Screening of Microsatellite Loci for Identifying Genome Barcoding of Cotton Cultivars

Abstract

Microsatellites or simple sequence repeats (SSRs) loci with high information content, reproducibility and locus specificity can be used effectively to construct DNA barcode in plant. In this study, 12 cotton cultivars derived from different germplasm pedigrees and planted widely in three ecological cotton growing areas were selected to screen the SSR loci with high polymorphism. Based on our newly updated high-density genetic linkage map from G. hirsutum×G. barbadense BC 1 mapping population, we selected 51 primer pairs with clear amplification products and high polymorphism from 376 genome-wide SSR primer pairs. In total, 155 polymorphic loci in 12 cultivars were produced by using the selected 51 primer pairs. Alleles ranging from two to seven with an average of 3.04 were detected by each SSR primer pair. Of them, 26 SSR primer pairs, which amplified SSR loci were tagged on corresponding 26 chromosomes in cultivated tetraploid cotton species, were recommended as first selected primer pairs to establish DNA barcode of cotton cultivars, and other 25 SSR primer pairs could be used as candidate primer pairs. DNA barcodes of 12 cultivars were further constructed effectively using these microsatellite loci with high polymorphism. In the future, these microsatellite loci can be used to construct DNA barcode for a large number of cotton varieties, and applied effectively in the identification of genuineness and purity in cotton cultivar seeds.