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Ninety two sugarcane varieties from sub-tropical India were subjected to molecular profiling with 174 simple sequence repeat markers and characterized for 23 qualitative (morphological descriptors) and nine quantitative traits that directly or indirectly contribute to yield and juice quality. Using STRUCTURE-based population stratification study and a mixed linear model for marker-trait association (MTA) analysis, a total of 60 MTAs were identified for 22 qualitative traits that were able to explain a significantly higher (up to 40%) proportion of the phenotypic variations compared to all the previous reports of MTA studies in sugarcane. In addition, 21 MTAs stable over the three years of study were also identified for nine quantitative traits that explained 16-37% of the total trait variation. It could be concluded that the qualitative traits that are governed mostly by one or a few genes are more responsive to MTA studies and hence have a better potential to be adopted in marker-assisted breeding programmes in sugarcane. The MTAs identified in this study could also find significant applications in upcoming more stringent IP regime, which may necessitate tracking of specific alleles integrated in breeding programmes.

Identification of marker-trait associations for morphological descriptors and yield component traits in sugarcane