Study of genetic diversity and evaluation of interspecific hybrids of Saccharum spp. using SSR markers.

Abstract

SSR marker analysis was done to assess the genetic diversity among 18 improved hybrids of Saccharum officinarum and 21 hybrids of Saccharum robustum. A total of 327 polymorphic loci were detected with 23 SSR primer pairs. The number of loci per marker ranged from five (NKS 8) to 22 (NKS 43). The primers NKS 34, NKS 43, NKS 33 and NKS 46 produced more number of polymorphic bands numbering 15, 22, 21 and 20, respectively. Marker size ranged from 103 bp to 1.3 Kb and 11 primers generated unique fingerprints for 10 genotypes. Four S. robustum specific markers, viz. SMC 477 GC(279), NKS 43(1049) & (143) and NKS 16(380), and five S. officinarum specific markers, viz. NKS 6(873), mSSCIR 54(1138), NKS 42(179), NKS 40(133) and NKS 45(213) were identified. The jaccard similarity coefficient ranged from 0.60 to 0.84 with a mean of 0.72. Most of the SSR based pair-wise comparisons exhibited least genetic similarities with coefficient values of less than 0.65. The molecular markers clearly grouped S. officinarum and S. robustum clones into two distinct clusters with moderate genetic diversity as indicated by Unweighted Pair Group Method. To investigate the introgression and stability of species specific alleles against the commercial genetic background, two generations of introgression breeding was done. First generation introgressed hybrids (IH1) showed 15.1% improvement for HR brix% (300 days) over the S. robustum parents. Second generation introgressed hybrids (IH2) showed 65.5% improvement for single cane weight and 24.6% for HR brix% at 300 days against S. robustum. Eighty six introgressed hybrids were screened with eight SSR primers which produced nine polymorphic markers between S. officinarum and S. robustum to identify the true hybrids. Among these markers, SMC 477 GC(279) and NKS 40(133) were stably transmitted with maximum frequency in the introgressed hybrids. Significant correlations were identified with marker SMC 477 GC(279) for fibre% (r=0.754; P<0.001) and NKS 40(133) for sucrose% (r=0.685; P<0.001). These markers also showed stability and strong correlation with the respective traits over successive generations of breeding and, hence, the marker trait association identified can be used in marker-assisted breeding programmes.