Identification of loci and candidate genes for plant height in soybean (Glycine max) via genome-wide association study

Plant height (PH) of soybean (Glycine max (L.) Merr.) is an important and complex architecture trait significantly related to soybean yield. A natural population of 185 elite soybean accessions was used to identify QTN (quantitative trait nucleotide) and candidate genes of PH through genome-wide association study (GWAS). A total of 33,149 SNPs were identified based on the Specific Locus Amplified Fragment Sequencing (SLAF-seq). Finally, 14 signals associated with PH through GWAS were detected, including seven novel SNPs and seven known ones which were overlapped or located in the linked regions of known QTL. Numbers of functional genes located in the 200-kb genomic region of each peak SNP were found. Furthermore, a total of 103 SNPs based on 28 genes were scanned. Among them, six novel genes containing cis-acting elements involved in gibberellin or auxin responsiveness were predicted significantly related with PH according to transcript abundance analysis. The identified loci with beneficial alleles and the candidate genes might be useful for studying the molecular mechanisms of soybean PH and further for improving the potential yield of soybean.