Single Nucleotide Polymorphism for Assessing Genetic Diversity in

Single Nucleotide Polymorphism (SNPs) has become the most widely used markers in many current genetic applications. We analyzed the population genetic of Vitex trifolia L. collected from five different locations of Western Ghats of India. To assess genetic diversity we conducted sequencing of the genomes of five populations of V. trifolia and compared the data to a reference genome assembly. Three SNPs were discovered when compared the sequence of five different populations by direct partial sequencing of genes (rbcL). UPGMA clustering indicated two main groups. Our genome-wide assessment of SNP variation in V. trifolia revealed low levels of genetic variation. This approach determining population genetic structure using SNPs from genome-wide comparison constitute a framework for high-throughput analyses genetic diversity in plants, particularly in species with limited genetic diversity.