Foliar transcriptomes reveal candidate genes for late blight resistance in cultivars of diploid potato Solanum tuberosum L. Andigenum Group.

Characterization of major resistance (R) genes to late blight (LB) -caused by the oomycete Phytophthora infestans- is very important for potato breeding. The objective of this study was to identify novel genes for resistance to LB from diploid Solanum tuberosum L. Andigenum Group (StAG) cultivar accessions. Using comparative analysis with a edgeR bioconductor package for differential expression analysis of transcriptomes, two of these accessions with contrasting levels of resistance to LB were analyzed using digital gene expression data. As a result, various differentially expressed genes (P ≤ 0.0001, Log2FC ≥ 2, FDR < 0.001) were noted. The combination of transcriptomic analysis provided 303 candidate genes that are overexpressed and underexpressed, thereby giving high resistance to LB. The functional analysis showed differential expression of R genes and their corresponding proteins related to disease resistance, NBS-LRR domain proteins, and specific disease resistance proteins. Comparative analysis of specific tissue transcriptomes in resistant and susceptible genotypes can be used for rapidly identifying candidate R genes, thus adding novel genes from diploid StAG cultivar accessions for host plant resistance to P. infestans in potato.

Screening South American Potato Landraces and Potato Wild Relatives for Novel Sources of Late Blight Resistance.

Late blight (LB) caused by the oomycete Phytophthora infestans is one of the most important biotic constraints for potato production worldwide. This study assessed 508 accessions (79 wild potato species and 429 landraces from a cultivated core collection) held at the International Potato Center genebank for resistance to LB. One P. infestans isolate belonging to the EC-1 lineage, which is currently the predominant type of P. infestans in Peru, Ecuador, and Colombia, was used in whole plant assays under greenhouse conditions. Novel sources of resistance to LB were found in accessions of Solanum albornozii, S. andreanum, S. lesteri, S. longiconicum, S. morelliforme, S. stenophyllidium, S. mochiquense, S. cajamarquense, and S. huancabambense. All of these species are endemic to South America and thus could provide novel sources of resistance for potato breeding programs. We found that the level of resistance to LB in wild species and potato landraces cannot be predicted from altitude and bioclimatic variables of the locations where the accessions were collected. The high percentage (73%) of potato landraces susceptible to LB in our study suggests the importance of implementing disease control measures, including planting susceptible genotypes in less humid areas and seasons or switching to genotypes identified as resistant. In addition, this study points out a high risk of genetic erosion in potato biodiversity at high altitudes of the Andes due to susceptibility to LB in the native landraces, which has been exacerbated by climatic change that favors the development of LB in those regions.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Phenotypic stability and genome-wide association study of late blight resistance in potato genotypes adapted to the tropical highlands.

Potato genotypes from a breeding population adapted to tropical highlands were analyzed for the stability of late blight resistance and also for marker-phenotype association. We harmonized the historical evaluation data, consisting of observations spanning 6 years from two field sites utilizing a resistance scale constructed by comparing the area under the disease progress curve (AUDPC) values of 172 genotypes with that of susceptible control 'Yungay'. In total, 70 potato genotypes had a coefficient of variability <0.5 and were considered stable across the environments tested. A principal component analysis demonstrated that the ensemble of experiments formed two distinct groups that reflect the stability of genotype resistance to late blight. Phytophthora infestans isolates present in the experimental fields belonged to the EC-1 clonal lineage and showed variation in virulence beyond the concept of the avirulence determined by the conventionally used R1-R11 differential set. A single-nucleotide polymorphism (SNP) marker on chromosome 9 was associated with late blight resistance and linked to instability. Genotypes with either AACC or AAAC combinations for this SNP were highly resistant only in some environments, while the genotypes with the AAAA combination had more moderate levels of resistance but were stable across environments.

Wide Phenotypic Diversity for Resistance to Phytophthora infestans Found in Potato Landraces from Peru.

