Identification of quantitative trait loci controlling sucrose content based on an enriched genetic linkage map of sugarcane ( Saccharum spp. hybrids) cultivar ‘LCP 85-384’

Sucrose content is one of the most important traits considered in sugarcane breeding. Since sugarcane cultivars possess >100 chromosomes (2 n = 100–130) and are genetically complex polyploid and aneuploids, identification of quantitative trait loci (QTLs) associated with sucrose content is considered the best option to improve sucrose content through molecular breeding. A preliminary genetic linkage map of Louisiana sugarcane cultivar ‘LCP 85-384’ from a previous study was enriched using 65 additional polymorphism simple-sequence-repeats (SSR) primer-pairs to identify more co-segregated and homologous groups (CGs and HGs) and QTLs controlling sucrose content. Eighty-four SSR primer-pairs produced 456 markers, of which 441 were polymorphic. Both simplex (993) and duplex (225) amplified fragment length polymorphism (AFLP) and target region amplification polymorphism (TRAP) markers reported previously were also included to construct the LCP 85-384 map. These simplex and duplex markers were assigned to 108 CGs successfully using JoinMap ® . This map had a cumulative genome length of 7406.3 cM that included 675 AFLP (69.8 %), 90 TRAP (9.3 %), and 202 SSR (20.9 %) markers. The 202 SSR markers were assigned to 65 CGs and 8 HGs. Based on this map, 24 putative QTLs affecting sucrose content were identified. Five QTLs were unlinked and the other 19 QTLs were located on nine CGs within four HGs. Of these QTLs, 11 had an effect in both plant-cane (20.33 %) and first-stubble (25.68 %) crops. A higher efficiency of QTLs’ identification with AFLP, TRAP and SSR markers in such a genetically complex crop, proposes its wider utility in molecular breeding in sugarcane.