Genetic mapping for QTL associated with seed nickel and molybdenum accumulation in the soybean ‘Forrest’ by 'Williams 82’ RIL population

Authors: Bellaloui, Nacer; KNIZIA, DOUNYA - Southern Illinois University; YUAN, JIAZHENG - Fayetteville State 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 - University Of Missouri; MEKSEM, KHALID - Southern Illinois University; Mengistu, Alemu; KASSEM, ABDELMAJID - Fayetteville State University

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/23/2023
Publication Date: 10/28/2023
Citation: Bellaloui, N., Knizia, D., Yuan, J., Song, Q., Betts, F., Register, T., Williams, E., Lakhssassi, N., Mazouz, H., Nguyen, H., Meksem, K., Mengistu, A., Kassem, A. 2023. Genetic mapping for QTL associated with seed nickel and molybdenum accumulation in the soybean ‘Forrest’ by 'Williams 82’ RIL population. Plants. 12:1-24. https://doi.org/10.3390/plants12213709.
DOI: https://doi.org/10.3390/plants12213709

Interpretive Summary: Nickel (Ni) and molybdenum (Mo) are essential nutrients for human and animal health and nutrition, and for crop growth and production. Soybean seed is an important source for Ni and Mo. Therefore, understanding the genetics of soybean seed Ni and Mo is essential. The objective of the current research was to identify the genetic regions (these regions are called quantitative trait loci, QTL) associated with Ni and Mo content in soybean seed. A soybean population (306 individuals) was created from a cross between ‘Forrest’ by ‘Williams 82’ 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 4 QTL for Ni and a total of 7 QTL for Mo were identified. Based on the search of the available literature, 4 QTL for Ni and 5 QTL associated with Mo are novel and not previously reported. The current research provides new knowledge of the genetics of Ni and Mo soybean nutrition. The genetic regions identified here can be used as an effective tool by soybean breeders to select for desirable levels of Ni and Mo in soybean seed.

Technical Abstract: Nickel (Ni) and molybdenum (Mo) are trace minerals, essential for human and animal health and nutrition, and for crop growth, development, and production. Both elements are involved in several physiological, biochemical reactions, and metabolic pathways. Although deficiency or toxicity in human diet or soil is rare, if it occurs, it will lead to negative health consequences to humans and plants. Therefore, understanding the genetic basis of seed Ni and Mo is essential. Since soybean is a major crop in the word and a major source for nutrients, including Ni and Mo, thus, the objective of the current research was to map genetic regions (quantitative trait loci, QTL) linked to Ni and Mo concentrations in soybean seed. A recombinant inbred line (RIL) population derived from a cross between ‘Forrest’ by ‘Williams 82’ (F×W82). A total of 306 lines was used to genotype using 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 and included the parents and the RILs population. One experiment was conducted in 2018 in North Carolina (NC), and the second experiment was conducted in Illinois in 2020 (IL). Logarithm of the odds (LOD) of = 2.5 was set as a threshold to report identified QTL using composite interval mapping (CIM) method. A wide range of Ni and Mo concentrations among RILs. A total of 4 QTL for Ni (qNi-01, qNi-02, and qNi-03 in 2018 on Chr 2, 8, and 9, respectively in 2018); and one QTL (qNi-01 on Ch 20 in 2020) were identified for seed Ni. All these QTL were significantly (LOD threshold >2.5) associated with seed Ni with LOD scores ranged between 2.71-3.44, and with phenotypic variance explained ranged from 4.48%-6.97%. A total of 7 QTL for Mo (qMo-01, qMo-02, and qMo-03 on Chr 1, 3, 17, respectively, in 2018; and 4 QTL (qMo-01, qMo-02, qMo-03, and qMo-04, on Chr 5, 11, 14, and 16, respectively, in 2020) were identified. Some of the current QTL had high LOD and significantly contributed to the phenotypic variance for the trait. For example, in 2018, Mo QTL (qMo-01 on Chr 1) had LOD of 7.8, explaining a phenotypic variance of 41.17%; and qMo-03 on Chr 17 with LOD of 5.33, and with phenotypic variance explained of 41.49%. In addition, Mo QTL (qMo-03 on Chr 14) had LOD of 9.77, explaining 51.57% of phenotypic variance related to the trait; and another Mo QTL(qMo-04 on Chr 16) which had LOD of 7.62 and explained 49.95% of phenotypic variance. None of the QTL identified here were identified twice across locations/years. Based on the search of the available literature and of Soybase, the 4 QTL for Ni, identified on Chr 2, 8, 9, and 20; and the 5 QTL associated with Mo, identified on Chr 1, 17, 11, 14, and 16, are novel and not previously reported. The current research provides new knowledge of Ni and Mo genetic mapping, and useful QTL and molecular markers that can be potentially used for molecular assisted selection for levels of Ni and Mo in soybean seed.