Evaluation and Exploration of Favorable QTL Alleles for Salt Stress Related Traits in Cotton Cultivars (G. hirsutum L.)
Soil salinization is one of the major problems in global agricultural production. Cotton is a pioneer crop with regard to salt stress tolerance, and can be used for saline-alkali land improvement. The large-scale detection of salt tolerance traits in cotton accessions, and the identification of elit...
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| description | Soil salinization is one of the major problems in global agricultural production. Cotton is a pioneer crop with regard to salt stress tolerance, and can be used for saline-alkali land improvement. The large-scale detection of salt tolerance traits in cotton accessions, and the identification of elite quantitative trait loci (QTLs)/genes for salt-tolerance have been very important in salt tolerance breeding. Here, 43 advanced salt-tolerant and 31 highly salt-sensitive cultivars were detected by analyzing ten salt tolerance related traits in 304 upland cotton cultivars. Among them, 11 advanced salt-tolerance and eight highly salt-sensitive cultivars were consistent with previously reported results. Association analysis of ten salt-tolerance related traits and 145 SSRs was performed, and a total of 95 significant associations were detected; 17, 41, and 37 of which were associated with germinative index, seedling stage physiological index, and four seedling stage biochemical indexes, respectively. Of these associations, 20 SSR loci were simultaneously associated with two or more traits. Furthermore, we detected 117 elite alleles associated with salt-tolerance traits, 4 of which were reported previously. Among these loci, 44 (37.60%) were rare alleles with a frequency of less than 5%, 6 only existed in advanced salt-tolerant cultivars, and 2 only in highly salt-sensitive cultivars. As a result, 13 advanced salt-tolerant cultivars were selected to assemble the optimal cross combinations by computer simulation for the development of salt-tolerant accessions. This study lays solid foundations for further improvements in cotton salt-tolerance by referencing elite germplasms, alleles associated with salt-tolerance traits, and optimal crosses. |
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Cotton is a pioneer crop with regard to salt stress tolerance, and can be used for saline-alkali land improvement. The large-scale detection of salt tolerance traits in cotton accessions, and the identification of elite quantitative trait loci (QTLs)/genes for salt-tolerance have been very important in salt tolerance breeding. Here, 43 advanced salt-tolerant and 31 highly salt-sensitive cultivars were detected by analyzing ten salt tolerance related traits in 304 upland cotton cultivars. Among them, 11 advanced salt-tolerance and eight highly salt-sensitive cultivars were consistent with previously reported results. Association analysis of ten salt-tolerance related traits and 145 SSRs was performed, and a total of 95 significant associations were detected; 17, 41, and 37 of which were associated with germinative index, seedling stage physiological index, and four seedling stage biochemical indexes, respectively. Of these associations, 20 SSR loci were simultaneously associated with two or more traits. Furthermore, we detected 117 elite alleles associated with salt-tolerance traits, 4 of which were reported previously. Among these loci, 44 (37.60%) were rare alleles with a frequency of less than 5%, 6 only existed in advanced salt-tolerant cultivars, and 2 only in highly salt-sensitive cultivars. As a result, 13 advanced salt-tolerant cultivars were selected to assemble the optimal cross combinations by computer simulation for the development of salt-tolerant accessions. This study lays solid foundations for further improvements in cotton salt-tolerance by referencing elite germplasms, alleles associated with salt-tolerance traits, and optimal crosses.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0151076</identifier><identifier>PMID: 26943816</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Abiotic stress ; Agricultural production ; Alleles ; Association analysis ; Biology and Life Sciences ; Breeding ; Computational Biology ; Computer simulation ; Cotton ; Cotton (Plant) ; Cultivars ; Data analysis ; Data Mining ; Ecology and Environmental Sciences ; Education ; Engineering research ; Environmental aspects ; Gene frequency ; Genetic aspects ; Genetic Markers - genetics ; Genetic Variation ; Genetics ; Genomes ; Germplasm ; Gossypium - drug effects ; Gossypium - genetics ; Gossypium - physiology ; Gossypium hirsutum ; Laboratories ; Land improvement ; Linkage Disequilibrium ; Loci ; Microsatellite Repeats - genetics ; Models, Genetic ; Phenotype ; Physical Sciences ; Physiological