Optimizing Plant Disease Management in Agricultural Ecosystems Through Rational In-Crop Diversification

Biodiversity plays multifaceted roles in societal development and ecological sustainability. In agricultural ecosystems, using biodiversity to mitigate plant diseases has received renewed attention in recent years but our knowledge of the best ways of using biodiversity to control plant diseases is still incomplete. In term of in-crop diversification, it is not clear how genetic diversity per se in host populations interacts with identifiable resistance and other functional traits of component genotypes to mitigate disease epidemics and what is the best way of structuring mixture populations. In this study, we created a series of host populations by mixing different numbers of potato varieties showing different late blight resistance levels in different proportions. The amount of naturally occurring late blight disease in the mixture populations was recorded weekly during the potato growing seasons. The percentage of disease reduction (PDR) in the mixture populations was calculated by comparing their observed late blight levels relative to that expected when they were planted in pure stands. We found that PDR in the mixtures increased as the number of varieties and the difference in host resistance (DHR) between the component varieties increased. However, the level of host resistance in the potato varieties had little impact on PDR. In mixtures involving two varieties, the optimum proportion of component varieties for the best PDR depended on their DHR, with an increasing skewness to one of the component varieties as the DHR between the component varieties increased. These results indicate that mixing crop varieties can significantly reduce disease epidemics in the field. To achieve the best disease mitigation, growers should include as many varieties as possible in mixtures or, if only two component mixtures are possible, increase DHR among the component varieties.

Comparative analysis of late blight resistance R genes and their coding proteins in some potato genotypes

Late blight (LB) disease can cause potato yield losses in both Egypt and the world. Therefore, the structural analysis of resistance (R) genes responsible for LB resistance will help in understanding their functions. This work aimed to identify the variations between the dominant and recessive alleles of two genes, R3a and R8 at the nucleotide and amino acid levels in five potato genotypes. Two genes of R3a and R8 representing the broad-spectrum LB resistance were amplified by specific primers, which gave one amplicon of 194 and 220 bp of each gene, respectively. Two fragments were sequenced after purification using an ABI 3730xl System DNA Sequencer. The DNA sequence alignments of two genes, R3a and R8, were determined among five selected potato genotypes. The percentage of genetic similarity of the nucleotide sequences of the R3a and R8 genes ranged between (82–83%) and (86–87%), respectively, in comparison to the reference sequences in the nucleotide BLAST. We report on the existence of positional differences in the nucleotide sequences, and base-pair substitutions of two fragments, resulting in amino acid changes between the resistant and susceptible potato genotypes. On the other hand, the highest total number of base-pair substitutions was recorded as 16 in the recessive allele r8 of the varieties Bellini and Cara. However, the lowest number was recorded as four in the dominant allele R3a of the variety Cara. The dendrograms of the five potato genotypes were made up of phylogenetically different clusters, separate from all the other named potato accessions of the two genes. The results of this study will create a solid base for the further understanding of the mechanism of plant-pathogen interactions and supply a theoretical reference for durable resistance to late blight diseases in the potato.

Breeding Late Blight Resistant Potatoes for Organic Farming—a Collaborative Model of Participatory Plant Breeding: the Bioimpuls Project

In organic potato production, the need for varieties with durable late blight resistance developed through classical breeding programmes is urgent. Besides late blight resistance, other variety characteristics needed in organic potato production are early canopy closure for weed suppression and good tuber dormancy to eliminate the need for (chemical) sprouting inhibition during storage, amongst others. This paper is a unique example of collaboration between researchers, farmers and professional breeders of both large, medium and small breeding companies. The aim of the resulting breeding project, Bioimpuls, was to provide a substantial impulse to both the organic and conventional potato breeding sector by enlarging the access to various sources of late blight resistance. The Bioimpuls activities include providing true seed populations for variety selection with five available sources of R-genes against Phytophthora infestans, early and advanced introgression breeding with six new R-genes, and education and communication. The results achieved over the 11-year period (2009–2019) are analysed. Many true seed populations containing multiple resistance genes are produced and selected, and a constant flow of breeding clones is entering the evaluation and positioning trials of companies. However, it will still take a considerable amount of time before varieties with stacked resistance genes will replace the new resistant single gene varieties entering the market in the next few years. Five out of six new sources of R-genes need more years of backcrossing before they are ready for commercial use. Bioimpuls successfully introduced a training course for farmer breeders, and published a manual for potato breeding.

