Genome-wide identification and characterization of ABA receptorPYLgene family in rice

Background Abscisic acid (ABA), a key phytohormone that controls plant growth and stress responses, is sensed by the pyrabactin resistance 1(PYR1)/PYR1-like (PYL)/regulatory components of the ABA receptor (RCAR) family of proteins. Comprehensive information on evolution and function ofPYLgene family in rice (Oryza sativa) needs further investigation. This study made detailed analysis on evolutionary relationship between PYL family members, collinearity, synteny, gene structure, protein motifs,cis-regulatory elements (CREs), SNP variations, miRNAs targetingPYLsand expression profiles in different tissues and stress responses. Results Based on sequence homology withArabidopsisPYL proteins, we identified a total of 13 PYLs in rice (BOP clade) and maize (PACCMAD clade), while other members of BOP (wheat - each diploid genome, barley andBrachypodium) and PACCMAD (sorghum and foxtail millet) have 8-9 PYLs. The phylogenetic analysis divided PYLs into three subfamilies that are structurally and functionally conserved across species. Gene structure and motif analysis ofOsPYLs revealed that members of each subfamily have similar gene and motif structure. Segmental duplication appears be the driving force for the expansion ofPYLs, and the majority of thePYLsunderwent evolution under purifying selection in rice. 32 unique potential miRNAs that might targetPYLswere identified in rice. Thus, the predicted regulation ofPYLsthrough miRNAs in rice is more elaborate as compared withB. napus. Further, the miRNAs identified to in this study were also regulated by stresses, which adds additional layer of regulation ofPYLs. The frequency of SAPs identified was higher inindicacultivars and were predominantly located in START domain that participate in ABA binding. The promoters of most of theOsPYLs havecis-regulatory elements involved in imparting abiotic stress responsive expression. In silico and q-RT-PCR expression analyses ofPYLgenes revealed multifaceted role of ABARs in shaping plant development as well as abiotic stress responses. Conclusion The predicted miRNA mediated regulation ofOsPYLsand stress regulated expression of allOsPYLs, at least, under one stress, lays foundation for further validation and fine tuning ABA receptors for stress tolerance without yield penalty in rice.