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Genic and nongenic contributions to natural variation of quantitative traits in maize

The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic technology need to be integrated with strategic genetic design...

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Autores principales: Li, Xianran, Zhu, Chengsong, Yeh, Cheng-Ting, Wu, Wei, Takacs, Elizabeth M., Petsch, Katherine A., Tian, Feng, Bai, Guihua, Buckler, Edward S., Muehlbauer, Gary J., Timmermans, Marja C.P., Scanlon, Michael J., Schnable, Patrick S., Yu, Jianming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514673/
https://www.ncbi.nlm.nih.gov/pubmed/22701078
http://dx.doi.org/10.1101/gr.140277.112
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author Li, Xianran
Zhu, Chengsong
Yeh, Cheng-Ting
Wu, Wei
Takacs, Elizabeth M.
Petsch, Katherine A.
Tian, Feng
Bai, Guihua
Buckler, Edward S.
Muehlbauer, Gary J.
Timmermans, Marja C.P.
Scanlon, Michael J.
Schnable, Patrick S.
Yu, Jianming
author_facet Li, Xianran
Zhu, Chengsong
Yeh, Cheng-Ting
Wu, Wei
Takacs, Elizabeth M.
Petsch, Katherine A.
Tian, Feng
Bai, Guihua
Buckler, Edward S.
Muehlbauer, Gary J.
Timmermans, Marja C.P.
Scanlon, Michael J.
Schnable, Patrick S.
Yu, Jianming
author_sort Li, Xianran
collection PubMed
description The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic technology need to be integrated with strategic genetic design and novel perspectives to break new ground. Complementary to individual-gene–targeted research, which remains challenging, a global assessment of the genomic distribution of trait-associated SNPs (TASs) discovered from genome scans of quantitative traits can provide insights into the genetic architecture and contribute to the design of future studies. Here we report the first systematic tabulation of the relative contribution of different genomic regions to quantitative trait variation in maize. We found that TASs were enriched in the nongenic regions, particularly within a 5-kb window upstream of genes, which highlights the importance of polymorphisms regulating gene expression in shaping the natural variation. Consistent with these findings, TASs collectively explained 44%–59% of the total phenotypic variation across maize quantitative traits, and on average, 79% of the explained variation could be attributed to TASs located in genes or within 5 kb upstream of genes, which together comprise only 13% of the genome. Our findings suggest that efficient, cost-effective genome-wide association studies (GWAS) in species with complex genomes can focus on genic and promoter regions.
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spelling pubmed-35146732012-12-20 Genic and nongenic contributions to natural variation of quantitative traits in maize Li, Xianran Zhu, Chengsong Yeh, Cheng-Ting Wu, Wei Takacs, Elizabeth M. Petsch, Katherine A. Tian, Feng Bai, Guihua Buckler, Edward S. Muehlbauer, Gary J. Timmermans, Marja C.P. Scanlon, Michael J. Schnable, Patrick S. Yu, Jianming Genome Res Research The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic technology need to be integrated with strategic genetic design and novel perspectives to break new ground. Complementary to individual-gene–targeted research, which remains challenging, a global assessment of the genomic distribution of trait-associated SNPs (TASs) discovered from genome scans of quantitative traits can provide insights into the genetic architecture and contribute to the design of future studies. Here we report the first systematic tabulation of the relative contribution of different genomic regions to quantitative trait variation in maize. We found that TASs were enriched in the nongenic regions, particularly within a 5-kb window upstream of genes, which highlights the importance of polymorphisms regulating gene expression in shaping the natural variation. Consistent with these findings, TASs collectively explained 44%–59% of the total phenotypic variation across maize quantitative traits, and on average, 79% of the explained variation could be attributed to TASs located in genes or within 5 kb upstream of genes, which together comprise only 13% of the genome. Our findings suggest that efficient, cost-effective genome-wide association studies (GWAS) in species with complex genomes can focus on genic and promoter regions. Cold Spring Harbor Laboratory Press 2012-12 /pmc/articles/PMC3514673/ /pubmed/22701078 http://dx.doi.org/10.1101/gr.140277.112 Text en © 2012, Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/3.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.
spellingShingle Research
Li, Xianran
Zhu, Chengsong
Yeh, Cheng-Ting
Wu, Wei
Takacs, Elizabeth M.
Petsch, Katherine A.
Tian, Feng
Bai, Guihua
Buckler, Edward S.
Muehlbauer, Gary J.
Timmermans, Marja C.P.
Scanlon, Michael J.
Schnable, Patrick S.
Yu, Jianming
Genic and nongenic contributions to natural variation of quantitative traits in maize
title Genic and nongenic contributions to natural variation of quantitative traits in maize
title_full Genic and nongenic contributions to natural variation of quantitative traits in maize
title_fullStr Genic and nongenic contributions to natural variation of quantitative traits in maize
title_full_unstemmed Genic and nongenic contributions to natural variation of quantitative traits in maize
title_short Genic and nongenic contributions to natural variation of quantitative traits in maize
title_sort genic and nongenic contributions to natural variation of quantitative traits in maize
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514673/
https://www.ncbi.nlm.nih.gov/pubmed/22701078
http://dx.doi.org/10.1101/gr.140277.112
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