Contrasting Potato Foliage and Tuber Defense Mechanisms against the Late Blight Pathogen Phytophthora infestans

Transcriptome analysis reveals genes associated with late blight resistance in potato

Late blight is a serious disease of potato worldwide. Our study aimed to unveil genes involved in late blight resistance in potato by RNA-seq analysis after artificial inoculation under controlled conditions. In this study, two potato somatic hybrids (P7 and Crd6) and three varieties such as Kufri Girdhari, Kufri Jyoti and Kufri Bahar (control) were used. Transcriptiome analysis revealed statistically significant (p < 0.05) differentially expressed genes (DEGs), which were analysed into up-regulated and down-regulated genes. Further, DEGs were functionally characterized by the Gene Ontology annotations and the Kyoto Encyclopedia of Genes and Genomes pathways. Overall, some of the up-regulated genes in resistant genotypes were disease resistance proteins such as CC-NBS-LRR resistance protein, ankyrin repeat family protein, cytochrome P450, leucine-rich repeat family protein/protein kinase family, and MYB transcription factor. Sequence diversity analysis based on 38 peptide sequences representing 18 genes showed distinct variation and the presence of three motifs in 15 amino acid sequences. Selected genes were also validated by real-time quantitative polymerase chain reaction analysis. Interestingly, gene expression markers were developed for late blight resistant genotypes. Our study elucidates genes involved in imparting late blight resistance in potato, which will be beneficial for its management strategies in the future.

Global expression patterns of R-genes in tomato and potato

Introduction

As key-players of plant immunity, the proteins encoded by resistance genes (R-genes) recognize pathogens and initiate pathogen-specific defense responses. The expression of some R-genes carry fitness costs and therefore inducible immune responses are likely advantageous. To what degree inducible resistance driven by R-genes is triggered by pathogen infection is currently an open question.

Methods

In this study we analyzed the expression of 940 R-genes of tomato and potato across 315 transcriptome libraries to investigate how interspecific interactions with microbes influence R-gene expression in plants.

Results

We found that most R-genes are expressed at a low level. A small subset of R-genes had moderate to high levels of expression and were expressed across many independent libraries, irrespective of infection status. These R-genes include members of the class of genes called NRCs (NLR required for cell death). Approximately 10% of all R-genes were differentially expressed during infection and this included both up- and down-regulation. One factor associated with the large differences in R-gene expression was host tissue, reflecting a considerable degree of tissue-specific transcriptional regulation of this class of genes.

Discussion

These results call into question the widespread view that R-gene expression is induced upon pathogen attack. Instead, a small core set of R-genes is constitutively expressed, imparting upon the plant a ready-to-detect and defend status.

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 of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potato

Late blight (Phytophthora infestans) is a serious disease of potatoes. The aim of this study was to screen wild potato species and identify differentially expressed genes (DEGs) associated with late blight resistance. Wild potato species such as PIN45 (Solanum pinnatisectum), CPH62 (Solanum cardiophyllum), JAM07 (Solanum jamesii), MCD24 (Solanum microdontum), PLD47 (Solanum polyadenium), and cv. Kufri Bahar (control) were tested by artificial inoculation of P. infestans under controlled conditions. Transcriptomes of the leaf tissues (96 h post-inoculation) were sequenced using the Illumina platform. Statistically significant (p < 0.05) DEGs were analyzed in wild species by comparison with the control, and upregulated (>2 log₂ fold change, FC) and downregulated (<-2 log₂ FC) genes were identified. DEGs were functionally characterized with Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Selected genes were validated by real-time PCR analysis to confirm RNA-seq results. We identified some upregulated genes associated with late blight resistance in wild species such as cytochrome P450, proline-rich protein, MYB transcription factor MYB139, ankyrin repeat-containing protein, and LRR receptor-like serine/threonine-protein kinase in PIN45; glucosyltransferase, fructose-bisphosphate aldolase, and phytophthora-inhibited protease 1 in CPH62; steroid binding protein and cysteine proteinase 3 in JAM07; glycine-rich cell wall structural protein 1 and RING finger protein in MCD24; and cysteine proteinase 3 and major latex protein in PLD47. On the other hand, downregulated genes in these species were snakin-2 and WRKY transcription factor 3 in PIN45; lichenase and phenylalanine ammonia-lyase 1 in CPH62; metallothionein and LRR receptor-like serine/threonine-protein kinase in JAM07; UDP-glucoronosyl/UDP-glucosyl transferase family protein and steroid binding protein in MCD24; and cytoplasmic small heat shock protein class I and phosphatase PLD47. Our study identified highly resistant wild potato species and underlying genes such as disease resistance, stress response, phytohormones, and transcription factors (e.g., MYB, WRKY, AP2/ERF, and AN1) associated with late blight resistance in wild potato species.

