Molecular Diversity Analysis of Mid-late Maturing Sugarcane Clones Derived from Bi-parental and General Crosses Using SSR Markers

Abstract

Genetic diversity has been assessed based on morphological and agronomic traits. However, these traits are greatly influenced by environmental conditions and genotype × environment interactions, often leading to unreliable estimates of true genetic relationships. In contrast, molecular marker systems enable direct assessment of genetic variation at the DNA level, independent of environmental influences, thus providing a more accurate and stable measure of genetic diversity. The study aims to evaluate genetic similarity, clustering patterns, and intra-cross variability to facilitate effective parent selection and enhance genetic gain in sugarcane breeding programmes. The study was conducted during 2022–23 to characterise the molecular diversity among twenty mid-late maturing sugarcane genotypes derived from bi-parental and general crosses using Simple Sequence Repeat (SSR) markers. All the genotypes, along with one check, were planted at the research farm of Dr Rajendra Prasad Central Agricultural University (RPCAU), Pusa, in a Randomised Block Design with two replications.  Genomic DNA was isolated from young leaf tissues of all twenty genotypes. Eleven polymorphic SSR primer pairs were used for amplification of DNA, generating a total of 53 alleles, including 37 shared and 16 unique alleles. The number of alleles per locus ranged from three to seven. The Polymorphism Information Content (PIC) values ranged from 0.39 (SOSSR 48) to 0.78 (SOSSR 31), with an average of 0.61, indicating a high level of marker informativeness. Genetic similarity coefficients among the genotypes ranged from 0.800 to 0.892. UPGMA-based cluster analysis grouped the genotypes into four major clusters, largely corresponding to their parental lineage. Clones with common parentage were predominantly grouped together, whereas genotypes derived from the same cross but placed in separate clusters revealed substantial intra-cross genetic variability. The results demonstrate that SSR markers are highly efficient in detecting molecular diversity. It is concluded that using an SSR marker is a very reliable approach for identifying diverse genotypes where phenotypic similarity of the cultivars leads to difficulty while selecting parents for hybridisation.