Pepper (Capsicum spp.) is an important vegetable crop that provides a unique pungent sensation when eaten. Through construction of a pepper variome map, we examined the main groups that emerged during domestication and breeding of C. annuum, their relationships and temporal succession, and the molecular events underlying the main transitions. The results showed that the initial differentiation in fruit shape and pungency, increase in fruit weight, and transition from erect to pendent fruits, as well as the recent appearance of large, blocky, sweet fruits (bell peppers), were accompanied by strong selection/fixation of key alleles and introgressions in two large genomic regions. Furthermore, we identified Up, which encodes a BIG GRAIN protein involved in auxin transport, as a key domestication gene that controls erect vs pendent fruit orientation. The up mutation gained increased expression especially in the fruit pedicel through a 579-bp sequence deletion in its 5' upstream region, resulting in the phenotype of pendent fruit. The function of Up was confirmed by virus-induced gene silencing. Taken together, these findings constitute a cornerstone for understanding the domestication and differentiation of a key horticultural crop.

Anthracnose (Colletotrichum spp.) is a serious disease worldwide in pepper (Capsicum) production. Inheritance of resistance to Colletotrichum acutatum from a Capsicum chinense accession (PBC932) was studied in a BC1 population derived from a hybrid with Capsicum annuum line 77013 (susceptible) using a QTL analysis method. Resistance test was performed on detached mature green and mature red fruit under laboratory conditions by evaluated in disease incidence, true lesion diameter and overall lesion diameter. Based on a linkage map with 14 linkage groups, 385 markers (SSR, InDel and CAPS), 1310.2cM in length, inclusive Composite Interval Mapping (ICIM) revealed main effect QTLs located in a close marker interval on P5 chromosome for all fruit stages and resistance criteria, and four minor-effect QTLs only at green mature stage. Identification of recombinant individuals suggested that resistance in green versus red fruit may be controlled by distinct genes within the QTL interval on P5

Genetic diversity plays an essential role in plant breeding and utilization. Pepper is an important vegetable and spice crop worldwide. The genetic diversity of 1 904 accessions of pepper conserved at the National Mid-term Genebank for Vegetables, Beijing, China was analyzed based on 29 simple sequence repeat (SSR) markers, which were evenly distributed over 12 pepper chromosomes. The pepper accessions were divided into two groups in a genetic structure analysis, and the two groups showed obvious differences in fruit type and geographical distribution. We finally selected 248 accessions capturing 75.6% of the SSR alleles as the core collection for further research. Insights into the genetic structure of pepper provide the basis for population-level gene mining and genetic improvement.