Genome-wide association study and genomic selection for yield and related traits in soybean

Soybean [Glycine max (L.) Merr.] is a crop of great interest worldwide. Exploring molecular approaches to increase yield genetic gain has been one of the main challenges for soybean breeders and geneticists. Agronomic traits such as maturity, plant height, and seed weight have been found to contribute to yield. In this study, a total of 250 soybean accessions were genotyped with 10,259 high-quality SNPs postulated from genotyping by sequencing (GBS) and evaluated for grain yield, maturity, plant height, and seed weight over three years. A genome-wide association study (GWAS) was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model. Genomic selection (GS) was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that 20, 31, 37, and 23 SNPs were significantly associated with maturity, plant height, seed weight, and yield, respectively; Many SNPs were mapped to previously described maturity and plant height loci (E2, E4, and Dt1) and a new plant height locus was mapped to chromosome 20. Candidate genes were found in the vicinity of the two SNPs with the highest significant levels associated with yield, maturity, plant height, seed weight, respectively. A 11.5-Mb region of chromosome 10 was associated with both yield and seed weight. Overall, the accuracy of GS was dependent on the trait, year, and population structure, and high accuracy indicates that these agronomic traits can be selected in molecular breeding through GS. The SNP markers identified in this study can be used to improve yield and agronomic traits through the marker-assisted selection and GS in breeding programs.