Journal
JOURNAL OF EXPERIMENTAL BOTANY
Volume 69, Issue 3, Pages 413-421Publisher
OXFORD UNIV PRESS
DOI: 10.1093/jxb/erx413
Keywords
Gene expression; germination; rice; GWAS; low temperature; natural variation; OsSAP16
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Funding
- National Science Foundation of China the Xinjiang Key Laboratory Special Funds of China [31670269]
- Open Project Program of the State Key Laboratory of Plant Physiology and Biochemistry [SKLPPBKF1501]
- Jiangsu Collaborative Innovation Center for Modern Crop Production
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Low temperature affects seed germination in plants, and low-temperature germination (LTG) is an important agronomic trait. Natural variation of LTG has been reported in rice, but the molecular basis for this variation is largely unknown. Here we report the phenotypic analysis of LTG in 187 rice natural accessions and a genome-wide association study (GWAS) of LTG in this collection. A total of 53 quantitative trait loci (QTLs) were found to be associated with LTG, of which 20 were located in previously reported QTLs. We further identified Stress-Associated Protein 16 (OsSAP16), coding for a zinc-finger domain protein, as a causal gene for one of the major LTG QTLs. Loss of OsSAP16 function reduces germination while greater expression of OsSAP16 enhances germination at low temperature. In addition, accessions with extremely high and low LTG values have correspondingly high and low OsSAP16 expression at low temperatures, suggesting that variation in expression of the OsSAP16 gene contributes to LTG variation. As the first case of identification of an LTG gene through GWAS, this study indicates that GWAS of natural accessions is an effective strategy in genetically dissecting LTG processes and gaining molecular understanding of low-temperature response and germination.
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