Genome-wide associations and epistatic interactions for internode number, plant height, seed weight and seed yield in soybean

Abstract

Background: Breeding programs benefit from information about marker-trait associations for many traits, whether the goal is to place those traits under active selection or to maintain them through background selection. Association studies are also important for identifying accessions bearing potentially useful alleles by characterizing marker-trait associations and allelic states across germplasm collections. This study reports the results of a genome-wide association study and evaluation of epistatic interactions for four agronomic and seed-related traits in soybean.

Results: Using 419 diverse soybean accessions, together with genotyping data from the SoySNP50K Illumina Infinium BeadChip, we identified marker-trait associations for internode number (IN), plant height (PH), seed weight (SW), and seed yield per plant (SYP). We conducted a genome-wide epistatic study (GWES), identifying candidate genes that show evidence of SNP-SNP interactions. Although these candidate genes will require further experimental validation, several appear to be involved in developmental processes related to the respective traits. For IN and PH, these include the Dt1 determinacy locus (a soybean meristematic transcription factor), as well as a pectinesterase gene and a squamosa promoter binding gene that in other plants are involved in cell elongation and the vegetative-to-reproductive transition, respectively. For SW, candidate genes include an ortholog of the AP2 gene, which in other species is involved in maintaining seed size, embryo size, seed weight and seed yield. Another SW candidate gene is a histidine phosphotransfer protein - orthologs of which are involved in cytokinin-mediated seed weight regulating pathways. The SYP association loci overlap with regions reported in previous QTL studies to be involved in seed yield.

Conclusions: This study further confirms the utility of GWAS and GWES approaches for identifying marker-trait associations and interactions within a diverse germplasm collection.

Keywords: Epistasis; GWAS; GWES; Internode number; Plant height; QTL; Seed weight; Seed yield per plant; Soybean.

Fig. 1

Manhattan plots of GWAS for internode number. The horizontal black line in each panel shows a selected genome-wide significance threshold at FDR < 0.05. The panels give GWAS values for (a) internode number (IN), (b) plant height (PH), (c) seed weight (SW), and (d) seed yield per plant (SYP). See Table 2 for regions and candidate genes

Fig. 2

An association region for internode length (IN), on chromosome 19. Top panel: -log₁₀ of P transformed values from GWAS for IN, within a 300 kb window; bottom panel: LD, measured in r². The most significant SNP is ss715635024 (red dot), at a genomic position of 40,683,097. A candidate gene in this region is Glyma.19 g145700, a pectinestrase, at 14 kb from the significant SNP (location marked in green)

Fig. 3

An association region for plant height (PH), on chromosome 19. Top panel: -log₁₀ of P transformed values from GWAS for IN, within a 300 kb window; bottom panel: LD, measured in r². The most significant SNP is ss715635425 (red dot), at a genomic position of 45,204,441. A candidate gene in this region is Glyma.19 g194300, the determinacy (Dt1) gene, at 20 kb from the significant SNP (location marked in green)