress and Germplasm Development Research, PA, CSRL, USDA-ARS, Lubbock, TX, United States
| | - Tra T. Duong
- Department of Nematology, University of California, Riverside, Riverside, CA, United States
| | - Philip A. Roberts
- Department of Nematology, University of California, Riverside, Riverside, CA, United States
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Abdullaev AA, Salakhutdinov IB, Egamberdiev SS, Khurshut EE, Rizaeva SM, Ulloa M, Abdurakhmonov IY. Genetic diversity, linkage disequilibrium, and association mapping analyses of Gossypium barbadense L. germplasm. PLoS One 2017; 12:e0188125. [PMID: 29136656 PMCID: PMC5685624 DOI: 10.1371/journal.pone.0188125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/01/2017] [Indexed: 02/05/2023] Open
Abstract
Limited polymorphism and narrow genetic base, due to genetic bottleneck through historic domestication, highlight a need for comprehensive characterization and utilization of existing genetic diversity in cotton germplasm collections. In this study, 288 worldwide Gossypium barbadense L. cotton germplasm accessions were evaluated in two diverse environments (Uzbekistan and USA). These accessions were assessed for genetic diversity, population structure, linkage disequilibrium (LD), and LD-based association mapping (AM) of fiber quality traits using 108 genome-wide simple sequence repeat (SSR) markers. Analyses revealed structured population characteristics and a high level of intra-variability (67.2%) and moderate interpopulation differentiation (32.8%). Eight percent and 4.3% of markers revealed LD in the genome of the G. barbadense at critical values of r2 ≥ 0.1 and r2 ≥ 0.2, respectively. The LD decay was on average 24.8 cM at the threshold of r2 ≥ 0.05. LD retained on average distance of 3.36 cM at the threshold of r2 ≥ 0.1. Based on the phenotypic evaluations in the two diverse environments, 100 marker loci revealed a strong association with major fiber quality traits using mixed linear model (MLM) based association mapping approach. Fourteen marker loci were found to be consistent with previously identified quantitative trait loci (QTLs), and 86 were found to be new unreported marker loci. Our results provide insights into the breeding history and genetic relationship of G. barbadense germplasm and should be helpful for the improvement of cotton cultivars using molecular breeding and omics-based technologies.
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Affiliation(s)
- Alisher A. Abdullaev
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Ilkhom B. Salakhutdinov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Sharof S. Egamberdiev
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Ernest E. Khurshut
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Sofiya M. Rizaeva
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Mauricio Ulloa
- Cropping Systems Research Laboratory, United States Department of Agriculture - Agricultural Research Services, Lubbock, Texas, United States of America
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Bohra A, Jha R, Pandey G, Patil PG, Saxena RK, Singh IP, Singh D, Mishra RK, Mishra A, Singh F, Varshney RK, Singh NP. New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [ Cajanus cajan (L.) Millspaugh]. FRONTIERS IN PLANT SCIENCE 2017; 8:377. [PMID: 28408910 PMCID: PMC5374739 DOI: 10.3389/fpls.2017.00377] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/06/2017] [Indexed: 05/21/2023]
Abstract
Draft genome sequence in pigeonpea offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, 421 hypervariable simple sequence repeat (SSR) markers from the pigeonpea genome were screened on a panel of eight pigeonpea genotypes yielding marker validation and polymorphism percentages of 95.24 and 54.11%, respectively. The SSR marker assay uncovered a total of 570 alleles with three as an average number of alleles per marker. Similarly, the mean values for gene diversity and PIC were 0.44 and 0.37, respectively. The number of polymorphic markers ranged from 39 to 89 for different parental combinations. Further, 60 of these SSRs were assayed on 94 genotypes, and model based clustering using STRUCTURE resulted in the identification of the two subpopulations (K = 2). This remained in close agreement with the clustering patterns inferred from genetic distance (GD)-based approaches i.e., dendrogram, factorial and principal coordinate analysis (PCoA). The AMOVA accounted majority of the genetic variation within groups (89%) in comparison to the variation existing between the groups (11%). A subset of these markers was implicated for hybrid purity testing. We also demonstrated utility of these SSR markers in trait mapping through association and bi-parental linkage analyses. The general linear (GLM) and mixed linear (MLM) models both detected a single SSR marker (CcGM03681) with R2 = 16.4 as associated with the resistance to Fusarium wilt variant 2. Similarly, by using SSR data in a segregating backcross population, the corresponding restorer-of-fertility (Rf) locus was putatively mapped at 39 cM with the marker CcGM08896. However, The marker-trait associations (MTAs) detected here represent a very preliminary type and hence demand deeper investigations for conclusive evidence. Given their ability to reveal polymorphism in simple agarose gels, the hypervariable SSRs are valuable genomic resource for pigeonpea research community, particularly in South Asia and East Africa where pigeonpea is primarily grown.
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Affiliation(s)
- Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
- *Correspondence: Abhishek Bohra
| | - Rintu Jha
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Gaurav Pandey
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
| | | | - Rachit K. Saxena
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Indra P. Singh
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - D. Singh
- ICAR-Indian Agricultural Statistics Research InstituteNew Delhi, India
| | - R. K. Mishra
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Ankita Mishra
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - F. Singh
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- Rajeev K. Varshney
| | - N. P. Singh
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
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