Analysis of genetic divergence and population structure through microsatellite markers in normal and quality protein maize genotypes from NW Himalayan region of India

Abstract

Maize is a self-compatible but largely cross pollinated crop and considered as the staple food in many developing countries. The present study was designed to examine the best polymorphic SSR markers of any maize variety and the assessment of population structure variation and genetic diversity among normal and quality protein maize genotypes. The markers used were found highly polymorphic, that can be effectively used for maize genotypes across the geographical regions. The PIC values for all SSR markers in 47 maize genotypes varied from 0.20 to 0.85 with a mean of 0.57 whereas, gene diversity ranged from 0.23 to 0.86. On the basis of SSR analysis and obtained PIC value (≥ 0.75), gene diversity (≥ 0.79), inbreeding coefficient (≥ 0.97) and polymorphic alleles (≥ 8), six highly polymorphic SSR loci, umc2071, umc1077, umc2163, umc1804, phi026 and umc1799 were observed. The clustering of the maize genotypes was found to be largely based on their centre of development, quality nature and parentage involved. The clustering of the maize genotypes was largely based on their centre of development, quality nature and parentage involved. The genotype CM212 is one of the parent of VQL1 which was converted through MAS, hence clustered with CM212. Likewise, the QPM inbred line VQL373 was derived from the V373 recipient parent through marker assisted conversion, hence clustered together. The finding of this study showed parentage influencing more than the quality related genes. The inferred ancestry at K = 2 suggested that the maize genotypes were grouped into two populations.