Characterization of Indian and exotic quality protein maize (QPM) and normal maize (Zea mays L.) inbreds using simple sequence repeat (SSR) markers

Abstract

Polymorphism analysis and genetic diversity of normal maize and quality protein maize (QPM) inbreds among locally well adapted germplasm is a prerequisite for hybrid maize breeding program. The diversity analyses of 48 maize accessions including Indian and exotic germplasm using 75 simple sequence repeat (SSR) markers yielded 258 scorable alleles, out of which 251 alleles were polymorphic with an average of 3.35 alleles per locus. The polymorphism information content (PIC) values of all the polymorphic primers across the maize genotypes varied from 0.11 to 0.91, with an average value of 0.56. Di-nucleated repeats showed more number of average alleles (4.2) with more mean PIC value (0.61) than tri-, tetra-, penta- and hexa- nucleotide repeats. Gene diversity (He) was in the range of 0.11 ( umc 1766) to 0.81 ( mmc 0371 and bnlg 1600) with an average value of 0.59, while heterozygosity (Ho) was observed with an average of 0.19, ranging from 0.02 ( umc 1495) to 0.98 ( umc 1906). Inbreeding coefficient (F) varied from 0.06 ( umc 2075) to 1.00 (15 SSR loci). Thus, the present study resulted to the identification of highly polymorphic SSR loci mmc 0371, umc 2364, umc 1568, bnlg 1600, phi 026, umc 2071 and bnlg 1904 by considering the parameters of PIC value (≥0.74), gene diversity (≥0.75), inbreeding coefficient (≥0.62) and polymorphic alleles (≥4). These 7 polymorphic primers can be effectively used in a molecular breeding programs and quantitative trait loci (QTL) mapping studies since they exhibited very high polymorphism over other loci. Genotype pairs VQL 2 and CML 173 was observed to serve as ideal parents for mapping modifiers since they differ significantly for tryptophan content and also showed lowest similarity of 27% between them. Among all the genotypes, V 370 and B 06-7 (22%), V 25 and CM 152 (22%) and V 341 and CM 145 (24%) genotype pairs can be used in maize hybrid breeding programs for producing high yielding hybrids. Key words: Quality protein maize (QPM), gene diversity, heterozygosity, inbreeding coefficient, SSR markers, allele frequency.