Evaluation of microsatellite markers for genetic diversity analysis among sugarcane species and commercial hybrids

Increasing sugar productivity is the main concern of sugarcane (Saccharum officinarum) breeding programs. The complexity and size of the sugarcane genome is a major limitation in genetic improvement. Characterization of sugarcane wild germplasm provides essential information on genetic diversity that breeders utilize for crop improvement. The objective of this study was to evaluate the utility of 7 sugarcane cDNA derived microsatellite markers (SCM), 9 genomic microsatellites and 16 unigene sugarcane microsatellite markers (UGSM) for accessing genetic diversity and interrelationships in sugarcane germplasm collections. Eighty four genotypes from the Saccharum barberi, S. spontaneum, S. officinarum, Indian and non Indian commercial cultivars were used in the study. The UGSM and SCM yielded a higher mean number of alleles per locus and superior polymorphism information content (PIC) values than the sugarcane genomic markers (SGM). The number of amplified fragments ranged from 4 (UGSM312) to 14 (UGSM667) indicating that high polyploidy and hetrozygosity exist in sugarcane. The Saccharum spontaneum clones retained significantly higher number of DNA fragments (20%) than S. barberi clones (14%). Based on cluster analysis, the 84 Saccharum species clones and commercial cultivars were grouped into 10 distinct classes. Clusters showing grouping of individual genetic relationship among the sugarcane species clones, Indian and non Indian sugarcane commercial cultivars based on geographical origin, available pedigree information, adaptation zone and morphological characters. The cultivar B29-228, S. spontaneum clones N-56, N-75 and Inter-specific hybrids (ISH-112) were found most diverse pairs but unfortunately these were not extensively utilized in the development of other sugarcane cultivars. These sources which have desirable agronomic characteristic should be used as progenitors for the creation of cultivars with a wider genetic base.