Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice
Zhaoyuan Pan,
Bin Tan,
Guiyuan Cao,
Rongqi Zheng,
Meng Liu,
Ruizhen Zeng,
Shaokui Wang,
Haitao Zhu,
Heng Ye,
Guangmiao Zhao,
Wei Cao,
Guifu Liu,
Guiquan Zhang,
Yuliang Zhou
Affiliations
Zhaoyuan Pan
Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University
Bin Tan
Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University
Guiyuan Cao
Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University
Rongqi Zheng
Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University
Meng Liu
Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University
Ruizhen Zeng
Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University
Shaokui Wang
Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University
Haitao Zhu
Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University
Heng Ye
Division of Plant Sciences, University of Missouri
Guangmiao Zhao
Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University
Wei Cao
Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University
Guifu Liu
Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University
Guiquan Zhang
Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University
Yuliang Zhou
Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University
Abstract Low-temperature germinability (LTG) is an important agronomic trait that can affect the planting time, planting area, and grain yield of staple crops, such as rice. However, the genetic mechanism of LTG is still unclear. In this study, a multi-parental permanent population with 208 single segment substitution lines (SSSLs) was used to conduct a genetic dissection for LTG across four cropping seasons. LTG was a typical quantitative trait with a high combined broad-sense heritability of 0.71. By comparison with the recipient parent, Huajingxian74, 24 SSSLs were identified as carrying LTG QTLs, which were further merged into integrated QTLs with shorter genetic distances by substitution mapping. Finally, 14 LTG QTLs were mapped on ten chromosomes, including seven positive-effect and seven negative-effect QTLs, with additive effect contributions ranging from 19.2 to 39.9%. qLTG3a, a main-effect and novel QTL, was confirmed by bulk segregant analysis using an F2 segregating population, and five key recombinants were selected to develop F3 populations for progeny testing. Marker-trait association analysis fine mapped qLTG3a to a 332.7-kb physical region between markers M6026 and M6341. Within this interval, 40 annotated genes were revealed, and three genes (Os03g0213300, Os03g0214400, and Os03g0214600) were considered as pivotal candidate genes for qLTG3a based on their sequence variations and expression patterns. Besides low temperature, qLTG3a can also enhance seed germination under standard temperature and osmotic stress. In summary, this study identified some genetic factors regulating LTG and opened a new window for breeding elite direct-seeded rice varieties. It will help reduce the climate risk in the production process of rice, which is of great significance to ensuring food security.
