Genetic Diversity of Soybeans (Glycine max (L.) Merr.) with Black Seed Coats and Green Cotyledons in Korean Germplasm

Abstract

Soybeans (Glycine max (L.) Merr.) with black seed coats and green cotyledons are rich in anthocyanins and chlorophylls known as functional nutrients, antioxidants and compounds with anticarcinogenic properties. Understanding the genetic diversity of germplasm is important to determine effective strategies for improving the economic traits of these soybeans. We aimed to analyze the genetic diversity of 470 soybean accessions by 6K single nucleotide polymorphic loci to determine genetic architecture of the soybeans with black seed coats and green cotyledons. We found soybeans with black seed coats and green cotyledons showed narrow genetic variability in South Korea. The genotypic frequency of the d1d2 and psbM variants for green cotyledon indicated that soybean collections from Korea were intermingled with soybean accessions from Japan and China. Regarding the chlorophyll content, the nuclear gene variant pair d1d2 produced significantly higher chlorophyll a content than that of chloroplast genome psbM variants. Among the soybean accessions in this study, flower color plays an important role in the anthocyanin composition of seed coats. We provide 36 accessions as a core collection representing 99.5% of the genetic diversity from the total accessions used in this study to show potential as useful breeding materials for cultivars with black seed coats and green cotyledons.

Genome-Wide Association Mapping for Seed Weight in Soybean with Black Seed Coats and Green Cotyledons

“…We assumed that BLG accessions could be valuable materials to identify the genes to increase seed size in soybeans. In addition, with BLG accessions, our previous study reported that most significant SNPs related to anthocyanin compositions were colocalized with the O locus, which corresponded with an anthocyanidin reductase gene and R locus, which is the R2R3 MYB transcription factor for upregulating UDP-glycose: flavonoid 3-O-glycosyltranferase (UF3GT) in black soybeans [55].…”

“…In addition, our previous study reported the analyses of population structure and PCA to reveal three clusters in 470 BLG accessions. Small-seed sizes of BLG accessions with "AA" of Gm02_8896955 were in cluster 3, whereas the ones with the "aabb" genotype belonged to cluster 2, which had relatively higher genetic diversity than clusters 1 and 3 [55]. As small-seed sizes in the "AA" genotype of Gm02_8896955 may be associated with other genes for HSW, further research like linkage analysis with a bi-parental mapping population will be required to identify genes to control seed weight with BLG accessions in "AA" genotype of Gm02_8896955.…”

“…Our previous study reported that BLG collections exhibited narrow genetic variability [55]. BLG accessions may spread over a wide range of geographical areas by farmers' distribution due to better performance and yield for a long history of soybean cultivation in South Korea.…”

“…To conduct the GWAS analysis, 470 BLG accessions, including three cultivars (Cheongja, Cheongja 3 and Uram), formed the total population [45,55]. The 470 BLG accessions were grown at Gyeongsanbuk-do Agricultural Research and Extension, Daegu, Republic of Korea in the years 2013, 2014 and 2015 with the planting dates over the three years being 14 June, 29 May, and 15 June, respectively.…”

“…Online tools and databases have been developed with publicly available genome sequencing data, such as SoyBase [10], Phytozome [53], and SoyKB [54]. In this study, we have conducted GWAS with agronomic traits of 470 BLG accessions [45] and 6K SNPs [55], and application of online tools with publicly available genome sequencing data. The objective of this study was to identify the QTLs in the soybean genome, which are associated with HSW, and to identify the candidate genes in LD blocks where the most significant SNPs are located.…”