Genome-Wide Identification and Expression Analysis of RCC1 Gene Family under Abiotic Stresses in Rice (Oryza sativa L.)

Abstract

In plants, the essential roles played by the regulator of chromosome condensation 1 (RCC1) in diverse biological processes, including UV-B (ultraviolet-B radiation) response, hormonal signal transduction, cold tolerance and phenotypic plasticity, have been identified. No comprehensive study on the evolution and function of RCC1 gene family in rice has been carried out. A genome-wide analysis of this gene family is thus required. In this study, a total of 26 OsRCC1s unevenly distributed across 10 chromosomes were identified in rice. Based on their phylogenetic relationship and sequence composition, the OsRCC1 family could be classified into six groups. Members within the same group share a similar gene structure and protein motif/domain composition. Gene duplication analysis revealed that segmental duplication might be the main contributor to the expansion of the RCC1 gene family in rice. Several cis-regulatory elements (CREs) relevant to light, abscisic acid (ABA) and methyl jasmonate (MeJA) are abundant in the promoters of OsRCC1s. A large number of microRNA (miRNA) target sites were present in OsRCC1 mRNAs. Additionally, we used data from gene microarray and qRT-PCR to analyze the expression of OsRCC1 genes during various developmental stages and under abiotic stress conditions. OsRCC1s were found to be highly expressed in panicles and seeds, and most OsRCC1s were differentially expressed under abiotic stresses. Taken together, our study provides a systematic characterization of OsRCC1s and preliminarily explores their diversity as well as their biological functions. Evidence demonstrates that OsRCC1s may play vital roles in both development and abiotic stress response. The results presented here lay a foundation for further investigating the functions of OsRCC1s.

Expression profiling of ALOG family genes during inflorescence development and abiotic stress responses in rice (Oryza sativa L.)

“…Gene duplication events, such as tandem and segmental duplication, provide major forces that drive the expansion of gene families and the evolution of the entire genome ( Cen et al, 2023 ). To reveal the origin and evolutionary information of ALOG genes, a collinearity analysis was respectively performed between the genome of rice and two other species, including Arabidopsis (dicotyledon plant) and B. distachyon (monocotyledon plant) ( Figure 3A ).…”

Characterization of the Fatty Acyl-CoA Reductase (FAR) Gene Family and Its Response to Abiotic Stress in Rice (Oryza sativa L.)

“…The CDS sequences of OsFARs were used as inputs files and searched against the reference miRNAs in rice. All parameters were kept at default values [65]. The interaction network between the predicted miRNAs and their corresponding target genes was constructed using Cytoscape v3.9.1 software.…”