Marker-trait association study for sucrose and yield contributing traits in sugarcane (Saccharum spp. hybrid)

Linkage disequilibrium (LD)-based marker-trait association (MTA) was used to identify markers for sucrose and yield contributing traits in a panel of 108 sugarcane genotypes from sub-tropical India. Population structure (Q), kinship (K), and MTA study exploited a set of 989 marker loci generated from 123 genomic- and expressed sequence tag-SSR primers. The mixed linear model (MLM) coupled with a modified algorithm for population structure (Q) analysis was able to control both type I and type II errors and provided a deeper understanding of the genetics, population stratification and its manifestations on LD in the sugarcane genome. Significant associations were identified for four markers with cane diameter, seven markers each with cane length and number of millable canes (NMCs), eleven markers with number of nodes, six with sucrose per cent, and five markers with average cane weight. A total of 15 markers stable for all the 3 years of study explained 57 % trait variation for NMCs, 34 % for cane width, 27 % for cane length, 20 % for sucrose content, and 19 % for number of nodes. The frequent deviation of structure-based profiles from pedigree-based grouping in this complex heterozygous system reinforced the importance of using genotypic data for selection and breeding. The results contribute to a deeper insight of the complex genome and the identified MTAs could be exploited to fine-tune marker-assisted breeding programmes in genetically complex sugarcane crop.