Sequence-based analysis of the rice CAMTA family: haplotype and network analyses

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The calmodulin-binding transcription activator (CAMTA) family contributes to stress responses in many plant species. The Oryza sativa ssp. japonica genome harbors seven CAMTA genes; however, intraspecific variation and functional roles of this gene family have not been determined. Here, we comprehensively evaluated the structure and characteristics of the CAMTA genes in japonica rice using bioinformatics approaches and RT-qPCR. Within the CAMTA gene and promoter sequences, 527 single nucleotide polymorphisms were retrieved from 3,024 rice accessions. The CAMTA genes could be subdivided into 5–14 haplotypes. Association analyses between haplotypes and phenotypic traits, such as grain weight and salt stress parameters, identified phenotypic differences between rice subpopulations harboring different CAMTA haplotypes. Co-expression analyses and the identification of CAMTA-specific binding motifs revealed candidate genes regulated by CAMTA. A Gene Ontology functional enrichment analysis of 690 co-expressed genes revealed that CAMTA genes have key roles in defense responses. An interaction analysis identified 30 putative CAMTA interactors. Three genes were identified in co-expression and interaction network analyses, suggesting that they are potentially regulated by CAMTAs. Based on all information obtained together with the phenotypes of the CRISPR-Cas9 knockout mutant lines of three OskCAMTA genes generated, CAMTA1 likely plays important roles in the response to salt stress in rice. Overall, our findings suggest that the CAMTA gene family is involved in development and the salt stress response and reveal candidate target genes, providing a basis for further functional characterization.