A mixed model QTL analysis for sugarcane multiple-harvest-location trial data
Identifieur interne : 001808 ( Main/Exploration ); précédent : 001807; suivant : 001809A mixed model QTL analysis for sugarcane multiple-harvest-location trial data
Auteurs : M. M. Pastina [Brésil] ; M. Malosetti [Pays-Bas] ; R. Gazaffi [Brésil] ; M. Mollinari [Brésil] ; G. R. A. Margarido [Brésil] ; K. M. Oliveira [Brésil] ; L. R. Pinto ; A. P. Souza ; F. A. Van Eeuwijk [Pays-Bas] ; A. A. F. Garcia [Brésil]Source :
- TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik [ 0040-5752 ] ; 2011.
Abstract
Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane.
The online version of this article (doi:10.1007/s00122-011-1748-8) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1007/s00122-011-1748-8
PubMed: 22159754
PubMed Central: 3284670
Affiliations:
- Brésil, Pays-Bas
- Gueldre (province), État de São Paulo
- São Paulo, Wageningue
- Université de São Paulo, Université de Wageningue
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Souza</name><affiliation><nlm:aff id="Aff4">Centro de Biologia Molecular e Engenharia Genética (CBMEG), Departamento de Genética e Evolução, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, 13083-875 Campinas, SP Brazil</nlm:aff><wicri:noCountry code="subfield">SP Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Van Eeuwijk, F A" sort="Van Eeuwijk, F A" uniqKey="Van Eeuwijk F" first="F. A." last="Van Eeuwijk">F. A. Van Eeuwijk</name><affiliation wicri:level="4"><nlm:aff id="Aff5">Biometris, Wageningen University, P.O. Box 100, 6700 AC Wageningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Biometris, Wageningen University, P.O. 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M." last="Pastina">M. M. Pastina</name><affiliation wicri:level="4"><nlm:aff id="Aff1">Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, 13400-970 Piracicaba, SP Brazil</nlm:aff><orgName type="university">Université de São Paulo</orgName><country>Brésil</country><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Malosetti, M" sort="Malosetti, M" uniqKey="Malosetti M" first="M." last="Malosetti">M. Malosetti</name><affiliation wicri:level="4"><nlm:aff id="Aff5">Biometris, Wageningen University, P.O. Box 100, 6700 AC Wageningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Biometris, Wageningen University, P.O. 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Oliveira</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Centro de Tecnologia Canavieira (CTC), CP 162, 13400-970 Piracicaba-SP, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Centro de Tecnologia Canavieira (CTC), CP 162, 13400-970 Piracicaba-SP</wicri:regionArea><placeName><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Pinto, L R" sort="Pinto, L R" uniqKey="Pinto L" first="L. R." last="Pinto">L. R. Pinto</name><affiliation><nlm:aff id="Aff3">Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana, IAC/Apta, CP 206, 14001-970 Ribeirão Preto, SP Brazil</nlm:aff><wicri:noCountry code="subfield">SP Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Souza, A P" sort="Souza, A P" uniqKey="Souza A" first="A. P." last="Souza">A. P. Souza</name><affiliation><nlm:aff id="Aff4">Centro de Biologia Molecular e Engenharia Genética (CBMEG), Departamento de Genética e Evolução, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, 13083-875 Campinas, SP Brazil</nlm:aff><wicri:noCountry code="subfield">SP Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Van Eeuwijk, F A" sort="Van Eeuwijk, F A" uniqKey="Van Eeuwijk F" first="F. A." last="Van Eeuwijk">F. A. Van Eeuwijk</name><affiliation wicri:level="4"><nlm:aff id="Aff5">Biometris, Wageningen University, P.O. Box 100, 6700 AC Wageningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Biometris, Wageningen University, P.O. Box 100, 6700 AC Wageningen</wicri:regionArea><orgName type="university">Université de