Association mapping across numerous traits reveals patterns of functional variation in maize.
Phenotypic variation in natural populations results from a combination of genetic effects, environmental effects, and gene-by-environment interactions. Despite the vast amount of genomic data becoming available, many pressing questions remain about the nature of genetic mutations that underlie funct...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-12-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC4256217?pdf=render |
| _version_ | 1811336920230264832 |
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| author | Jason G Wallace Peter J Bradbury Nengyi Zhang Yves Gibon Mark Stitt Edward S Buckler |
| author_facet | Jason G Wallace Peter J Bradbury Nengyi Zhang Yves Gibon Mark Stitt Edward S Buckler |
| author_sort | Jason G Wallace |
| collection | DOAJ |
| description | Phenotypic variation in natural populations results from a combination of genetic effects, environmental effects, and gene-by-environment interactions. Despite the vast amount of genomic data becoming available, many pressing questions remain about the nature of genetic mutations that underlie functional variation. We present the results of combining genome-wide association analysis of 41 different phenotypes in ∼ 5,000 inbred maize lines to analyze patterns of high-resolution genetic association among of 28.9 million single-nucleotide polymorphisms (SNPs) and ∼ 800,000 copy-number variants (CNVs). We show that genic and intergenic regions have opposite patterns of enrichment, minor allele frequencies, and effect sizes, implying tradeoffs among the probability that a given polymorphism will have an effect, the detectable size of that effect, and its frequency in the population. We also find that genes tagged by GWAS are enriched for regulatory functions and are ∼ 50% more likely to have a paralog than expected by chance, indicating that gene regulation and gene duplication are strong drivers of phenotypic variation. These results will likely apply to many other organisms, especially ones with large and complex genomes like maize. |
| first_indexed | 2024-04-13T17:46:34Z |
| format | Article |
| id | doaj.art-fcc22df3ecb04079a07a775dcb682480 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-13T17:46:34Z |
| publishDate | 2014-12-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-fcc22df3ecb04079a07a775dcb6824802022-12-22T02:36:57ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042014-12-011012e100484510.1371/journal.pgen.1004845Association mapping across numerous traits reveals patterns of functional variation in maize.Jason G WallacePeter J BradburyNengyi ZhangYves GibonMark StittEdward S BucklerPhenotypic variation in natural populations results from a combination of genetic effects, environmental effects, and gene-by-environment interactions. Despite the vast amount of genomic data becoming available, many pressing questions remain about the nature of genetic mutations that underlie functional variation. We present the results of combining genome-wide association analysis of 41 different phenotypes in ∼ 5,000 inbred maize lines to analyze patterns of high-resolution genetic association among of 28.9 million single-nucleotide polymorphisms (SNPs) and ∼ 800,000 copy-number variants (CNVs). We show that genic and intergenic regions have opposite patterns of enrichment, minor allele frequencies, and effect sizes, implying tradeoffs among the probability that a given polymorphism will have an effect, the detectable size of that effect, and its frequency in the population. We also find that genes tagged by GWAS are enriched for regulatory functions and are ∼ 50% more likely to have a paralog than expected by chance, indicating that gene regulation and gene duplication are strong drivers of phenotypic variation. These results will likely apply to many other organisms, especially ones with large and complex genomes like maize.http://europepmc.org/articles/PMC4256217?pdf=render |
| spellingShingle | Jason G Wallace Peter J Bradbury Nengyi Zhang Yves Gibon Mark Stitt Edward S Buckler Association mapping across numerous traits reveals patterns of functional variation in maize. PLoS Genetics |
| title | Association mapping across numerous traits reveals patterns of functional variation in maize. |
| title_full | Association mapping across numerous traits reveals patterns of functional variation in maize. |
| title_fullStr | Association mapping across numerous traits reveals patterns of functional variation in maize. |
| title_full_unstemmed | Association mapping across numerous traits reveals patterns of functional variation in maize. |
| title_short | Association mapping across numerous traits reveals patterns of functional variation in maize. |
| title_sort | association mapping across numerous traits reveals patterns of functional variation in maize |
| url | http://europepmc.org/articles/PMC4256217?pdf=render |
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