Abstract
SummaryVitamin 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. A new proposed evolutionary model for hexaploid oat formation is 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 with 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.
Highlights
Cereal crops have experienced a nearly 2.2-fold increase in production in the last 50 years (FAOSTATS, 2015)
1.1 M of Roche/ 454 reads averaging 457 bp were produced. These reads, together with the Illumina reads from the aforementioned oat seed transcriptome study, were used as a framework to reconstruct oat vitamin E pathway homeologs, through an in silico iterative procedure designed to recover oat homeolog-specific consensus sequences from the orthologous sequences of the close relatives wheat, barley and Brachypodium
Reads were mapped to the consensus sequences and visually inspected to identify SNP polymorphisms that differentiate each specific homeolog for each catalytic step in the pathway (Figure S1)
Summary
Cereal crops have experienced a nearly 2.2-fold increase in production in the last 50 years (FAOSTATS, 2015) This is due both to the use of improved cultural practices and genetic enhancement, and to an increase in cultivated land area. This increased production is largely biased towards generally less nutritious but high-yielding staple cereals such as rice, wheat and maize, at the expense of other more nutrient-rich cereals including oats, barley, sorghum, rye and millet (DeFries et al, 2015). Oats and barley have higher concentrations of vitamin E than other cereals (Gutierrez-Gonzalez et al, 2013a; Panfili et al, 2003). Vitamin E, the synthesis of which has been intensively investigated in plants, plays a role in cell membrane stability, protection against lipid oxidation and stress tolerance
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