Genome-wide association study of seed protein, oil and amino acid contents in soybean from maturity groups I to IV

Mikyung Sung,Randall Nelson,Leah K Mchale,Kyujung Van,Sungwoo Lee,M A Rouf Mian,Jonathan Lamantia

doi:10.1007/s00122-019-03304-5

Abstract

Key messageGenomic regions associated with seed protein, oil and amino acid contents were identified by genome-wide association analyses. Geographic distributions of haplotypes indicate scope of improvement of these traits.Soybean [Glycine max (L.) Merr.] protein and oil are used worldwide in feed, food and industrial materials. Increasing seed protein and oil contents is important; however, protein content is generally negatively correlated with oil content. We conducted a genome-wide association study using phenotypic data collected from five environments for 621 accessions in maturity groups I–IV and 34,014 markers to identify quantitative trait loci (QTL) for seed content of protein, oil and several essential amino acids. Three and five genomic regions were associated with seed protein and oil contents, respectively. One, three, one and four genomic regions were associated with cysteine, methionine, lysine and threonine content (g kg−1 crude protein), respectively. As previously shown, QTL on chromosomes 15 and 20 were associated with seed protein and oil contents, with both exhibiting opposite effects on the two traits, and the chromosome 20 QTL having the most significant effect. A multi-trait mixed model identified trait-specific QTL. A QTL on chromosome 5 increased oil with no effect on protein content, and a QTL on chromosome 10 increased protein content with little effect on oil content. The chromosome 10 QTL co-localized with maturity gene E2/GmGIa. Identification of trait-specific QTL indicates feasibility to reduce the negative correlation between protein and oil contents. Haplotype blocks were defined at the QTL identified on chromosomes 5, 10, 15 and 20. Frequencies of positive effect haplotypes varied across maturity groups and geographic regions, providing guidance on which alleles have potential to contribute to soybean improvement for specific regions.

Highlights

Soybean [Glycine max (L.) Merr.] is a highly valued source of protein and oil for feed, food and industrial uses across the world
Wide and continuous phenotypic distributions were observed for both seed protein and oil contents (Fig. 1; Tables S3, S4)
Historical phenotypic data collected over time have important limitations, because the data often originated from various subsets of soybean accessions, which are frequently grown in un-replicated and incomplete blocks in different locations and years

Summary

Introduction

Soybean [Glycine max (L.) Merr.] is a highly valued source of protein and oil for feed, food and industrial uses across the world. In 2016, soybean represented 71% of protein meal used worldwide (SoyStat 2017). Theoretical and Applied Genetics (2019) 132:1639–1659 source of protein in the feed mixtures of commercial poultry, livestock and fish farms worldwide, there is a growing interest in elevating the protein content of soybean seed and, in turn, elevating the protein content of the meal obtained from seed (Gatrell et al 2014). In cultivar development, breeders generally select for the best seed yield potential with little attention to seed protein or oil content. Since seed protein contents of US soybean cultivars have been declining slowly over many decades, while the seed yields have been increasing (Rinker et al 2014), developing high protein and high yield soybean cultivars would benefit farmers (Chung et al 2003; Bandillo et al 2015; Brzostowski and Diers 2017)

Methods

Results

Conclusion