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Diversity and DNA fingerprinting of sugarcane (Saccharum officinarum L.) genotypes using microsatellite markers

Muhammad Khalid, Zabta Khan Shinwari, Ahmad Zubair, Humaira and Malik Ashiq Rabbani

Large genome size and deficiency of adequate informative molecular markers bottlenecked genetic improvement in sugarcane. DNA fingerprinting and diversity analysis of sugarcane genotypes provide essential genetic evidences that breeders could utilize in crop improvement program. To investigate the genetic diversity based on 46 microsatellite markers, 16 promising exotic sugarcane genotypes were utilized. Twenty (20) out of 46 microsatellite markers were examined at Germplasm Evaluation Lab of BCI, National Agricultural Research Centre, Islamabad, whereas the remaining 26 were tested at the genomics lab of SIU-Carbondale, USA. The genotypes portrayed substantial level of genetic polymorphism. Ratio of monomorphic loci was 28.66% out of 164, whereas polymorphic loci were 71.34% with an average 3.57 alleles/locus. Out of 46 microsatellite markers, 10 (21.74%) produced monomorphic, 13 (28.26%) produced polymorphic bands and 23 (50%) produced both monomorphic and polymorphic bands. SSR markers SCM16 and UGSM574 produced maximum number of bands (10), whereas markers SMC7CUQ, SMC1604SA, MCSA053C10, SOMS118, UGSM154, UGSM312, mSSCIR3, SMC851MS, SOMS156, SMC336BS and SMC1751CLproduced the least number of band i.e., 1. In all 16 sugarcane genotypes, the PIC value of the polymorphic loci ranged between 0.009 and 0.947 with the mean value of 0.490/locus. Mean number of alleles/polymorphic locus was 3.30, whereas mean number of alleles/locus was calculated as 3.57. Through similarity matrix extent of genetic relatedness among the sugarcane genotypes was determined. Genetic similarity as pair-wise ranged between 71 to 93%. Minimum genetic similarity was noted 71% between genotypes CP89831 and MS94CP15, while the maximum between genotypes S97CP288 and MS99HO391. The phenogram categorized the 16 cultivars into main four (4) clusters/groups. Cluster-1/group-1 consisted two (2) genotypes only, 2nd cluster consisted of five (5) genotypes, whereas 3rd cluster consisted only one genotype (MS92CP979) which was branched solitary. The 4th cluster was comparatively a large one and consisted of eight genotypes. This was suggested that the genotypes showed maximum level of genetic polymorphism might be further utilized in sugarcane varietal development and breeding plans.

To Cite this article: Khalid, M., Z.K. Shinwari, A. Zubair, Humaira and M.A. Rabbani. 2019. Diversity and DNA fingerprinting of sugarcane (Saccharum officinarum L.) genotypes using microsatellite markers. Pak. J. Bot., 51(4): DOI:

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