Comparative transcriptomic responses of European and Japanese larches to infection by Phytophthora ramorum

BACKGROUND AND OBJECTIVES

Phytophthora ramorum severely affects both European larch (EL) and Japanese larch (JL) trees as indicated by high levels of mortality particularly in the UK. Field observations suggested that EL is less severely affected and so may be less susceptible to P. ramorum than JL; however, controlled inoculations have produced inconsistent or non-statistically significant differences. The present study aimed to compare RNA transcript accumulation profiles in EL and JL in response to inoculation with P. ramorum to improve our understanding of their defence responses.

METHODOLOGY

RNA-sequencing was carried out on bark tissues following the inoculation with P. ramorum of potted saplings in both EL and JL carried out under controlled environment conditions, with sampling at 1, 3, 10, and 25 days post inoculation in infected and control plants.

RESULTS

All of the inoculated trees rapidly developed lesions but no statistically significant differences were found in lesion lengths between EL and JL. RNA-Sequencing comparing control and inoculate saplings identified key differences in differentially expressed genes (DEGs) between the two larch species. European larch had rapid induction of defence genes within 24 hours of infection followed by sustained expression until 25 days after inoculation. Results in JL were more varied; upregulation was stronger but more transient and represented fewer defence pathways. Gene enrichment analyses highlighted differences in jasmonate signalling and regulation including NPR1 upregulation in EL only, and specific aspects of secondary metabolism. Some DEGs were represented by multiple responsive copies including lipoxygenase, chalcone synthase and nucleotide-binding, leucine-rich-repeat genes.

CONCLUSION

The variations between EL and JL in responsive DEGs of interest as potentially related to differences seen in the field and should be considered in the selection of trees for planting and future breeding.

Genome-wide identification of long intergenic non-coding RNAs for Ralstonia solanacearum resistance in tomato (Solanum lycopersicum)

There is growing evidences indicating that long intergenic ncRNAs (lincRNAs) play key roles in plant development and stress responses. To research tomato lincRNA functions during the interaction between tomato and Ralstonia solanacearum, RNA-seq data of tomato plants inoculated with R. solanacearum was analyzed. In this study, 315 possible lincRNAs were identified from RNA-seq data. Then 23 differentially expressed lincRNAs between tomato plants inoculated with R. solanacearum and control were identified and a total of 171 possible target genes for these differentially expressed lincRNAs were predicted. Through GO and KEGG analysis, we found that lincRNA might be involved in jasmonic acid and ethylene signaling pathways to respond to tomato bacterial wilt infection. Furthermore, lincRNA may also be involved in regulating the expression of AGO protein. Subsequently, analysis of expression patterns between differentially expressed lincRNAs and adjacent mRNAs by qRT-PCR revealed that part of lincRNAs and their possible target genes exhibited positive correlation. Taken together, these results suggest that lincRNAs play potential roles in tomato against R. solanacearum infection and will provide fundamental information about the lincRNA-based plant defense mechanisms.

