Comparative alternative splicing analysis of two contrasting rice cultivars under drought stress and association of differential splicing genes with drought response QTLs

Alternative splicing (AS) of precursor mRNA is often regulated by different developmental stages, environments, and genotypes. Little is known about how AS is regulated between different rice cultivars with distinctive response to certain abiotic stress. This study aimed to elucidate the AS patterns in contrasting rice (Oryza sativa L.) cultivars and examine its role during rice adaptation to drought environment. By comparing AS patterns between IRAT109 and ZS97 rice cultivars under drought stress, drought tolerant and susceptible respectively, 8034 shared, 11,086 ZS97-specific, and 12,057 IRAT109-specific AS events were observed where intron retention is the predominant AS pattern. Gene ontology (GO) as well as Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses suggested that the spliceosome and DNA repair represented the most significant functional categories among the genes with genotype-specific AS patterns. Other categories include basal transcription factors, environmental information, adaptation related pathways, oxidative phosphorylation, etc. Through integrating the drought-response related quantitative trait locus (QTLs) from 2006 to 2016 manually and mapping spliceosome and DNA repair genes with different AS patterns on chromosomes, we identified 14 out of 31 genes involved in splicesome and 4 out of 14 genes in DNA repair co-localized in drought stress related QTLs. We therefore propose that during long domestication, genes responsive to drought stress evolved specific AS patterns in upland rice, and spliceosome and DNA repair genes play potential roles in rice tolerance to drought stress. Genes with diversity AS patterns and co-localized with drought QTLs will serve as important resources for genetic improvement of rice adaptation to drought stress.