Identification of QTLs for symbiotic nitrogen fixation and related traits in a soybean recombinant inbred line population

Authors: KRUEGER, CHARLES - University Of Missouri; Ray, Jeffery - Jeff; Smith, James - Rusty; DHANAPAL, ARUN - University Of Missouri; ARIFUZZAMAN, MUHMAMMAD - University Of Missouri; GAO, FEI - University Of Missouri; FRITSCHI, FLEIX - University Of Missouri

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/28/2024
Publication Date: 3/27/2024
Citation: Krueger, C.B., Ray, J.D., Smith, J.R., Dhanapal, A.P., Arifuzzaman, M., Gao, F., Fritschi, F.B. 2024. Identification of QTLs for symbiotic nitrogen fixation and related traits in a soybean recombinant inbred line population. Theoretical and Applied Genetics. 137:89. https://doi.org/10.1007/s00122-024-04591-3.
DOI: https://doi.org/10.1007/s00122-024-04591-3

Interpretive Summary: Soybeans are grown all over the world and are the most plentiful and important source of plant-based protein, providing high-quality protein meal for livestock, poultry, and fish. The ability of soybeans and bacteria, working together in a relationship, to convert nitrogen in the air into organic forms of nitrogen in soybean plants (called nitrogen fixation) is critical for producing the high levels of protein in soybean seeds. In this positive relationship, the soybeans receive organic nitrogen from the bacteria, and the bacteria receive simple sugars from the soybeans. In spite of this mutually beneficial relationship, soybean plants may still not have enough nitrogen to reach their full potential in terms of seed yield and total seed protein. The purpose of this research was to better understand the genetic factors that control the soybean-bacteria relationship to fix nitrogen from the air, accumulate organic nitrogen in the soybean, and provide enough sugars for the bacteria to have optimal growth. An improved understanding of these processes will facilitate the development of high-yielding varieties with high protein for sustainable soybean production in stressful environments. To accomplish these objectives, a family of plants was created consisting of 190 members derived from two soybean parents. Each family member was measured for nitrogen derived from the atmosphere, nitrogen concentration in the plant, and the ratio of carbon to nitrogen (C/N) in three growing environments. For all three traits, the family members did not perform equally across the three environments in relation to each other, but there were still impactful effects identified for nitrogen concentration and C/N. Using the genetic information from all family members, two newly identified sequences of DNA were found to be associated with nitrogen fixation and eight were found to be associated with C/N. Four of the eight DNA sequences associated with C/N were also found to be associated with nitrogen concentration in the plant. Some of the DNA sequences associated differently with the traits, depending on where the plants were grown. Sometimes DNA sequences interacted with each other to affect the three traits. The identification of the specific DNA sequences associated with these important nitrogen traits may help breeders develop improved soybeans with higher protein in the seeds.

Technical Abstract: Soybean [Glycine max (L.) Merr.] is cultivated worldwide and is the most abundant source of plant-based protein. Symbiotic N2 fixation (SNF) in legumes such as soybean is of great importance, however, yields may still be limited by N in both high yielding and stressful environments. To better understand the genetic architecture of SNF and facilitate the development of high yielding cultivars and sustainable soybean production in stressful environments, a recombinant inbred line (RIL) population consisting of 190 lines developed from a cross between PI 442012A and PI 404199 was evaluated for N derived from the atmosphere (Ndfa), N concentration ([N]), and C to N ratio (C/N) in three environments. Significant genotype x environment effects were observed for all three traits, and environment main effects were identified for [N] and C/N. A linkage map was constructed containing 3,309 single nucleotide polymorphism (SNP) markers. QTL analysis was performed for additive effects of QTLs, QTL x environment interactions, and QTL x QTL interactions. Ten unique additive QTLs were identified across all traits and environments. Of these, two QTLs were detected for Ndfa and eight for C/N. Of the eight QTLs for C/N, four were also detected for [N]. Using QTL x environment analysis, six QTLs were detected, of which five were also identified in the additive QTL analysis. The QTL x QTL analysis identified four unique epistatic interactions. The results of this study may be used for genomic selection and introgression of favorable alleles for increased SNF, [N], and C/N via marker assisted selection.