Investigation on genetic discriminating ability of EST-SSR primers across the Indian population of yellow stem borer (YSB)

The present study is the first record of genetic diversity analysis of rice yellow stem borer (Scirpophaga incertulas) using SSR marker. Amplification of the genomic DNA was achieved with 100 set of designed EST-SSR primers. Here we discussed the criteria for the selection of primers for genetic study. The feasibility of the primers in discriminating the populations of YSB was determined by expected heterozygosity (H_e), polymorphism information content (PIC), Effective multiplex ratio (EMR), Marker index (MI), and Resolution power (RP). Out of 100 primers, only 20 primers were polymorphic, and among them, ten were very informative with (PIC > 0.5), five were somewhat informative (PIC = 0.25 - 0.50), and five were not much informative (PIC < 0.25). DNA from YSB larva or adult from 27 locations in India was extracted through CTAB extraction method, and they were amplified using 100 sets of designed primers through polymerase chain reaction. The gel images were obtained for all the amplified products, and only those gel images were used for genetic analysis, which produced polymorphic bands. The bands were scored by gel Analyzer 19.1 for every primer, and these binary data were utilized to perform the molecular analysis on NTSYS pc version 2.2.