Genome-wide association studies of leaf photosynthetic gas exchange parameters in sugarcane

Introduction As the global food crisis intensifies, improving photosynthesis is a primary strategy to enhance crop yield. Methods The analysis was based on whole-genome sequencing data from updated abstract based on this version. 219 elite sugarcane clones of worldwide origin, grown across two sites over two years. The genetic bases of intercellular CO2 concentration (Ci), net photosynthetic rate (A), transpiration rate (E), and stomatal conductance (Gs) were investigated across four environments using 5,964,084 high-quality single nucleotide polymorphisms (SNPs). Results and discussion A total of eight genomic intervals associated with gas exchange parameters were identified on six chromosomes (2A, 2C, 4B, 5B, 6A, and 8C), encompassing 10 significant SNPs within 20-kb windows. These SNPs showed P-values below 1.5 × 10 -6 and were consistently detected in at least two environments. Among the eight predicted genes located within these intervals, three genes were identified as putative candidates affecting leaf photosynthesis. These genes are related to a WRKY transcription factor, the UV-B (Ultraviolet-B) receptor UVR8, and an R2R3 Myb protein. Overall, this study provides valuable molecular markers and candidate genes that could facilitate marker-assisted breeding for improved photosynthetic efficiency in sugarcane.