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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Bibliographic Details
Published in:	PloS one Vol. 9; no. 5; p. e96276
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:	Journal Article
Language:	English
Published:	United States Public Library of Science 12-05-2014 Public Library of Science (PLoS)
Subjects:	Alleles Analysis Barley Biology and Life Sciences Biosynthesis Chromosome Mapping Crops Dissection Enzymes Gene expression Gene polymorphism Genes Genetic polymorphisms Genetics Genomes Genomics Genotypes Germplasm Hordeum - genetics Hordeum vulgare Nutrient deficiency Orthology Plant stress Polymorphism Polymorphism, Single Nucleotide - genetics Quantitative genetics Quantitative trait loci Quantitative Trait Loci - genetics Seeds Single-nucleotide polymorphism Soil sciences Systems Biology - methods Tissues Vitamin E North Carolina United States > US Wisconsin Idaho
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Conceived and designed the experiments: REO EI DEO GH EWJ. Performed the experiments: REO DEO LLH AH SAH AI JMM. Analyzed the data: REO EI MLW LLH KJM GRL EWJ. Contributed reagents/materials/analysis tools: DEO MLW AH JMM. Wrote the paper: REO MLW GRL EWJ. Competing Interests: Scientists DEO and EWJ contributed to the manuscript prior to employment at General Mills Inc. and Limagrain Cereal Seeds, and these authors declare that the work presented was not in any way influenced by their current relationship with their employer. KJM is an employee of SAS Institute Inc. There are no patents, products in development or marketed products to declare. This does not alter adherence to all the PLOS ONE policies on sharing data and materials.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0096276