STUDY OF GLOBAL PANEL OF SOYBEAN ACCESSIONS FOR NITROGEN USE EFFICIENCY USING ASSOCIATION MAPPING

Author

• Rita Bhandari, Southern Illinois University CarbondaleFollow

Date of Award

5-1-2026

Degree Name

Master of Science

Department

Plant, Soil, and Agricultural Systems

First Advisor

Kantartzi, Stella

Abstract

Soybean (Glycine max [L.] Merr.) is a leguminous crop valued for its high protein, oil content, and other essential nutrients. Global production has significantly increased, with Brazil, the United States, and Argentina being the leading producers. In the U.S., Illinois, Iowa, and Minnesota rank as the top soybean-producing states. Nitrogen (N) is a predominant nutrient required for optimal soybean growth and productivity, particularly in high-yielding varieties. While biological nitrogen fixation and soil mineral N supply part of the plant’s N requirement, synthetic fertilizers are commonly used to meet the remaining demand. However, only 30–50% of applied N is taken up by plants, with the rest lost to the environment, contributing to issues such as eutrophication and greenhouse gas emissions. Enhancing nitrogen use efficiency (NUE) is a key strategy for achieving sustainable yield improvements. Breeding for improved NUE requires identifying the genes underlying NUE-related traits as well as the lines with superior genetic value. Considering this, greenhouse and field experiments were conducted in 2023 and 2024 to identify single-nucleotide polymorphisms (SNPs) and candidate genes significantly associated with seed weight, SPAD score (an indicator of chlorophyll content), 100-seed weight, and protein content traits linked to NUE, in global soybean accessions through association mapping. In both experiments, population structure and genome-wide association analysis (GWAS) were performed using 1,242 high-quality SNP markers. The GWAS was carried out using two consecutive years of SPAD data, and protein content data in the greenhouse experiment revealed one significant SNP each for SPAD score and protein content, located on chromosomes (Chr.) 15 and 3, respectively. Within the GlymaWm82.a2 genome assembly, three candidate genes were identified within 10 kb flanking regions of the SNP associated with SPAD score, and one candidate gene was found near the SNP associated with protein content. Among these, a gene located on Chr. 3 encodes a RING/U-box superfamily protein, which has been previously associated with protein content in soybeans. Likewise, the field experiment analysis identified 30 significant SNPs under N-treated conditions and 49 under without N fertilizer conditions. A total of 63 candidate genes were identified under N-treated and 107 under without N fertilizer conditions, based on the Glyma.Wm82.a2 genome within 10 kb flanking regions of each significant SNP. Among these, six genes on chromosomes 1, 4, 6, 9, and 16 were related to seed weight, photosynthesis, N allocation and fixation, and chloroplast development. Overall, our findings contribute to a better understanding of the molecular mechanisms underlying NUE.