Soybean Hypocotyls Prevent Calonectria ilicicola Invasion by Multi-Layered Defenses

In plants, many pathogens infect a specific set of host organs to cause disease, yet the underlying mechanisms remain unclear. Here, we show that inoculation of soybean plants with Calonectria ilicicola, the soil-borne causal agent of soybean red crown rot, caused typical disease symptoms of root rot and leaf chlorosis and necrosis. However, the pathogen DNA was only detected in the roots and stem (hypocotyl) base but not other aerial parts of the plants. As we observed vigorous fungal growth in all culture media made of extracts from roots, stems, and leaves, differences in key components including available nutrients did not determine organ-specific infection and reproduction by C. ilicicola. Furthermore, inoculation of stems both with and without a surface wound showed that the stems resisted C. ilicicola infection via both the pre- and post-invasion defense layers. Transcriptomic comparison of roots and stems using RNA-seq analysis further revealed that upon C. ilicicola inoculation, a greater expression of genes involved in stress response was induced in the plant stems, including receptor-like kinase, AP2/ERF, MYB, and WRKY. In addition, pathways related to amino acid metabolism were also more upregulated in the stems in response to C. ilicicola infection. These results suggest that soybean stems provide C. ilicicola resistance, at least in part, by activating an organ-specific defense response.

Comparison of the Distinct, Host-Specific Response of Three Solanaceae Hosts Induced by Phytophthora infestans

Three Solanaceae hosts (TSHs), S. tuberosum, N. benthamiana and S. lycopersicum, represent the three major phylogenetic clades of Solanaceae plants infected by Phytophthora infestans, which causes late blight, one of the most devastating diseases seriously affecting crop production. However, details regarding how different Solanaceae hosts respond to P. infestans are lacking. Here, we conducted RNA-seq to analyze the transcriptomic data from the TSHs at 12 and 24 h post P. infestans inoculation to capture early expression effects. Macroscopic and microscopic observations showed faster infection processes in S. tuberosum than in N. benthamiana and S. lycopersicum under the same conditions. Analysis of the number of genes and their level of expression indicated that distinct response models were adopted by the TSHs in response to P. infestans. The host-specific infection process led to overlapping but distinct in GO terms and KEGG pathways enriched for differentially expressed genes; many were tightly linked to the immune response in the TSHs. S. tuberosum showed the fastest response and strongest accumulation of reactive oxygen species compared with N. benthamiana and S. lycopersicum, which also had similarities and differences in hormone regulation. Collectively, our study provides an important reference for a better understanding of late blight response mechanisms of different Solanaceae host interactions.

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.

Volatile Compounds From Bacillus, Serratia, and Pseudomonas Promote Growth and Alter the Transcriptional Landscape of Solanum tuberosum in a Passively Ventilated Growth System

The interaction of an array of volatile organic compounds (VOCs) termed bacterial volatile compounds (BVCs) with plants is now a major area of study under the umbrella of plant-microbe interactions. Many growth systems have been developed to determine the nature of these interactions in vitro. However, each of these systems have their benefits and drawbacks with respect to one another and can greatly influence the end-point interpretation of the BVC effect on plant physiology. To address the need for novel growth systems in BVC-plant interactions, our study investigated the use of a passively ventilated growth system, made possible via Microbox^® growth chambers, to determine the effect of BVCs emitted by six bacterial isolates from the genera Bacillus, Serratia, and Pseudomonas. Solid-phase microextraction GC/MS was utilized to determine the BVC profile of each bacterial isolate when cultured in three different growth media each with varying carbon content. 66 BVCs were identified in total, with alcohols and alkanes being the most abundant. When cultured in tryptic soy broth, all six isolates were capable of producing 2,5-dimethylpyrazine, however BVC emission associated with this media were deemed to have negative effects on plant growth. The two remaining media types, namely Methyl Red-Voges Proskeur (MR-VP) and Murashige and Skoog (M + S), were selected for bacterial growth in co-cultivation experiments with Solanum tuberosum L. cv. ‘Golden Wonder.’ The BVC emissions of Bacillus and Serratia isolates cultured on MR-VP induced alterations in the transcriptional landscape of potato across all treatments with 956 significantly differentially expressed genes. This study has yielded interesting results which indicate that BVCs may not always broadly upregulate expression of defense genes and this may be due to choice of plant-bacteria co-cultivation apparatus, bacterial growth media and/or strain, or likely, a complex interaction between these factors. The multifactorial complexities of observed effects of BVCs on target organisms, while intensely studied in recent years, need to be further elucidated before the translation of lab to open-field applications can be fully realized.

