Genetic Diversity of Pepper Germplasm with RAPD,ISSR and Phenotypic Data

Thirteen accessions from five cultivated Capsicum species were analyzed with RAPD and ISSR markers,and 28 phenotypic traits.Twenty-three RAPD primers and sixteen ISSR primers generated 209 and 94 fragments,respectively.The number of fragments per primer,the percentage of polymorphic loci was in turn 9.09,83.73% for RAPD markers,and 5.88,79.79% for ISSR markers.But ISSR had higher percentage of polymorphic loci in C.annuum than RAPD,and effective number of alleles(Ne),Shannon's Information index(I),heterozygosity(Ht),the genetic differentiation coefficient(Gst) based on ISSR markers were bigger than those based on RAPD as well.The results showed that ISSR markers could detect more genetic diversity in the pepper accessions and be more suitable for assessment of genetic diversity among accessions that have higher consanguinity levels.Three dendrograms for the 13 accessions were formed based on RAPD,ISSR-generated bands and phenotypic data.The correlation analysis among genetic similarities based on RAPD,ISSR markers and phenotypic data indicated they were significantly correlated.All the dendrograms could separate C.annuum from the other cultivated Capsicum species.