Identification of genetic loci and domestication gene GmZFP1 associated with soybean hypocotyl elongation in seedling stage by genome-wide association study

BACKGROUND: The hypocotyl length and elongation is an important characteristic that affect the soybean seedling emergence and photosynthesis. However, the basic genetic mechanism of this feature remains incompletely understood. RESULTS: In this study, the hypocotyl length of four-day germinated soybean seedlings was evaluated before and after 24 h cultivation to assess hypocotyl elongation (HE) in 330 soybean accessions. Five quantitative trait loci (QTLs) that significantly associated with HE trait were detected by genome-wide association study (GWAS) in two models, and they are located on chromosome (Chr.) 2, 3, 11, 15, and 17, respectively. A total of 84 gene models have been found in HE QTLs candidate regions, and with a large proportion enriched in the biological processes of photosynthesis and cell differentiation. A CCCH zinc finger protein gene of GmZFP1 (Glyma.15G262900) was identified as the candidate in the major locus qHE_8 through the analysis of linkage disequilibrium (LD) blocks, gene expression patterns, and natural variation. Three SNPs substantially associated with HE in the GmZFP1 area resulted in 12 haplotypes (Hap 1-12) and four haplotype groups (Hap Ⅰ-Ⅳ). Soybean accessions carrying superior Hap Ⅲ showed significantly higher HE than the soybean lines containing Hap I, and the Hap Ⅲ made up 13.4% of the G. soja subpopulation and 61.98% of the G. max subpopulation, respectively. In genetic diversity and molecular evolution analysis, the GmZFP1 was also located in the genome selective sweep region during soybean domestication. CONCLUSIONS: Five QTLs were mapped by GWAS in both EMMAX and TASSEL models that significantly associated with soybean hypocotyl elongation (HE). The major candidate gene GmZFP1 underlying the qHE_8 locus was identified, and the superior haplotypes and selective sweep signals were also detected in the GmZFP1 region. The QTLs and GmZFP1 discovered in this study provided potential genetic resources for the soybean molecular breeding in the future.