Genome-Wide Identification and Characterization of Potato Long Non-coding RNAs Associated With Phytophthora infestans Resistance

Long non-coding RNA (lncRNA) is a crucial regulatory mechanism in the plant response to biotic and abiotic stress. However, their roles in potato (Solanum tuberosum L.) resistance to Phytophthora infestans (P. infestans) largely remain unknown. In this study, we identify 2857 lncRNAs and 33,150 mRNAs of the potato from large-scale published RNA sequencing data. Characteristic analysis indicates a similar distribution pattern of lncRNAs and mRNAs on the potato chromosomes, and the mRNAs were longer and had more exons than lncRNAs. Identification of alternative splicing (AS) shows that there were a total of 2491 lncRNAs generated from AS and the highest frequency (46.49%) of alternative acceptors (AA). We performed R package TCseq to cluster 133 specific differentially expressed lncRNAs from resistance lines and found that the lncRNAs of cluster 2 were upregulated. The lncRNA targets were subject to KEGG pathway enrichment analysis, and the interactive network between lncRNAs and mRNAs was constructed by using GENIE3, a random forest machine learning algorithm. Transient overexpression of StLNC0004 in Nicotiana benthamiana significantly suppresses P. infestans growth compared with a control, and the expression of extensin (NbEXT), the ortholog of the StLNC0004 target gene, was significantly upregulated in the overexpression line. Together, these results suggest that lncRNAs play potential functional roles in the potato response to P. infestans infection.

Comparative proteomics of three Chinese potato cultivars to improve understanding of potato molecular response to late blight disease

Background

Late blight disease (LBD) caused by the pathogen Phytophthora infestans (PI), is the most devastating disease limiting potato (Solanum tuberosum) production globally. Currently, this disease pathogen is re-emerging and appearing in new areas at a very high intensity. A better understanding of the natural defense mechanisms against PI in different potato cultivars especially at the protein level is still lacking. Therefore, to elucidate potato proteome response to PI, we investigated changes in the proteome and leaf morphology of three potato cultivars, namely; Favorita (FA), Mira (MA), and E-malingshu N0.14 (E14) infected with PI by using the iTRAQ-based quantitative proteomics analysis.

Results

A total of 3306 proteins were found in the three potato genotypes, and 2044 proteins were quantified. Cluster analysis revealed MA and E14 clustered together separately from FA. The protein profile and related functions revealed that the cultivars shared a typical hypersensitive response to PI, including induction of elicitors, oxidative burst, and suppression of photosynthesis in the potato leaves. Meanwhile, MA and E14 deployed additional specific response mechanism different from FA, involving high induction of protease inhibitors, serine/threonine kinases, terpenoid, hormone signaling, and transport, which contributed to MA tolerance of LBD. Furthermore, inductions of pathogenesis-related proteins, LRR receptor-like kinases, mitogen-activated protein kinase, WRKY transcription factors, jasmonic acid, and phenolic compounds mediate E14 resistance against LBD. These proteins were confirmed at the transcription level by a quantitative polymerase chain reaction and at the translation level by western-blot.

Conclusions

We found several proteins that were differentially abundant among the cultivars, that includes common and cultivar specific proteins which highlighted similarities and significant differences between FA, MA, and E14 in terms of their defense response to PI. Here the specific accumulation of mitogen-activated protein kinase, Serine/threonine kinases, WRKY transcription played a positive role in E14 immunity against PI. The candidate proteins identified reported in this study will form the basis of future studies and may improve our understanding of the molecular mechanisms of late blight disease resistance in potato.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07286-3.

