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Article

The Soybean High Density ‘Forrest’ by ‘Williams 82’ SNP-Based Genetic Linkage Map Identifies QTL and Candidate Genes for Seed Isoflavone Content

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Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
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Laboratoire de Biotechnologies & Valorisation des Bio-Ressources (BioVar), Department de Biology, Faculté des Sciences, Université Moulay Ismail, Meknès 50000, Morocco
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Plant Genomics and Biotechnology Laboratory, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA
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Crop Genetics Research Unit, USDA, Agriculture Research Service, 141 Experiment Station Road, Stoneville, MS 38776, USA
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Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
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Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, USA
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Crop Genetics Research Unit, USDA, Agricultural Research Service, Jackson, TN 38301, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Toyoaki Anai
Plants 2021, 10(10), 2029; https://doi.org/10.3390/plants10102029
Received: 23 August 2021 / Revised: 13 September 2021 / Accepted: 21 September 2021 / Published: 27 September 2021
(This article belongs to the Special Issue QTL Mapping of Seed Quality Traits in Crops)
Isoflavones are secondary metabolites that are abundant in soybean and other legume seeds providing health and nutrition benefits for both humans and animals. The objectives of this study were to construct a single nucleotide polymorphism (SNP)-based genetic linkage map using the ‘Forrest’ by ‘Williams 82’ (F×W82) recombinant inbred line (RIL) population (n = 306); map quantitative trait loci (QTL) for seed daidzein, genistein, glycitein, and total isoflavone contents in two environments over two years (NC-2018 and IL-2020); identify candidate genes for seed isoflavone. The FXW82 SNP-based map was composed of 2075 SNPs and covered 4029.9 cM. A total of 27 QTL that control various seed isoflavone traits have been identified and mapped on chromosomes (Chrs.) 2, 4, 5, 6, 10, 12, 15, 19, and 20 in both NC-2018 (13 QTL) and IL-2020 (14 QTL). The six QTL regions on Chrs. 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). A total of 130 candidate genes involved in isoflavone biosynthetic pathways have been identified on all 20 Chrs. And among them 16 have been identified and located within or close to the QTL identified in this study. Moreover, transcripts from four genes (Glyma.10G058200, Glyma.06G143000, Glyma.06G137100, and Glyma.06G137300) were highly abundant in Forrest and Williams 82 seeds. The identified QTL and four candidate genes will be useful in breeding programs to develop soybean cultivars with high beneficial isoflavone contents. View Full-Text
Keywords: soybean; RIL; Forrest; Williams 82; linkage map; isoflavone; daidzein; genistein; glycitein; SNP soybean; RIL; Forrest; Williams 82; linkage map; isoflavone; daidzein; genistein; glycitein; SNP
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MDPI and ACS Style

Knizia, D.; Yuan, J.; Bellaloui, N.; Vuong, T.; Usovsky, M.; Song, Q.; Betts, F.; Register, T.; Williams, E.; Lakhssassi, N.; Mazouz, H.; Nguyen, H.T.; Meksem, K.; Mengistu, A.; Kassem, M.A. The Soybean High Density ‘Forrest’ by ‘Williams 82’ SNP-Based Genetic Linkage Map Identifies QTL and Candidate Genes for Seed Isoflavone Content. Plants 2021, 10, 2029. https://doi.org/10.3390/plants10102029

AMA Style

Knizia D, Yuan J, Bellaloui N, Vuong T, Usovsky M, Song Q, Betts F, Register T, Williams E, Lakhssassi N, Mazouz H, Nguyen HT, Meksem K, Mengistu A, Kassem MA. The Soybean High Density ‘Forrest’ by ‘Williams 82’ SNP-Based Genetic Linkage Map Identifies QTL and Candidate Genes for Seed Isoflavone Content. Plants. 2021; 10(10):2029. https://doi.org/10.3390/plants10102029

Chicago/Turabian Style

Knizia, Dounya, Jiazheng Yuan, Nacer Bellaloui, Tri Vuong, Mariola Usovsky, Qijian Song, Frances Betts, Teresa Register, Earl Williams, Naoufal Lakhssassi, Hamid Mazouz, Henry T. Nguyen, Khalid Meksem, Alemu Mengistu, and My A. Kassem 2021. "The Soybean High Density ‘Forrest’ by ‘Williams 82’ SNP-Based Genetic Linkage Map Identifies QTL and Candidate Genes for Seed Isoflavone Content" Plants 10, no. 10: 2029. https://doi.org/10.3390/plants10102029

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