Rapeseed (Brassica napus L.) is a major agricultural crop with diverse applications, particularly in the production of seed oil for both culinary use and biodiesel. However, its photosynthetic efficiency, a pivotal determinant of yield, remains relatively low compared with other C3 plants such as rice and soybean, highlighting the necessity of identifying the genetic loci and genes regulating photosynthesis in rapeseed. In this study, we investigated 5 photosynthesis traits and 5 leaf morphology traits in a natural population of rapeseed, and conducted a genome-wide association study (GWAS) to identify significantly associated loci and genes. The results showed that the gas-exchange parameters of the dark reactions in photosynthesis exhibited a significant positive correlation with the chlorophyll content, whereas they showed a weaker negative correlation with the leaf area. By GWAS, a total of 538 quantitative trait nucleotides (QTNs) were identified as significantly associated with traits related to both leaf morphology and photosynthesis. These QTNs were classified into 84 QTL clusters, of which, 21 clusters exhibited remarkable stability across different traits and environmental conditions. In addition, a total of 3,129 potential candidate genes were identified to be significantly associated with the above-mentioned 10 traits, most of which were shared by certain traits, further indicating the reliability of the findings. By integrating GWAS data with GO enrichment analysis and gene expression analysis, we further identified 8 key candidate genes that are associated with the regulation of photosynthesis, chlorophyll content, leaf area, and leaf petiole angle. Taken together, this study identified key genetic loci and candidate genes with the potential to improve photosynthetic efficiency in rapeseed. These findings provide a theoretical framework for breeding new rapeseed varieties with enhanced photosynthetic capabilities.
