Global multi-environment resistance QTL for foliar late blight resistance in tetraploid potato with tropical adaptation

Abstract The identification of environmentally-stable and globally-predictable resistance to potato late blight is challenged by the clonal and polyploid nature of the crop and the rapid evolution of the pathogen. A diversity panel of tetraploid potato germplasm bred for multiple resistance and quality traits was genotyped by genotyping by sequencing (GBS) and evaluated for late blight resistance in three countries where the International Potato Center (CIP) has established breeding work. Health-indexed, in vitro plants of 380 clones and varieties were distributed from CIP headquarters and tuber seed was produced centrally in Peru, China and Ethiopia. Phenotypes were recorded following field exposure to local isolates of Phytophthora infestans. QTL explaining resistance in four experiments conducted across the three countries were identified in chromosome IX, and environment-specific QTL were found in chromosomes III, V, and X. Different genetic models were evaluated for prediction ability to identify best performing germplasm in each and all environments. The best prediction ability (0.868) was identified with the genomic best linear unbiased predictors (GBLUPs) when using the diploid marker data and QTL-linked markers as fixed effects. Genotypes with high levels of resistance in all environments were identified from the B3, LBHT, and B3-LTVR populations. The results show that many of the advanced clones bred in Peru for high levels of late blight resistance maintain their resistance in Ethiopia and China, suggesting that the centralized selection strategy has been largely successful.

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Global multi-environment resistance QTL for foliar late blight resistance in tetraploid potato with tropical adaptation

10.1101/2020.02.16.950618 ◽

2020 ◽

Author(s):

Hannele Lindqvist-Kreuze ◽

Bert de Boeck ◽

Paula Unger ◽

Dorcus Gemenet ◽

Xianping Li ◽

...

Keyword(s):

Late Blight ◽

Complex Traits ◽

Prediction Models ◽

Late Blight Resistance ◽

Read Depth ◽

Chromosome 9 ◽

Blight Resistance ◽

Field Exposure ◽

Tetraploid Potato

AbstractThe identification of environmentally stable and globally predictable resistance to potato late blight is challenged by the crop’s clonal and polyploid nature and the pathogen’s rapid evolution. Genome-wide analysis (GWA) of multi-environment trials can add precision to breeding for complex traits. A diversity panel of tetraploid potato germplasm bread for multiple resistance and quality traits was genotyped by genotyping by sequencing (GBS) and phenotyped for late blight resistance in a trait observation network spanning three continents addressed by the International Potato Center’s (CIP’s) breeding program. The aims of this study were to (i) identify QTL underlying resistance in and across environments and (ii) develop prediction models to support the global deployment and use of promising resistance sources in local breeding and variety development programs. Health-indexed in vitro plants of 380 clones and varieties were distributed from CIP headquarters in Peru to China and Ethiopia and tuber seed was produced centrally in each country. Phenotypes were recorded as rAUDPC following field exposure to local isolates of Phytophthora infestans, Stringent filtering for individual read depth >60 resulted in 3,239 tetraploid SNPs. Meanwhile, 55,748 diploid SNPs were identified using diploidized data and individual read depth>17. The kinship matrix was utilized to obtain BLUP and identify best performing germplasm in each and all environments. Genotypes with high levels of resistance in all environments were identified from the B3, LBHT and B3-LTVR populations. GWA identified stable QTL for late blight resistance in chromosome 9 and environment specific QTL in chromosomes 3, 5, 6 and 10.

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Marker-assisted pyramiding of potato late blight resistance genes Rpi-rzc1 and Rpi-phu1 on di- and tetraploid levels

Molecular Breeding ◽

10.1007/s11032-020-01169-x ◽

2020 ◽

Vol 40 (9) ◽

Author(s):

Emil Stefańczyk ◽

Jarosław Plich ◽

Marta Janiszewska ◽

Paulina Smyda-Dajmund ◽

Sylwester Sobkowiak ◽

...

Keyword(s):

Late Blight ◽

Resistance Genes ◽

Potato Breeding ◽

Late Blight Resistance ◽

Breeding Strategy ◽

Blight Resistance ◽

Pcr Markers ◽

Tetraploid Potato ◽

Potato Wild Relatives ◽

Tetraploid Level

Abstract Late blight is a disease with the biggest economic impact on potato cultivation worldwide. Pyramiding of the resistance genes originating from potato wild relatives is a breeding strategy that has a potential to produce potato cultivars durably resistant to late blight. Growing such cultivars would allow limiting the intensive chemical control of the disease. The goal of this work was to transfer the late blight resistance gene Rpi-rzc1 from Solanum ruiz-ceballosii to the tetraploid level of cultivated potato and to pyramid it with the Rpi-phu1 gene. We obtained two diploid and, through 4x-2x cross, a tetraploid potato population segregating for the Rpi-rzc1 presence, as well as one diploid and one tetraploid population where both genes were introgressed. In total, 754 progeny clones were tested for resistance to late blight in detached leaflet assays. Pathogen isolates avirulent on plants with both genes and virulent on plants with the Rpi-phu1 were used. The selection was assisted by two PCR markers flanking the Rpi-rzc1 gene and a newly designed, highly specific intragenic marker indicating the Rpi-phu1 gene presence. We obtained 26 diploid and 49 tetraploid potato clones with pyramid of both genes that should enhance the durability and spectrum of their late blight resistance and that can be exploited in potato breeding. The specificity of the marker for the Rpi-phu1 gene and the precision of the Rpi-rzc1 mapping were improved in this work.

