Molecular identification and genetic diversity analysis of sugarcane clones by SSR markers

Sugarcane is one of the important crops with high heterozygosity and phenotypic polymorphism. Varietal identification and characterization is one of the important aspects in any breeding programme. Forty sugarcane clones from Pre -zonal varietal trial (PZVT) conducted at Ugar, North Karnataka were characterized through Simple sequence repeats (SSR) markers using a set of 15 sugarcane specific primer pairs which amplified a total of 164 alleles with an average of 10.93 alleles per pair. Primer NKS 33 was highly polymorphic and produced more than 15 polymorphic alleles and was unique in all the clones studied. Six primers i.e., NKS 2, NKS 6, NKS 7, NKS 40, NKS 42 and NKS 11 were moderately polymorphic by producing 10 to 13 alleles. Percentage of polymorphic bands ranged from 75.0 % (NKS 3) to 100.0 % (NKS 40 and NKS 42). Primers viz., SMC 1039 GC, mSSCIR 54, NKS 2, NKS 7, NKS 9, NKS 33, NKS 40, NKS 42 and NKS 11 were highly informative and generated above 85.0 % of polymorphic bands. Among the primers used, SMC 1039 GC, NKS 33, NKS 42 and NKS 43 produced the maximum number of unique markers in different clones and hence the combined application of these primers will be useful in unambiguous varietal identification. The cluster analysis based on the genetic similarity matrix grouped the 40 clones into two major clusters CI and CII. The largest cluster CII contained the maximum of 38 clones. Cluster C II was further sub-grouped into IIa, IIb, IIc and IId and each sub-cluster comprised 7, 11, 6 and 14 clones respectively. The unique DNA markers and the genetically diverse combinations identified in the present study will enhance the exploitation of genetic diversity present in the clones in breeding programmes and promising twenty eight entries for yield and quality.