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The receptor like kinases (RLKs) belong to the RLK/Pelle superfamily, one of the largest gene families in plants. RLKs play an important role in plant development, as well as in response to biotic and abiotic stresses. The lysine motif receptor like kinases (LysM-RLKs) are a subfamily of RLKs containing at least one lysine motif (LysM) that are involved in the perception of elicitors or pathogen-associated molecular patterns (PAMPs). In the present study, 77 putative RLKs genes and three receptor like proteins were identified in potato (Solanum tuberosum) genome, following a genome-wide search. The 77 potato RLK proteins are classified into two major phylogenetic groups based on their kinase domain amino acid sequence similarities. Out of 77 RLKs, 10 proteins had at least one LysM. Among them three RLP proteins were found in potato genome with either 2 or three tandem LysM but these lacked a cytoplasmic kinase domain. Expression analyses of a potato LysM-RLKs (StLysM-RLK05) was carried out by a Real time RT-PCR, following inoculation of potato leaves and immature tubers with late blight and common scab pathogens, respectively. The expression was significantly higher in resistant than in susceptible following S. scabies inoculation. The StLysM-RLK05 sequence was verified and it was polymorphic in scab susceptible cultivar. The present study provides an overview of the StLysM-RLKs gene family in potato genome. This information is helpful for future functional analysis of such an important protein family, in Solanaceae species.

Crop plant resistance against pathogens is governed by dynamic molecular and biochemical responses driven by complex transcriptional networks. However, the underlying mechanisms are largely unclear. Here we report an interesting role of HvWRKY23 transcription factor (TF) in modulating defense response against Fusarium head blight (FHB) in barley. The combined approach of gene silencing, metabolomics, real time expression analysis and ab initio bioinformatics tools led to the identification of the HvWRKY23 role in FHB resistance. The knock-down of HvWRKY23 gene in the FHB resistant barley genotype CI9831, followed by inoculation with Fusarium graminearum, led to the down regulation of key flavonoid and hydroxycinnamic acid amide biosynthetic genes resulting in reduced accumulation of resistant related (RR) secondary metabolites such as pelargonidin 3-rutinoside, peonidin 3-rhamnoside-5-glucoside, kaempferol 3-O-arabinoside and other flavonoid glycosides. Reduced abundances of RR metabolites in TF silenced plants were also associated with an increased proportion of spikelets diseased and amount of fungal biomass in spikelets, depicting the role of HvWRKY23 in disease resistance. The luciferase reporter assay demonstrated binding of HvWRKY23 protein to promoters of key flavonoid and hydroxycinnamic acid amides (HCAA) biosynthetic genes, such as HvPAL2, HvCHS1, HvHCT, HvLAC15 and HvUDPGT. The accumulation of high abundances of HCAAs and flavonoid glycosides reinforce cell walls to contain the pathogen to initial infection area. This gene in commercial cultivars can be edited, if non-functional, to enhance resistance against FHB.

Metabolic pathway gene editing in tetraploid potato enhanced resistance to late blight. Multiallelic mutation correction of a caffeoyl-CoA O-methyltransferase gene increased accumulation of resistance metabolites in Russet Burbank potato. Late blight of potato is a devastating disease worldwide and requires weekly applications of fungicides to manage. Genetic improvement is the best option, but the self-incompatibility and inter-specific incompatibility makes potato breeding very challenging. Immune receptor gene stacking has increased resistance, but its durability is limited. Quantitative resistance is durable, and it mainly involves secondary cell wall thickening due to several metabolites and their conjugates. Deleterious mutations in biosynthetic genes can hinder resistance metabolite biosynthesis. Here a probable resistance role of the StCCoAOMT gene was first confirmed by an in-planta transient overexpression of the functional StCCoAOMT allele in late blight susceptible Russet Burbank (RB) genotype. Following this, a precise single nucleotide polymorphism (SNP) mutation correction of the StCCoAOMT gene in RB potato was carried out using CRISPR-Cas9 mediated homology directed repair (HDR). The StCCoAOMT gene editing increased the transcript abundance of downstream biosynthetic resistance genes. Following pathogen inoculation, several phenylpropanoid pathway genes were highly expressed in the edited RB plants, as compared to the non-edited. The disease severity (fold change = 3.76) and pathogen biomass in inoculated stems of gene-edited RB significantly reduced (FC = 21.14), relative to non-edited control. The metabolic profiling revealed a significant increase in the accumulation of resistance-related metabolites in StCCoAOMT edited RB plants. Most of these metabolites are involved in suberization and lignification. The StCCoAOMT gene, if mutated, can be edited in other potato cultivars to enhance resistance to late blight, provided it is associated with other functional genes in the metabolic pathway network.

