Investigating Alternative Splicing Landscape in Maize - Analysis from B73/Mo17 Hybrids and B73 x Mo17 Recombinant Inbred Line (IBM RIL) Population

Alternative Splicing (AS) produces multiple isoforms from a single pre-mRNA through selective use of splice sites. AS can influence protein diversity or affect protein levels by regulating message processing. AS is known to play roles during plant development, stress response, and flowering, but the extent of AS in plants is not well understood. Maize as the major crop plant in the U.S.A. is lack of information about genome-wise alternative splicing. We are examining RNA-Seq data to investigate tissue specific AS within endosperm, embryo and root in B73 and Mo17 maize, identify parent of origin alternative splicing events or isoforms, cis- and trans- regulation in the hybrids and splicing QTL in the IBM RIL population. The results identified here will help us to further understand the cross talk between endosperm and embryo during seed development and embryogenesis, the regulation of AS in the hybrids and IBM RIL population. By comparing AS between B73 and Mo17 we can test for the existence of genotype-specific AS. Currently we are developing new computational approach to detect parent of origin effects in B73/Mo17 hybrids, cis- and trans- regulation in the IBM RIL to identify genome-wide patterns of regulation of isoform abundance and alternative splicing. Our analysis centers on huge amount of RNA-Seq read alignment, allele specific splice site detection, alternate isoform detection and identification of allelic gene structures and isoforms. Our current results have identified differences in transcript isoform abundance between embryo and endosperm as well as some evidence for genotype-specific AS and parent of origin AS.