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SSR-based assessment of genetic diversity and population structure in 144 sugarcane genotypes
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DOI：10.1016/j.cropd.2026.100139.png)
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Abstract
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Genetic diversity is crucial for breeding program to develop improved varieties. Estimating genetic diversity and population structure among genotypes of a given population is compulsory to select the most divergent parents in breeding programs. This study evaluated 144 sugarcane genotypes using 20 microsatellite markers. The markers produced 482 alleles, and 88.59% (434) of the alleles were polymorphic. The number of alleles per locus ranged from 14 to 40, with a mean of 24.1, while polymorphic information content values ranged from 0.42 to 0.92, with an average value of 0.67 for all markers evaluated. In this study, high genetic diversity within the population was recorded with an average value of number alleles of 1.75, effective alleles of 1.53, Shannon's information index of 0.45, Nei's gene diversity of 0.30, and polymorphic percentage loci of 79.25%. Among the populations, India showed the highest observed number of alleles (1.86), the effective number of alleles (1.60), Shannon's information index (0.49), Nei's gene diversity (0.34), and unexpected heterozygosity (0.34). Thus, the genotypes from India could be a source of divergent parents to use in sugarcane breeding programs. Cluster analysis using the UPGMA method showed four main clusters, further grouped into eight sub-clusters. Population structure analysis also identified six subpopulations within the genotype set. AMOVA analysis revealed that 96% and 4% of the total variability was attributed to within- and between-population variation, respectively. The principal coordinate analysis showed that the distribution of genotypes in the scatter plot was considerably dispersed, indicating a wide genetic diversity between genotypes originating from different populations. The overall results offer valuable information for future genetic study of the sugarcane genotypes and better utilization of sugarcane germplasm resources in sugarcane breeding.
Keywords:
Allele
Cluster
Heterozygosity
Microsatellite markers
Polymorphic loci
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