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Tagging Quantitative Trait Loci for Maturity-Corrected Late Blight Resistance in Tetraploid Potato with PCR-Based Candidate Gene Markers

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2004.17.10.1126 ◽

2004 ◽

Vol 17 (10) ◽

pp. 1126-1138 ◽

Cited By ~ 65

Author(s):

Christina Angelika Bormann ◽

Andreas Marcus Rickert ◽

Rosa Angela Castillo Ruiz ◽

Jürgen Paal ◽

Jens Lübeck ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Late Blight ◽

Candidate Genes ◽

Quantitative Trait ◽

Quantitative Resistance ◽

Late Blight Resistance ◽

Blight Resistance ◽

Resistance Qtl ◽

Tetraploid Potato ◽

Plant Maturity

Late blight caused by the oomycete Phytophthora infestans is the economically most important and destructive disease in potato cultivation. Quantitative resistance to late blight available in tetraploid cultivars is correlated with late maturity in temperate climates, which is an undesirable characteristic. A total of 30 DNA-based markers known to be linked to loci for pathogen resistance in diploid potato were selected and tested as polymerase chain reaction-based markers for linkage with quantitative trait loci (QTL) for late blight resistance and plant maturity in two half-sib families of tetraploid potatoes. Most markers originated from within or were physically closely linked to candidate genes for quantitative resistance factors. The families were repeatedly evaluated in the field for quantitative resistance to late blight and maturity. Resistance was corrected for the maturity effect. Nine of eleven different map segments tagged by the markers harbored QTL affecting maturity-corrected resistance. Interactions were found between unlinked resistance QTL, providing testable strategies for marker-assisted selection in tetraploid potato. Based on the linkage observed between QTL for resistance and plant maturity and based on the genetic interactions observed between candidate genes tagging resistance QTL, we discuss models for the molecular basis of quantitative resistance and maturity.

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Prediction based on estimated breeding values using genealogy for tuber yield and late blight resistance in auto-tetraploid potato (Solanum tuberosum L.)

Heliyon ◽

10.1016/j.heliyon.2020.e05624 ◽

2020 ◽

Vol 6 (11) ◽

pp. e05624

Author(s):

Salej Sood ◽

Vinay Bhardwaj ◽

S.K. Kaushik ◽

Sanjeev Sharma

Keyword(s):

Solanum Tuberosum ◽

Late Blight ◽

Tuber Yield ◽

Solanum Tuberosum L ◽

Late Blight Resistance ◽

Blight Resistance ◽

Breeding Values ◽

Tetraploid Potato ◽

Estimated Breeding Values

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Transcriptome Analysis of Grafted Potato Rootstock for Improvement of Scion Late-Blight Resistance

10.21203/rs.3.rs-58639/v1 ◽

2020 ◽

Author(s):

Yuexin Li ◽

Degang Zhao

Keyword(s):

Late Blight ◽

Molecular Mechanisms ◽

Enrichment Analysis ◽

Late Blight Resistance ◽

Potato Late Blight ◽

Mapk Signaling ◽

Susceptible Variety ◽

Resistant Variety ◽

Blight Resistance

Abstract Late blight seriously threatens potato cultivation worldwide. Damage caused by the fungus, which is severe and widespread, can lead to drastic reductions in potato yield and even total loss. Although grafting technology has been widely used to improve crop resistance, the effects and associated molecular mechanisms of grafting on resistance to potato late blight are unclear. In this study, we therefore performed RNA transcriptome sequencing of the scion when potato late blight-resistant variety Qingshu 9 and susceptible variety Favorita were used as the rootstock and scion, respectively, and vice versa. Using the sequencing results, we analyzed the influence of the rootstock on scion resistance and related molecular mechanisms. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that plant–pathogen interactions, the plant MAPK signaling pathway, and genes on the SA pathway were significantly up-regulated in the scion when Qingshu 9 was used as the rootstock. When Favorita was used as the rootstock, β-ketoacyl-CoA synthase-related genes in the scion, Qingshu 9, were significantly down-regulated. Resistance to late blight on scion leaves were also tested in vitro, which results consistent with those obtained by sequencing. All the generated evidence indicates that the use of resistant and susceptible varieties as rootstocks can respectively increase and reduce resistance to late blight. Our sequencing results further elucidate the molecular mechanism underlying the post-grafting effects of rootstocks on late blight resistance and provide a theoretical basis for the transfer of resistance genes between scions and rootstocks after grafting.

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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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