Genomic regions and candidate genes for seed iron and seed zinc accumulation identified in the soybean 'Forrest' by 'Williams 82' RIL population

Authors: Bellaloui, Nacer; KNIZA, DOUNYA - Southern Illinois University; YUAN, JIAZHENG - Fayetteville State University; Song, Qijian; BETTS, FRANCE - 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 - University Of Missouri; MEKSEM, KHALID - Southern Illinois University; Mengistu, Alemu; KASSEM, ABDELMAJID - Fayetteville State University

Submitted to: International Journal of Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/22/2024
Publication Date: 5/27/2024
Citation: Bellaloui, N., Kniza, D., Yuan, J., Song, Q., Betts, F., Register, T., Williams, E., Lakhssassi, N., Mazouz, H., Nguyen, H., Meksem, K., Mengistu, A., Kassem, A. 2024. Genomic regions and candidate genes for seed iron and seed zinc accumulation identified in the soybean 'Forrest' by 'Williams 82' RIL population. International Journal of Plant Biology. 15:452-467. https://doi.org/10.3390/ijpb15020035.
DOI: https://doi.org/10.3390/ijpb15020035

Interpretive Summary: Iron (Fe) and zinc (Zn) are major micronutrients for human and animal nutrition, and plant growth and production. Deficiencies of Fe and Zn in human diet leads to malnutrition, and deficiencies of Fe and Zn in soil result in loss of crop production and poor seed quality. Therefore, identifying genetic regions controlling the content of Fe and Zn in crop seeds is essential. Soybean is a major food and feed crop in the world and an essential source for nutrients, including Fe and Zn. Thus, the objective of the current research was to identify genetic regions (these regions are called quantitative trait loci, QTL) associated with Fe and Zn content in soybean seed. A soybean population (306 individuals) was created to be used to identify these genetic regions. One experiment was conducted in 2018 in North Carolina, and the second experiment was conducted in Illinois in 2020. A total of 6 genetic regions were identified for seed Fe content. A total of 6 genetic regions associated with seed Zn were identified. To our knowledge, and based on the literature available, 2 genetic regions identified here are novel and were not previously identified. This current research provides new knowledge of the genetic basis of seed Fe and Zn nutrition in soybean. These newly identified genetic regions can be potentially used by public and private sector plant breeders to efficiently select for higher Fe and Zn content in soybean seed.

Technical Abstract: Iron (Fe) and zinc (Zn) are major micronutrients for human and animal nutrition, and plant growth and development. Deficiencies of Fe and Zn in human diet leads to malnutrition, and deficiencies of Fe and Zn in soil result in loss of crop production and poor seed quality. Therefore, identifying genomic regions and candidate genes controlling the accumulation of Fe and Zn in crop seeds is essential. Soybean is a major crop in the world and an essential source for minerals, including Fe and Zn. Thus, the objective of the current research was to identify genetic regions (quantitative trait loci, QTL) controlling Fe and Zn accumulation (concentration) in soybean seed. A ‘Forrest’ by ‘Williams 82’ (F×W82) recombinant inbred line (RIL) population (n = 306) was used and genotyped using a total of 5405 single nucleotides polymorphism (SNP) markers using Infinium SNP6K BeadChips. A total 2075 polymorphic SNPs were mapped on the 20 soybean chromosomes (Chr). The F×W82 genetic map covered 4029.9 cM with an average marker density of 1.94 cM, and the genetic length ranged from 153.7 cM for Chr 18 to 308.3 cM for Chr 2. A two-year experiment was conducted in two environments [(North Carolina, 2018 (NC)]; and Illinois, 2020 (IL)]. Only QTL with logarithm of odds (LOD) scores = 2.5 and identified by the composite interval mapping (CIM) method were reported here. A total of 6 QTL were identified for seed Fe; 3 QTL (qFe-01-qFe-03) on Chr 1, 2, and 6, respectively, in NC, and 3 QTL (qFe-01-qFe-03), respectively, on Chr 1, 2, and 12, in IL. A total of 6 QTL associated with seed Zn were identified; 4 QTL (qZn-01- qZn-04), respectively on Chr 2, 3, 7, and 19 in NC; and 2 QTL (qZn-01- qZn-02), respectively, on Chr 5 and 8 in IL. To our knowledge, and based on the literature available, the QTL identified here on Chr 2 and 6 are novel and were not previously identified. This current research provides a new knowledge of the genetic basis of seed Fe and Zn and the markers associated with QTL. The QTL identified here will contribute to efficient marker assisted selection for higher Fe and Zn content in soybean seeds.