Analysis of genotype-by-environment interactions in a maize mapping population
Genotype-by-environment interactions are a significant challenge for crop breeding as well as being important for understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype-by-environment interactions in a maize multiparent advanced generation intercross populat...
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| Published in: | G3 : genes - genomes - genetics Vol. 12; no. 3 |
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| Language: | English |
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Oxford University Press
04-03-2022
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| Abstract | Genotype-by-environment interactions are a significant challenge for crop breeding as well as being important for understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype-by-environment interactions in a maize multiparent advanced generation intercross population grown across 5 environments. We found that genotype-by-environment interactions contributed as much as genotypic effects to the variation in some agronomically important traits. To understand how genetic correlations between traits change across environments, we estimated the genetic variance-covariance matrix in each environment. Changes in genetic covariances between traits across environments were common, even among traits that show low genotype-by-environment variance. We also performed a genome-wide association study to identify markers associated with genotype-by-environment interactions but found only a small number of significantly associated markers, possibly due to the highly polygenic nature of genotype-by-environment interactions in this population. |
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| AbstractList | Abstract
Genotype-by-environment interactions are a significant challenge for crop breeding as well as being important for understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype-by-environment interactions in a maize multiparent advanced generation intercross population grown across 5 environments. We found that genotype-by-environment interactions contributed as much as genotypic effects to the variation in some agronomically important traits. To understand how genetic correlations between traits change across environments, we estimated the genetic variance–covariance matrix in each environment. Changes in genetic covariances between traits across environments were common, even among traits that show low genotype-by-environment variance. We also performed a genome-wide association study to identify markers associated with genotype-by-environment interactions but found only a small number of significantly associated markers, possibly due to the highly polygenic nature of genotype-by-environment interactions in this population. Genotype-by-environment interactions are a significant challenge for crop breeding as well as being important for understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype-by-environment interactions in a maize multiparent advanced generation intercross population grown across 5 environments. We found that genotype-by-environment interactions contributed as much as genotypic effects to the variation in some agronomically important traits. To understand how genetic correlations between traits change across environments, we estimated the genetic variance-covariance matrix in each environment. Changes in genetic covariances between traits across environments were common, even among traits that show low genotype-by-environment variance. We also performed a genome-wide association study to identify markers associated with genotype-by-environment interactions but found only a small number of significantly associated markers, possibly due to the highly polygenic nature of genotype-by-environment interactions in this population. |
| Author | Tixier, Marie-Helene Hudson, Asher I Dubreuil, Pierre Runcie, Daniel E Ross-Ibarra, Jeffrey Odell, Sarah G Praud, Sebastien |
| AuthorAffiliation | 5 Genome Center, University of California , Davis, CA 95616, USA 4 Center of Research of Chappes, Limagrain , Chappes 63720, France 1 Department of Evolution and Ecology, University of California , Davis, CA 95616, USA 3 Department of Plant Sciences, University of California , Davis, CA 95616, USA 2 Center for Population Biology, University of California , Davis, CA 95616, USA |
| AuthorAffiliation_xml | – name: 5 Genome Center, University of California , Davis, CA 95616, USA – name: 1 Department of Evolution and Ecology, University of California , Davis, CA 95616, USA – name: 4 Center of Research of Chappes, Limagrain , Chappes 63720, France – name: 2 Center for Population Biology, University of California , Davis, CA 95616, USA – name: 3 Department of Plant Sciences, University of California , Davis, CA 95616, USA |
| Author_xml | – sequence: 1 givenname: Asher I orcidid: 0000-0001-9520-8901 surname: Hudson fullname: Hudson, Asher I organization: Center for Population Biology, University of California, Davis, CA 95616, USA – sequence: 2 givenname: Sarah G orcidid: 0000-0002-0316-7506 surname: Odell fullname: Odell, Sarah G organization: Department of Plant Sciences, University of California, Davis, CA 95616, USA – sequence: 3 givenname: Pierre surname: Dubreuil fullname: Dubreuil, Pierre organization: Center of Research of Chappes, Limagrain, Chappes 63720, France – sequence: 4 givenname: Marie-Helene surname: Tixier fullname: Tixier, Marie-Helene organization: Center of Research of Chappes, Limagrain, Chappes 63720, France – sequence: 5 givenname: Sebastien orcidid: 0000-0002-4474-9115 surname: Praud fullname: Praud, Sebastien organization: Center of Research of Chappes, Limagrain, Chappes 63720, France – sequence: 6 givenname: Daniel E orcidid: 0000-0002-3008-9312 surname: Runcie fullname: Runcie, Daniel E organization: Department of Plant Sciences, University of California, Davis, CA 95616, USA – sequence: 7 givenname: Jeffrey orcidid: 0000-0003-1656-4954 surname: Ross-Ibarra fullname: Ross-Ibarra, Jeffrey organization: Genome Center, University of California, Davis, CA 95616, USA |
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| Cites_doi | 10.1038/nrg3688 10.1038/sj.hdy.6800532 10.1146/annurev-ecolsys-110512-135806 10.1111/nph.15103 10.1038/nature04920 10.1186/s13059-015-0716-z 10.1093/genetics/130.1.195 10.7554/eLife.05861 10.2135/cropsci1964.0011183X000400050021x 10.1111/evo.12795 10.1038/hdy.2013.12 10.1038/nmeth.1681 10.1016/j.spasta.2017.10.003 10.1093/g3journal/jkac011 10.1071/AR9630742 10.1186/1746-4811-9-29 10.1371/journal.pone.0156744 10.1126/science.1174276 10.1101/706739 10.18637/jss.v080.i01 10.1126/science.1159978 10.1093/g3journal/jkaa050 10.1111/j.1461-0248.2004.00684.x 10.1093/jxb/erv441 10.1371/journal.pgen.1007978 10.3168/jds.2007-0980 10.1371/journal.pgen.1002589 10.1038/s41467-017-01450-2 10.1111/j.1558-5646.2008.00580.x 10.1111/pce.12418 10.1086/519795 10.1111/evo.12776 |
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| Copyright | The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. 2022 |
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| Keywords | environment interactions maize multiparental populations genotype |
| Language | English |
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| Title | Analysis of genotype-by-environment interactions in a maize mapping population |
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