Identification of SNP markers associated with soybean fatty acids contents by genome-wide association analyses

Authors: SUNG, MIKYUNG - North Carolina State University; VAN, KYUJUNG - The Ohio State University; LEE, SUNGWOO - Chungnam National University; MCHALE, LEAH - The Ohio State University; NELSON, RANDALL - University Of Illinois; La Mantia, Jonathan; Taliercio, Earl; Mian, Rouf

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/12/2021
Publication Date: 3/20/2021
Citation: Sung, M., Van, K., Lee, S., Mchale, L.K., Nelson, R., La Mantia, J.M., Taliercio, E.W., Mian, R.M. 2021. Identification of SNP markers associated with soybean fatty acids contents by genome-wide association analyses. Molecular Breeding. https://doi.org/10.1007/s11032-021-01216-1.
DOI: https://doi.org/10.1007/s11032-021-01216-1

Interpretive Summary: With the recent market focus on high oleic and low linolenic soybean oil and the trans fatty acid issues, the compositions of fatty acids (FAs) in soybean oil has become very important. Using gas chromatography, we have measured soybean FAs profiles of 621 soybean accessions (maturity groups I through IV) grown in five different environments - Columbus, OH (2015), Wooster, OH (2014 and 2015), Plymouth, NC (2015), and Urbana, IL (2015). Using publicly available SoySNP50K genotypic data and the FA profiles from this study, a genome-wide association analysis was completed with a compressed mixed linear model to identify six significant genomic regions associated with palmitic acid, 35 stearic acid-associated regions, and one genomic region each associated with oleic acid and linoleic acid across five environments at a genome-wide significance threshold. One and three novel genomic regions associated with palmitic acid and stearic acid, respectively, were identified across all five environments. Additionally, nine novel environment-specific FA related genomic regions were discovered providing new insights into the genetics of soybean FAs. Previously reported FA related loci, such as FatB1a encoding palmitoyl-acyl carrier protein thioesterase, SACPD-C for '9-stearoyl-acyl carrier protein-desaturase, and KASIII for 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III were also among the significant genomic regions identified in this study. Our results will be useful for future functional studies and marker-assisted breeding for soybean FAs.

Technical Abstract: Compositions of fatty acids (FAs) in soybean seed are very important for the quality and uses of the soybean oil. Using gas chromatography, we have measured soybean FAs profiles of 621 soybean accessions (maturity groups I through IV) grown in five different environments - Columbus, OH (2015), Wooster, OH (2014 and 2015), Plymouth, NC (2015), and Urbana, IL (2015). Using publicly available SoySNP50K genotypic data and the FA profiles from this study, a genome-wide association analysis was completed with a compressed mixed linear model to identify six significant genomic regions associated with palmitic acid, 35 stearic acid-associated regions, and one genomic region each associated with oleic acid and linoleic acid across five environments at a genome-wide significance threshold. One and three novel genomic regions associated with palmitic acid and stearic acid, respectively, were identified across all five environments. Additionally, nine novel environment-specific FA related genomic regions were discovered providing new insights into the genetics of soybean FAs. Previously reported FA related loci, such as FatB1a encoding palmitoyl-acyl carrier protein thioesterase, SACPD-C for '9-stearoyl-acyl carrier protein-desaturase, and KASIII for 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III were also among the significant genomic regions identified in this study. . Our results will be useful for future functional studies and marker-assisted breeding for soybean FAs.