An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize
Identifieur interne : 000146 ( Main/Exploration ); précédent : 000145; suivant : 000147An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize
Auteurs : Hongjun Liu [République populaire de Chine] ; Yongchao Niu [République populaire de Chine] ; Pedro J. Gonzalez-Portilla [États-Unis] ; Huangkai Zhou [République populaire de Chine] ; Liya Wang [États-Unis] ; Tao Zuo [États-Unis] ; Cheng Qin [République populaire de Chine] ; Shuaishuai Tai [République populaire de Chine] ; Constantin Jansen [États-Unis] ; Yaou Shen [République populaire de Chine] ; Haijian Lin [République populaire de Chine] ; Michael Lee [États-Unis] ; Doreen Ware [États-Unis] ; Zhiming Zhang [République populaire de Chine] ; Thomas Lübberstedt [États-Unis] ; Guangtang Pan [République populaire de Chine]Source :
- BMC Genomics [ 1471-2164 ] ; 2015.
Abstract
To safeguard the food supply for the growing human population, it is important to understand and exploit the genetic basis of quantitative traits. Next-generation sequencing technology performs advantageously and effectively in genetic mapping and genome analysis of diverse genetic resources. Hence, we combined re-sequencing technology and a bin map strategy to construct an ultra-high-density bin map with thousands of bin markers to precisely map a quantitative trait locus.
In this study, we generated a linkage map containing 1,151,856 high quality SNPs between Mo17 and B73, which were verified in the maize intermated B73 × Mo17 (IBM) Syn10 population. This resource is an excellent complement to existing maize genetic maps available in an online database (iPlant,
Our findings provide basic essential genetic data for the maize genetic research community. An updated IBM Syn10 population and a reliable, verified high-quality SNP set between Mo17 and B73 will aid in future molecular breeding efforts.
The online version of this article (doi:10.1186/s12864-015-2242-5) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-015-2242-5
PubMed: 26691201
PubMed Central: 4687334
Affiliations:
- République populaire de Chine, États-Unis
- Guangdong, Iowa, État de New York
- Ames (Iowa), Shenzhen
- Université d'État de l'Iowa
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Gonzalez-Portilla</name><affiliation wicri:level="2"><nlm:aff id="Aff3">Department of Agronomy, Iowa State University, Ames, IA 50011 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Iowa</region></placeName><wicri:cityArea>Department of Agronomy, Iowa State University, Ames</wicri:cityArea></affiliation></author><author><name sortKey="Zhou, Huangkai" sort="Zhou, Huangkai" uniqKey="Zhou H" first="Huangkai" last="Zhou">Huangkai Zhou</name><affiliation wicri:level="3"><nlm:aff id="Aff2">BGI-Shenzhen, Shenzhen, 518083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>BGI-Shenzhen, Shenzhen</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Wang, Liya" sort="Wang, Liya" uniqKey="Wang L" first="Liya" last="Wang">Liya Wang</name><affiliation wicri:level="2"><nlm:aff id="Aff4">Cold Spring Harbor Laboratory and USDA: USDA ARS NAA Robert W. 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Gonzalez-Portilla</name><affiliation wicri:level="2"><nlm:aff id="Aff3">Department of Agronomy, Iowa State University, Ames, IA 50011 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Iowa</region></placeName><wicri:cityArea>Department of Agronomy, Iowa State University, Ames</wicri:cityArea></affiliation></author><author><name sortKey="Zhou, Huangkai" sort="Zhou, Huangkai" uniqKey="Zhou H" first="Huangkai" last="Zhou">Huangkai Zhou</name><affiliation wicri:level="3"><nlm:aff id="Aff2">BGI-Shenzhen, Shenzhen, 518083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>BGI-Shenzhen, Shenzhen</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Wang, Liya" sort="Wang, Liya" uniqKey="Wang L" first="Liya" last="Wang">Liya Wang</name><affiliation wicri:level="2"><nlm:aff id="Aff4">Cold Spring Harbor Laboratory and USDA: USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, 14853 Ithaca, NY USA</nlm:aff><country>États-Unis</country><placeName><region type="state">État de New York</region></placeName><wicri:cityArea>Cold Spring Harbor Laboratory and USDA: USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, 14853 Ithaca</wicri:cityArea></affiliation></author><author><name sortKey="Zuo, Tao" sort="Zuo, Tao" uniqKey="Zuo T" first="Tao" last="Zuo">Tao Zuo</name><affiliation