Applications of next-generation sequencing towards identifying novel disease resistance genes

Improving disease resistance is a fundamental goal of plant breeding. The identification of novel resistance genes is a key step towards developing resistant potato varieties. Nucleotide-binding site leucine-rich repeat (NLR) genes are a common class of resistance genes in plants. Their conserved and modular structure makes them ideal for automated identification in plant genomes through computational methods. Here, the novel NLR annotation program Resistify is presented, which is rapid, easy-to-use, and is the most sensitive NLR annotator to date. By applying Resistify to a Solanaceae pangenome, its performance is demonstrated, and a previously undescribed association between NLRs and Helitron transposable elements is revealed. Wild potato genomes are a valuable source of novel resistance genes. The wild species Solanum verrucosum contains the Rpi-ver1 gene which confers resistance to the late-blight pathogen Phytophthora infestans. Through a combination of HiFi and Nanopore sequencing, the genome of S. verrucosum is assembled, and the complete identity of the Rpi-ver1 locus is resolved. Candidate genes within the locus are revealed including a severed NLR and a Jacalin-like lectin gene. S. verrucosum has the unusual and advantageous trait of being self-compatible - the S-RNase gene which imparts self-compatibility is identified within the genome. The genome of S. verrucosum also gives new insights into the centromeres of potato chromosomes. Some are formed of large tandem repeats which show evidence of being derived from transposable elements, whilst others are entirely repeatless and rich in transposable elements of the Tekay and CRM subfamilies. In Scotland, the recent encroachment of the potato cyst nematode Globodera pallida has become an existential threat to the potato industry. The G. pallida resistance genes H2 and H3 are valuable sources of resistance, but their identity is unknown. Through a combination of RenSeq sequencing and association genetics, candidates of the H2 and H3 genes are identified, which are determined to be homologs of the NRC3 and R2 NLRs.