The soybean high density Forrest by Williams 82 SNP-based genetic linkage map identifies QTL and candidate genes for seed isoflavones content

Authors: KNIZIA, DOUNYA - Southern Illinois University; YUAN, JIAZHENG - Fayetteville State University; Bellaloui, Nacer; VUONG, TRI - University Of Missouri; BETTS, FRANCES - Fayetteville State University; REGISTER, TERESA - Fayetteville State University; WILLIAMS, EARL - Fayetteville State University; LAKHSSASI, NAOUFAL - Southern Illinois University; NGUYEN, HENRY - University Of Missouri; MEKSEM, KHALID - Southern Illinois University; Mengistu, Alemu; KASSEM, MY - Fayetteville State University

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/21/2021
Publication Date: 9/27/2021
Citation: Knizia, D., Yuan, J., Bellaloui, N., Vuong, T., Betts, F., Register, T., Williams, E., Lakhssasi, N., Nguyen, H., Meksem, K., Mengistu, A., Kassem, M.A. 2021. The soybean high density Forrest by Williams 82 SNP-based genetic linkage map identifies QTL and candidate genes for seed isoflavones content. Plants. 10:1-23. https://doi.org/10.3390/plants10102029.
DOI: https://doi.org/10.3390/plants10102029

Interpretive Summary: Soybean seed contains high value nutrients such as isoflavones. Isoflavones are plant hormones that are thought to have beneficial effects on human health. Therefore, increasing these compounds and controlling their production genetically is crucial. The objectives of this study were to construct a genetic map and identify gene regions or genes controlling the main isoflavones in soybean seed using 309 individuals resulting from a cross between Forrest and Williams 82 cultivars. To achieve this goal, DNA was extracted from plants and isoflavones were analyzed in seeds in experiments conducted in two locations (North Carolina in 2018 and Illinois in 2020). A total of 26 QTL (Quantitative Trait Loci, a region of DNA which is associated with a trait; in our case isoflavones) that control various seed isoflavone have been identified and mapped on soybean chromosomes 2, 4, 5, 6, 10, 12, 15, 19, and 20 in both location. Six of these QTLs are novel regions on chromosomes 2, 4, 5, 12, 15, and 19, while the other 21 QTLs have been previously identified by other studies. Since limited information is available on soybean isoflavone QTLs, the QTLs identified in this research and their candidate genes could be used in breeding programs to develop soybean cultivars with high beneficial isoflavone content, and to advance our knowledge of isoflavone metabolism.

Technical Abstract: Isoflavones are secondary metabolites abundant in soybean and other legumes seed and have health and nutrition benefits for both humans and animals. The objectives of this study were to (1) construct a single nucleotide polymorphism (SNP)-based genetic linkage map using the ‘Forrest’ by ‘Williams 82’ (FXW82) recombinant inbred line (RIL) population (n=309), (2), map quantitative trait loci (QTL) for seed isoflavones daidzein, genistein, glycitein, and total isoflavones contents in two environments over two years (North Carolina in 2018, NC-2018; and Illinois in 2020; IL-2020) in this population, and (3) identify candidate genes for seed isoflavones. The FXW82 SNP-based map was composed of 2,075 SNPs and covered 4,029.9 cM. A total of 26 QTL that control various seed isoflavone have been identified and mapped on chromosomes 2, 4, 5, 6, 10, 12, 15, 19, and 20 in both NC-2018 (13 QTL) and IL-2020 (14 QTL). The 6 QTL regions on chromosomes 2, 4, 5, 12, 15, and 19 are novel regions while the other 21 QTL have been identified by other studies using different biparental mapping populations or genome-wide association studies (GWAS). Since limited information is available on soybean isoflavones QTLs, the QTLs identified here and their candidate genes could be used in breeding programs to develop soybean cultivars with high beneficial isoflavone contents, and to advance our knowledge of isoflavones metabolic pathways.