Genome-wide association analysis of natural variation in seed tocochromanols of barley

Authors: Mahalingam, Ramamurthy; SALLAM, AHMAD - University Of Minnesota; STEFFENSON, BRIAN - University Of Minnesota; Fiedler, Jason; Walling, Jason

Submitted to: Journal of Experimental Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/6/2020
Publication Date: 9/28/2020
Citation: Mahalingam, R., Sallam, A.H., Steffenson, B.J., Fiedler, J.D., Walling, J.G. 2020. Genome-wide association analysis of natural variation in seed tocochromanols of barley. The Plant Genome. e20039. https://doi.org/10.1002/tpg2.20039.
DOI: https://doi.org/10.1002/tpg2.20039

Interpretive Summary: Barley seeds form the most important raw material for the malting and brewing industry. The quality of the barley seeds has a significant bearing on seed germination process, a key step in the malting process. Tocochromanols, commonly referred to as Vitamin E comprises of eight different isoforms and has been shown to play a key role in seed longevity. Vitamin E acts as an antioxidant by protecting membrane structures by preventing the build-up of toxic molecules such as reactive oxygen species that occurs as a part of normal respiration during seed storage and during the process of seed germination. In this study we have analyzed the eight forms of vitamin E in 297 wild barley accessions and 160 spring domesticated barley accessions from the mini-core collection. These 457 lines were genotyped for nearly 50,000 markers spanning the entire barley genome. Using the genotyping data we identified markers that show significant associations with each of the eight vitamin E isoforms. All the enzymes associated with vitamin E biosynthetic pathway were tagged by one or more markers. We also identified several new loci associated with seed vitamin E that may play a regulatory role in modulating the levels of these metabolites. This study provides a valuable resource for selecting lines that can be valuable for breeding barley varieties that are enriched for particular isoforms of vitamin E. Increased levels of vitamin E in barley malt has been shown to protect the yeasts from oxidative stress and improve fermentation. This study paves the way to conduct functional studies on the role of vitamin E isoforms in the process of seed germination during malting. We speculate these vitamin E isoforms also play a protective role against abiotic stresses such as drought and heat in the germinating seedlings.

Technical Abstract: All the eight different isoforms of tocochromanols (Vitamin E) in barley seeds were quantified from a diverse collection of 457 accessions comprised of 297 wild lines from the diversity collection and 160 domesticated spring lines from the mini-core collection. Significant differences were observed in the concentration of seed alpha-tocopherol contents from these two populations. The mini-core collection was genotyped using the 50K illumina arrays. To identify quantitative trait loci associated with vitamin E (QVEs), Genome Wide Association Analysis was conducted using the 50K illumina arrays for the mini-core. Genotyping-by-sequencing based SNP markers was used for GWAS in the wild barley panel. Based on a highly stringent cut-off, 41 unique SNPs in the wild barley and 27 in the mini-core collection were identified as significantly associated with various tocochromanols. Apart from the previously reported QTLs associated with key enzymes, HGGT and VTE2 on chromosome 7, all other known structural genes associated with the tocol biosynthetic pathway were tagged by one or more SNPs in one or both the populations. In addition, we report several novel QVEs that explained more than 10% of the variation in the concentrations of the various tocols on chromosomes 2, 3, 4 and 5. Zinc finger transcription factors with high expression in developing caryposes were identified in the proximity of few of the novel QVEs. This study paves the way for selecting the apt germplasm for breeding programs focused on increasing particular isoforms of tocols in barley cultivars. Barley cultivars with higher levels of tocochromanols will aid in improving malting quality of seeds via increased seed germination and conferring stress tolerance.