Development of Single Nucleotide Polymorphism Markers Using High Resolution Melting Analysis and Construction and Application of an Inter-Specific Genetic Maps of Capsicum

To develop the single nucleotide polymorphism (SNP) markers for facilitating marker-assisted breeding and the analysis of structure and/or organization of Capsicum genomes, expressed sequence tag (EST) from pepper genome is utilised. We developed three kinds of PCR-based markers derived from pepper EST; intron based polymorphic marker (IBP), conserved ortholog set (COSII) and eSNP (EST-SNP). Among 1592 IBP marker, 1086 pepper introns were amplified as the average intron size (420 bp). A pepper interspecific genetic map was constructed with IBP, COSII and eSNP by using HRM analysis. A total of 514 markers, comprised of 211 IBP, 121 COSII and 48 Esnp and, were mapped on 12 linkage groups, corresponding to 12 chromosomes in published inter-specific ‘AC99’ F₂ population which NuMex RNaky (C. Annuum ”RNaky”) x PI159234 (C. Chinense,”CA4”) is crossed. This interspecific map (New AC99) was covered 2335.6 cM with average marker interval distance of 4.5 cM and was aligned directly with two another interspecific maps, previously reported map (AC99) and another published interspecific map (Pepper-COSII). Using developed SNP markers, chromosome specific markers, from 1 to 6 markers each chromosome, were developed and elucidation of the difference of genome structure by reciprocal translocation between chromosome 1 and 8 was observed by fluorescent in situ hybridization (FISH) analysis. As the results, the reciprocal translocation was also observed between wild types and cultivated types of pepper genome. The results from this study might be used for subsequent studies such as genome sequencing and evolution study.