Pangenome architecture and differentiation of agronomical traits in the Capsicum clade
Several studies have indicated the association of structural variations (SVs), such as inversions, translocations, presence/absence variations (PAVs) and copy number variations (CNVs) with important agronomic traits. To further provide insight into the genetic diversity and harnessing the potential of SVs in crop improvement, we will apply a Capsicum pangenome.
The importance of the approach was recently demonstrated for identification of causal PAVs underlying disease resistance, (a)biotic stress tolerance, flowering time, silique length and seed weight. Furthermore, several studies showed identification of new loci associated with important agronomical traits, providing direct targets for crop improvement using a GWAS based on large-scale resequencing approach. Within the Capsicum Genome Initiative (CGI) we previously profiled species accessions with agronomical traits linked to yield and disease resistance that can be used to improve Capsicum crops. For example, wild annuum accessions and related wild species displayed different combinations of growth habit and flowering phenotype.
The underlying genes represent an interesting resource that potentially can be used to breed for annuum varieties with more concentrated fruit set and higher yield. In addition, Chili anthracnose, caused by Colletotrichum species, is a serious problem constraining pepper production. Currently, we have sequenced several accessions that exhibit anthracnose resistance, which might be used to introduce Colletotrichum species specific anthracnose resistance into Capsicum crop accessions. Several viral resistant (TMV, TSWV, CMV), fungal resistant (Phytophtora capsici) and low temperature tolerant accessions have been characterized within the CGI project as well. At present we have a unique combination of Capsicum genome sequences, bioinformatics and genetics, which permits the development of new insights and breeding tools that will drive innovation in Dutch plant breeding and horticulture.
We will construct a pangenome from representative C. annuum, C. baccatum, C. cardenasii, C. chinense, C. chacoense, C. frutescens, C. pubescens, C. tovarii accessions, that were recently profiled within CGI. We aim to develop new pangenome technology and functionality of existing tools like PanTools by integrating annotation and proteome layers as well as query and visualization functionality using a graph database technology. The pangenome and extended functionality of tools like PanTools will support intergenomic comparisons to establish the capsicum core-genome and identify individual-specific genetic variation and prioritize (putative) genes, by comparing against annotated reference genomes, providing further insight into candidate variations that may be causal to target traits.