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.
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.
Genetic diversity in 92 sugarcane varieties of subtropical India was assessed using 30 morphological descriptors and 643 simple sequence repeat (SSR) marker loci. Out of the 30 morphological descriptors, 14 were found polymorphic, and significant variability was recorded for plant height, cane diameter and number of millable canes. Grouping traits like plant growth habit, leaf blade curvature and leaf sheath adherence were found to be predominantly monomorphic. There were a few pairs of varieties (e.g., CoP 9702 and CoP 9302, CoP 9301 and CoSe 01424, UP 05 and Co 1336, CoS 96258 and CoH 110) that showed similar DUS profiles except differing for a few descriptors. The STRU CTU RE profile suggest that all the 92 sugarcane varieties had admixtures and no subgroup had a pure unblemished structure profile. An average Nei's genetic distance of 0.49 was found to be a better measure of diversity, whereas, the average band informativeness (Ib av) value of all the 80 SSR primers was 0.434. Although, the mean Ib av values for EST-SSR and genomic-SSR primers were same (0.43), the range of Ib av of EST-SSR (0.04-0.85) was more compared to genomic-SSR (0.12-0.63) primers. The segregation of the varieties based on morphological traits was not in accordance with their geographical distribution or maturity groups, but principal component analysis was able to group the sugarcane varieties that had similar pedigree together. Results indicate that the SSRs have a potential use in the DNA fingerprinting of varieties to prevent any malpractice like unauthorised reregistration of a previously registered sugarcane variety under PPV&FR Act. The marker profiles could also be utilised for variety identification and release, since at present, it has been made mandatory to include it in addition to the morphological descriptors.
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