Natural variation in the evolutionarily conserved F-box gene SDEF promotes seed dormancy in rice.
- 1Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
- 2Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210014, China.
Abstract
Insufficient seed dormancy causes pre-harvest sprouting (PHS) and severe yield losses in rice; however, genetic resources with practical breeding value remain limited. Here, we isolated a major dormancy gene, SDEF, via map-based cloning using chromosomal single segment substitution lines (SSSLs), identifying a functional SNP (Arg-to-Trp) as the causal mutation. CRISPR/Cas9-mediated knockout of SDEF led to PHS susceptibility, while overexpression significantly enhanced dormancy. Importantly, SDEF enhanced seed dormancy without compromising grain yield in SSSLs, confirming it as a promising breeding target. Moreover, SDEF encodes an angiosperm-conserved, nuclear-localized F-box protein and is preferentially expressed in the embryo, with expression increasing during seed maturation and declining upon germination. Mechanistically, protein interaction assays confirmed that SDEF recruits OSK1, with the Trp-type SDEFK exhibiting a more stable interaction than the Arg-type SDEFH. SDEF is induced by abscisic acid (ABA) and appears to promote seed dormancy through the ABA pathway by activating ABA signaling genes and repressing α-amylase genes, as evidenced by the reduced ABA sensitivity of sdef mutants. Additionally, haplotype analysis revealed that natural variation in SDEF is associated with divergent dormancy levels, and reduced nucleotide diversity in cultivated rice indicates that SDEF was selected during domestication. Collectively, our results provide insights into the molecular basis of SDEF-mediated dormancy, providing an ideal target for breeding PHS-resistant rice.
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BibTeX
@article{zhou2026natural,
title = {{Natural variation in the evolutionarily conserved F-box gene SDEF promotes seed dormancy in rice.}},
author = {Yuliang Zhou and Yueping Wang and Guangmiao Zhao and Chunbao Liu and Ruizhen Zeng and Wenxuan Liang and Ru Han and Hui Kong and Xiaofan Cao and Minshi Li and Huhui Chen and Bin Tan and Hong Liu and Zhenjiang Xu},
journal = {The Plant journal : for cell and molecular biology},
year = {2026},
month = oct,
doi = {10.1111/tpj.71203},
url = {https://europepmc.org/article/MED/42958909},
note = {CC BY},
}
RIS
TY - JOUR
TI - Natural variation in the evolutionarily conserved F-box gene SDEF promotes seed dormancy in rice.
AU - Yuliang Zhou
AU - Yueping Wang
AU - Guangmiao Zhao
AU - Chunbao Liu
AU - Ruizhen Zeng
AU - Wenxuan Liang
AU - Ru Han
AU - Hui Kong
AU - Xiaofan Cao
AU - Minshi Li
AU - Huhui Chen
AU - Bin Tan
AU - Hong Liu
AU - Zhenjiang Xu
PY - 2026
DA - 2026/10/30
JO - The Plant journal : for cell and molecular biology
DO - 10.1111/tpj.71203
UR - https://europepmc.org/article/MED/42958909
AB - Insufficient seed dormancy causes pre-harvest sprouting (PHS) and severe yield losses in rice; however, genetic resources with practical breeding value remain limited. Here, we isolated a major dormancy gene, SDEF, via map-based cloning using chromosomal single segment substitution lines (SSSLs), identifying a functional SNP (Arg-to-Trp) as the causal mutation. CRISPR/Cas9-mediated knockout of SDEF led to PHS susceptibility, while overexpression significantly enhanced dormancy. Importantly, SDEF enhanced seed dormancy without compromising grain yield in SSSLs, confirming it as a promising breeding target. Moreover, SDEF encodes an angiosperm-conserved, nuclear-localized F-box protein and is preferentially expressed in the embryo, with expression increasing during seed maturation and declining upon germination. Mechanistically, protein interaction assays confirmed that SDEF recruits OSK1, with the Trp-type SDEFK exhibiting a more stable interaction than the Arg-type SDEFH. SDEF is induced by abscisic acid (ABA) and appears to promote seed dormancy through the ABA pathway by activating ABA signaling genes and repressing α-amylase genes, as evidenced by the reduced ABA sensitivity of sdef mutants. Additionally, haplotype analysis revealed that natural variation in SDEF is associated with divergent dormancy levels, and reduced nucleotide diversity in cultivated rice indicates that SDEF was selected during domestication. Collectively, our results provide insights into the molecular basis of SDEF-mediated dormancy, providing an ideal target for breeding PHS-resistant rice.
SN - 0960-7412
SN - 1365-313X
ER -