Development And Characterization Of SSR Markers Providing Genome-wide Coverage And High Resolution In Maize

Simple sequence repeats (SSRs) also known as microsatellite DNA have been developed rapidly in recent years, which is a specific primer PCR-based molecular marker technology. SSRs are tandemly repeated mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide sequence motifs flanked by unique sequences. SSRs have been the genetic markers of choice, because they are easy to score, and have multiallelic nature, codominant inheritance, and clear advantages over restriction fragment length polymorphism (RFLP) and amplified fragment length polymorphism (AFLP) markers as well as SNP markers in terms of technical simplicity, throughput level and automation. SSRs are abundant and well distributed throughout the maize genome, which can be employed as a preferred marker system. SSR markers have been utilized extensively in maize to characterize the genetic structure and diversity, construct phylogenetic trees and define potential heterotic groups, and identify unique sources of allelic diversity.In this study, SSR motifs were identified across the whole genome using MISA, and a large number of SSR loci was observed in17genotypes. We analyzed the composition and distribution of SSR loci, and some representative primers were chose to experimental validation, the main results are summarized as follows:1. A total of264,658SSRs were identified across the17genomes, with an average of135,693SSRs per genome. Marker density was one SSR every of15.48Kb.(C/G) n,(AT)n,(CAG/CTG)n and (AAAT/ATTT)n were the most frequent motifs for mono, di-, tri-, tetra-nucleotide SSRs, respectively.2. SSRs were most abundant in intergenic region and least frequent in UTR regions as revealed by comparing SSR distributions of three representative resequenced genomes.3. Comparing SSR sequences and e-PCR analysis among the17tested genomes created a new database including111,887SSR loci could be developed as polymorphic markers in silico. Among these markers、58.00%、26.09%、7.20%、3.00%、3.93%and1.78%of them had mono, di-, tri-, tetra-, penta-and hexa-nucleotide motifs, respectively, and polymorphic information content for SSRs with these motifs varied from0.05to0.83, with an average of0.31in the17tested genotypes. 4. Experimental validation of polymorphic SSR markers showed that over70%of the primer pairs could generate the target bands with length polymorphism, and these markers would be very powerful when they are used for genetic populations derived from various types of maize germplasm that were sampled for this study.