Wageningue</orgName><placeName><settlement type="city">Wageningue</settlement><region nuts="2">Gueldre (province)</region></placeName></affiliation></author><author><name sortKey="Garcia, A A F" sort="Garcia, A A F" uniqKey="Garcia A" first="A. A. F." last="Garcia">A. A. F. Garcia</name><affiliation wicri:level="4"><nlm:aff id="Aff1">Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, 13400-970 Piracicaba, SP Brazil</nlm:aff><orgName type="university">Université de São Paulo</orgName><country>Brésil</country><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></affiliation></author></analytic><series><title level="j">TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik</title><idno type="ISSN">0040-5752</idno><idno type="eISSN">1432-2242</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane.</p><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1007/s00122-011-1748-8) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Aitken, Ks" uniqKey="Aitken K">KS Aitken</name></author><author><name sortKey="Jackson, Pa" uniqKey="Jackson P">PA Jackson</name></author><author><name sortKey="Mcintyre, Cl" uniqKey="Mcintyre C">CL McIntyre</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Aitken, Ks" uniqKey="Aitken K">KS Aitken</name></author><author><name sortKey="Hermann, S" uniqKey="Hermann S">S Hermann</name></author><author><name sortKey="Karno, K" uniqKey="Karno K">K Karno</name></author><author><name 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sortKey="Painter, I" uniqKey="Painter I">I Painter</name></author><author><name sortKey="Zeng, Zb" uniqKey="Zeng Z">ZB Zeng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, R" uniqKey="Wu R">R Wu</name></author><author><name sortKey="Ma, Cx" uniqKey="Ma C">CX Ma</name></author><author><name sortKey="Wu, Ss" uniqKey="Wu S">SS Wu</name></author><author><name sortKey="Zeng, Zb" uniqKey="Zeng Z">ZB Zeng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, R" uniqKey="Wu R">R Wu</name></author><author><name sortKey="Ma, Cx" uniqKey="Ma C">CX Ma</name></author><author><name sortKey="Casella, G" uniqKey="Casella G">G Casella</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Brésil</li><li>Pays-Bas</li></country><region><li>Gueldre (province)</li><li>État de São Paulo</li></region><settlement><li>São Paulo</li><li>Wageningue</li></settlement><orgName><li>Université de São Paulo</li><li>Université de Wageningue</li></orgName></list><tree><noCountry><name sortKey="Pinto, L R" sort="Pinto, L R" uniqKey="Pinto L" first="L. R." last="Pinto">L. R. Pinto</name><name sortKey="Souza, A P" sort="Souza, A P" uniqKey="Souza A" first="A. P." last="Souza">A. P. Souza</name></noCountry><country name="Brésil"><region name="État de São Paulo"><name sortKey="Pastina, M M" sort="Pastina, M M" uniqKey="Pastina M" first="M. M." last="Pastina">M. M. Pastina</name></region><name sortKey="Garcia, A A F" sort="Garcia, A A F" uniqKey="Garcia A" first="A. A. F." last="Garcia">A. A. F. Garcia</name><name sortKey="Gazaffi, R" sort="Gazaffi, R" uniqKey="Gazaffi R" first="R." last="Gazaffi">R. Gazaffi</name><name sortKey="Margarido, G R A" sort="Margarido, G R A" uniqKey="Margarido G" first="G. R. A." last="Margarido">G. R. A. Margarido</name><name sortKey="Mollinari, M" sort="Mollinari, M" uniqKey="Mollinari M" first="M." last="Mollinari">M. Mollinari</name><name sortKey="Oliveira, K M" sort="Oliveira, K M" uniqKey="Oliveira K" first="K. M." last="Oliveira">K. M. Oliveira</name></country><country name="Pays-Bas"><region name="Gueldre (province)"><name sortKey="Malosetti, M" sort="Malosetti, M" uniqKey="Malosetti M" first="M." last="Malosetti">M. Malosetti</name></region><name sortKey="Van Eeuwijk, F A" sort="Van Eeuwijk, F A" uniqKey="Van Eeuwijk F" first="F. A." last="Van Eeuwijk">F. A. Van Eeuwijk</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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