Genetic structure of populations is under constant pressure from varying geographical conditions that induce phenotypic plasticity in insects. Spatial distribution of 15 populations of Indian eri silkworm, Samia cynthia ricini originated at various altitudes of sub Himalayas based on Euclidean distance realized from yield attributes showed two population clusters irrespective of their place of origin and altitude. However, DNA amplification profile by inter SSR (ISSR) markers showed genetic variations among the populations depend on low and high altitudes. One ISSR locus each specific to high and low altitude population was identified. The locus from high altitude showed deviation from Hardy-Weinberg equilibrium but that from low altitude was in neutrality suggests that the high altitude loci could be under pressure from the altitudinal variations. In association with different yield traits, 18 loci were identified. Of which, three markers showed association with more than one trait indicative of pleiotropic influence. Stepwise addition of markers enhanced the correlation between markers and the associated trait pointed to polygenic influence. Association of markers with altitude and yield traits suggests an imperative relation of rare genetic loci with gene-environment interaction and phenotypic variability in S. c. ricini.
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