Simple sequence repeat polymorphism in Quality Protein Maize (QPM) lines

Abstract

A set of 23 Quality Protein Maize (QPM) lines, including 13 lines developed in India and 10 lines at CIMMYT (International Maize and Wheat Improvement Center), Mexico, was analyzed using microsatellite or simple sequence repeat (SSR) markers. Polymorphic profiles for 36 SSR loci have aided in differentiating the QPM inbred lines. The study resulted in identification of SSR markers, such as bnlg439, phi037, bnlg125, dupssr34 andbnlg105, with high polymorphism information content in the selected QPM genotypes. Detection of 30 unique/rare SSR alleles could contribute to effective differentiation of 14 of the 23 QPM inbreds. An opaque2-specific microsatellite marker, phi057, also facilitated differentiation of opaque2-carrying QPM inbreds from the non-opaque genotypes. Analysis using SSR markers indicated high levels of heterozygosity in majority of the Indian QPM lines and in one CIMMYT QPM inbred, CML188. Cluster analysis using SSR data, followed by canonical discriminant analysis, clearly distinguished the Indian QPM inbreds from those developed at CIMMYT. The cluster patterns were largely in congruence with the available pedigree information of the QPM inbreds studied. The study demonstrates the effectiveness of SSR markers in QPM genotype discrimination and analysis of genetic relationships, and could potentially contribute towards effective utilization of the elite QPM germplasm in Indian maize breeding programmes.