The wild and cultivated species of potato have been utilized in potato breeding to good effect but only a very small sample of the available biodiversity has been exploited. In total, 468 accessions of wild and cultivated species of potato were assessed for resistance to the oomycete pathogen Phytophthora infestans using greenhouse assays. Wide phenotypic variation for resistance was found within a species (i.e., among accessions) but not among species which, on average, were similar. Nineteen accessions had resistance levels better than or similar to the variety Chucmarina, which is routinely used by the International Potato Center as a resistant control. Surprisingly, a number of accessions were significantly more susceptible than the susceptible control, Tomasa Condemayta. Frequency histograms of species indicated continuous variation for resistance with little evidence for functional resistance genes.

Use of Phosphonate to Manage Foliar Potato Late Blight in Developing Countries.

Twenty phosphonate products found in the agrochemical market in Ecuador and Peru were evaluated in bioassays for the control of foliar potato late blight, caused by Phytophthora infestans. Eight phosphonate products were evaluated in 16 field experiments done in Peru, Ecuador, Kenya, and Nepal. A meta-analysis across locations involving 71 combinations of potato genotype by site and year demonstrated a significant relationship between phosphonate application rate and efficacy for controlling late blight on potato foliage. The meta-analysis revealed that phosphonate rates of approximately 2.5 g a.i./liter provided efficacy similar to that of the conventional contact fungicides mancozeb and chlorothalonil used at similar rates. At rates higher than 2.5 g a.i./liter, the efficacy of phosphonate was superior to the contact fungicides. Overall, late blight control by phosphonate appeared relatively stable in field experiments across locations. An analysis of field experiments and 64 combinations of potato genotype by site and year showed no correlation between the susceptibility level of potato genotypes and efficacy of phosphonates. The cost of both phosphonate compounds and contact fungicides varied greatly among the countries of the field study; however, in Kenya, control with phosphonate was clearly less expensive than with mancozeb.

Comparison of transcript profiles in late blight-challenged Solanum cajamarquense and B3C1 potato clones.

Two Solanum genotypes, a wild relative of cultivated potato S. cajamarquense (Cjm) and an advanced tetraploid clone B3C1 (B3), were inoculated with two Phytophthora infestans isolates and leaves were sampled at 72 and 96 h after inoculation. Gene expression in the inoculated versus noninoculated samples was monitored using the Institute of Genomic Research (TIGR) 10K potato array and real-time reverse transcriptase-polymerase chain reaction (RT-PCR). The current experiment is study number 83 of the TIGR expression profiling service project, and all data are publicly available in the Solanaceae Gene Expression Database (SGED) at ftp://ftp.tigr.org/pub/data/s_tuberosum/SGED. Differentially regulated cDNA clones were selected separately for each isolate-time point interaction by significant analysis of microarray (SAM), and differentially regulated clones were classified into functional categories by MapMan. The results show that the genes activated in B3 and Cjm have largely the same biological functions and are commonly activated when plants respond to pathogen attack. The genes activated within biological function categories were considerably different between the genotypes studied, suggesting that the defence pathways activated in B3 and Cjm during the tested conditions may involve unique genes. However, as indicated by real-time RT-PCR, some of the genes thought to be genotype specific may be activated across genotypes at other time points during disease development.

Rainfall Thresholds as Support for Timing Fungicide Applications in the Control of Potato Late Blight in Ecuador and Peru.

Accumulated rainfall thresholds were studied in seven field experiments conducted in Ecuador and Peru for their value in timing applications of fungicide to control potato late blight, caused by Phytophthora infestans. Fungicide regimes based on accumulated rainfall thresholds ranging from 10 to 70 mm were compared with calendar spray schemes of every 5 or 7 days. Very low thresholds of 10 to 20 mm gave similar levels of control and resulted in similar number of sprays as did calendar spraying. However, neither low thresholds nor calendar sprays were effective in protecting susceptible potato genotypes in over half of the experiments. Thresholds of 25 to 50 mm of rainfall led to reduction in the number of sprays needed to protect resistant cultivars but also resulted in high levels of disease on susceptible cultivars. We conclude that timing fungicide sprays based on accumulated rainfall thresholds could be a successful component of integrated management strategies that include cultivars with moderate or high levels of resistance. The simplicity of measuring accumulated rainfall means that the technology can potentially be used by resource-poor farmers in developing countries.