Identification of genomic regions and candidate genes associated with seed boron and manganese accumulation in the soybean ‘Forrest’ by ‘Williams 82’ RIL population

Authors: Bellaloui, Nacer; YUAN, JIAZHENG - Fayetteville State University; KNIZIA, DOUNYA - Southern Illinois University; Song, Qijian; BETTS, FRANCES - Fayetteville State University; REGISTER, TERESA - Fayetteville State University; WILLIAMS, EARL - Fayetteville State University; LAKHSSASSI, NAOUFAL - Southern Illinois University; MAZOUZ, HAMID - Moulay Ismail University; NGUYEN, HENRY - Lincoln University Of Missouri; MEKSEM, KHALID - Southern Illinois University; Mengistu, Alemu; KASSEM, ABDELMAJID - Fayetteville State University

Submitted to: Journal of the Mississippi Academy of Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/6/2026
Publication Date: N/A
Citation: N/A

Interpretive Summary: Boron (B) and manganese (Mn) are important nutrients for human health, plant growth and development, and crop production. Their deficiencies in the human diet will result in malnutrition, and their deficiencies or toxicities in soil will result in yield loss and poor seed quality in soybean. Because soybean seed is an important source for nutrients, including B and Mn, identifying genetic regions controlling seed content of B and Mn is essential. Two field experiments were conducted, one in Spring Lake in North Carolina in 2018 and the other in Carbondale, Illinois in 2020. A soybean population (306 individuals) was used. We were able to identify eight genetic regions for B and 6 for Mn that are novel and were not previously identified. Also, we were able to identify several genes within these genetic regions that are associated with B and Mn content in seeds. The genetic regions and specific genes identified in this research provide new knowledge of physiological and genetic basis of seed mineral nutrition and provide breeders with potential tools for soybean seed selection for B and Mn nutrition. The identified genes controlling these nutrients will allow us to alter their functions to increase soybean seed B and Mn to improve human and livestock nutrition

Technical Abstract: Boron (B) and manganese (Mn) are important nutrients for human health, plant growth and development, and crop production. Their deficiencies in the human diet will result in human malnutrition, and their deficiencies or toxicities in soil will result in yield loss and poor seed quality. Therefore, maintaining adequate or optimum concentration within the plant for higher production and seed quality is essential. Since soybean seed is an important source of B and Mn, understanding the physiology and genetics of B and Mn accumulation in soybean seed, and identifying their genomic regions, molecular markers, and associated genes controlling B and Mn seed content in the genome are crucial. Two field experiments were conducted at two locations (in Spring Lake, NC in 2018; in Carbondale, IL in 2020). The ‘Forrest’ × ‘Williams 82’ recombinant inbred lines (RILs) population were used. A total of 306 RILs were analyzed by 2075 single nucleotide polymorphism (SNP) markers in the genetic map. The results showed a great range of B and Mn seed concentrations observed in RILs at both locations. The broad-sense heritability (H2) analysis showed that 13.3% (for B) and 44.2% (for Mn) of nutrient concentrations were due to genetic effects. In 2018 at the NC location, a total of 5 significant Quantitative trait loci (QTLs) were identified (qB-01-[NC-2018] on Chr 2; qB-02-[NC-2018] on Chr 6; qB-03-[NC-2018] on Chr 11; qB-04-[NC-2018] on Chr 18; and qB-05-[NC-2018]) on Chr 19. A total of three QTLs were identified for seed Mn (qMn-01-[NC-2018] on Chr 5; qMn-02-[NC-2018] on Chr 9; and qMn-03-[NC-2018]) on Chr 20. For the RILs planted at IL in 2020, a total of three QTL were detected for seed B concentrations (qB-01-[IL-2020] on Chr 10; qB-02-[IL-2020] on Chr 12; and qB-03-[IL-2020] on Chr 20. A total of three QTL for seed Mn concentrations were identified (qMn-01-[IL-2020] on Chr 1; qMn-02-[IL-2020] on Chr 7; and qMn-03-[IL-2020] on Chr 12. Several functional candidate genes encoding Mn-proteins, transporters, transcription factors, and cation transport domains were identified within the intervals of the detected QTLs. The QTLs identified are novel and were not previously reported. QTLs, genes, and molecular markers found in the current study will provide breeders with knowledge and tools for soybean seed selection for B and Mn nutrition and advance our knowledge in physiology and genetics of seed mineral nutrition. The identified candidate genes here will help molecular biologists with new knowledge for possible use in genetic engineering.