[Genome-wide identification, subcellular localization, and expression analysis of the RNA-dependent RNA polymerase...

Helianthus annuus L., as one of the important oil crops, has strong salt and drought tolerance. The RNA-dependent RNA polymerase (RDR) plays an irreplaceable role in plant growth and development and in the formation of small-molecule RNA. To clarify the functions and regulatory mechanisms of this gene family, in this study, bioinformatics analysis was performed to identify the members of the RDR gene family in H. annuus, and the physicochemical properties, chromosome location, phylogenetic relationship, and subcellular localization of the family members were analyzed in depth. Meanwhile, RT-qPCR was conducted to explore the expression patterns of the family members under salt, alkali, and drought stresses. The results showed that a total of 10 members of the RDR gene family were identified in H. annuus, and they were distributed on chromosomes 1, 3, 6, 8, and 16. The phylogenetic analysis indicated that the RDRs of H. annuus and Arabidopsis were clustered into 4 groups. The results of multiple amino acid sequence alignment showed that all the members of this family contained the conserved domain of RdRP. Protein structure prediction revealed that the secondary structure of the protein family members was mainly composed of α-helixes and random coils. STRING interaction network analysis revealed that HaRDR interacted with Argonaute (HaAGO) and Dicer-like (HaDCL) proteins. The results of RT-qPCR revealed that the expression levels of the HaRDR gene family members were significantly upregulated in stems under salt stress and in leaves under alkali stress. The subcellular localization results indicated that HaRDR3c was located in the cytoplasm. The results of this study suggest that the HaRDR family members are highly conserved during evolution while exhibiting functional diversity. The RT-qPCR results indicate that the HaRDR family members can respond to abiotic stresses. The findings not only provide a basis for exploring the role of HaRDR in regulating stress resistance but also lays a foundation for revealing the molecular mechanism of HaRDR in plant stress responses.