Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species Solanum verrucosum through DNA capture technologies

Abstract

Key messageA broad-spectrum late blight disease-resistance gene from Solanum verrucosum has been mapped to potato chromosome 9. The gene is distinct from previously identified-resistance genes.AbstractWe have identified and characterised a broad-spectrum resistance to Phytophthora infestans from the wild Mexican species Solanum verrucosum. Diagnostic resistance gene enrichment (dRenSeq) revealed that the resistance is not conferred by previously identified nucleotide-binding, leucine-rich repeat genes. Utilising the sequenced potato genome as a reference, two complementary enrichment strategies that target resistance genes (RenSeq) and single/low-copy number genes (Generic-mapping enrichment Sequencing; GenSeq), respectively, were deployed for the rapid, SNP-based mapping of the resistance through bulked-segregant analysis. Both approaches independently positioned the resistance, referred to as Rpi-ver1, to the distal end of potato chromosome 9. Stringent post-enrichment read filtering identified a total of 64 informative SNPs that corresponded to the expected ratio for significant polymorphisms in the parents as well as the bulks. Of these, 61 SNPs are located on potato chromosome 9 and reside within 27 individual genes, which in the sequenced potato clone DM locate to positions 45.9 to 60.9 Mb. RenSeq- and GenSeq-derived SNPs within the target region were converted into allele-specific PCR-based KASP markers and further defined the position of the resistance to a 4.3 Mb interval at the bottom end of chromosome 9 between positions 52.62–56.98 Mb.Electronic supplementary materialThe online version of this article (10.1007/s00122-018-3078-6) contains supplementary material, which is available to authorized users.

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

“…Secondly, even when these fragments were translatable, the proof of functionality of Rpi homologues in S. alandiae and S. okadae must await further studies by independent methods. Our data match the evidence that the Rpi-vnt1 gene is specific to South American species of series Tuberosa (Pel, 2010) and is absent in Mexican S. verrucosum (Chen et al, 2018), despite the fact that the latter species is often grouped with South American Tuberosa germplasm (Hardigan et al, 2015). Other Rpi homologues found in S. alandiae and S. okadae resemble the R2, R8, R9 and Rpi-blb2 genes of Mexican species S. demissum and S. bulbocastanum.…”

“…accessions k-24995, k-24991, k-23760, k-24313, k-23015, k-23760, and PI195171, the only Tuberosa species in North and Central Americas (Spooner et al, 2014). The absence of Rpi-vnt1 in S. verrucosum was also reported using dRenSeq technology (Chen et al, 2018).…”

“…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).…”

Tracking disease resistance deployment in potato breeding by enrichment sequencing

“…The methodology takes advantage of the focused re-sequencing of NLRs through RenSeq (Jupe et al, 2013). RenSeq has previously been used for improving genome annotations and genetic mapping of plant NLRs (Chen et al, 2018;Jupe et al, 2013), the prioritisation of novel NLRs in wild diploid species (Jiang et al, 2018;Van Weymers et al, 2016), and identification of candidate NLRs when combined with long-read sequencing technology (Giolai et al, 2016;Witek et al, 2016).…”

Tracking disease resistance deployment in potato breeding by enrichment sequencing

“…The methodology takes advantage of the focused re-sequencing of NLRs through RenSeq (Jupe et al, 2013). RenSeq has previously been used for improving genome annotations and genetic mapping of plant NLRs (Jupe et al, 2013;Chen et al, 2018), the prioritisation of novel NLRs in wild diploid species (Van Weymers et al, 2016;Jiang et al, 2018), and of candidate NLRs in combination with long-read sequencing technology (Giolai et al, 2016;Witek et al, 2016).…”