Genomic regions and candidate genes associated with seed nitrogen, phosphorus, and sulfur accumulation identified 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: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/12/2025
Publication Date: 9/3/2025
Citation: Bellaloui, N., Yuan, J., Knizia, D., Song, Q., Betts, F., Register, T., Williams, E., Lakhssassi, N., Mazouz, H., Nguyen, H.T., Meksem, K., Mengistu, A., Kassem, A.M. 2025. Genomic regions and candidate genes associated with seed nitrogen, phosphorus, and sulfur accumulation identified in the soybean ‘Forrest’ by ‘Williams 82’ RIL population. PLOS ONE. 9:1-19. https://doi.org/10.1371/journal.pone.0331214.
DOI: https://doi.org/10.1371/journal.pone.0331214

Interpretive Summary: Nitrogen (N), phosphorus (P), and sulfur (S) are essential nutrients for plant health. Deficiencies in N, P, or S in plants lead to lower seed production and poor seed quality in seeds. Soybean seed is a source of protein, oil, essential amino acids, and minerals including N, P, and S for human and livestock nutrition. Maintaining high levels of N, P, and S in soybean seed contributes to high quality soybean meal. The objective of this research was to identify genetic regions and specific genes associated with seed N, P, and S content. Two experiments were conducted in two locations; one experiment was conducted in 2018 in Spring Lake, North Carolina and the second experiment was conducted in 2020 in Carbondale, Illinois. A soybean population containing 306 individuals was evaluated at each location. A total of 11 new genetic regions associated with levels of N, P, and S in seed were discovered. Several specific genes associated with seed N, P, and S content were identified within these genetic regions. The genetic regions, genes, and molecular markers discovered in this research will help breeders for soybean seed selection for optimum seed N, P, and S nutritional qualities. Also, these findings will advance our knowledge of physiology and genetics of seed mineral accumulation; and provide new knowledge on seed N, P, and S candidate genes and their possible use in genetic engineering.

Technical Abstract: Nitrogen (N), phosphorus (P), and sulfur (S) are essential nutrients for plant health. Deficiencies in N, P, or S in plants lead to lower seed production and seed quality in grain crops, including soybean seed. Soybean seed is a source of protein, oil, essential amino acids, and minerals. These nutrient components are essential for human and livestock nutrition and plant health, and maintaining N, P, and S levels in soybean seed is crucial for higher seed nutritional value and amino acids quality. Therefore, identifying genomic regions, candidate genes, and molecular markers associated with N, P, and S metabolism are important. The objective of this research was to identify genomic regions and candidate genes associated with N, P, and S accumulation in soybean seed. Two experiments were conducted in two locations using a ‘Forrest’ × ‘Williams 82’ recombinant inbred lines (RIL) population. The genetic map used in the current research was based on 306 RILs and 2075 SNP markers. One experiment was conducted in 2018 in Spring Lake, NC; the second experiment was conducted in 2020 in Carbondale, IL. The results showed a wide range of N, P, and S concentrations in both locations among RIL population lines. Based on the broad-sense heritability (H2), 91.7% of seed N concentration variation was due to genetic effects, followed by 48.2% for S seed concentration, and a heritability of close to zero for seed P concentration. Eleven QTL were identified for seed N, 7 QTL for seed P, and 9 QTL for seed S in two locations. All these QTL had a significant linkage to the trait as their LOD ranged from 2.5 to 6.48 in 2018 and from 2.75 to 128.72 in 2020. Two QTL for seed N (qN-02-[IL-2020] on Chr 4, and qN-03-[IL-2020] on Chr 4 were identified at the marker Gm04_4687302-Gm04_7672403 and Gm04_7672403, and their LOD were 45.06 and 96.98, and their contribution to the phenotypic variation were 45.85% and 48.37%, respectively. Except for the seed N, P, and S QTL identified on Chr 16, 11 QTL reported here were not previously identified and therefore are novel. Several functional genes encoding N-, P-, and S-proteins, enzymes, and transporters were identified and located within the QTL interval. To our knowledge, the QTL identified here on Chr 2 and 6 are novel and were not previously identified. QTL, genes, and molecular markers discovered in this research will help breeders for soybean select for optimum seed mineral nutritional qualities. These findings also advance our knowledge of physiology and genetics of seed mineral accumulation and provide new knowledge on seed N and S candidate genes for possible application in genetic engineering.