Discovery of genetic loci and causal genes for seed germination via deep re-sequencing in soybean.

High seed germination is crucial for mechanical sowing, seedling establishment, growth potential, multiple resistances, and the formation of yield and quality. However, few genetic loci and candidate genes conferring seed germination were explored in soybean at present. In view of this, a natural population containing 199 accessions was assessed for the germination potential (GP) and germination rate (GR) and also was re-sequenced at the average sequencing depth of 18.4 × for each accession. In total, 5,665,469 SNPs were obtained for association analysis, and 470 SNPs in 55 loci on 18 chromosomes were identified to associate with seed germination. Of them, 85 SNPs on chromosomes 1, 10, and 14 were associated with mean value and BLUP value for GP and GR, simultaneously. Moreover, 324 SNPs (68.9% of the total) in four loci were located on chromosome 14 for seed germination, of which 11 SNPs were located in the exons, 30 in introns, 17 in 5'UTR or 3'UTR, and 46 in upstream or downstream. Based on these, 131 candidate genes flanking the associated SNPs were analyzed for gene annotation, SNP mutation, and RNA expression, and three causal genes, Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01316-6.