Genome-Wide Association Study Identifies Loci and a Candidate Gene Regulating Tomato Seed Germination
- 1State Key Laboratory for Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- 2Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- 3Xianghu Laboratory, Hangzhou 311200, China
Abstract
Seed germination is the first critical transition in the plant life cycle, strongly influencing seedling establishment, crop uniformity, and subsequent productivity. However, the genetic basis of seed germination in tomato remains incompletely understood. Here, we performed a genome-wide association study (GWAS) using 319 diverse tomato accessions to identify new loci and candidate genes associated with seed germination. Five significant variants were detected across the genome. Among them, SNP_59508294 on chromosome 3 was consistently associated with the seed germination index (SGI), and accessions carrying the GG haplotype exhibited a significantly higher SGI than those carrying the TT haplotype. Seven α-expansin (EXPA) genes were located within or near the associated interval. Integration of transcriptomic data from contrasting accessions and expression profiles across tomato tissues showed SlEXPA10 to be the most plausible candidate gene. The InDels in the SlEXPA10 promoter were highly associated with its low expression level in low SGI varieties. CRISPR/Cas9-mediated disruption of SlEXPA10 significantly reduced the rate and speed of seed germination relative to the wild type. Collectively, these results identify SlEXPA10 as a positive regulator of tomato seed germination and provide a candidate locus for improving seed vigor and emergence uniformity.
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BibTeX
@article{liu2026genomewide,
title = {{Genome-Wide Association Study Identifies Loci and a Candidate Gene Regulating Tomato Seed Germination}},
author = {Chenxu Liu and Yihang Zhu and Jiashun Miao and Hongjian Wan and Zhuping Yao and Meiying Ruan and Qingjing Ye and Zhimiao Li and Guozhi Zhou and Yuan Cheng and Xiaobin Zhang and Rongqing Wang},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = oct,
doi = {10.3390/ijms27219478},
url = {https://www.mdpi.com/1422-0067/27/21/9478},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Genome-Wide Association Study Identifies Loci and a Candidate Gene Regulating Tomato Seed Germination
AU - Chenxu Liu
AU - Yihang Zhu
AU - Jiashun Miao
AU - Hongjian Wan
AU - Zhuping Yao
AU - Meiying Ruan
AU - Qingjing Ye
AU - Zhimiao Li
AU - Guozhi Zhou
AU - Yuan Cheng
AU - Xiaobin Zhang
AU - Rongqing Wang
PY - 2026
DA - 2026/10/23
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27219478
UR - https://www.mdpi.com/1422-0067/27/21/9478
AB - Seed germination is the first critical transition in the plant life cycle, strongly influencing seedling establishment, crop uniformity, and subsequent productivity. However, the genetic basis of seed germination in tomato remains incompletely understood. Here, we performed a genome-wide association study (GWAS) using 319 diverse tomato accessions to identify new loci and candidate genes associated with seed germination. Five significant variants were detected across the genome. Among them, SNP_59508294 on chromosome 3 was consistently associated with the seed germination index (SGI), and accessions carrying the GG haplotype exhibited a significantly higher SGI than those carrying the TT haplotype. Seven α-expansin (EXPA) genes were located within or near the associated interval. Integration of transcriptomic data from contrasting accessions and expression profiles across tomato tissues showed SlEXPA10 to be the most plausible candidate gene. The InDels in the SlEXPA10 promoter were highly associated with its low expression level in low SGI varieties. CRISPR/Cas9-mediated disruption of SlEXPA10 significantly reduced the rate and speed of seed germination relative to the wild type. Collectively, these results identify SlEXPA10 as a positive regulator of tomato seed germination and provide a candidate locus for improving seed vigor and emergence uniformity.
SN - 1422-0067
ER -