In silico Identification of Alternatively Spliced Variants from Transcriptome Data of Rice Lines Exhibiting Complete Panicle Exsertion

Abstract

Alternative splicing (AS) is a molecular mechanism governing gene expression, particularly in plants, wherein a single gene can yield multiple mRNA transcripts, thereby diversifying the resulting protein isoforms. Panicle exsertion (PE) is an important trait associated with grain yield in rice. We deployed the mRNA sequencing (transcriptome) data from incompletely exserted panicle genotype, BPT-5204 and its ethyl methanesulphonate (EMS) mutant lines viz., CPE-109 and CPE-110 exhibiting completely exserted panicle for identification of Alternative Splicing (AS) events. Our systematic analysis using rMATS package revealed 414 and 368 genes alternatively spliced upon the comparison of CPE-109 with BPT-5204 and CPE-110 with BPT-5204 respectively. We identified alternative 3′ splice site (A3SS) as the predominant AS type upon comparison of CPE-109 with BPT-5204 (51.20% A3SS) and CPE-110 with BPT-5204 (48.91% A3SS) at panicle initiation stage. In total 23 and 19 genes emanated multiple transcripts via., AS. Remarkably, upon comparison of splicing data of CPE-109 with BPT-5204 and CPE-110 with BPT-5204, we found three common genes namely, Os07g0406600 encoding DDHD domain containing protein, Os10g0442100 encoding tRNA methyltransferase and Os04g0675800 encoding H0103C06.10 protein, that generated more than two transcripts via., AS. These genes can be further validated for determining its role in panicle exsertion through gene expression studies, overexpression and functional characterization.