Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage

Dan Wang,Yong Liu,Zhuo Zhang,Zhuo Liu,Xinqiu Tan,Xuli Wang,Chenggang Li,Houxiang Kang,Xionglun Liu,Deyong Zhang,Yinghui Xiao,Yue Chen,Guo-Liang Wang,Shasha Peng,Su Jiang

doi:10.1186/s12284-021-00538-0

Abstract

Cold tolerance at the bud burst stage (CTB) is a key trait for direct-seeded rice. Although quantitative trait loci (QTL) affecting CTB in rice have been mapped using traditional linkage mapping and genome-wide association study (GWAS) methods, the underlying genes remain unknown. In this study, we evaluated the CTB phenotype of 339 cultivars in the Rice Diversity Panel II (RDP II) collection. GWAS identified four QTLs associated with CTB (qCTBs), distributed on chromosomes 1–3. Among them, qCTB-1-1 overlaps with Osa-miR319b, a known cold tolerance micro RNA gene. The other three qCTBs have not been reported. In addition, we characterised the candidate gene OsRab11C1 for qCTB-1-2 that encodes a Rab protein belonging to the small GTP-binding protein family. Overexpression of OsRab11C1 significantly reduced CTB, while gene knockout elevated CTB as well as cold tolerance at the seedling stage, suggesting that OsRab11C1 negatively regulates rice cold tolerance. Molecular analysis revealed that OsRab11C1 modulates cold tolerance by suppressing the abscisic acid signalling pathway and proline biosynthesis. Using RDP II and GWAS, we identified four qCTBs that are involved in CTB and determined the function of the candidate gene OsRab11C1 in cold tolerance. Our results demonstrate that OsRab11C1 is a negative regulator of cold tolerance and knocking out of the gene by genome-editing may provide enhanced cold tolerance in rice.

Highlights

Rice (Oryza sativa L.), a major food resource for humans, grows in tropical to temperate regions worldwide
The population comprised 102 indica (IND), 22 temperate japonica (TEJ), 88 tropical japonica (TRJ), 56 aromatic (ARO), 64 aus (AUS), and 7 admixture (ADM) cultivars, and their Cold tolerance at the bud burst stage (CTB) phenotypes are shown in Additional file 1: Table S1
From the RDP Rice Diversity Panel II (II) population, we identified 40 highly tolerant rice cultivars with survival rate over 90% after cold treatment at the bud burst stage

Summary

Introduction

Rice (Oryza sativa L.), a major food resource for humans, grows in tropical to temperate regions worldwide. At the early seedling stage, low temperature. Both LTG and CTB are complex genetic traits controlled by multi-genes or quantitative trait loci (QTL). OsSAP16 have been cloned and functionally characterised from two identified QTLs for LTG in rice (Fujino et al 2008; Wang et al 2018). The QTL gene qLTG3-1, encoding a protein of unknown function, is conserved in many plants and is highly expressed in the embryo, which may accelerate vacuolation to weaken tissues covering the embryo, and promote seed germination (Fujino et al 2008). The rice zinc finger domain protein OsSAP16 (Stress-Associated Protein 16) is the causal gene of the QTL qLVG7-2 (Wang et al 2018); loss of OsSAP16 function reduces germination, while overexpression enhances germination under low temperature

Results

Discussion

Conclusion