Detection of splicing variants in the leaf and spike transcripts of wild diploid wheat Aegilops tauschii and transmission of the splicing patterns to synthetic hexaploid wheat

Abstract

Alternative splicing produces multiple transcripts from a single gene, and RNA sequencing using next-generation sequencing apparatus has contributed to comprehensive detection of splicing variants in higher plants. Here, we completed a large-scale survey of alternatively spliced transcripts from RNA samples derived from seedling leaves and young spikes of two distinct accessions of wild diploid wheat Aegilops tauschii under normal growth conditions. Alternative splicing for 23,778 loci were analyzed in this study, and at least two splicing variants were found in 4712 genes. The proportion of events for intron retention was much smaller in Ae. tauschii than in other plant species, whereas the proportions of exon skipping and splice donor site events were higher. In at least some genes, alternative splicing patterns were clearly distinct between the two Ae. tauschii accessions. Distinct splicing patterns were transmitted from the parental Ae. tauschii accessions into their synthetic hexaploid wheat lines. Alternative splicing patterns in one of the two synthetic hexaploid wheat lines analyzed appeared to be generally similar to patterns intermediate between the parental lines under normal growth conditions, and seemed to be slightly altered in the other synthetic wheat.