Late blight caused by Phytophthora infestans is a devastating disease affecting potato production worldwide. The quantitative resistance is durable, but the underlying molecular and biochemical mechanisms are poorly understood, limiting its application in breeding. Integrated transcriptomics and metabolomics approach was used for the first time to study the hierarchies of molecular events occurring, following inoculation of resistant and susceptible potato genotypes with P. infestans. RNA sequencing revealed a total of 4216 genes that were differentially expressed in the resistant than in the susceptible genotype. Genes that were highly expressed and associated with their biosynthetic metabolites that were highly accumulated, through metabolic pathway regulation, were selected. Quantitative real-time PCR was performed to confirm the RNA-seq expression levels. The induced leucine-rich repeat receptor-like kinases (LRR-RLKs) are considered to be involved in pathogen recognition. These receptor genes are considered to trigger downstream oxidative burst, phytohormone signalling-related genes, and transcription factors that regulated the resistance genes to produce resistance related metabolites to suppress the pathogen infection. It was noted that several resistance genes in metabolic pathways related to phenylpropanoids, flavonoids, alkaloids and terpenoid biosynthesis were strongly induced in the resistant genotypes. The pathway specific gene induction provided key insights into the metabolic reprogramming of induced defence responses in resistant genotypes.

Fusarium head blight (FHB), caused mainly by Fusarium graminearum (Fg), is one of the most severe diseases of wheat. It affects grain yield and quality due to mycotoxin contamination, which is harmful for both human and livestock consumption. Cell wall lignification, following pathogen invasion, is one of the innate defense responses. Plant laccases are known to lignify the secondary cell walls. A metabolo-genomics study identified laccase as one of the candidate genes in QTL-Fhb1 of wheat NILs derived from Sumai 3*5/Thatcher cross. Based on phylogenetics, it was named as TaLAC4. Real-time qPCR revealed a strongly induced expression of TaLAC4 in NIL-R. The VIGS based transient silencing of TaLAC4 in NIL-R resulted in an increased susceptibility leading to Fg spread within the entire spike in 15dpi, contrasting to non-silenced where the infection was limited to inoculated spikelets. Histopathology revealed thickened cell walls, mainly due to G-lignin, in non-silenced NIL-R, relative to silenced, in conjunction with higher total lignin content. Metabolic profiling of TaLAC4 silenced NILs identified the accumulation of several precursor metabolites higher in abundances upstream TaLAC4. These results confirm that the resistance function of TaLAC4 in NIL-R is due to pathogen-induced lignification of secondary cell walls in the rachis.

Macronutrient contents of 94 genotypes from the Colombian Central Collection (CCC) and 13 genotypes from the Native Collection (NC) of diploid potatoes (Solanum tuberosum Group Phureja) were evaluated, considering six genotypes, four diploid and two tetraploid potato commercial cultivars, as control. Dry matter, protein, soluble dietary fibre (SDF) and insoluble dietary fibre (IDF), fat, and ash contents were determined in entire boiled tubers. Macronutrient contents varied widely among the 113 genotypes. Protein contents found in CCC and NC (1.8–17.2 g/100 g dry weight, DW) were greater than those in commercial cultivars (3.1–9.5 g/100 g DW). Total dietary fibre (TDF), SDF, and IDF were greater in CCC and NC (9.4–27.1 g/100 g DW, 1.6–6.6 g/100 g DW, and 6.4–20.9 g/100 g DW, respectively) than in the commercial cultivars (9.0–15.3 g/100 g DW, 2.7–4.4 g/100 g DW, and 6.4–12.3 g/100 g DW, respectively). Several genotypes from CCC and NC are good candidates as parental materials for developing new cultivars, with the highest protein content in CCC-76 (17.2 ± 0.3 g/100 g DW) and NC-8 (16.7 ± 0.7 g/100 g DW) and the highest TDF in CCC-110 (27.1 ± 4.0 g/100 g DW).

Resistance to late blight is highly complex and quantitative in nature but has proven difficult to harness due to poor understanding of its molecular and biochemical mechanisms. Secondary cell wall (SCW) biosynthesis is a critical process in late blight resistance, regulated by an array of transcription factors (TF). In the present study, metabolo-transcriptomics approaches were used to functionally characterize that the upregulated StNAC43 and StMYB8 in potato genotypes were linked to SCW biosynthetic phenylpropanoid metabolites produced in high fold change following Phytophthora infestans infection. The promoter analysis of StNAC43 revealed the presence of ethylene responsive element (ERE), which is the proposed binding site for ethylene responsive factor, ERF3. Sequencing of the ERF3 revealed a frameshift mutation in the susceptible potato genotype. Simultaneous induction of both the ERF3 and StNAC43, following pathogen invasion, enables functioning of the latter to interact with the ERE present in the resistant StNAC43 promoter region. Further, the StNAC43 binds to the secondary NAC binding element in StMYB8 promoter and activates StMYB8 TF. A luciferase transient expression assay elucidated a direct regulatory role of the StMYB8 on SCW biosynthetic genes, by binding to promoters of downstream genes: HCT, PHT, CHS, and flavanone 3-hydroxylase (F3H). Silencing of StNAC43 and StMYB8 affected the late blight resistance by significantly increasing pathogen biomass and decreasing the amounts of hydroxycinnamic acid amides (HCAAs) and flavonoid glycosides. The StNAC43 and StMYB8 TFs are positive activators of SCW biosynthetic genes, which deposit resistance-related metabolites to reinforce SCW and improve resistance against late blight.

