Sucrose-Specific Genic Microsatellites to Analyse the Genetic Structure Among the Commercial Hybrids and Clones of Interspecific and Intergeneric Origin in Saccharum Complex

Mining of non-redundant transcript assemblies from Saccharum spp. associated with sucrose synthesis located a higher number of repeat units in the open reading frames (ORF) of sucrose biosynthesis pathway. Functional annotation of these SSR motifs revealed that the two paralogs of soluble acid invertase (SAI) consisting of trimer motifs (TGC) 5 and (TTC) 10 were located in the coding region of the genome (ORFs). Molecular diversity analysis of the 44 unigenic microsatellite markers associated with six major sucrose-metabolizing enzymes indicated that Shannon’s information index (SI) was highest for neutral invertase (0.8743), but lowest for SSR allele specific to cell wall invertase (0.4506). Dendrogram based on dissimilarity coefficients grouped 40 genotypes into two major clusters. Cluster I had 26 genotypes that comprised high-sucrose Indian Co canes, while 14 low-sugar clones of S. spontaneum , S. officinarum and Erianthus genotypes formed cluster II. Population structure analysis revealed the presence of three different sub-populations with 24 high-sucrose clones grouped into two clusters and the remaining 14 low-sugar genotypes in a separate cluster. The first two factors in principal component analysis (PCA) had the highest contribution in variability as PC1 (34.47%) and PC2 (11.76%). Results of PCA from this study highlighted the importance of eight Indian Co canes (Co 11015, Co 94012, Co 87044, Co 86011, Co 86002, Co 86032, Co 85002 and CoC 671) exhibiting high diversity for sucrose-specific SSR alleles and utilization of these clones is expected to enhance the genetic gain for sucrose content in sugarcane improvement programmes. The SSR mined were of highly informative and able to distinguish high- and low-sugar genotypes, and are candidate markers for sucrose content. After marker traits association analysis, validation and precise estimation of marker effect could serve as markers for selecting high-sucrose genotypes in sugarcane.