A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding

A new map showing variable sites in the pepper (Capsicum) genome provides a platform to support rapid improvement of the crop. Capsicums, including sweet ‘bell’ and hot ‘chile’ types, are an increasingly important crop worldwide. Breeding new varities of pepper requires efficient searching for differences between the genomes of different varieties which might be associated with desirable traits. An international team led by Allen Van Deynze of the University of California-Davis, USA, used new high-throughput ‘microarray’ technology to generate a map of variable sites known as ‘single nucleotide polymorphisms’ (SNPs) in the pepper genome. They found almost 15,000 functional SNPs across both types of pepper. These findings provide an easy-to-use standardized resource for pepper researchers and breeders across the world to discover and exploit the genetic differences associated with economically important traits.