Sugarcane is an important cash crop of the entire world including India. It alone contributes to 75% of the worldwide sugar trade. Molecular markers are powerful tools and provide the basis for the estimation of genetic variability to start reasonable breeding program. Microsatellite markers have unique ability to determine the extent of genetic divergence among sugarcane genotypes. The objective of this study was to evaluate the genetic divergence of 12 early maturing sugarcane clones using 11 SSR markers. A total 55 alleles were found during the amplification of the primers out of which 21 alleles were found unique and 34 alleles were shared. The number of shared alleles per locus ranged from two out of five alleles in the case of primer NKS 1 and nine out of ten alleles in NKS 34. Similarly no. of unique alleles per locus ranged from one out of ten alleles in NKS 34, three out of six alleles in NKS 57. The primer pairs NKS 1 and NKS 8 generated considerably greater percentage of unique alleles. The PIC values revealing allelic diversity and frequency among the genotypes varied from 0.034 in case of NKS 48 to 0.778 in case of NKS 9 with an average of 0.549. Pair-wise combinations of CoSe15451 and CoSe15452 showed the highest similarity with the value of similarity coefficient (0.890). The lowest value of similarity coefficient was found to be 0.490 in the pair CoBln15501 and CoSe01421. The dendogram based on SSR marker analysis grouped the 12 sugarcane clones into four clusters which shows the CoSe15451 and CoSe15452 clones had maximum similarity and CoBln15501 and CoSe15452 clones had maximum diversity between each other.
A total of 56 alleles were obtained, of which 41 shared and 15 unique allelic variants were generated as the amplified product by polymerase chain reaction using eleven primer pairs. The PIC values revealing allelic diversity and frequency among the genotypes varied from 0.36 in the case of NKS 57 to 0.90 in the case of NKS 1 with an average of 0.62. The similarity coefficients revealing genetic similarity with respect to the size of the amplified products generated from targeted regions of the genome varied from 0.518 to 0.857 for the pairwise combinations amongst the thirteen entries under evaluation. Two Clusters were obtained when the phenol line was drawn at twenty-five similarity units. Cluster I consist of ten genotypes. The tri-genotypic cluster II consists of three genotypes. When phenol level drew at fifty similarity unit clusters I and II were further divided into sub-clusters. It is concluded that using an SSR marker is a very reliable approach for identifying diverse genotype(s) where phenotypic similarity of the cultivars leads to difficulty while selecting parents for hybridization.
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