In plants, the biosynthesis of the phenylpropanoid, flavonoid and fatty acid pathway monomers, polymers and conjugated metabolites play a vital role in disease resistance. These are generally deposited to reinforce cell walls to contain the pathogen to the site of infection. Identification of sequence variants in genes that biosynthesise these resistance metabolites can explain the mechanisms of disease resistance. The resistant and susceptible genotypes inoculated with Phytophthora infestans were RNA sequenced to identify the single nucleotide polymorphisms (SNPs) and insertion/deletion (InDel) variations. The SNPs/InDels were annotated and classified into different categories based on their effect on gene functions. In the selected 25 biosynthetic genes overlapping 39 transcripts, a total of 52 SNPs/InDels were identified in the protein-coding (CDS) regions. These were categorised as deleterious based on prediction of their effects on protein structure and function. The SNPs/InDels data obtained in this study can be used in genome editing to enhance late blight resistance in Russet Burbank and other potato cultivars.

An analysis of various systems, with special reference to coffee rust management systems, had led to various disease management practices. In coffee rust epidemiology, the lack of such an approach has lead to various parallel and repetitive experiments. For coffee rust control two of these epidemiological principles can be applied: reduction of initial inoculum; and reduction of infection rate. The methods used in coffee-rust management to reduce initial inoculum are exclusion, eradication, chemical control, cultural practices, and vertical resistance. When coffee rust broke out in various countries in Latin America, the neighboring countries sprayed protective and/or systemic fungicides along the border to exclude the pathogen from entering and establishing in their country. Copper-based fungicides have been most effective and economical for the control of coffee rust under field conditions. The copper fungicides are by far the most commonly used protective fungicides, not only for the control of coffee rust but also for various other plant diseases.

Fusarium head blight (FHB) is a destructive disease affecting cereal crops globally due to mycotoxin contamination of grains that reduce yield and quality. Among hundreds of QTLs identified for resistance, the QTL-Fhb1 is of significant interest even today, for its major contribution to FHB resistance. Previously, QTL-Fhb1 dissection based on a combined metabolo-genomics approach, identified a few potential resistance genes, including a NAC like transcription factor for FHB resistance. Sequencing and phylogenetic analysis confirmed NAC to be the wheat TaNAC032. Also, the quantitative RT-PCR studies revealed a greater induced expression of TaNAC032 in resistant NIL in comparison to susceptible NIL upon Fusarium graminearum (Fg) infection. The virus-induced gene silencing (VIGS) based functional validation of TaNAC032 in resistant NIL confirmed increased disease severity and fungal biomass. Metabolic profiling revealed low abundances of resistance-related (RR) metabolites in TaNAC032 silenced NIL-R compared to non-silenced. Silenced plants showed decreased transcript abundances of RR metabolite biosynthetic genes associated with a reduction in total lignin content in rachis, confirming the regulatory role of TaNAC032 in wheat in response to Fg infection. If TaNA032 is mutated in an FHB susceptible cultivar, it can be edited to enhance FHB resistance.

We report plausible disease resistance mechanisms induced by barley resistant genotype CI89831 against Fusarium head blight (FHB) based on metabolo-transcriptomics approach. We identified HvCERK1 as a candidate gene for FHB resistance, which is functional in resistant genotype CI9831 but non-functional in susceptible cultivars H106-371 and Zhedar-2. For the first time, we were able to show a hierarchy of regulatory genes that regulated downstream biosynthetic genes that eventually produced resistance related metabolites that reinforce the cell walls to contain the pathogen progress in plant. The HvCERK1 can be used for replacing in susceptible commercial cultivars, if non-functional, based on genome editing. Fusarium head blight (FHB) management is a great challenge in barley and wheat production worldwide. Though barley genome sequence and advanced omics technologies are available, till date none of the resistance mechanisms has been clearly deciphered. Hence, this study was aimed at identifying candidate gene(s) and elucidating resistance mechanisms induced by barley resistant genotype CI9831 based on integrated metabolomics and transcriptomics approach. Following Fusarium graminearum infection, we identified accumulation of specific set of induced secondary metabolites, belonging to phenylpropanoid, hydroxycinnamic acid (HCAA) and jasmonic acid pathways, and their biosynthetic genes. In association with these, receptor kinases such as chitin elicitor receptor kinase (HvCERK1) and protein kinases such as MAP kinase 3 (HvMPK3) and MAPK substrate 1 (HvMKS1), and transcription factors such as HvERF1/5, HvNAC42, HvWRKY23 and HvWRKY70 were also found upregulated with high fold change. Polymorphism studies across three barley genotypes confirmed the presence of mutations in HvCERK1 gene in two susceptible genotypes, isolating this gene as a potential candidate for FHB resistance. Further, the silencing of functional HvCERK1 gene in the resistant genotype CI9831, followed by gene expression and metabolite analysis revealed its role as an elicitor recognition receptor that triggered downstream regulatory genes, which in turn, regulated downstream metabolic pathway genes to biosynthesize resistance related (RR) metabolites to contain the pathogen to spikelet infection. A putative model on metabolic pathway regulation is proposed.

