Title: Comparative systems biology reveals allelic variation modulating tocochromanol profiles in barley Authors
|Oliver, Rebekah -|
|Obert, Donald -|
|Hang, An -|
|Harrison, Steven -|
|Ibrahim, Amir -|
|Marshall, Juliet -|
|Miclaus, Kelci -|
|Jackson, Eric -|
Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 6, 2014
Publication Date: May 12, 2014
Repository URL: http://doi:10.1371/journal.pone.0096276
Citation: Oliver, R.E., Islamovic, E., Obert, D.E., Wise, M.L., Herrin, L.L., Hang, A., Harrison, S.A., Ibrahim, A., Marshall, J.M., Miclaus, K.J., Lazo, G.R., Chao, S., Hu, G., Jackson, E. 2014. Comparative systems biology reveals allelic variation modulating tocochromanol profiles in barley. PLoS One. 9:e96276. Interpretive Summary: Barley is used as feed for livestock, malted beverages and food products. Vitamin E (tocochromanols) has many biological functions and the antioxidant function is the most important for human health and plants stress response. Enrichment with Vitamin E would lead to production of barley varieties resistant to stress (drought, cold) and barley grain that is high in antioxidants. In this study we identified regions of barley genome that are influencing Vitamin E levels in barley grain. We have identified three regions affecting Vitamin E levels and we sequenced specific genes that are involved in Vitamin E synthesis. We also identified molecular markers (specific DNA sequences) that correlate with high levels of specific Vitamin E forms. This is the first step in developing a screening technique that uses molecular markers for assisting barley breeders during selection process.
Technical Abstract: Background: Tocochromanols are recognized for beneficial effects in plant stress response, seed storage longevity, and nutritional content. Efforts to elucidate specific bioactive forms and develop new crops with beneficial amounts and ratios have been hindered due to costly analytical methods. Objectives of this study were to evaluate content of the eight tocochromanol forms in the Falcon/Azhul RIL barley population; characterize candidate genes causing tocochromanol variation in the population using a novel systems biological approach termed Comparative Genomics Candidate Gene Identification [(CG)2I]; and develop predictive assays for novel alleles modulating tocochromanol grain levels and compound ratios in barley. Results: Variation caused by location and year suggest that tocochromanol content is impacted by environment, with cool temperatures favoring increased production. Major QTL, defined by a significant peak in at least three environments, were identified in three regions, on barley chromosomes 6H and 7H. All three loci affected multiple forms. Barley/rice synteny allowed identification of candidate genes, using SNP sequences defining each QTL to localize the barley locus to the rice genome sequence. Analysis of gene and promoter sequences for homogentisate geranylgeranyltransferase (HGGT) and tocopherol methyltransferase (VTE4) revealed polymorphism between Falcon and Azhul. Polymorphism within promoter regions corresponded with motifs known to influence gene expression. Based on genomic sequence differences, molecular markers were developed, genotyped across the FA population, and appended to the FA linkage map. Gene-based markers for both VTE4 and HGGT mapped to the originating QTL, and inclusion of these markers in QTL analysis increased R2¬ values at the respective loci. Quantitative PCR analysis of both genes revealed a trend of increased expression in tissues grown at cold temperatures. Conclusions: Tocochromanols appear to play critical and unique roles in plant function, stress response, and nutritional content. Here we report genetic dissection of two key tocochromanol genes. This research will allow use of marker-assisted breeding for rapid development of barley lines with improved tocochromanol profiles, with applications in plant cold tolerance, seed longevity, and human nutrition.