Association Mapping for Sugarcane Quality Traits at Three Harvest Times

Sugarcane is a major crop cultivated globally for sugar and bioenergy production, with increasing relevance as a biomass source. Association mapping studies, in turn, identify markers associated with target traits that may assist genotype selection. Here, we used a diversity panel comprising 100 sugarcane genotypes to investigate the clustering patterns using phenotypic data, i.e., sugar content (Pol%Cane) and fiber, and Amplified Fragment Length Polymorphism (AFLP) markers, and perform association mapping to identify marker-trait associations (MTAs) that are consistent across harvesting times, i.e., autumn, winter and spring harvest, and across 2 years for the spring harvest. The K-means clustering of phenotypic and genotypic data revealed discontinuities among genotypes, indicating a distribution into two groups with high intra- and inter-group diversity. A subset of 640 AFLP markers across 93 genotypes was selected after quality control and subjected to association analysis via the Bayes C method. Different sets of MTAs were detected across harvest times for each trait, with each set collectively explaining 68.44-99.75% of the phenotypic variation (R-2). The detection in more than one harvest time was observed for 32 and 12 MTAs for Pol%Cane and fiber, respectively, while none was detected in all the harvest times. The most important markers selected by the stepwise process individually explained 1.61-67.55% of the phenotypic variation, with highlights for the MTAs with high individual R-2 values and/or detection in two or more harvest times with consistent positive effects, which may correspond to new genomic regions associated with Pol%Cane and fiber and should be further investigated.