Summary Fusarium head blight (FHB) resistance in wheat is considered to be polygenic in nature. Cell wall fortification is one of the best resistance mechanisms in wheat against Fusarium graminearum which causes FHB. Metabolomics approach in our study led to the identification of a wide array of resistance related (RR) metabolites, among which hydroxycinnamic acid amides (HCAAs), such as, coumaroylagmatine and coumaroylputrescine were the highest fold-change RR metabolites in the rachis of a resistant near-isogenic line (NIL-R) upon F. graminearum infection. Placement of these metabolites in the secondary metabolic pathway led to the identification of a gene encoding agmatinecoumaroyl transferase, herein referred to as TaACT, as a candidate gene. Based on wheat survey sequence TaACT was located within a FHB quantitative trait loci on chromosome 2DL (FHB QTL-2DL) between the flanking markers WMC245 and GWM608. Phylogenetic analysis suggested that TaACT shared closest phylogenetic relationship with an ACT ortholog in barley. Sequence analysis of TaACT in resistant and susceptible NILs, with contrasting levels of resistance to FHB, led to the identification of several single nucleotide polymorphisms (SNPs) and two inversions that may be important for gene function. Further, a role for TaACT in FHB resistance was functionally validated by virus induced gene silencing (VIGS) in wheat NIL-R and based on complementation studies in Arabidopsis with act mutant background. The disease severity, fungal biomass, and RR metabolite analysis confirmed TaACT as an important gene in wheat FHB QTL-2DL, conferring resistance to F. graminearum. This article is protected by copyright. All rights reserved.

Resistance in plants against pathogen infection is defined as a spectrum of reduced susceptibility, ranging from moderate susceptibility to a hypersensitive response (complete resistance). The genetic improvement of plants is one option to manage diseases. Several quantitative trait loci (QTLs) for disease resistance have been identified, but these contain many genes and the mechanisms by which resistance is imparted are unknown. These operative factors are crucial to assure precise breeding. Several OMICs tools have emerged, along with genomics, to elucidate resistance mechanisms of plants to pathogens. For example, metabolomics of plant–pathogen interactions have led to the discovery of several complex metabolites that are deposited to reinforce secondary cell walls and prevent the spread of the pathogen beyond the initial infection site. Resistance in plants is largely due to antimicrobial biochemicals and/or the structures formed from them; both these lines of defence may be constitutive or in...

Plant diseases, caused by microbes, threaten world food, feed, and bioproduct security. Plant resistance has not been effectively deployed to improve resistance in plants for lack of understanding of biochemical mechanisms and genetic bedrock of resistance. With the advent of genome sequencing, the forward and reverse genetic approaches have enabled deciphering the riddle of resistance. Invading pathogens produce elicitors and effectors that are recognized by the host membrane-localized receptors, which in turn induce a cascade of downstream regulatory and resistance metabolite and protein biosynthetic genes (R) to produce resistance metabolites and proteins, which reduce pathogen advancement through their antimicrobial and cell wall enforcement properties. The resistance in plants to pathogen attack is expressed as reduced susceptibility, ranging from high susceptibility to hypersensitive response, the shades of gray. The hypersensitive response or cell death is considered as qualitative resistan...

Selection of disease resistant potato varieties for conventional breeders is a time consuming and labor intensive process and most of the times lead to the results that are spatiotemporally inconsistent. Metabolic phenotyping was employed to develop metabolic criteria that can be used to distinguish potato genotypes with disease resistance. Tubers of potato varieties (Caesar and AC Novachip) moderately resistant and susceptible to Phytophthora infestans were inoculated with pathogen or water, and metabolites were analyzed using Gas Chromatography-mass Spectrometry (GS/MS). Disease severity was measured as the volume of diseased tissue calculated based on lesions volume at 2-day intervals after inoculation. Disease severity was 4.17 and 0.61 cm3 for varieties Caesar and AC Novachip respectively. Seventy seven metabolites were tentatively identified using Automated Mass spectral Deconvolution and Identification System (AMDIS) and univariate ANOVA showed that 37 metabolites had significant treatment effects with nine identified as resistance related and five as constitutive metabolites. Four metabolites, constitutive or induced showed significant increase in their abundance in pathogen inoculated tubers. A total of 21 metabolites were considered as pathogenesis related which showed changes in abundance after pathogen challenge. A canonical discriminant analysis of the 37 metabolites identified metabolic phenotypes correlating to disease severity phenotypes. The metabolites were mainly from sugars, fatty acids, and phenolic compounds which of some may have potential antimicrobial activity. Among resistance related metabolites, the abundances of 1H-Indole-3-acetonitrile, trihydroxybutyrate, D-Mannitol, dihydocoumarin, and propanoate were significantly higher in Caesar. The potential application of metabolic profiling technology for high throughput screening of potato breeding lines against potato late blight is discussed.

