Allele Mining and Genomic Tools to Improve Capsicums

There are five species of Capsicum that are used worldwide as vegetable crops and as important spice crops. In this review, we examine recent developments in analyzing genomes of Capsicum species. Much progress has been made in the identification of chromosomal regions or candidate genes important for valuable phenotypes related to plant growth and development, fruit qualities, and resistance to diseases. This progress was possible due to improvements in technologies and reduction in costs to genotype plants including genotyping-by-sequencing, whole genome sequencing, mapping, and fine-mapping of quantitative trait loci and functional validation of candidate genes. DNA markers and candidate genes uncovered so far can be expected to open many new opportunities for researchers to develop marker-assisted selection methods and genome editing strategies to achieve novel and improved new varieties of peppers. Large-scale semi-automated pipelines for phenotyping can be expected to be available with the development and application of computational tools. Specific candidate genes have been identified for many valuable traits and they will be used to generate more allelic variants for use in breeding and synthetic biology. Using examples, we illustrate both the progress and the challenges in developing and utilizing genomic resources for Capsicum breeding.