Mining of publicly available RNA-seq data to reveal phenotypic differences between Landsberg erecta-0 and Columbia-0 ecotypes in Arabidopsis thaliana

As common ecotypes of Arabidopsis thaliana, obvious phenotypic differences have been observed between Landsberg erecta-0 (Ler-0) and Columbia-0 (Col-0). However, it is unlikely to explain a phenotypic trait from each single-gene mutant. In this study, a genotype to phenotype prediction using comparative transcriptome analysis was established to study multigene regulation in biological processes. Analyses of RNA sequencing data of Ler-0 and Col-0 revealed that the differences on gene expression in different organs were larger than those in different ecotypes. Totally 671 differentially expressed genes (DEGs) between Ler-0 and Col-0 were detected, including 273 genes up-regulated and 398 genes down-regulated in Ler-0. Gene Ontology (GO) analysis by using the 671 DEGs showed that 43, 31 and 58 genes were enriched in response to cold, response to abscisic acid stimulus and response to hormone stimulus respectively. Due to these data, the sensitivity of Col-0 and Ler-0 to cold and abscisic acid (ABA) stress were tested, and Col-0 ecotype exhibited more tolerance to cold stress and ABA. We also quantified the cell and leaf length of Col-0 and Ler-0, and these different growth phenotypes may be partly caused by the genes which enriched in response to hormone stimulus. The differentially expressed genes identified through the mRNA transcriptome provide a revealing insight into guiding phenotyping of organisms and providing genotype to phenotype relations for better understanding of plant growth, development and response to environments. This approach could also be applied to discovery of novel phenotypes thus better understanding of the mutant gene functions.