Whole-Genome Analysis of Multienvironment or Multitrait QTL in MAGIC

Multiparent Advanced Generation Inter-Cross (MAGIC) populations are now being utilized to more accurately identify the underlying genetic basis of quantitative traits through quantitative trait loci (QTL) analyses and subsequent gene discovery. The expanded genetic diversity present in such populati...

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Main Authors:	Verbyla, Arūnas P., Cavanagh, Colin R., Verbyla, Klara L.
Format:	Online
Language:	English
Published:	Genetics Society of America 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169149/

id	pubmed-4169149
recordtype	oai_dc
spelling	pubmed-41691492014-09-24 Whole-Genome Analysis of Multienvironment or Multitrait QTL in MAGIC Verbyla, Arūnas P. Cavanagh, Colin R. Verbyla, Klara L. Multiparental Populations Multiparent Advanced Generation Inter-Cross (MAGIC) populations are now being utilized to more accurately identify the underlying genetic basis of quantitative traits through quantitative trait loci (QTL) analyses and subsequent gene discovery. The expanded genetic diversity present in such populations and the amplified number of recombination events mean that QTL can be identified at a higher resolution. Most QTL analyses are conducted separately for each trait within a single environment. Separate analysis does not take advantage of the underlying correlation structure found in multienvironment or multitrait data. By using this information in a joint analysis—be it multienvironment or multitrait — it is possible to gain a greater understanding of genotype- or QTL-by-environment interactions or of pleiotropic effects across traits. Furthermore, this can result in improvements in accuracy for a range of traits or in a specific target environment and can influence selection decisions. Data derived from MAGIC populations allow for founder probabilities of all founder alleles to be calculated for each individual within the population. This presents an additional layer of complexity and information that can be utilized to identify QTL. A whole-genome approach is proposed for multienvironment and multitrait QTL analysis in MAGIC. The whole-genome approach simultaneously incorporates all founder probabilities at each marker for all individuals in the analysis, rather than using a genome scan. A dimension reduction technique is implemented, which allows for high-dimensional genetic data. For each QTL identified, sizes of effects for each founder allele, the percentage of genetic variance explained, and a score to reflect the strength of the QTL are found. The approach was demonstrated to perform well in a small simulation study and for two experiments, using a wheat MAGIC population. Genetics Society of America 2014-09-01 /pmc/articles/PMC4169149/ /pubmed/25237109 http://dx.doi.org/10.1534/g3.114.012971 Text en Copyright © 2014 Verbyla 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.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Verbyla, Arūnas P. Cavanagh, Colin R. Verbyla, Klara L.
spellingShingle	Verbyla, Arūnas P. Cavanagh, Colin R. Verbyla, Klara L. Whole-Genome Analysis of Multienvironment or Multitrait QTL in MAGIC
author_facet	Verbyla, Arūnas P. Cavanagh, Colin R. Verbyla, Klara L.
author_sort	Verbyla, Arūnas P.
title	Whole-Genome Analysis of Multienvironment or Multitrait QTL in MAGIC
title_short	Whole-Genome Analysis of Multienvironment or Multitrait QTL in MAGIC
title_full	Whole-Genome Analysis of Multienvironment or Multitrait QTL in MAGIC
title_fullStr	Whole-Genome Analysis of Multienvironment or Multitrait QTL in MAGIC
title_full_unstemmed	Whole-Genome Analysis of Multienvironment or Multitrait QTL in MAGIC
title_sort	whole-genome analysis of multienvironment or multitrait qtl in magic
description	Multiparent Advanced Generation Inter-Cross (MAGIC) populations are now being utilized to more accurately identify the underlying genetic basis of quantitative traits through quantitative trait loci (QTL) analyses and subsequent gene discovery. The expanded genetic diversity present in such populations and the amplified number of recombination events mean that QTL can be identified at a higher resolution. Most QTL analyses are conducted separately for each trait within a single environment. Separate analysis does not take advantage of the underlying correlation structure found in multienvironment or multitrait data. By using this information in a joint analysis—be it multienvironment or multitrait — it is possible to gain a greater understanding of genotype- or QTL-by-environment interactions or of pleiotropic effects across traits. Furthermore, this can result in improvements in accuracy for a range of traits or in a specific target environment and can influence selection decisions. Data derived from MAGIC populations allow for founder probabilities of all founder alleles to be calculated for each individual within the population. This presents an additional layer of complexity and information that can be utilized to identify QTL. A whole-genome approach is proposed for multienvironment and multitrait QTL analysis in MAGIC. The whole-genome approach simultaneously incorporates all founder probabilities at each marker for all individuals in the analysis, rather than using a genome scan. A dimension reduction technique is implemented, which allows for high-dimensional genetic data. For each QTL identified, sizes of effects for each founder allele, the percentage of genetic variance explained, and a score to reflect the strength of the QTL are found. The approach was demonstrated to perform well in a small simulation study and for two experiments, using a wheat MAGIC population.
publisher	Genetics Society of America
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169149/
_version_	1613135513425805312

Whole-Genome Analysis of Multienvironment or Multitrait QTL in MAGIC

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