Late Blight Resistance Evaluation and Genome-Wide Assessment of Genetic Diversity in Wild and Cultivated Potato Species

Late blight, caused by the oomycete Phytophthora infestans, is the most devastating disease in potato-producing regions of the world. Cultivation of resistant varieties is the most effective and environmentally friendly way to control potato late blight disease, and identification of germplasms with late blight resistance and clarification their genetic relationship would promote the development of the resistant varieties. In this study, a diverse population of 189 genotypes with potential late blight resistance, consisting of 20 wild species and cultivated Solanum tuberosum Andigenum group and Chilotanum group, was screened for the presence of late blight resistance by performing challenge inoculation with four Phytophthora infestans isolates including one 13_A2 isolate, CN152. Ten elite resources with broad-spectrum resistance and 127 with isolate-specific resistance against P. infestans were identified. To improve the available gene pool for future potato breeding programs, the population was genotyped using 30 simple sequence repeat (SSR) markers covering the entire potato genome. A total of 173 alleles were detected with an average of 5.77 alleles per locus. Structure analysis discriminated the 189 potato genotypes into five populations based on taxonomic classification and genetic origin with some deviations. There was no obvious clustering by country of origin, ploidy level, EBN (endosperm balance number) value, or nuclear clade. Analysis of molecular variance showed 10.08% genetic variation existed among populations. The genetic differentiation (Fst) ranged from 0.0937 to 0.1764, and the nucleotide diversity (π) was 0.2269 across populations with the range from 0.1942 to 0.2489. Further genotyping of 20K SNP array confirmed the classification of SSRs and could uncover the genetic relationships of Solanum germplasms. Our results indicate that there exits abundant genetic variation in wild and cultivated potato germplasms, while the cultivated S. tuberosum Chilotanum group has lower genetic diversity. The phenotypic and genetic information obtained in this study provide a useful guide for hybrid combination and resistance introgression from wild gene pool into cultivated species for cultivar improvement, as well as for germplasm conservation efforts and resistance gene mining.

Virulence of Phytophthora infestans isolates from potato in Spain

The oomycete Phytophthora infestans is responsible for the disease known as late blight in potato and tomato. It is the plant pathogen that has caused the greatest impact on humankind so far and, despite all the studies that have been made, it remains the most important in this crop. In Spain during the last years a greater severity of the disease has been observed in both, potato and tomato, probably due to genetic changes in pathogen populations described recently. The aim of this study was the characterization of the physiological strains of 52 isolates of P. infestans obtained in different potato-growing areas in Spain. For this purpose, inoculations on detached leaves were performed in order to determine compatibility or incompatibility reactions. A total of 17 physiological races were found. The less frequent virulence factors were Avr5 and Avr8. By studying the epidemiology of the pathogen, a specific breeding program for late blight resistance can be implemented.

Serial Transcriptome Analysis Reveals Genes Associated with Late Blight Resistance in Potato Cultivar Qingshu 9

The late blight caused by Phytophthora infestans (P. infestans) has been a major constraint for worldwide sustainable potato production. Chinese potato cultivar Qingshu 9 has shown excellent field performance against late blight. To understand the mechanism underlying its resistance, the transcriptomic dynamics of Qingshu 9 infected with P. infestans was systematically investigated to identify the resistance-related genes. In total, 2027 shared differentially expressed genes (DEGs) were identified when infected with P. infestans at 24, 48 and 72 h post-inoculation. Based on k-mean cluster analysis, the DEGs showed four types of expression patterns, suggesting their divergent functions in response to P. infestans infection. KEGG enrichment analysis showed that the significantly enriched DEGs were involved in the biosynthesis of secondary metabolites, plant–pathogen interaction, and photosynthesis. Furthermore, 980 transcription factor genes belonging to 68 families were found in the DEGs, of which AP2-EREBP and MYB genes were the most abundant. Moreover, many genes related to disease resistance showed differential expression during infection. Finally, the expression of nine DEGs was validated by quantitative real-time PCR. These results provide valuable information for understanding late resistance in potato cultivar Qingshu 9.

