Tracking disease resistance deployment in potato breeding by enrichment sequencing

Abstract

SummaryFollowing the molecular characterisation of functional disease resistance genes in recent years, methods to track and verify the integrity of multiple genes in varieties are needed for crop improvement through resistance stacking. Diagnostic resistance gene enrichment sequencing (dRenSeq) enables the high-confidence identification and complete sequence validation of known functional resistance genes in crops. As demonstrated for tetraploid potato varieties, the methodology is more robust and cost-effective in monitoring resistances than whole-genome sequencing and can be used to appraise (trans)gene integrity efficiently. All currently known NB-LRRs effective against viruses, nematodes and the late blight pathogen Phytophthora infestans can be tracked with dRenSeq in potato and hitherto unknown polymorphisms have been identified. The methodology provides a means to improve the speed and efficiency of future disease resistance breeding in crops by directing parental and progeny selection towards effective combinations of resistance genes.

RLP/K enrichment sequencing; a novel method to identify receptor‐like protein (RLP) and receptor‐like kinase (RLK) genes

“…A dRenSeq‐type analysis was conducted to ascertain the presence and sequence integrity of the known functional target gene ELR . The mapping condition for the diagnostic analysis of the RLP/KSeq‐derived reads was as described previously (Armstrong et al , 2019), and adapted for RLP/KSeq. For this, the ELR sequence was used as reference (GenBank no.…”

“…RenSeq has also been successfully applied to other crops and has led to the cloning of two stem rust resistance genes, Sr22 and Sr45 , from hexaploid bread wheat (Steuernagel et al , 2016). Furthermore, used as a diagnostic tool and referred to as dRenSeq, the methodology enables the identification of known functional NLRs in potatoes (Van Weymers et al , 2016; Jiang et al , 2018; Armstrong et al , 2019). These successful advances in enrichment sequencing indicate that, with adaption and optimization, the sequence capture technology can be applied to other types of immune receptors, such as RLPs and RLKs.…”

South American species <i>Solanum alandiae</i> Card. and <i>S. okadae</i> Hawkes et Hjerting as potential sources of genes for potato late blight resistance

“…Following the marker-assisted mapping and cloning of Rpi genes, recent years have seen a considerable progress in this direction. New methodologies, such as effectoromics, allele profiling and diagnostic resistance gene enrichment sequencing (dRenSeq), tremendously facilitated the search for new Rpi genes and new alleles of Rpi genes already characterized in other species of Solanum L. within the section Petota Dumort van Weymers et al, 2016;Chen et al, 2018;Jiang et al, 2018;Armstrong et al, 2019). Currently some of these genes have been introgressed into commercial potato cultivars (Haesaert et al, 2015).…”

Extreme resistance toPotato Virus Yin potato carrying theRystogene is mediated by a TIR-NLR immune receptor

“…It has been estimated that controlling major diseases through the informed deployment of resistance genes could contribute over 30% towards crop yield whilst reducing the requirements for chemical applications (Gebhardt and Valkonen 2001). This might be achieved by implementation of new breeding tools to select resistant genotypes and deploy them as varieties (Armstrong et al 2018).…”

“…The methodology is more robust and cost-effective in monitoring NLR sequences than whole-genome sequencing. All currently known NLRs effective against viruses, nematodes and the late blight pathogen Phytophthora infestans can be tracked with SMRT RenSeq in potato and their polymorphisms defined (Armstrong et al 2018).…”