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

Authors: ASSEFA, TESHALE - Orise Fellow; OTYAMA, PAUL - Iowa State University; Brown, Anne; Kalberer, Scott; KULKARNI, ROSHAN - Orise Fellow; Cannon, Steven

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/17/2019
Publication Date: 6/26/2019
Citation: Assefa, T., Otyama, P., Brown, A.V., Kalberer, S.R., Kulkarni, R.S., Cannon, S.B. 2019. Genome-wide associations and epistatic interactions for internode number, plant height, seed weight and seed yield in soybean. BMC Genomics. 20(527). https://doi.org/10.1186/s12864-019-5907-7.
DOI: https://doi.org/10.1186/s12864-019-5907-7

Interpretive Summary: Efficient modern breeding methods typically involve genetic markers for selecting plants that have desired characteristics. Genetic markers enable breeders to identify desirable varieties much earlier than in methods that rely solely on field evaluation of plant traits in each year. The research reported in this paper identifies genetic markers that breeders can use for several important soybean traits related to growth characteristics and yield, and also reports the performance of more than 400 diverse soybean varieties. Evaluation of diverse varieties is especially important in soybean, because commonly grown soybean varieties in the U.S. have relatively limited genetic variation. Breeders will be able to use the research described in this paper to identify little-used but potentially valuable varieties to use in breeding programs, and to select genetic markers to use for efficient selection for traits including yield, seed weight, and plant height. This work will benefit farmers and consumers by helping breeders to develop new, high-yielding and resilient soybean varieties.

Technical Abstract: 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. 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. Associations with several well-established genes are described, including the Dt1 locus for plant height. This study further confirms the utility of GWAS and GWES approaches for identifying marker-trait associations and interactions within a diverse germplasm collection.