Highlight StWRKY1 transcription factor mediates secondary cell wall thickening in potato by regulating expression of tyramine-related hydroxycinnamic acid amide biosynthetic genes, thus contributing to resistance to late blight disease., Quantitative resistance is polygenically controlled and durable, but the underlying molecular and biochemical mechanisms are poorly understood. Secondary cell wall thickening is a critical process in quantitative resistance, regulated by transcriptional networks. This paper provides compelling evidence on the functionality of StWRKY1 transcription factor, in a compatible interaction of potato–Phytophthora infestans, to extend our knowledge on the regulation of the metabolic pathway genes leading to strengthening the secondary cell wall. A metabolomics approach was used to identify resistance-related metabolites belonging to the phenylpropanoid pathway and their biosynthetic genes regulated by StWRKY1. The StWRKY1 gene in resistant potato was silenced to decipher its role in the regulation of phenylpropanoid pathway genes to strengthen the secondary cell wall. Sequencing of the promoter region of StWRKY1 in susceptible genotypes revealed the absence of heat shock elements (HSEs). Simultaneous induction of both the heat shock protein (sHSP17.8) and StWRKY1 following pathogen invasion enables functioning of the latter to interact with the HSE present in the resistant StWRKY1 promoter region. EMSA and luciferase transient expression assays further revealed direct binding of StWRKY1 to promoters of hydroxycinnamic acid amide (HCAA) biosynthetic genes encoding 4-coumarate:CoA ligase and tyramine hydroxycinnamoyl transferase. Silencing of the StWRKY1 gene was associated with signs of reduced late blight resistance by significantly increasing the pathogen biomass and decreasing the abundance of HCAAs. This study provides convincing evidence on the role of StWRKY1 in the regulation of downstream genes to biosynthesize HCAAs, which are deposited to reinforce secondary cell walls.

Fusarium head blight (FHB) caused by Fusarium graminearum is one of the devastating diseases of small grain crops, including barley and wheat. Breeding for resistance is one of the best and ecofriendly strategies to manage the FHB. However, the existing methods used for screening genotypes, both under field and greenhouse conditions, often resulted in high experimental error, leading to inconsistent ranking of genotypes over years. In the postgenomic era, precise assessment of resistance is crucial to identify candidate genes. Here, we report a pathogen inoculation procedure and a real-time quantitative polymerase chain reaction (qPCR) based protocol for the quantification and discrimination of quantitative resistance among barley and wheat genotypes to FHB. Using Fusarium specific primer pair Tri6_10, for the trichothecene biosynthetic cluster (Tri6) gene, we successfully quantified the relative fungal biomass in both spikelets and rachis. A qPCR of spikelets and rachis collected on 6 dpi, from inoculated three alternate spikelet regions, discriminated resistance with less experimental error than those based on the proportion of spikelets diseased (PSD) at 9 dpi. This method can be applied for medium to high-throughput barley and wheat breeding programmes to discriminate quantitative resistance among genotypes against FHB.

This project was supported by the International Development Research Center and Department of Foreign Affairs, Trade and Development Canada (Project number 106926, “Improving Potato Production for Increasing Food Security of Indigenous Communities in Colombia”). The authors are grateful with Ministry of Environment and Sustainable Development for the granted access to S. tuberosum group Phureja genetic resources through the Contract No. 53.

Metabolomics has become a widely-used tool in plants to phenotype different genotypes with varying levels of resistance to stresses. Two near-isogenic lines (NILs) of wheat QTL-2DL, with contrasting levels of resistance to fusarium head blight (FHB), were grown under greenhouse conditions, spikelets were individually inoculated, fungal biomass quantified and the metabolome profiled. The NILs significantly varied in resistance to FHB. The metabolites in phenylpropanoid, fatty acid and glycerophospholipid pathways were highly induced in NIL-R (resistant NIL) relative to NIL-S (susceptible NIL) upon Fusarium graminearum (Fg) inoculation. Key genes involved in the biosynthesis of high fold-change resistance related (RR) metabolites such as genes encoding a glyceraldehyde 3-phosphate acyltransferase (GPAT), an ABC transporter eceriferum 5 (CER5), and a phenylalanine ammonium lyase (PAL), were identified from the QTL-2DL region based on wheat genome survey sequence. Concurrently, relative transcript expressions of these candidate genes were also up-regulated in NIL-R after pathogen inoculation, confirming their potential involvement in the biosynthesis of high fold-change RR metabolites. The spikelet resistance to FHB observed in this study was mainly associated with cell wall reinforcement through deposition of cutin and suberin molecules.

