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. Electronic supplementary material The online version of this article (10.1186/s12864-019-5907-7) contains supplementary material, which is available to authorized users.

Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

“…These significant SNPs were associated with seed weight and yield. A 4-Mb region of chromosome of chromosome 19 was found to be associated with maturity, plant height, and yield in soybean, which was in agreement with a study investigated by Assefa et al (2019). A 5.4-MB region of chromosome 20 harbored loci that were associated with maturity, plant height, and seed weight.…”

“…Diers et al (2018) reported 23 loci affecting soybean yield on chromosome 16 alone. Two of the SNPs on chromosome 19 reported in this study were in the vicinity of a significant yield SNP marker identified by Assefa et al (2019). Despite the lack of overlapping SNPs between traits, overlapping significant loci were identified to control two or more traits.…”

“…A total of 19, 29, 15, and 23 SNPs were reported to be associated with maturity, seed weight, plant height, and yield, respectively (Diers et al 2018). Assefa et al (2019) found a total of 14, 10, and 9 SNPs associated with seed weight, plant height, and yield, respectively, upon a GWAS study involving a total of 419 soybean accessions. After SNP validation is performed, the information from this report could be used in trait introgression efforts in soybean breeding programs.…”

Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

“…Diers et al [31] reported 23 loci affecting soybean yield on chromosome 16 alone. Two of the SNPs on chromosome 19 reported in this study were in the vicinity of a signi cant yield SNP marker identi ed by Assefa et al [32]. Despite the lack of overlapping SNPs between traits, overlapping signi cant loci were identi ed to control two or more traits.…”

“…A total of 19, 29, 15, and 23 SNPs were reported to be associated with maturity, seed weight, plant height, and yield, respectively [31]. Assefa et al [32] found a total of 14, 10, and 9 SNPs associated with seed weight, plant height, and yield, respectively, upon a GWAS study involving a total of 419 soybean accessions. After SNP validation is performed, the information from this report could be used in trait introgression efforts in soybean breeding programs.…”