Development of a highly specific co-dominant marker for genotyping the Ph-3 (tomato late blight resistance) locus by comparing cultivated and wild ancestor species

Late blight, caused by Phytophthora infestans, is one of the most devastating diseases in cultivated potato. Breeding of new potato cultivars with high levels of resistance to P. infestans is considered the most durable strategy for future potato cultivation. In this study, we report the identification of a new late-blight resistance (R) locus from the wild potato species Solanum bulbocastanum. Using several different approaches, a high-resolution genetic map of the new locus was generated, delimiting Rpi-blb3 to a 0.93 cM interval on chromosome 4. One amplification fragment length polymorphism marker was identified that cosegregated in 1,396 progeny plants of an intraspecific mapping population with Rpi-blb3. For comparative genomics purposes, markers linked to Rpi-blb3 were tested in mapping populations used to map the three other late-blight R loci Rpi-abpt, R2, and R2-like also to chromosome 4. Marker order and allelic conservation suggest that Rpi-blb3, Rpiabpt, R2, and R2-like reside in the same R gene cluster on chromosome 4 and likely belong to the same gene family. Our findings provide novel insights in the evolution of R gene clusters conferring late-blight resistance in Solanum spp.

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Exploiting Knowledge of R/Avr Genes to Rapidly Clone a New LZ-NBS-LRR Family of Late Blight Resistance Genes from Potato Linkage Group IV

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-22-6-0630 ◽

2009 ◽

Vol 22 (6) ◽

pp. 630-641 ◽

Cited By ~ 132

Author(s):

Anoma A. Lokossou ◽

Tae-ho Park ◽

Gert van Arkel ◽

Marjon Arens ◽

Carolien Ruyter-Spira ◽

...

Keyword(s):

Late Blight ◽

Leucine Zipper ◽

Late Blight Resistance ◽

Amino Acid Sequences ◽

Blight Resistance ◽

Resistance Locus ◽

Solanum Bulbocastanum ◽

Rxlr Effector ◽

Signature Sequences ◽

Functional Analyses

In addition to the resistance to Phytophthora infestans (Rpi) genes Rpi-blb1 and Rpi-blb2, Solanum bulbocastanum appears to harbor Rpi-blb3 located at a major late blight resistance locus on LG IV, which also harbors Rpi-abpt, R2, R2-like, and Rpi-mcd1 in other Solanum spp. Here, we report the cloning and functional analyses of four Rpi genes, using a map-based cloning approach, allele-mining strategy, Gateway technology, and transient complementation assays in Nicotiana benthamiana. Rpi-blb3, Rpi-abpt, R2, and R2-like contain all signature sequences characteristic of leucine zipper nucleotide binding site leucine-rich repeat (LZ-NBS-LRR) proteins, and share amino-acid sequences 34.9% similar to RPP13 from Arabidopsis thaliana. The LRR domains of all four Rpi proteins are highly homologous whereas LZ and NBS domains are more polymorphic, those of R2 being the most divergent. Clear blocks of sequence affiliation between the four functional resistance proteins and those encoded by additional Rpi-blb3 gene homologs suggest exchange of LZ, NBS, and LRR domains, underlining the modular nature of these proteins. All four Rpi genes recognize the recently identified RXLR effector PiAVR2.

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Characterization and high-resolution mapping of a late blight resistance locus similar to R2 in potato

Theoretical and Applied Genetics ◽

10.1007/s00122-005-2050-4 ◽

2005 ◽

Vol 111 (3) ◽

pp. 591-597 ◽

Cited By ~ 32

Author(s):

T. H. Park ◽

V. G. A. A. Vleeshouwers ◽

D. J. Huigen ◽

E. A. G. van der Vossen ◽

H. J. van Eck ◽

...

Keyword(s):

High Resolution ◽

Late Blight ◽

Late Blight Resistance ◽

Blight Resistance ◽

Resistance Locus ◽

High Resolution Mapping ◽

Resolution Mapping

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A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector

10.1101/2020.05.15.095497 ◽

2020 ◽

Cited By ~ 4

Author(s):

Kamil Witek ◽

Xiao Lin ◽

Hari S Karki ◽

Florian Jupe ◽

Agnieszka I Witek ◽

...

