Association of a Specific OsCULLIN3c Haplotype with Salt Stress Responses in Local Thai Rice

Author:

Herwibawa Bagus1ORCID,Lekklar Chakkree2ORCID,Chadchawan Supachitra34,Buaboocha Teerapong45

Affiliation:

1. Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand

2. Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand

3. Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand

4. Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand

5. Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand

Abstract

We previously found that OsCUL3c is involved in the salt stress response. However, there are no definitive reports on the diversity of OsCUL3c in local Thai rice. In this study, we showed that the CUL3 group was clearly separated from the other CUL groups; next, we focused on OsCUL3c, the third CUL3 of the CUL3 family in rice, which is absent in Arabidopsis. A total of 111 SNPs and 28 indels over the OsCUL3c 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 LTR, MYC, [AP2; ERF], and NF-YB, 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 OsCUL3c 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 OsCUL3c influences the regulation of salt-related responses, and haplotype variations play a role in this regulation.

Funder

Second Century Fund (C2F) from Chulalongkorn University, Thailand

Universitas Diponegoro Postgraduate Scholarship, Indonesia

100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship

an Overseas Research Experience Scholarship for Graduate Students from the Graduate School, Chulalongkorn University, Thailand

Publisher

MDPI AG

Reference42 articles.

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