Pattern and causes of the establishment of the invasive bacterial potato pathogen Dickeya solani and of the maintenance of the resident pathogen D. dianthicola

Invasive pathogens can be a threat when they affect human health, food production or ecosystem services, by displacing resident species, and we need to understand the cause of their establishment. We studied the patterns and causes of the establishment of the pathogen Dickeya solani that recently invaded potato agrosystems in Europe by assessing its invasion dynamics and its competitive ability against the closely related resident D. dianthicola species. Epidemiological records over one decade in France revealed the establishment of D. solani and the maintenance of the resident D. dianthicola in potato fields exhibiting blackleg symptoms. Using experimentations, we showed that D. dianthicola caused a higher symptom incidence on aerial parts of potato plants than D. solani, while D. solani was more aggressive on tubers (i.e. with more severe symptoms). In co-infection assays, D. dianthicola outcompeted D. solani in aerial parts, while the two species co-existed in tubers. A comparison of 76 D. solani genomes (56 of which have been sequenced here) revealed balanced frequencies of two previously uncharacterized alleles, VfmB_Pro and VfmB_Ser , at the vfmB virulence gene. Experimental inoculations showed that the VfmB_Ser population was more aggressive on tubers, while the VfmB_Pro population outcompeted the VfmB_Ser population in stem lesions, suggesting an important role of the vfmB virulence gene in the ecology of the pathogens. This study thus brings novel insights allowing a better understanding of the pattern and causes of the D.solani invasion into potato production agrosystems, and the reasons why the endemic D. dianthicola nevertheless persisted.

Structural specificity in plant-filamentous pathogen interactions

Plant diseases bear names such as leaf blights, root rots, sheath blights, tuber scabs, and stem cankers, indicating that symptoms occur preferentially on specific parts of host plants. Accordingly, many plant pathogens are specialized to infect and cause disease in specific tissues and organs. Conversely, others are able to infect a range of tissues, albeit often disease symptoms fluctuate in different organs infected by the same pathogen. The structural specificity of a pathogen defines the degree to which it is reliant on a given tissue, organ, or host developmental stage. It is influenced by both the microbe and the host but the processes shaping it are not well established. Here we review the current status on structural specificity of plant-filamentous pathogen interactions and highlight important research questions. Notably, this review addresses how constitutive defence and induced immunity as well as virulence processes vary across plant organs, tissues, and even cells. A better understanding of the mechanisms underlying structural specificity will aid targeted approaches for plant health, for instance by considering the variation in the nature and the amplitude of defence responses across distinct plant organs and tissues when performing selective breeding.

Peptide Extracts from Seven Medicinal Plants Discovered to Inhibit Oomycete Phytophthora infestans, a Causative Agent of Potato Late Blight Disease

We report the inhibitory effect of peptide extracts obtained from seven medicinal plants against a causative agent of late blight disease Phytophthora infestans. We find that all the extracts possess inhibitory activity toward the zoospores output, zoosporangium germination, and the development of P. infestans on potato disc tubers at different quantitative levels. Based on the biological effects detected, an extract of common horsetail (Equisetum arvense) biomass is recognized as the most effective and is selected for further structural analysis. We perform a combination of amino acid analysis and MALDI-TOF mass spectrometry, which reveal the presence of Asn/Asp- and Gln/Glu-rich short peptides with molecular masses in the range of 500-900 Da and not exceeding 1500 Da as the maximum. Analytical anion-exchange HPLC is successfully applied for separation of the peptide extract from common horsetail (E. arvense). We collect nine dominant components that are combined in two groups with differences in retention times. The N-terminal amino acid sequence of the prevalent compounds after analytical ion-exchange HPLC allows us to identify them as peptide fragments of functionally active proteins associated with photosynthesis, aquatic transport, and chitin binding. The anti-oomycete effects may be associated with the conversion of ribulose-1,5-bisphosphate carboxylase/oxygenase to produce a number of biologically active anionic peptides with possible regulatory functions. These data inform our knowledge regarding biologically active peptide fragments; they are the components of programmed or induced proteolysis of plant proteins and can realize secondary antimicrobial functions.