A semi-comprehensive metabolomics was used to identify the candidate metabolites and genes to decipher mechanisms of resistance in wheat near-isogenic lines (NILs) containing QTL-2DL against Fusarium graminearum (Fg). Metabolites, with high fold-change in abundance, belonging to hydroxycinnamic acid amides (HCAAs): such as coumaroylagmatine, coumaroylputrescine and Fatty acids: phosphatidic acids (PAs) were identified as resistance related induced (RRI) metabolites in rachis of resistant NIL (NIL-R), inoculated with Fg. A WRKY like transcription factor (TF) was identified within the QTL-2DL region, along with three resistance genes that biosynthesized RRI metabolites. Sequencing and in-silico analysis of WRKY confirmed it to be wheat TaWRKY70. Quantitative real time-PCR studies showed a higher expression of TaWRKY70 in NIL-R as compared to NIL-S after Fg inoculation. Further, the functional validation of TaWRKY70 based on virus induced gene silencing (VIGS) in NIL-R, not only confirmed an increased fungal biomass but also decreased expressions of downstream resistance genes: TaACT, TaDGK and TaGLI1, along with decreased abundances of RRI metabolites biosynthesized by them. Among more than 200 FHB resistance QTL identified in wheat, this is the first QTL from which a TF was identified, and its downstream target genes as well as the FHB resistance functions were deciphered.

Late blight is a serious economic threat to potato crop, sometimes leading to complete crop loss. The resistance in potato to late blight can be qualitative or quantitative in nature. Qualitative resistance is not durable. Though quantitative resistance is durable, the breeding is challenging due to polygenic inheritance. Several quantitative trait loci (QTLs) have been identified, but the mechanisms of resistance are largely unknown. A nontargeted metabolomics approach was used to identify resistance-related (RR) metabolites in a resistant genotype (F06025), as compared to a susceptible (Shepody) genotype, mock- or pathogen-inoculated. The RR metabolites, which had high fold change in abundance, mainly belonged to phenylpropanoid, flavonoid, fatty acid, and alkaloid chemical groups. The most important phenylpropanoids identified were hydroxycinnamic acid amides, the polyaromatic domain of suberin that is known to be associated with cell wall reinforcement. These metabolites were mapped on to the potato metabolic pathways, and the candidate enzymes and their coding genes were identified. A quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay revealed a higher upregulation of 4-coumarate: CoA ligase (4-CL), tyrosine decarboxylase (TyDC), and tyramine hydroxycinnamoyl transferase (THT) in the pathogen-inoculated resistant genotype than in susceptible. These genes were sequenced in both resistant and susceptible genotypes, and nonsynonymous single-nucleotide polymorphisms (nsSNPs) were found. The application of these genes in potato resistance improvement, following validation, is discussed.

Late blight of potato (Solanum tuberosum) caused by Phytophthora infestans significantly reduces the productivity of potato around the world. Resistance to late blight in potato is either qualitative or quantitative. Qualitative resistance governed by race-specific single R genes is well characterized and gives complete resistance, but is not durable. Quantitative resistance governed by polygenes gives partial resistance, but is durable in nature. However, the quantitative resistance mechanisms are poorly studied and are not efficiently exploited in potato breeding. A nontargeted metabolic profiling of resistant (F06037) and susceptible (Shepody) potato cultivars, using high-resolution liquid chromatography–mass spectrometry, was applied to elucidate the quantitative resistance mechanisms against P. infestans (US-8 genotype). The hydroxycinnamic acid amides (HCAAs) of the shunt phenylpropanoid pathway were highly induced following pathogen inoculation in F06037. In parallel, the transcript abundances of genes that catalyze the biosynthesis of these metabolites, such as 4-coumarate:CoA ligase, tyrosine decarboxylase, ornithine decarboxylase, tyramine hydroxycinnamoyl transferase, and putrescine hydroxycinnamoyl transferase, were also higher in the resistant genotype. Sequencing of the coding genes of these enzymes revealed single-nucleotide polymorphisms between resistant and susceptible genotypes, and the amino acid changes caused missense mutations altering protein functions. HCAAs deposited at host cell walls inhibit pathogen colonization, thus reducing lesion expansion. In addition, these also act as phytoalexins, leading to the reduced biomass of the pathogen. Following validation, the HCAAs can be used as biomarker metabolites for late blight resistance. The putative candidate genes can be either used to develop allele-specific markers for marker-assisted breeding programs or suitably stacked into elite cultivars through cisgenic approaches, following validation.

