Abstract
Identifying and characterizing alternative splicing (AS) enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined. Additionally, differences in AS between the two genotypes B73 and Mo17 are greatest within genes expressed in seed. We demonstrate that changes in the level of alternatively spliced transcripts (intron retention and exon skipping) do not solely reflect differences in total transcript abundance, and we present evidence that intron retention may act to fine-tune gene expression across seed development stages. Furthermore, we have identified temperature sensitive AS in maize and demonstrate that drought-induced changes in AS involve distinct sets of genes in reproductive and vegetative tissues. Examining our identified AS isoforms within B73 × Mo17 recombinant inbred lines (RILs) identified splicing QTL (sQTL). The 43.3% of cis-sQTL regulated junctions are actually identified as alternatively spliced junctions in our analysis, while 10 Mb windows on each side of 48.2% of trans-sQTLs overlap with splicing related genes. Using sorghum as an out-group enabled direct examination of loss or conservation of AS between homeologous genes representing the two subgenomes of maize. We identify several instances where AS isoforms that are conserved between one maize homeolog and its sorghum ortholog are absent from the second maize homeolog, suggesting that these AS isoforms may have been lost after the maize whole genome duplication event. This comprehensive analysis provides new insights into the complexity of AS in maize.
Highlights
Alternative splicing (AS) is a mechanism for generating multiple isoforms from a single pre-mRNA by the regulated selection of splice sites during mRNA processing
We present a comparative genomics analysis of alternative splicing (AS) between maize homeologs and their orthologous genes in sorghum that identified conserved AS events, and revealed instances of AS absence in one versus the other maize homeolog that likely represent AS loss after the maize whole genome duplication (WGD) event
Our analysis suggests that similar proportions of maize small nuclear ribonucleoprotein (snRNP) and splicing factor genes undergo AS, while a greater proportion of splicing regulator genes undergo AS relative to snRNP and splicing factor genes (Supplemental Table 2)
Summary
Alternative splicing (AS) is a mechanism for generating multiple isoforms from a single pre-mRNA by the regulated selection of splice sites during mRNA processing. While exon skipping is the dominant AS event in animals, intron retention events prevail in plants (Barbazuk et al, 2008). AS contributes to increased protein diversity (Graveley, 2001; Kazan, 2003), and may regulate protein levels by influencing relative isoform ratios (Wang et al, 2008). The study of UPF (up-frameshift) mutants has suggested that purposeful production of unproductive messages by AS in combination with nonsense-mediated decay is a strategy used for post-transcriptional regulation of gene expression by plants (Kalyna et al, 2012; Drechsel et al, 2013)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