adaptation ; Physiological aspects ; Plant breeding ; Quantitative trait loci ; Quantitative Trait Loci - genetics ; Research and Analysis Methods ; Salinity ; Salinity tolerance ; Salinization ; Salt ; Salt tolerance ; Salts ; Salts - pharmacology ; Seedlings ; Soil salinity ; Stress, Physiological - drug effects ; Stress, Physiological - genetics</subject><ispartof>PloS one, 2016-03, Vol.11 (3), p.e0151076-e0151076</ispartof><rights>COPYRIGHT 2016 Public Library of Science</rights><rights>2016 Du et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2016 Du et al 2016 Du et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-fcbaa411c7897741a8e1ad62bdafb24540fb6b70aa029bf933df7aed39b285063</citedby><cites>FETCH-LOGICAL-c692t-fcbaa411c7897741a8e1ad62bdafb24540fb6b70aa029bf933df7aed39b285063</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778925/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778925/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26943816$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Fang, David D</contributor><creatorcontrib>Du, Lei</creatorcontrib><creatorcontrib>Cai, Caiping</creatorcontrib><creatorcontrib>Wu, Shuang</creatorcontrib><creatorcontrib>Zhang, Fang</creatorcontrib><creatorcontrib>Hou, Sen</creatorcontrib><creatorcontrib>Guo, Wangzhen</creatorcontrib><title>Evaluation and Exploration of Favorable QTL Alleles for Salt Stress Related Traits in Cotton Cultivars (G. hirsutum L.)</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Soil salinization is one of the major problems in global agricultural production. Cotton is a pioneer crop with regard to salt stress tolerance, and can be used for saline-alkali land improvement. The large-scale detection of salt tolerance traits in cotton accessions, and the identification of elite quantitative trait loci (QTLs)/genes for salt-tolerance have been very important in salt tolerance breeding. Here, 43 advanced salt-tolerant and 31 highly salt-sensitive cultivars were detected by analyzing ten salt tolerance related traits in 304 upland cotton cultivars. Among them, 11 advanced salt-tolerance and eight highly salt-sensitive cultivars were consistent with previously reported results. Association analysis of ten salt-tolerance related traits and 145 SSRs was performed, and a total of 95 significant associations were detected; 17, 41, and 37 of which were associated with germinative index, seedling stage physiological index, and four seedling stage biochemical indexes, respectively. Of these associations, 20 SSR loci were simultaneously associated with two or more traits. Furthermore, we detected 117 elite alleles associated with salt-tolerance traits, 4 of which were reported previously. Among these loci, 44 (37.60%) were rare alleles with a frequency of less than 5%, 6 only existed in advanced salt-tolerant cultivars, and 2 only in highly salt-sensitive cultivars. As a result, 13 advanced salt-tolerant cultivars were selected to assemble the optimal cross combinations by computer simulation for the development of salt-tolerant accessions. This study lays solid foundations for further improvements in cotton salt-tolerance by referencing elite germplasms, alleles associated with salt-tolerance traits, and optimal crosses.</description><subject>Abiotic stress</subject><subject>Agricultural production</subject><subject>Alleles</subject><subject>Association analysis</subject><subject>Biology and Life Sciences</subject><subject>Breeding</subject><subject>Computational Biology</subject><subject>Computer simulation</subject><subject>Cotton</subject><subject>Cotton (Plant)</subject><subject>Cultivars</subject><subject>Data analysis</subject><subject>Data Mining</subject><subject>Ecology and Environmental Sciences</subject><subject>Education</subject><subject>Engineering research</subject><subject>Environmental aspects</subject><subject>Gene frequency</subject><subject>Genetic aspects</subject><subject>Genetic Markers - genetics</subject><subject>Genetic Variation</subject><subject>Genetics</subject><subject>Genomes</subject><subject>Germplasm</subject><subject>Gossypium - drug effects</subject><subject>Gossypium - genetics</subject><subject>Gossypium - physiology</subject><subject>Gossypium hirsutum</subject><subject>Laboratories</subject><subject>Land improvement</subject><subject>Linkage Disequilibrium</subject><subject>Loci</subject><subject>Microsatellite Repeats - genetics</subject><subject>Models, Genetic</subject><subject>Phenotype</subject><subject>Physical Sciences</subject><subject>Physiological adaptation</subject><subject>Physiological aspects</subject><subject>Plant breeding</subject><subject>Quantitative trait loci</subject><subject>Quantitative Trait Loci - genetics</subject><subject>Research and Analysis Methods</subject><subject>Salinity</subject><subject>Salinity tolerance</subject><subject>Salinization</subject><subject>Salt</subject><subject>Salt tolerance</subject><subject>Salts</subject><subject>Salts - pharmacology</subject><subject>Seedlings</subject><subject>Soil salinity</subject><subject>Stress, Physiological - drug effects</subject><subject>Stress, Physiological - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Du, Lei</au><au>Cai, Caiping</au><au>Wu, Shuang</au><au>Zhang, Fang</au><au>Hou, Sen</au><au>Guo, Wangzhen</au><au>Fang, David D</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Evaluation and Exploration of Favorable QTL Alleles for Salt Stress Related Traits in Cotton Cultivars (G. hirsutum L.)