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 2014-05, Vol.9 (5), p.e96276-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: Article
Language:English
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
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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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0096276