Construction of an integrated linkage map of sugarcane using unigene-derived microsatellite (SSR) markers

Sugarcane (Saccharum officinarum L.) is one of the key agro-industrial crops that produce raw sugar and bio-fuel ethanol, which contributes to sustainable national economy, food and nutritional security in tropical areas globally. Traditional sugarcane breeding practices are tedious and labour-intensive practice to develop elite high-yielding and resistant cultivars. Sugarcane improvement based on high-throughput techniques to develop traits linked DNA markers through establishing marker-trait associations using linkage analysis. The SSR and markers offer a user-friendly and cost-efficient genomic tool for marker-trait linkage analysis in crop species. In the current study, an integrated sugarcane genetic linkage map was constructed with SSR and TRAP molecular markers using 226 progenies derived from a bi-parental (UP 9530 × Co 86,011) mapping population. The biparental mapping population (266 progenies) was genotyped which generated a total of 815 polymorphic loci with 96 SSR and 11 TRAP primer combinations. Out of 815 markers, 324 markers were scattered onto 107 linkage groups (LGs) and for all the linkage maps, the cumulative genome length was found to be 7608.7 cM, with an average length of 71.11 cM per LG. The length of LGs was ranging from 0.06 to 238.44 cM, with an average of 23.48 cM between two adjacent markers and the number of markers per LG varied from 2 to 11. Out of 324 linked markers, 232 (71.60 %) were found to be single dose (1:1) and 92 (28.39 %) double single dose (3:1) in segregation pattern in genotyping. All the LGs with common markers on individual maps were merged to construct an integrated map using a map integration tool. Future research will be focused on validation of the linked markers in sugarcane involves a combination of phenotypic studies, molecular analysis, genetic mapping, and field trials. This ensures the marker is accurate, reliable, and applicable across different environments and genetic backgrounds. Moreover, the developed SSR-based linkage map will be a useful suit for understanding genetic architecture, marker-assisted breeding for improving yield and quality, identifying disease resistance genes, and accelerating genetic research in polyploid sugarcane and other related polyploidy crop species.