</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2016-03-04</date><risdate>2016</risdate><volume>11</volume><issue>3</issue><spage>e0151076</spage><epage>e0151076</epage><pages>e0151076-e0151076</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Soil salinization is one of the major problems in global agricultural production. Cotton is a pioneer crop with regard to salt stress tolerance, and can be used for saline-alkali land improvement. The large-scale detection of salt tolerance traits in cotton accessions, and the identification of elite quantitative trait loci (QTLs)/genes for salt-tolerance have been very important in salt tolerance breeding. Here, 43 advanced salt-tolerant and 31 highly salt-sensitive cultivars were detected by analyzing ten salt tolerance related traits in 304 upland cotton cultivars. Among them, 11 advanced salt-tolerance and eight highly salt-sensitive cultivars were consistent with previously reported results. Association analysis of ten salt-tolerance related traits and 145 SSRs was performed, and a total of 95 significant associations were detected; 17, 41, and 37 of which were associated with germinative index, seedling stage physiological index, and four seedling stage biochemical indexes, respectively. Of these associations, 20 SSR loci were simultaneously associated with two or more traits. Furthermore, we detected 117 elite alleles associated with salt-tolerance traits, 4 of which were reported previously. Among these loci, 44 (37.60%) were rare alleles with a frequency of less than 5%, 6 only existed in advanced salt-tolerant cultivars, and 2 only in highly salt-sensitive cultivars. As a result, 13 advanced salt-tolerant cultivars were selected to assemble the optimal cross combinations by computer simulation for the development of salt-tolerant accessions. This study lays solid foundations for further improvements in cotton salt-tolerance by referencing elite germplasms, alleles associated with salt-tolerance traits, and optimal crosses.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26943816</pmid><doi>10.1371/journal.pone.0151076</doi><oa>free_for_read</oa></addata></record> |
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| ispartof | PloS one, 2016-03, Vol.11 (3), p.e0151076-e0151076 |
| issn | 1932-6203 1932-6203 |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Abiotic stress Agricultural production Alleles Association analysis Biology and Life Sciences Breeding Computational Biology Computer simulation Cotton Cotton (Plant) Cultivars Data analysis Data Mining Ecology and Environmental Sciences Education Engineering research Environmental aspects Gene frequency Genetic aspects Genetic Markers - genetics Genetic Variation Genetics Genomes Germplasm Gossypium - drug effects Gossypium - genetics Gossypium - physiology Gossypium hirsutum Laboratories Land improvement Linkage Disequilibrium Loci Microsatellite Repeats - genetics Models, Genetic Phenotype Physical Sciences Physiological adaptation Physiological aspects Plant breeding Quantitative trait loci Quantitative Trait Loci - genetics Research and Analysis Methods Salinity Salinity tolerance Salinization Salt Salt tolerance Salts Salts - pharmacology Seedlings Soil salinity Stress, Physiological - drug effects Stress, Physiological - genetics |
| title | Evaluation and Exploration of Favorable QTL Alleles for Salt Stress Related Traits in Cotton Cultivars (G. hirsutum L.) |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-31T00%3A01%3A22IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Evaluation%20and%20Exploration%20of%20Favorable%20QTL%20Alleles%20for%20Salt%20Stress%20Related%20Traits%20in%20Cotton%20Cultivars%20(G.%20hirsutum%20L.)&rft.jtitle=PloS%20one&rft.au=Du,%20Lei&rft.date=2016-03-04&rft.volume=11&rft.issue=3&rft.spage=e0151076&rft.epage=e0151076&rft.pages=e0151076-e0151076&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0151076&rft_dat=%3Cgale_plos_%3EA445095526%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1770505002&rft_id=info:pmid/26943816&rft_galeid=A445095526&rft_doaj_id=oai_doaj_org_article_8f50600874f444daa777cbb4c278d8b5&rfr_iscdi=true |