Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand.
Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
Sci Rep. 2024 Oct 5;14(1):23156. doi: 10.1038/s41598-024-73668-2.
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.
钙调素结合转录激活因子（CAMTA）家族在许多植物物种的应激反应中发挥作用。水稻亚种粳稻基因组含有七个 CAMTA 基因；然而，该基因家族的种内变异和功能作用尚未确定。在这里，我们使用生物信息学方法和 RT-qPCR 全面评估了粳稻中 CAMTA 基因的结构和特征。在 CAMTA 基因和启动子序列中，从 3024 个水稻品系中检索到 527 个单核苷酸多态性。CAMTA 基因可分为 5-14 个单倍型。单倍型与表型性状（如粒重和盐胁迫参数）之间的关联分析确定了携带不同 CAMTA 单倍型的水稻亚群之间的表型差异。共表达分析和 CAMTA 特异性结合基序的鉴定揭示了受 CAMTA 调控的候选基因。690 个共表达基因的基因本体功能富集分析表明，CAMTA 基因在防御反应中具有关键作用。相互作用分析鉴定了 30 个潜在的 CAMTA 相互作用蛋白。在共表达和相互作用网络分析中鉴定出三个基因，表明它们可能受 CAMTAs 调控。基于共获得的所有信息以及三种 OskCAMTA 基因的 CRISPR-Cas9 敲除突变体系的表型，CAMTA1 可能在水稻对盐胁迫的反应中发挥重要作用。总之，我们的研究结果表明，CAMTA 基因家族参与了水稻的发育和盐胁迫反应，并揭示了候选靶基因，为进一步的功能表征提供了基础。
