Association of a Specific Haplotype with Salt Stress Responses in Local Thai Rice

We previously found that is involved in the salt stress response. However, there are no definitive reports on the diversity of in local Thai rice. In this study, we showed that the group was clearly separated from the other CUL groups; next, we focused on , the third of the family in rice, which is absent in Arabidopsis. A total of 111 SNPs and 28 indels over the region, representing 79 haplotypes (haps), were found. Haplotyping revealed that group I (hap A and hap C) and group II (hap B1 and hap D) were different mutated variants, which showed their association with phenotypes under salt stress. These results were supported by cis-regulatory elements (CREs) and transcription factor binding sites (TFBSs) analyses. We found that , , [; ], and -, which are related to salt stress, drought stress, and the response to abscisic acid (ABA), have distinct positions and numbers in the haplotypes of group I and group II. An RNA Seq analysis of the two predominant haplotypes from each group showed that the expression of the group I representative was upregulated and that of group II was downregulated, which was confirmed by RT-qPCR. Promoter changes might affect the transcriptional responses to salt stress, leading to different regulatory mechanisms for the expression of different haplotypes. We speculate that influences the regulation of salt-related responses, and haplotype variations play a role in this regulation.