Keyword(s):

Late Blight ◽

Broad Spectrum ◽

Durable Resistance ◽

Late Blight Resistance ◽

Potato Production ◽

Blight Resistance ◽

Resistance Locus ◽

Family Diversity ◽

Long Read ◽

Solanum Americanum

AbstractLate blight caused by Phytophthora infestans greatly constrains potato production. Many Resistance (R) genes were cloned from wild Solanum species and/or introduced into potato cultivars by breeding. However, individual R genes have been overcome by P. infestans evolution; durable resistance remains elusive. We positionally cloned a new R gene, Rpi-amr1, from Solanum americanum, that encodes an NRC helper-dependent CC-NLR protein. Rpi-amr1 confers resistance in potato to all 19 P. infestans isolates tested. Using association genomics and long-read RenSeq, we defined eight additional Rpi-amr1 alleles from different S. americanum and related species. Despite only ∼90% identity between Rpi-amr1 proteins, all confer late blight resistance but differentially recognize Avramr1 orthologs and paralogs. We propose that Rpi-amr1 gene family diversity facilitates detection of diverse paralogs and alleles of the recognized effector, enabling broad-spectrum and durable resistance against P. infestans.

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(2) A Unique Late-blight Resistance Locus from Solanum pinnatisectum

HortScience ◽

10.21273/hortsci.40.4.998b ◽

2005 ◽

Vol 40 (4) ◽

pp. 998B-998 ◽

Cited By ~ 1

Author(s):

Monica J. Norby ◽

Michael J. Havey

Keyword(s):

Late Blight ◽

Primary Source ◽

Late Blight Resistance ◽

Potato Production ◽

Avirulence Gene ◽

Blight Resistance ◽

Endosperm Balance Number ◽

Resistance Locus ◽

Cultivated Potato ◽

The Relationship

Phytophthorainfestans is the casual agent of late blight and is a major threat to potato production worldwide. There are no curative control agents available and resistance genes offer promise in controlling late blight. To date, the primary source of late-blight resistance has been from hexaploid (6x) [4 Endosperm Balance Number (EBN)] Solanum demissum. Mexican diploid (2x) (1EBN) Solanum species possess a wealth of late-blight resistances, but have been neglected due to crossing barriers. Manipulation of EBN and ploidies should allow integration of 2x (1EBN) germplasm into cultivated potato. Synteny between late-blight resistance loci from Solanum species of disparate ploidies and EBNs may facilitate the identification of unique resistance alleles and loci. Isolate MSU96 (US8/A2) of P. infestans revealed a late-blight resistance locus (Rpi1) from 2x(1EBN) S. pinnatisectum (PI 253214) that mapped to chromosome seven (MGG 265:977-985). MSU96 was also avirulent on the late-blight differential R9-Hodgson 2573 (LB3), revealing the presence of the avirulence gene for R9 originating from S. demissum. To test the relationship between Rpi1 and R9, we evaluated a family segregating for R9 and revealed that it does not map to chromosome seven. The independent inheritance of R9 and Rpi1 indicates that Rpi1 is a unique resistance locus. We are conducting a variety of crossing schemes to introgress Rpi1 into cultivated potato.

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Mutations introduced in susceptibility genes through CRISPR/Cas9 genome editing confer increased late blight resistance in potatoes

Scientific Reports ◽

10.1038/s41598-021-83972-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Nam Phuong Kieu ◽

Marit Lenman ◽

Eu Sheng Wang ◽

Bent Larsen Petersen ◽

Erik Andreasson

Keyword(s):

Late Blight ◽

Late Blight Resistance ◽

Susceptibility Genes ◽

Blight Resistance ◽

R Genes ◽

Guide Rnas ◽

Knockout Mutants ◽

Growth Phenotype ◽

Allelic Deletion ◽

S Genes

AbstractThe use of pathogen-resistant cultivars is expected to increase yield and decrease fungicide use in agriculture. However, in potato breeding, increased resistance obtained via resistance genes (R-genes) is hampered because R-gene(s) are often specific for a pathogen race and can be quickly overcome by the evolution of the pathogen. In parallel, susceptibility genes (S-genes) are important for pathogenesis, and loss of S-gene function confers increased resistance in several plants, such as rice, wheat, citrus and tomatoes. In this article, we present the mutation and screening of seven putative S-genes in potatoes, including two DMR6 potato homologues. Using a CRISPR/Cas9 system, which conferred co-expression of two guide RNAs, tetra-allelic deletion mutants were generated and resistance against late blight was assayed in the plants. Functional knockouts of StDND1, StCHL1, and DMG400000582 (StDMR6-1) generated potatoes with increased resistance against late blight. Plants mutated in StDND1 showed pleiotropic effects, whereas StDMR6-1 and StCHL1 mutated plants did not exhibit any growth phenotype, making them good candidates for further agricultural studies. Additionally, we showed that DMG401026923 (here denoted StDMR6-2) knockout mutants did not demonstrate any increased late blight resistance, but exhibited a growth phenotype, indicating that StDMR6-1 and StDMR6-2 have different functions. To the best of our knowledge, this is the first report on the mutation and screening of putative S-genes in potatoes, including two DMR6 potato homologues.

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