wicri:level="4"><nlm:aff id="Aff5">Interdepartmental Genetics Graduate Program, Iowa State University, Ames, 50011 USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Interdepartmental Genetics Graduate Program, Iowa State University, Ames</wicri:regionArea><orgName type="university">Université d'État de l'Iowa</orgName><placeName><settlement type="city">Ames (Iowa)</settlement><region type="state">Iowa</region></placeName></affiliation></author><author><name sortKey="Qin, Cheng" sort="Qin, Cheng" uniqKey="Qin C" first="Cheng" last="Qin">Cheng Qin</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130 Chengdu, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130 Chengdu</wicri:regionArea><wicri:noRegion>611130 Chengdu</wicri:noRegion></affiliation></author><author><name sortKey="Tai, Shuaishuai" sort="Tai, Shuaishuai" uniqKey="Tai S" first="Shuaishuai" last="Tai">Shuaishuai Tai</name><affiliation wicri:level="3"><nlm:aff id="Aff2">BGI-Shenzhen, Shenzhen, 518083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>BGI-Shenzhen, Shenzhen</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Jansen, Constantin" sort="Jansen, Constantin" uniqKey="Jansen C" first="Constantin" last="Jansen">Constantin Jansen</name><affiliation wicri:level="2"><nlm:aff id="Aff3">Department of Agronomy, Iowa State University, Ames, IA 50011 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Iowa</region></placeName><wicri:cityArea>Department of Agronomy, Iowa State University, Ames</wicri:cityArea></affiliation></author><author><name sortKey="Shen, Yaou" sort="Shen, Yaou" uniqKey="Shen Y" first="Yaou" last="Shen">Yaou Shen</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130 Chengdu, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130 Chengdu</wicri:regionArea><wicri:noRegion>611130 Chengdu</wicri:noRegion></affiliation></author><author><name sortKey="Lin, Haijian" sort="Lin, Haijian" uniqKey="Lin H" first="Haijian" last="Lin">Haijian Lin</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130 Chengdu, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130 Chengdu</wicri:regionArea><wicri:noRegion>611130 Chengdu</wicri:noRegion></affiliation></author><author><name sortKey="Lee, Michael" sort="Lee, Michael" uniqKey="Lee M" first="Michael" last="Lee">Michael Lee</name><affiliation wicri:level="2"><nlm:aff id="Aff3">Department of Agronomy, Iowa State University, Ames, IA 50011 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Iowa</region></placeName><wicri:cityArea>Department of Agronomy, Iowa State University, Ames</wicri:cityArea></affiliation></author><author><name sortKey="Ware, Doreen" sort="Ware, Doreen" uniqKey="Ware D" first="Doreen" last="Ware">Doreen Ware</name><affiliation wicri:level="2"><nlm:aff id="Aff4">Cold Spring Harbor Laboratory and USDA: USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, 14853 Ithaca, NY USA</nlm:aff><country>États-Unis</country><placeName><region type="state">État de New York</region></placeName><wicri:cityArea>Cold Spring Harbor Laboratory and USDA: USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, 14853 Ithaca</wicri:cityArea></affiliation></author><author><name sortKey="Zhang, Zhiming" sort="Zhang, Zhiming" uniqKey="Zhang Z" first="Zhiming" last="Zhang">Zhiming Zhang</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130 Chengdu, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130 Chengdu</wicri:regionArea><wicri:noRegion>611130 Chengdu</wicri:noRegion></affiliation></author><author><name sortKey="Lubberstedt, Thomas" sort="Lubberstedt, Thomas" uniqKey="Lubberstedt T" first="Thomas" last="Lübberstedt">Thomas Lübberstedt</name><affiliation wicri:level="2"><nlm:aff id="Aff3">Department of Agronomy, Iowa State University, Ames, IA 50011 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Iowa</region></placeName><wicri:cityArea>Department of Agronomy, Iowa State University, Ames</wicri:cityArea></affiliation></author><author><name sortKey="Pan, Guangtang" sort="Pan, Guangtang" uniqKey="Pan G" first="Guangtang" last="Pan">Guangtang Pan</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130 Chengdu, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130 Chengdu</wicri:regionArea><wicri:noRegion>611130 Chengdu</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>To safeguard the food supply for the growing human population, it is important to understand and exploit the genetic basis of quantitative traits. Next-generation sequencing technology performs advantageously and effectively in genetic mapping and genome analysis of diverse genetic resources. Hence, we combined re-sequencing technology and a bin map strategy to construct an ultra-high-density bin map with thousands of bin markers to precisely map a quantitative trait locus.