Molecular Linkage Maps of Capsicum

Genetic mapping in Capsicum has been initiated more than 50 years ago using morphological markers for fruit traits. Since then, numerous maps have been constructed in pepper mostly consisting of various types of molecular markers. These maps were instrumental in identifi cation of genomic regions containing traits of interest and development of linked markers for use in marker-assisted selection. Furthermore, use of common markers with other Solanaceae crops, especially tomato, allowed comparative mapping between these species and determining the syntenic relationship among genomes. Early maps were based on mostly restriction fragment length polymorphism (RFLP) markers, while subsequent maps included mostly PCR-based markers such as random amplifi ed polymorphic DNA (RAPD ), amplifi ed fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. More recent maps include single nucleotide polymorphism (SNP) markers, often derived from next-generation sequencing studies of different parental lines. Until recently, most maps were generated in inter-specifi c crosses because of lack of suffi cient level of DNA polymorphism between closely related parents. However, with advancement of DNA sequencing and generation of large number of SNPs even between closely related parents, the limit in DNA polymorphism is much less critical, allowing the generation of maps consisting of thousands of markers on the basis of intra-specifi c crosses. Such saturated maps allow effi cient identifi cation of genes of interest by “map-based cloning approach”.