DEVELOPING GENOMIC RESOURCES FOR GENETIC IMPROVEMENT OF BELL PEPPER

Sweet or bell pepper [Capsicum annuum var. grossum (L.) Sendt.], a member of Solanaceae family is more of a horticultural group of C. annuum rather than taxonomically distinct. Bell pepper fruits are generally blocky, square, thick fleshed, three to four lobed and non-pungent. It is a versatile crop plant and its consumption is on the increase all over the world. Bell paper exhibits wide variation in fruit morphological traits such as size, shape, and color that are utilized for breeding diverse fruit types. Here, we propose to use genomic selection for the bell pepper breeding program, which greatly shortens the generation time and accelerates pepper breeding programs. This proposal aims to build genomic infrastructure that can accelerate introgression programs involving whole-genome sequencing of bell pepper, genomewide SNPs, and selections for fruit weight, size, shape, color, and total yield.Bell peppers show wide natural variation in fruit morphology and metabolomic traits, including non-pungent capsiates, carotenoids, and flavonoids. Previous association mapping in our laboratory allowed for the identification of several major QTL controlling fruit size, shape, capsaicinoids, carotenoids, and flavonoids. However, because of the lack of sufficient mapping resolution and functional tests, none of the genes underlying these QTL have been identified. For high-resolution mapping and identification of candidate genes, we will use RNA-seq and genomic resequencing of extreme phenotypic bulks from the mapping populations.The overall program is conceived to bring together and strengthen existing expertise in phenome analyses and infuse modern breeding technologies for bell pepper improvement that will establish a US food safety focus. The specific objectives are described below.Whole-genome sequence of bell pepper genome and resequencing of bell peppers;Assessing phenotypic diversity for fruit traits and molecular diversity among bell pepper germplasm accessions using single nucleotide polymorphisms; andImprove and integrate genome editing methods for altering fruit size, color, shape, and yield.