Multifamily QTL analysis and comprehensive design of genotypes for high-quality soft wheat
Milling properties and flour color are essential selection criteria in soft wheat breeding. However, high phenotypic screening costs restrict selection to relatively few breeding lines in late generations. To achieve marker-based selection of these traits in early generations, we performed genetic d...
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| creator | Ishikawa, Goro Hayashi, Takeshi Nakamura, Kazuhiro Tanaka, Tsuyoshi Kobayashi, Fuminori Saito, Mika Ito, Hiroyuki Ikenaga, Sachiko Taniguchi, Yoshinori Nakamura, Toshiki |
| description | Milling properties and flour color are essential selection criteria in soft wheat breeding. However, high phenotypic screening costs restrict selection to relatively few breeding lines in late generations. To achieve marker-based selection of these traits in early generations, we performed genetic dissection of quality traits using three doubled haploid populations that shared the high-quality soft wheat variety Kitahonami as the paternal parent. An amplicon sequencing approach allowed effective construction of well-saturated linkage maps of the populations. Marker-based heritability estimates revealed that target quality traits had relatively high values, indicating the possibility of selection in early generations. Taking advantage of Chinese Spring reference sequences, joint linkage maps of the three populations were generated. Based on the maps, multifamily quantitative trait locus (QTL) analysis revealed a total of 86 QTLs for ten traits investigated. In terms of target quality traits, 12 QTLs were detected for flour yield, and 12 were detected for flour redness (a* value). Among these QTLs, six for flour yield and nine for flour a* were segregating in more than two populations. Some relationships among traits were explained by QTL collocations on chromosomes, especially group 7 chromosomes. Ten different ideotypes with various combinations of favorable alleles for the flour yield and flour a* QTLs were generated. Phenotypes of derivatives from these ideotypes were predicted to design ideal genotypes for high-quality wheat. Simulations revealed the possibility of breeding varieties with better quality than Kitahonami. |
| doi_str_mv | 10.1371/journal.pone.0230326 |
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However, high phenotypic screening costs restrict selection to relatively few breeding lines in late generations. To achieve marker-based selection of these traits in early generations, we performed genetic dissection of quality traits using three doubled haploid populations that shared the high-quality soft wheat variety Kitahonami as the paternal parent. An amplicon sequencing approach allowed effective construction of well-saturated linkage maps of the populations. Marker-based heritability estimates revealed that target quality traits had relatively high values, indicating the possibility of selection in early generations. Taking advantage of Chinese Spring reference sequences, joint linkage maps of the three populations were generated. Based on the maps, multifamily quantitative trait locus (QTL) analysis revealed a total of 86 QTLs for ten traits investigated. In terms of target quality traits, 12 QTLs were detected for flour yield, and 12 were detected for flour redness (a* value). Among these QTLs, six for flour yield and nine for flour a* were segregating in more than two populations. Some relationships among traits were explained by QTL collocations on chromosomes, especially group 7 chromosomes. Ten different ideotypes with various combinations of favorable alleles for the flour yield and flour a* QTLs were generated. Phenotypes of derivatives from these ideotypes were predicted to design ideal genotypes for high-quality wheat. Simulations revealed the possibility of breeding varieties with better quality than Kitahonami.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0230326</identifier><identifier>PMID: 32160264</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agricultural production ; Agricultural research ; Alleles ; Biology and Life Sciences ; Chromosomes ; Crop science ; Crop yield ; Flour ; Food ; Gene mapping ; Genetic aspects ; Genomes ; Genotypes ; Heritability ; Horticulture ; Markers ; Medicine and Health Sciences ; Phenotypes ; Plant breeding ; Populations ; Proteins ; Quality ; Quantitative genetics ; Quantitative trait loci ; Research and Analysis Methods ; Surgery ; Wheat</subject><ispartof>PloS one, 2020-03, Vol.15 (3), p.e0230326-e0230326</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Ishikawa 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. 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However, high phenotypic screening costs restrict selection to relatively few breeding lines in late generations. To achieve marker-based selection of these traits in early generations, we performed genetic dissection of quality traits using three doubled haploid populations that shared the high-quality soft wheat variety Kitahonami as the paternal parent. An amplicon sequencing approach allowed effective construction of well-saturated linkage maps of the populations. Marker-based heritability estimates revealed that target quality traits had relatively high values, indicating the possibility of selection in early generations. Taking advantage of Chinese Spring reference sequences, joint linkage maps of the three populations were generated. Based on the maps, multifamily quantitative trait locus (QTL) analysis revealed a total of 86 QTLs for ten traits investigated. 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QTL analysis and comprehensive design of genotypes for high-quality soft wheat</title><author>Ishikawa, Goro ; Hayashi, Takeshi ; Nakamura, Kazuhiro ; Tanaka, Tsuyoshi ; Kobayashi, Fuminori ; Saito, Mika ; Ito, Hiroyuki ; Ikenaga, Sachiko ; Taniguchi, Yoshinori ; Nakamura, Toshiki</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c802t-e7710bf50c07eaf8b3be30446e8009a2c38bce5313f8773e051d58b107c0e0233</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Agricultural production</topic><topic>Agricultural research</topic><topic>Alleles</topic><topic>Biology and Life Sciences</topic><topic>Chromosomes</topic><topic>Crop science</topic><topic>Crop yield</topic><topic>Flour</topic><topic>Food</topic><topic>Gene mapping</topic><topic>Genetic 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and comprehensive design of genotypes for high-quality soft wheat</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2020-03-11</date><risdate>2020</risdate><volume>15</volume><issue>3</issue><spage>e0230326</spage><epage>e0230326</epage><pages>e0230326-e0230326</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Milling properties and flour color are essential selection criteria in soft wheat breeding. However, high phenotypic screening costs restrict selection to relatively few breeding lines in late generations. To achieve marker-based selection of these traits in early generations, we performed genetic dissection of quality traits using three doubled haploid populations that shared the high-quality soft wheat variety Kitahonami as the paternal parent. An amplicon sequencing approach allowed effective construction of well-saturated linkage maps of the populations. Marker-based heritability estimates revealed that target quality traits had relatively high values, indicating the possibility of selection in early generations. Taking advantage of Chinese Spring reference sequences, joint linkage maps of the three populations were generated. Based on the maps, multifamily quantitative trait locus (QTL) analysis revealed a total of 86 QTLs for ten traits investigated. In terms of target quality traits, 12 QTLs were detected for flour yield, and 12 were detected for flour redness (a* value). Among these QTLs, six for flour yield and nine for flour a* were segregating in more than two populations. Some relationships among traits were explained by QTL collocations on chromosomes, especially group 7 chromosomes. Ten different ideotypes with various combinations of favorable alleles for the flour yield and flour a* QTLs were generated. Phenotypes of derivatives from these ideotypes were predicted to design ideal genotypes for high-quality wheat. Simulations revealed the possibility of breeding varieties with better quality than Kitahonami.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>32160264</pmid><doi>10.1371/journal.pone.0230326</doi><tpages>e0230326</tpages><orcidid>https://orcid.org/0000-0002-5199-2308</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Agricultural production Agricultural research Alleles Biology and Life Sciences Chromosomes Crop science Crop yield Flour Food Gene mapping Genetic aspects Genomes Genotypes Heritability Horticulture Markers Medicine and Health Sciences Phenotypes Plant breeding Populations Proteins Quality Quantitative genetics Quantitative trait loci Research and Analysis Methods Surgery Wheat |
| title | Multifamily QTL analysis and comprehensive design of genotypes for high-quality soft wheat |
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