SSR Mining in Pepper(Capsicum annuum L.) Transcriptome and the Polymorphism Analysis

In this study,we investigated 221 037 unigenes(97.3 Mb)from two transcriptome in pepper using SSR finding soft.In total,17 319(7.83%)SSRs were identified from these SSR-containing unique ESTs with the occurring frequency of 1/56 kb.Among,single nucleotide type(56.30%)is the most abundant,followed by di-(19.16%),tri-(23.18%).A total of 10 468 primer pairs were successfully designed and 1 538 primer pairs exhibited polymorphism by E-PCR 19 out of 20 primer pairs selected at random yielded amplification products,of which 7 primer pairs showed polymorphism among 10 different pepper varieties,PIC ranged from 0.33–0.89,average 0.67,and 10 pepper breeds were grouped into three classes.This results indicate that molecular markers will be more usable in map structure,analysis of genetic polymorphism in pepper.