Comparative Systems Biology Reveals Allelic Variation Modulating Tocochromanol Profiles in Barley (Hordeum vulgare L.)

Tocochromanols are recognized for nutritional content, plant stress response, and seed longevity. Here we present a systems biological approach to characterize and develop predictive assays for genes affecting tocochromanol variation in barley. Major QTL, detected in three regions of a SNP linkage m...

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Main Authors:	Oliver, Rebekah E., Islamovic, Emir, Obert, Donald E., Wise, Mitchell L., Herrin, Lauri L., Hang, An, Harrison, Stephen A., Ibrahim, Amir, Marshall, Juliet M., Miclaus, Kelci J., Lazo, Gerard R., Hu, Gongshe, Jackson, Eric W.
Format:	Online
Language:	English
Published:	Public Library of Science 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018352/

id	pubmed-4018352
recordtype	oai_dc
spelling	pubmed-40183522014-05-16 Comparative Systems Biology Reveals Allelic Variation Modulating Tocochromanol Profiles in Barley (Hordeum vulgare L.) Oliver, Rebekah E. Islamovic, Emir Obert, Donald E. Wise, Mitchell L. Herrin, Lauri L. Hang, An Harrison, Stephen A. Ibrahim, Amir Marshall, Juliet M. Miclaus, Kelci J. Lazo, Gerard R. Hu, Gongshe Jackson, Eric W. Research Article Tocochromanols are recognized for nutritional content, plant stress response, and seed longevity. Here we present a systems biological approach to characterize and develop predictive assays for genes affecting tocochromanol variation in barley. Major QTL, detected in three regions of a SNP linkage map, affected multiple tocochromanol forms. Candidate genes were identified through barley/rice orthology and sequenced in genotypes with disparate tocochromanol profiles. Gene-specific markers, designed based on observed polymorphism, mapped to the originating QTL, increasing R2 values at the respective loci. Polymorphism within promoter regions corresponded to motifs known to influence gene expression. Quantitative PCR analysis revealed a trend of increased expression in tissues grown at cold temperatures. These results demonstrate utility of a novel method for rapid gene identification and characterization, and provide a resource for efficient development of barley lines with improved tocochromanol profiles. Public Library of Science 2014-05-12 /pmc/articles/PMC4018352/ /pubmed/24820172 http://dx.doi.org/10.1371/journal.pone.0096276 Text en © 2014 Oliver et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
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	Oliver, Rebekah E. Islamovic, Emir Obert, Donald E. Wise, Mitchell L. Herrin, Lauri L. Hang, An Harrison, Stephen A. Ibrahim, Amir Marshall, Juliet M. Miclaus, Kelci J. Lazo, Gerard R. Hu, Gongshe Jackson, Eric W.
spellingShingle	Oliver, Rebekah E. Islamovic, Emir Obert, Donald E. Wise, Mitchell L. Herrin, Lauri L. Hang, An Harrison, Stephen A. Ibrahim, Amir Marshall, Juliet M. Miclaus, Kelci J. Lazo, Gerard R. Hu, Gongshe Jackson, Eric W. Comparative Systems Biology Reveals Allelic Variation Modulating Tocochromanol Profiles in Barley (Hordeum vulgare L.)
author_facet	Oliver, Rebekah E. Islamovic, Emir Obert, Donald E. Wise, Mitchell L. Herrin, Lauri L. Hang, An Harrison, Stephen A. Ibrahim, Amir Marshall, Juliet M. Miclaus, Kelci J. Lazo, Gerard R. Hu, Gongshe Jackson, Eric W.
author_sort	Oliver, Rebekah E.
title	Comparative Systems Biology Reveals Allelic Variation Modulating Tocochromanol Profiles in Barley (Hordeum vulgare L.)
title_short	Comparative Systems Biology Reveals Allelic Variation Modulating Tocochromanol Profiles in Barley (Hordeum vulgare L.)
title_full	Comparative Systems Biology Reveals Allelic Variation Modulating Tocochromanol Profiles in Barley (Hordeum vulgare L.)
title_fullStr	Comparative Systems Biology Reveals Allelic Variation Modulating Tocochromanol Profiles in Barley (Hordeum vulgare L.)
title_full_unstemmed	Comparative Systems Biology Reveals Allelic Variation Modulating Tocochromanol Profiles in Barley (Hordeum vulgare L.)
title_sort	comparative systems biology reveals allelic variation modulating tocochromanol profiles in barley (hordeum vulgare l.)
description	Tocochromanols are recognized for nutritional content, plant stress response, and seed longevity. Here we present a systems biological approach to characterize and develop predictive assays for genes affecting tocochromanol variation in barley. Major QTL, detected in three regions of a SNP linkage map, affected multiple tocochromanol forms. Candidate genes were identified through barley/rice orthology and sequenced in genotypes with disparate tocochromanol profiles. Gene-specific markers, designed based on observed polymorphism, mapped to the originating QTL, increasing R2 values at the respective loci. Polymorphism within promoter regions corresponded to motifs known to influence gene expression. Quantitative PCR analysis revealed a trend of increased expression in tissues grown at cold temperatures. These results demonstrate utility of a novel method for rapid gene identification and characterization, and provide a resource for efficient development of barley lines with improved tocochromanol profiles.
publisher	Public Library of Science
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018352/
_version_	1612088151732387840

Comparative Systems Biology Reveals Allelic Variation Modulating Tocochromanol Profiles in Barley (Hordeum vulgare L.)

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