Comparison of defense responses of transgenic potato lines expressing three different Rpi genes to specific Phytophthora infestans races based on transcriptome profiling

Potato late blight, one of the most devastating diseases in potato, is caused by the oomycete Phytophthora infestans. Over 20 resistance genes have been cloned including R1, R3a, and R3b. The distinctions between defense response mechanisms mediated by different resistance genes are still unclear. Here we performed transcriptome profiling in three transgenic lines, R1, R3a, and R3b, and wild-type Desiree under inoculation with two P. infestans isolates, 89148 (race 0) and CN152 (super race), using RNA-seq. Compared with wild type, specific differentially expressed genes (DEGs) were identified in the three transgenic lines. The highest number of DEGs occurred in transgenic R3b, with 779 DEGs in response to isolate 89148 and 864 DEGs in response to infection by CN152, followed by transgenic R1 lines with 408 DEGs for isolate 89148 and 267 DEGs for CN152. Based on gene ontology, the most common GO terms (15 for 89148 and 20 for CN152) were enriched in transgenic R3a and R3b lines. This indicates that the defense pathways mediated by R3a and R3b are more similar than those mediated by R1. Further separate GO analysis of up- or down-regulated DEGs showed that the down-regulated DEGs mainly functioned in mediating the resistance of potato to P. infestans 89148 by response to stress biological process and to CN152 by oxidation reduction biological process. KEGG pathways of DNA replication, plant-pathogen interaction and pentose and glucuronate interconversions are unique for transgenic R1, R3a, and R3b lines in incompatible interactions. Quantitative real-time PCR experimental validation confirmed the induced expression of DEGs in the late blight resistance signaling pathway. Our results will lay a solid foundation for further understanding the mechanisms of plant-pathogen interactions, and provide a theoretical reference for durable resistance in potato.

Novel organ-specific genetic factors for quantitative resistance to late blight in potato

Potato, Solanum tuberosum, is one of the major consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused by Phytophtora infestans. Here, we present a multi-environmental analysis of the response to P. infestans using an association panel of 150 accessions of S. tuberosum Group Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site–associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain between 13.7% and 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively. In silico analysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candidate genes code for diverse proteins, including a leucine-rich repeat kinase.

Novel organ-specific genetic factors for quantitative resistance to late blight in potato

Potato, Solanum tuberosum, is one of the major consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused by Phytophtora infestans. Here, we present a multi-environmental analysis of the response to P. infestans using an association panel of 150 accessions of S. tuberosum Group Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site-associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain between 13.7% and 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively. In silico analysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candidate genes code for diverse proteins, including a leucine-rich repeat kinase.

Transcriptome analysis provides insights into the delayed sticky disease symptoms in Carica papaya

Global gene expression analysis indicates host stress responses, mainly those mediated by SA, associated to the tolerance to sticky disease symptoms at pre-flowering stage in Carica papaya. Carica papaya plants develop the papaya sticky disease (PSD) as a result of the combined infection of papaya meleira virus (PMeV) and papaya meleira virus 2 (PMeV2), or PMeV complex. PSD symptoms appear only after C. papaya flowers. To understand the mechanisms involved in this phenomenon, the global gene expression patterns of PMeV complex-infected C. papaya at pre-and post-flowering stages were assessed by RNA-Seq. The result was 633 and 88 differentially expressed genes at pre- and post-flowering stages, respectively. At pre-flowering stage, genes related to stress and transport were up-regulated while metabolism-related genes were down-regulated. It was observed that induction of several salicylic acid (SA)-activated genes, including PR1, PR2, PR5, WRKY transcription factors, ROS and callose genes, suggesting SA signaling involvement in the delayed symptoms. In fact, pre-flowering C. papaya treated with exogenous SA showed a tendency to decrease the PMeV and PMeV2 loads when compared to control plants. However, pre-flowering C. papaya also accumulated transcripts encoding a NPR1-inhibitor (NPR1-I/NIM1-I) candidate, genes coding for UDP-glucosyltransferases (UGTs) and several genes involved with ethylene pathway, known to be negative regulators of SA signaling. At post-flowering, when PSD symptoms appeared, the down-regulation of PR-1 encoding gene and the induction of BSMT1 and JA metabolism-related genes were observed. Hence, SA signaling likely operates at the pre-flowering stage of PMeV complex-infected C. papaya inhibiting the development of PSD symptoms, but the induction of its negative regulators prevents the full-scale and long-lasting tolerance.