</p></sec><sec><title>Results</title><p>In this study, we generated a linkage map containing 1,151,856 high quality SNPs between Mo17 and B73, which were verified in the maize intermated B73 × Mo17 (IBM) Syn10 population. This resource is an excellent complement to existing maize genetic maps available in an online database (iPlant, <ext-link ext-link-type="uri" xlink:href="http://data.maizecode.org/maize/qtl/syn10/">http://data.maizecode.org/maize/qtl/syn10/</ext-link>). Moreover, in this population combined with the IBM Syn4 RIL population, we detected 135 QTLs for flowering time and plant height traits across the two populations. Eighteen known functional genes and twenty-five candidate genes for flowering time and plant height trait were fine-mapped into a 2.21–4.96 Mb interval. Map expansion and segregation distortion were also analyzed, and evidence for inadvertent selection of early flowering time in the process of mapping population development was observed. Furthermore, an updated integrated map with 1,151,856 high-quality SNPs, 2,916 traditional markers and 6,618 bin markers was constructed. The data were deposited into the iPlant Discovery Environment (DE), which provides a fundamental resource of genetic data for the maize genetic research community.</p></sec><sec><title>Conclusions</title><p>Our findings provide basic essential genetic data for the maize genetic research community. An updated IBM Syn10 population and a reliable, verified high-quality SNP set between Mo17 and B73 will aid in future molecular breeding efforts.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-015-2242-5) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Tester, M" uniqKey="Tester M">M Tester</name></author><author><name sortKey="Langridge, P" uniqKey="Langridge P">P Langridge</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Lu, Y" uniqKey="Lu Y">Y Lu</name></author><author><name sortKey="Shah, T" uniqKey="Shah T">T Shah</name></author><author><name sortKey="Hao, Z" uniqKey="Hao Z">Z Hao</name></author><author><name sortKey="Taba, S" uniqKey="Taba S">S Taba</name></author><author><name sortKey="Zhang, S" uniqKey="Zhang S">S 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sortKey="Lin, Haijian" sort="Lin, Haijian" uniqKey="Lin H" first="Haijian" last="Lin">Haijian Lin</name><name sortKey="Niu, Yongchao" sort="Niu, Yongchao" uniqKey="Niu Y" first="Yongchao" last="Niu">Yongchao Niu</name><name sortKey="Pan, Guangtang" sort="Pan, Guangtang" uniqKey="Pan G" first="Guangtang" last="Pan">Guangtang Pan</name><name sortKey="Qin, Cheng" sort="Qin, Cheng" uniqKey="Qin C" first="Cheng" last="Qin">Cheng Qin</name><name sortKey="Shen, Yaou" sort="Shen, Yaou" uniqKey="Shen Y" first="Yaou" last="Shen">Yaou Shen</name><name sortKey="Tai, Shuaishuai" sort="Tai, Shuaishuai" uniqKey="Tai S" first="Shuaishuai" last="Tai">Shuaishuai Tai</name><name sortKey="Zhang, Zhiming" sort="Zhang, Zhiming" uniqKey="Zhang Z" first="Zhiming" last="Zhang">Zhiming Zhang</name><name sortKey="Zhou, Huangkai" sort="Zhou, Huangkai" uniqKey="Zhou H" first="Huangkai" last="Zhou">Huangkai Zhou</name></country><country name="États-Unis"><region name="Iowa"><name sortKey="Gonzalez Portilla, Pedro J" sort="Gonzalez Portilla, Pedro J" uniqKey="Gonzalez Portilla P" first="Pedro J." last="Gonzalez-Portilla">Pedro J. Gonzalez-Portilla</name></region><name sortKey="Jansen, Constantin" sort="Jansen, Constantin" uniqKey="Jansen C" first="Constantin" last="Jansen">Constantin Jansen</name><name sortKey="Lee, Michael" sort="Lee, Michael" uniqKey="Lee M" first="Michael" last="Lee">Michael Lee</name><name sortKey="Lubberstedt, Thomas" sort="Lubberstedt, Thomas" uniqKey="Lubberstedt T" first="Thomas" last="Lübberstedt">Thomas Lübberstedt</name><name sortKey="Wang, Liya" sort="Wang, Liya" uniqKey="Wang L" first="Liya" last="Wang">Liya Wang</name><name sortKey="Ware, Doreen" sort="Ware, Doreen" uniqKey="Ware D" first="Doreen" last="Ware">Doreen Ware</name><name sortKey="Zuo, Tao" sort="Zuo, Tao" uniqKey="Zuo T" first="Tao" last="Zuo">Tao Zuo</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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