Genome-Wide Association Mapping of Chlorophyll Dynamics and Seed Weight Under Contrasting Nitrogen Conditions in Soybean

Background: Nitrogen (N) availability is an important factor affecting soybean growth, photosynthetic capacity, and seed development. Identification of genomic regions associated with N-responsive traits may enable the development of cultivars with enhanced performance under reduced fertilizer inputs. Methods: A soybean diversity panel consisting of 193 accessions was evaluated under N-deficient (N−) and N-sufficient (N+) conditions during the 2024 and 2025 growing seasons. Best linear unbiased predictors were estimated for SPAD area under the curve (SPAD AUC) and 1000-seed weight (SW) under N− and N+ conditions and used for genome-wide association analysis with 37,429 single-nucleotide polymorphism (SNP) markers. Results: Six loci associated with SPAD AUC under N−, four with SW under N−, and 10 with SW under N+ exceeded the Bonferroni-corrected significance threshold, whereas no significant loci were detected for SPAD AUC under N+. Candidate genes near significant loci encoded proteins including receptor-like kinases, WRKY transcription factors, peroxidases, and protein kinases, which are involved in signal transduction, transcriptional regulation, oxidative stress responses, carbohydrate metabolism, and developmental processes. Allelic effect analyses revealed significant phenotypic differences between favorable and unfavorable alleles at representative loci, supporting the biological relevance of the identified associations. Conclusions: These findings provide insight into the genetic architecture of chlorophyll accumulation and seed weight under contrasting N environments and identify candidate loci that may facilitate the improvement of nitrogen-use efficiency and agronomic performance in soybean.