Gene Profiling in Late Blight Resistance in Potato Genotype SD20

Late blight caused by the oomycete fungus Phytophthora infestans (Pi) is the most serious obstacle to potato (Solanum tuberosum) production in the world. A super race isolate, CN152, which was identified from Sichuan Province, China, could overcome nearly all known late blight resistance genes and caused serious damage in China. The potato genotype SD20 was verified to be highly resistant to CN152; however, the molecular regulation network underlying late blight resistance pathway remains unclear in SD20. Here, we performed a time-course experiment to systematically profile the late blight resistance response genes using RNA-sequencing in SD20. We identified 3354 differentially expressed genes (DEGs), which mainly encoded transcription factors and protein kinases, and also included four NBS-LRR genes. The late blight responsive genes showed time-point-specific induction/repression. Multi-signaling pathways of salicylic acid, jasmonic acid, and ethylene signaling pathways involved in resistance and defense against Pi in SD20. Gene Ontology and KEGG analyses indicated that the DEGs were significantly enriched in metabolic process, protein serine/threonine kinase activity, and biosynthesis of secondary metabolites. Forty-three DEGs were involved in immune response, of which 19 were enriched in hypersensitive response reaction, which could play an important role in broad-spectrum resistance to Pi infection. Experimental verification confirmed the induced expression of the responsive genes in the late blight resistance signaling pathway, such as WRKY, ERF, MAPK, and NBS-LRR family genes. Our results provided valuable information for understanding late blight resistance mechanism of potato.

Genome-wide sequence variations between wild and cultivated tomato species revisited by whole genome sequence mapping

Background

Cultivated tomato (Solanum lycopersicum L.) is the second most important vegetable crop after potato and a member of thirteen interfertile species of Solanum genus. Domestication and continuous selection for desirable traits made cultivated tomato species susceptible to many stresses as compared to the wild species. In this study, we analyzed and compared the genomes of wild and cultivated tomato accessions to identify the genomic regions that encountered changes during domestication.

Results

Analysis was based on SNP and InDel mining of twentynine accessions of twelve wild tomato species and forty accessions of cultivated tomato. Percentage of common SNPs among the accessions within a species corresponded with the reproductive behavior of the species. SNP profiles of the wild tomato species within a phylogenetic subsection varied with their geographical distribution. Interestingly, the ratio of genic SNP to total SNPs increased with phylogenetic distance of the wild tomato species from the domesticated species, suggesting that variations in gene-coding region play a major role in speciation. We retrieved 2439 physical positions in 1594 genes including 32 resistance related genes where all the wild accessions possessed a common wild variant allele different from all the cultivated accessions studied. Tajima’s D analysis predicted a very strong purifying selection associated with domestication in nearly 1% of its genome, half of which is contributed by chromosome 11. This genomic region with a low Tajima’s D value hosts a variety of genes associated with important agronomic trait such as, fruit size, tiller number and wax deposition.

Conclusion

Our analysis revealed a broad-spectrum genetic base in wild tomato species and erosion of that in cultivated tomato due to recurrent selection for agronomically important traits. Identification of the common wild variant alleles and the genomic regions undergoing purifying selection during cultivation would facilitate future breeding program by introgression from wild species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3822-3) contains supplementary material, which is available to authorized users.

Extracellular Alkalinization as a Defense Response in Potato Cells

A quantitative and robust bioassay to assess plant defense response is important for studies of disease resistance and also for the early identification of disease during pre- or non-symptomatic phases. An increase in extracellular pH is known to be an early defense response in plants. In this study, we demonstrate extracellular alkalinization as a defense response in potatoes. Using potato suspension cell cultures, we observed an alkalinization response against various pathogen- and plant-derived elicitors in a dose- and time-dependent manner. We also assessed the defense response against a variety of potato pathogens, such as protists (Phytophthora infestans and Spongospora subterranea) and fungi (Verticillium dahliae and Colletotrichum coccodes). Our results show that extracellular pH increases within 30 min in proportion to the number of pathogen spores added. Consistently with the alkalinization effect, the higher transcription level of several defense-related genes and production of reactive oxygen species was observed. Our results demonstrate that the alkalinization response is an effective marker to study early stages of defense response in potatoes.