Fusarium head blight (FHB) and deoxy- nivalenol (DON) mycotoxin produced by Fusarium graminearum reduce barley yield and quality world- wide. Hundreds of quantitative trait loci (QTLs) have been identified in wheat and barley but their functions are largely unknown. Metabolic profiling was applied to better understand the mechanisms of resistance and to identify potential FHB resistance biomarker metab- olites in barley. Four FHB resistant (H15-2, H148-3, H203-2 and H379-2) and one susceptible (H97-2), two-row, purple, doubled-haploid (DH) lines of barley were inoculated with either the pathogen or mock- solution. The disease severity quantified as the area under the disease progress curve (AUDPC) significant- ly varied between the resistant and susceptible geno- types, but not among the resistant genotypes. Neither the amount of DON nor the detoxified product, pro- portion of total DON, was significant among lines. The resistance related (RR, higher in abundance in resistant than in susceptible) metabolites varied in numbers and fold changes among the DH resistant lines. A total of 144 RR constitutive (RRC) and 167 RR induced (RRI) metabolites were selected, of which 39 and 37, respec- tively, were putatively identified. These RR metabolites mainly belonged to six chemical groups: phenylpro- panoids, hydroxycinnamic acid amides, flavonoids, fatty acids, terpenoids, and alkaloids. The specific RR metabo- lites identified in each DH line, the possible mechanisms of resistance in each and their use as potential biomarkers are discussed.

Plants continuously encounter various environmental stresses and use qualitative and quantitative measures to resist pathogen attack. Qualitative stress responses, based on monogenic inheritance, have been elucidated and successfully used in plant improvement. By contrast, quantitative stress responses remain largely unexplored in plant breeding, due to complex polygenic inheritance, although hundreds of quantitative trait loci for resistance have been identified. Recent advances in metabolomic and proteomic technologies now offer opportunities to overcome the hurdle of polygenic inheritance and identify candidate genes for use in plant breeding, thus improving the global food security. In this review, we describe a conceptual background to the plant-pathogen relationship and propose ten heuristic steps streamlining the application of metabolo-proteomics to improve plant resistance to biotic stress.

The resistance to late blight is either qualitative or quantitative in nature. Quantitative resistance is durable, but challenging due to polygenic inheritance. In the present study, the diploid potato genotypes resistant and susceptible to late blight, were profiled for metabolites. Tissue specific metabolite analysis of benzylisoquinoline alkaloids (BIAs) in response to pathogen infection revealed increased accumulation of morphinone, codeine-6-glucuronide and morphine-3-glucuronides. These BIAs are antimicrobial compounds and possibly involved in cell wall reinforcement, especially through cross-linking cell wall pectins. Quantitative reverse transcription-PCR studies revealed higher expressions of TyDC, NCS, COR-2 and StWRKY8 transcription factor genes, in resistant genotypes than in susceptible genotype, following pathogen inoculation. A luciferase transient expression assay confirmed the binding of the StWRKY8 TF to promoters of downstream genes, elucidating a direct regulatory role on BIAs biosynthetic genes. Sequence analysis of StWRKY8 in potato genotypes revealed polymorphism in the WRKY DNA binding domain in the susceptible genotype, which is important for the regulatory function of this gene. A complementation assay of StWRKY8 in Arabidopsis wrky33 mutant background was associated with decreased fungal biomass. In conclusion, StWRKY8 regulates the biosynthesis of BIAs that are both antimicrobial and reinforce cell walls to contain the pathogen to initial infection.

Highlight WAX INDUCER1 (HvWIN1) transcription factor regulates cutin biosynthetic genes to reinforce cuticle to resist Fusarium head blight. CYP86A2, CYP89A2 and LACS2 are potential downstream targets of HvWIN1., Fusarium head blight (FHB), caused by Fusarium graminearum, is one of the most devastating diseases of wheat and barley. Resistance to FHB is highly complex and quantitative in nature, and is most often classified as resistance to spikelet infection and resistance to spread of pathogen through the rachis. In the present study, a resistant (CI9831) and a susceptible (H106-371) two-row barley genotypes, with contrasting levels of spikelet resistance to FHB, pathogen or mock-inoculated, were profiled for metabolites based on liquid chromatography and high resolution mass spectrometry. The key resistance-related (RR) metabolites belonging to fatty acids, phenylpropanoids, flavonoids and terpenoid biosynthetic pathways were identified. The free fatty acids (FFAs) linoleic and palmitic acids were among the highest fold change RR induced (RRI) metabolites. These FFAs are deposited as cutin monomers and oligomers to reinforce the cuticle, which acts as a barrier to pathogen entry. Quantitative real-time PCR studies revealed higher expressions of KAS2, CYP86A2, CYP89A2, LACS2 and WAX INDUCER1 (HvWIN1) transcription factor in the pathogen-inoculated resistant genotype than in the susceptible genotype. Knockdown of HvWIN1 by virus-induced genes silencing (VIGS) in resistant genotype upon pathogen inoculation increased the disease severity and fungal biomass, and decreased the abundance of FFAs like linoleic and palmitic acids. Notably, the expression of CYP86A2, CYP89A2 and LAC2 genes was also suppressed, proving the link of HvWIN1 in regulating these genes in cuticle biosynthesis as a defense response.

