Characterization of Simple Sequence Repeat (SSR) Markers and Genetic Relationships within Cultivated Peanut (Arachis hypogaeaL.)

Abstract

AbstractA total of 709 SSR markers were collected from public databases and 556 SSRs passed an initial screen and were used to characterize 16 peanut (Arachis hypogaea) genotypes. PIC (polymorphism information content) scores and heterozygosity indices for each marker were calculated to assess the genetic diversity revealed by SSR markers and genetic distances were estimated from shared allele distances for construction of a cladogram by the Neighbor-Joining method to illustrate the genetic relationships among the genotypes. Two hundred thirty-five (42.27%) markers showed polymorphisms in these genotypes. The average heterozygosity estimated from these 556 SSRs was 0.225 with a range of 0 to 0.992 and the average PIC was 0.209. The average number of alleles per SSR was 2.5 with a range of 1 to 13. However, 410 SSR markers had only one allele, confirming that diversity of cultivated peanuts is very limited. Among the polymorphic SSR markers, 26.4% were dinucleotide GA repeat motif markers, followed by dinucleotide CT (10.4%), and trinucleotide TAA (9.6%). The dinucleotide and trinucleotide repeat motifs are the most abundant type of SSRs, and dinucleotide GA repeat motif shows a higher polymorphism in comparison to other types. The genetic relationships revealed from the cladogram are in agreement with the pedigrees and origins of the tested peanut genotypes, indicating that these SSR markers are useful tools for evaluation of genetic diversity in peanuts.