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Dissecting Genome-Wide Association Signals for Loss-of-Function Phenotypes in Sorghum Flavonoid Pigmentation Traits
Genome-wide association studies are a powerful method to dissect the genetic basis of traits, although in practice the effects of complex genetic architecture and population structure remain poorly understood. To compare mapping strategies we dissected the genetic control of flavonoid pigmentation t...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Genetics Society of America
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815067/ https://www.ncbi.nlm.nih.gov/pubmed/24048646 http://dx.doi.org/10.1534/g3.113.008417 |
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author | Morris, Geoffrey P. Rhodes, Davina H. Brenton, Zachary Ramu, Punna Thayil, Vinayan Madhumal Deshpande, Santosh Hash, C. Thomas Acharya, Charlotte Mitchell, Sharon E. Buckler, Edward S. Yu, Jianming Kresovich, Stephen |
author_facet | Morris, Geoffrey P. Rhodes, Davina H. Brenton, Zachary Ramu, Punna Thayil, Vinayan Madhumal Deshpande, Santosh Hash, C. Thomas Acharya, Charlotte Mitchell, Sharon E. Buckler, Edward S. Yu, Jianming Kresovich, Stephen |
author_sort | Morris, Geoffrey P. |
collection | PubMed |
description | Genome-wide association studies are a powerful method to dissect the genetic basis of traits, although in practice the effects of complex genetic architecture and population structure remain poorly understood. To compare mapping strategies we dissected the genetic control of flavonoid pigmentation traits in the cereal grass sorghum by using high-resolution genotyping-by-sequencing single-nucleotide polymorphism markers. Studying the grain tannin trait, we find that general linear models (GLMs) are not able to precisely map tan1-a, a known loss-of-function allele of the Tannin1 gene, with either a small panel (n = 142) or large association panel (n = 336), and that indirect associations limit the mapping of the Tannin1 locus to Mb-resolution. A GLM that accounts for population structure (Q) or standard mixed linear model that accounts for kinship (K) can identify tan1-a, whereas a compressed mixed linear model performs worse than the naive GLM. Interestingly, a simple loss-of-function genome scan, for genotype-phenotype covariation only in the putative loss-of-function allele, is able to precisely identify the Tannin1 gene without considering relatedness. We also find that the tan1-a allele can be mapped with gene resolution in a biparental recombinant inbred line family (n = 263) using genotyping-by-sequencing markers but lower precision in the mapping of vegetative pigmentation traits suggest that consistent gene-level resolution will likely require larger families or multiple recombinant inbred lines. These findings highlight that complex association signals can emerge from even the simplest traits given epistasis and structured alleles, but that gene-resolution mapping of these traits is possible with high marker density and appropriate models. |
format | Online Article Text |
id | pubmed-3815067 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-38150672013-11-04 Dissecting Genome-Wide Association Signals for Loss-of-Function Phenotypes in Sorghum Flavonoid Pigmentation Traits Morris, Geoffrey P. Rhodes, Davina H. Brenton, Zachary Ramu, Punna Thayil, Vinayan Madhumal Deshpande, Santosh Hash, C. Thomas Acharya, Charlotte Mitchell, Sharon E. Buckler, Edward S. Yu, Jianming Kresovich, Stephen G3 (Bethesda) Investigations Genome-wide association studies are a powerful method to dissect the genetic basis of traits, although in practice the effects of complex genetic architecture and population structure remain poorly understood. To compare mapping strategies we dissected the genetic control of flavonoid pigmentation traits in the cereal grass sorghum by using high-resolution genotyping-by-sequencing single-nucleotide polymorphism markers. Studying the grain tannin trait, we find that general linear models (GLMs) are not able to precisely map tan1-a, a known loss-of-function allele of the Tannin1 gene, with either a small panel (n = 142) or large association panel (n = 336), and that indirect associations limit the mapping of the Tannin1 locus to Mb-resolution. A GLM that accounts for population structure (Q) or standard mixed linear model that accounts for kinship (K) can identify tan1-a, whereas a compressed mixed linear model performs worse than the naive GLM. Interestingly, a simple loss-of-function genome scan, for genotype-phenotype covariation only in the putative loss-of-function allele, is able to precisely identify the Tannin1 gene without considering relatedness. We also find that the tan1-a allele can be mapped with gene resolution in a biparental recombinant inbred line family (n = 263) using genotyping-by-sequencing markers but lower precision in the mapping of vegetative pigmentation traits suggest that consistent gene-level resolution will likely require larger families or multiple recombinant inbred lines. These findings highlight that complex association signals can emerge from even the simplest traits given epistasis and structured alleles, but that gene-resolution mapping of these traits is possible with high marker density and appropriate models. Genetics Society of America 2013-11-01 /pmc/articles/PMC3815067/ /pubmed/24048646 http://dx.doi.org/10.1534/g3.113.008417 Text en Copyright © 2013 Morris et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Investigations Morris, Geoffrey P. Rhodes, Davina H. Brenton, Zachary Ramu, Punna Thayil, Vinayan Madhumal Deshpande, Santosh Hash, C. Thomas Acharya, Charlotte Mitchell, Sharon E. Buckler, Edward S. Yu, Jianming Kresovich, Stephen Dissecting Genome-Wide Association Signals for Loss-of-Function Phenotypes in Sorghum Flavonoid Pigmentation Traits |
title | Dissecting Genome-Wide Association Signals for Loss-of-Function Phenotypes in Sorghum Flavonoid Pigmentation Traits |
title_full | Dissecting Genome-Wide Association Signals for Loss-of-Function Phenotypes in Sorghum Flavonoid Pigmentation Traits |
title_fullStr | Dissecting Genome-Wide Association Signals for Loss-of-Function Phenotypes in Sorghum Flavonoid Pigmentation Traits |
title_full_unstemmed | Dissecting Genome-Wide Association Signals for Loss-of-Function Phenotypes in Sorghum Flavonoid Pigmentation Traits |
title_short | Dissecting Genome-Wide Association Signals for Loss-of-Function Phenotypes in Sorghum Flavonoid Pigmentation Traits |
title_sort | dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits |
topic | Investigations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815067/ https://www.ncbi.nlm.nih.gov/pubmed/24048646 http://dx.doi.org/10.1534/g3.113.008417 |
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