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Title: Subgenome-specific assembly of vitamin E biosynthesis genes and expression patterns during seed development provide insight into the evolution of the oat genome

item GUTIERREZ-GONZALEZ, JUAN - University Of Minnesota
item Garvin, David

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/23/2016
Publication Date: 11/1/2016
Citation: Gutierrez-Gonzalez, J., Garvin, D.F. 2016. Subgenome-specific assembly of vitamin E biosynthesis genes and expression patterns during seed development provide insight into the evolution of the oat genome. Plant Biotechnology Journal. 14(11):2147-2157. doi:10.1111/pbi.12571.

Interpretive Summary: Oats are an important cereal grain for human diets. Despite being more nutritious than other grain crops, there is considerably less oat production than wheat or barley, and oat breeding efforts lag behind these crops. Oats have high levels of the essential vitamin E, and increasing the levels of this vitamin is a goal of breeding programs that may lead to more oat production. However, nothing is known about the structure of the genes that control the production of vitamin E in oats. Here, we deciphered the sequences of each gene involved in the synthesis of vitamin E in oat seeds. We also determined that two of these genes in particular are likely to be key control points for determining the amount of vitamin E that accumulates. We were then able to use the gene sequences to explore the unresolved mystery of how oat evolved. While the evolution of wheat, which has a genome with similar complexity as oat, was largely deduced many decades ago, the ancestors of oat evolution remain unidentified. We propose a new theory of oat evolution that explains why previous efforts to identify ancestral species have been unsuccessful. Our results are important because identifying and characterizing the genes that control vitamin E production in oats opens up new opportunities for breeders and geneticists to develop methods for increasing vitamin E content. This in turn will provide farmers an opportunity to diversify their crop production systems by growing more nutritious and more valuable oats, leading to improved nutritional quality of many oat-based foods in the U.S. food chain.

Technical Abstract: Vitamin E is essential for humans and thus must be a component of a healthy diet. Among the cereal grains, hexaploid oats (Avena sativa L.) have high vitamin E content. To date, no gene sequences in the vitamin E biosynthesis pathway have been reported for oats. Using deep sequencing and orthology-guided assembly, coding sequences of genes for each step in vitamin E synthesis in oats were reconstructed, including resolution of the sequences of homeologs. Three homeologs, presumably representing each of the three oat subgenomes, were identified for the main steps of the pathway. Partial sequences, likely representing pseudogenes, were recovered in some instances as well. Pairwise comparisons among homeologs revealed that two of the three putative subgenome-specific homeologs are almost identical for each gene. Synonymous substitution rates indicate the time of divergence of the two more similar subgenomes from the distinct one at 7.9-8.7 MYA, and a divergence between the similar subgenomes from a common ancestor 1.1 MYA. Several likely evolutionary models for hexaploid oat formation are discussed. Homeolog-specific gene expression was quantified during oat seed development and compared with vitamin E accumulation. Homeolog expression largely appears to be similar for most of genes; however, for some genes homoeolog-specific transcriptional bias was observed. The expression of HPPD, as well as certain homoeologs of VTE2 and VTE4, is highly correlated to seed vitamin E accumulation. Our findings expand our understanding of oat genome evolution, and will assist efforts to modify vitamin E content and composition in oats.