Abstract
Drought stress is one of the major adverse environmental factors reducing plant growth. With the aim to elucidate the underlying molecular basis of rice response to drought stress, comparative transcriptome analysis was conducted between drought susceptible rice cultivar Zhenshan97 and tolerant cultivar IRAT109 at the seedling stage. 436 genes showed differential expression and mainly enriched in the Gene Ontology (GO) terms of stress defence. A large number of variations exist between these two genotypes including 2564 high-quality insertion and deletions (INDELs) and 70,264 single nucleotide polymorphism (SNPs). 1041 orthologous gene pairs show the ratio of nonsynonymous nucleotide substitution rate to synonymous nucleotide substitutions rate (Ka/Ks) larger than 1.5, indicating the rapid adaptation to different environments during domestication. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of positive selection genes suggested that photosynthesis represents the most significant category. The collocation of positively selected genes with the QTLs of photosynthesis and the different photosynthesis performance of these two cultivars further illuminate the crucial function of photosynthesis in rice adaptation to drought stress. Our results also provide fruitful functional markers and candidate genes for future genetic research and improvement of drought tolerance in rice.
Highlights
Comparing transcriptomes of various genotypes of specific species is useful for exploring genes under selection and elucidating the role of various biological pathways and mechanisms for imparting stress tolerance to adverse environments[20,21]
To get deeper insight into the drought stress responses of upland drought-resistant (IRAT109) and lowland drought-sensitive (Zhenshan 97) rice cultivars, a genome-wide transcriptional analysis was performed by using Illumina Hiseq2500 platform
Merging of the predicted transcripts sets resulted in 103490 transcripts with 34832 novel transcripts which were not annotated in rice gene model (Supplemental Table 1)
Summary
Comparing transcriptomes of various genotypes of specific species is useful for exploring genes under selection and elucidating the role of various biological pathways and mechanisms for imparting stress tolerance to adverse environments[20,21]. Fundamental researches have provided significant insights into the physiological and molecular responses of plants to water deficit, but the divergence in transcriptome of rice genotypes with contrasting phenotypes remains unexplored. Techniques such as next-generation sequencing offer a unique opportunity to scan the transcriptomes of different genotypes. The comparative transcriptomes of drought-tolerant rice cultivar IRAT109 and sensitive rice cultivar Zhenshan[97] were analyzed comprehensively to provide insights into sequence variation, expression divergence, domestication selection of genes between drought-tolerant and sensitive rice genotypes under drought conditions. This study provides functional gene markers to promote future relevant research, and molecular breeding and genetic engineering projects for enhancing drought tolerance in rice
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 call
