GWAS of Leaf Morphological and Chlorophyll-Related Traits Provides Genetic Resources for Improving Photosynthetic Traits in Sugarcane

Photosynthesis is the ultimate source of energy for crop productivity, and leaf morphology as well as chlorophyll content are traditional, indirectly related traits of photosynthesis. However, the genetic basis of these traits remains unexplored in sugarcane. In this study, we conducted genome-wide association studies (GWAS) to identify loci controlling nine photosynthesis-related traits, including four leaf morphological traits (leaf length, leaf width, leaf ratio, and leaf area) and five chlorophyll-related traits (chlorophyll a, chlorophyll b, chlorophyll a/b ratio, total chlorophyll, and SPAD value). The analysis was performed using whole-genome resequencing data from 219 elite, globally diverse sugarcane materials evaluated at two locations across two years (four environments). Based on 5,964,084 high-quality single nucleotide polymorphisms (SNPs), we identified 308 GWAS-significant SNPs (p ≤ 1.5 × 10−6) that were consistently detected in two or more environments, defining 97 GWAS-associated intervals across 30 chromosomes. Within these intervals, 98 putative genes were predicted, of which 20 genes in 16 intervals were potentially associated with leaf photosynthesis based on functional annotation and literature mining. These candidates are primarily involved in pathways related to ADP-ribosylation factors, ATP-dependent Clp protease proteolytic subunits, protein kinases, F-box proteins, MYB and WRKY transcription factors, UVR8, pentatricopeptide repeat-containing (PPR) proteins, Aux/IAA proteins, monogalactosyldiacylglycerol (MGDG) synthase, Orange (OR) proteins, PsbP domain-containing (PPD) proteins, and chloroplast stem-loop binding proteins of 41 kDa b (CSP41b). Ten genes were prioritized for future functional validation. Notably, these photosynthesis-related structural and pigment traits represent a different regulatory layer from direct gas exchange parameters (e.g., net photosynthetic rate), and their associations with actual photosynthetic efficiency require further validation. Nevertheless, this study provides novel candidate genes and molecular markers to assist marker-assisted breeding aimed at improving the photosynthetic structure and light-harvesting capacity of sugarcane.