Insights into the genetic basis of the pre-breeding potato clones developed at the Julius Kühn Institute for high and durable late blight resistance

Due to the high yield losses caused by late blight in potato cultivation, the development of resistant pre-breeding material is of great importance for cultivar breeding. The gene pool of the Julius Kühn Institute (JKI) includes a large collection of resistant clones whose resistance has not yet been analysed in detail with markers for relevant resistance genes. A panel of 52 pre-breeding potato clones developed at the JKI via interspecific crosses and highly resistant to late blight were tested for the presence of seven resistance genes (Rpi-blb1/Rpi-sto1, Rpi-blb2, Rpi-blb3/R2/Rpi-abpt, R1, R3a, R3b, Rpi-phu1) and one QTL allele (QTL_phu-stn) from Solanum species S. bulbocastanum, S. demissum, S. phureja and S. stoloniferum, respectively. Molecular marker assays based on sequence-specific primers revealed that 36 of the 52 pre-breeding clones carried either 1, 2, 3 or 4 resistance genes introgressed from these wild Solanum species. Results indicate that these resistance genes were retained over generations of breeding. Although highly resistant to late blight, 16 pre-breeding clones did not carry any of these resistance genes. Resistance in the gene pool may, thus, be based not only on individual resistance genes but also on QTL effects. Results help to better understand both inheritance and expression of late blight resistance of this unique gene pool and may be used for breeding programmes.

First signs of late blight resistance in traditional native potatoes of Pasco—Peru, a preliminary assay

Background The native Andean potatoes, despite their low yield, have a large diversity that is conserved by subsistence farmers in Peru, due to their culinary characteristics and other qualities. However, this diversity is threatened by the impacts of climate change, which would directly affect the food security of these people, and eventually ours. Among its qualities of resistance to pests and diseases, there could be a genetic source of resistance to late blight, one of the most damaging diseases of the potato crop in the world. In this assay, 103 native landraces collected from local farmers in the Pasco region of Peru were subjected to natural infection conditions with Phytophthora infestans to identify potential resistant landraces within them. Results The 103 landraces assessed showed a broad variety of responses and were classified as “resistant” (22%), “moderately resistant” (57%), and “susceptible landraces” (21%). A relative effect of the disease in the yield is also shown, which is already low for commercial intentions. Conclusion Within this representative sample of the native potato diversity of the Pasco region, at least 23 local varieties grown by subsistence farmers have resistance qualities against eventual late blight disease.

Comparative transcriptome analysis of R3a and Avr3a-mediated defense responses in transgenic tomato

Late blight caused by Phytophthora infestans is one of the most devastating diseases in potatoes and tomatoes. At present, several late blight resistance genes have been mapped and cloned. To better understand the transcriptome changes during the incompatible interaction process between R3a and Avr3a, in this study, after spraying DEX, the leaves of MM-R3a-Avr3a and MM-Avr3a transgenic plants at different time points were used for comparative transcriptome analysis. A total of 7,324 repeated DEGs were detected in MM-R3a-Avr3a plants at 2-h and 6-h, and 729 genes were differentially expressed at 6-h compared with 2-h. Only 1,319 repeated DEGs were found in MM-Avr3a at 2-h and 6-h, of which 330 genes have the same expression pattern. Based on GO, KEGG and WCGNA analysis of DEGs, the phenylpropanoid biosynthesis, plant-pathogen interaction, and plant hormone signal transduction pathways were significantly up-regulated. Parts of the down-regulated DEGs were enriched in carbon metabolism and the photosynthesis process. Among these DEGs, most of the transcription factors, such as WRKY, MYB, and NAC, related to disease resistance or endogenous hormones SA and ET pathways, as well as PR, CML, SGT1 gene were also significantly induced. Our results provide transcriptome-wide insights into R3a and Avr3a-mediated incompatibility interaction.

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

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.