Potato is an ideal candidate for the delivery of functional ingredients due to its high worldwide consumption. The metabolites in cooked tubers of eight diploid potato genotypes from Colombia were explored. Potato tubers were harvested, cooked，lyophilized, and then stored at −80°C. Metabolites were extracted from flesh samples and analyzed using liquid chromatography and high-resolution mass spectrometry. A total of 294 metabolites were putatively identified, of which 87 metabolites were associated with health-benefiting roles for humans, such as anticancer and anti-inflammatory properties. Two metabolites, chlorogenic acid and N-Feruloyltyramine were detected in high abundance and were mapped on to the potato metabolic pathways to predict the related biosynthetic enzymes: hydroxycinnamoyl-CoA quinate transferase (HQT) and tyramine hydroxycinnamoyl transferase (THT), respectively. The coding genes of these enzymes identified nonsynonymous single-nucleotide polymorphisms (nsSNPs) in AC09, AC64, and Russet Burbank, with the highest enzyme stability found in AC09. This is consistent with the highest presence of hydroxycinnamic acids in the AC09 genotype. The metabolites detected at high fold change, their functional ingredient properties, and their enhancement through breeding to improve health of the indigenous communities’ of Colombia are discussed.

Resistance in Triticeae to fusarium head blight (FHB) is quantitatively inherited. Metabolomics as a tool was used to better understand the mechanisms of resistance and to identify potential FHB resistance biomarker metabolites in barley. Five FHB-resistant two-row barley genotypes (CIho 4196, Zhedar-1, Zhedar-2, Fredrickson, and Harbin-2r) and one FHB-susceptible genotype (CH 9520-30) were each inoculated with either pathogen-suspension or mock-solution. Disease severity, quantified as the proportion of spikelets diseased, varied among genotypes, being the greatest in CH 9520-30. Spikelets were sampled, metabolites extracted with aqueous methanol, and analyzed using an LC-ESI-LTQ-Orbitrap system. A pair wise, resistant vs. susceptible, t-test identified 1774 significant treatment peaks. Canonical discriminant analysis of peak abundance allowed the genotypes to be sorted into three clusters: (i) CH9520-30, (ii) Harbin-2r, (iii) the remaining four genotypes. The t-test was further used to identify resistance-related (RR) and pathogenesis-related (PR) metabolites. The pathogen-produced virulence factor deoxynivalenol (DON), and its detoxification product, DON-3-O-glucoside (D3G) were designated as resistance indicator (RI) metabolites. Metabolites (RR, PR, or RI) occurring in at least two resistant genotypes, showing a two-fold or greater abundance in resistant vs. susceptible lines, and also known to have plant defense functions were selected as potential FHB resistance biomarker metabolites. These included phenylalanine, p-coumaric acid, jasmonate, linolenic acid, total DON produced (TDP), and the proportion of DON converted to D3G (PDC). Total DON was the lowest in CIho 4196, while PDC was the highest in Zhedar-2. The application of RR, PR, and RI metabolites as potential biomarkers to enhance resistance is discussed.

The resistance in wheat to fusarium head blight (FHB) is controlled by several quantitative trait loci (QTLs), which are mainly expressed as two different types of resistance. The objective of this study was to assess the potential of a metabolomics approach to identify resistance-related metabolites associated with a QTL that confers resistance to FHB. Two near isogenic lines (NIL), with alternate alleles for the FHB resistance/susceptibility QTL on chromosome 2DL, were grown under greenhouse conditions and spikelets were inoculated with F. graminearum. Metabolites were extracted from the rachis and spikelets using a mixture of methanol-water and chloroform, and subsequently analyzed using GC/MS. Compound identification and quantification were achieved using AMDIS, GMD and NIST libraries, and MET-IDEA as the software platform. A total of 182 components were detected. A t-test of the quantities of these metabolites identified 27 resistance-related (RR) metabolites, including 22 constitutive (RRC) and 8 induced (RRI), with three common metabolites. Canonical discriminant analysis was used to classify treatments and to identify the associated metabolic functions. The putative metabolic pathways linking the RR-metabolites identified here are discussed. Key words: Functional genomics, metabolomics, fusarium head blight, Triticum aestivum, Fusarium graminearum

Fusarium head blight (FHB) [Fusarium graminearum (teleomorph Gibberella zeae)] causes considerable losses in wheat (Triticum aestivum) yield and grain quality. Because conventional screening for disease resistance based on five separate types of resistance is inefficient, a metabolomics approach to discriminating resistance was investigated. Spikelets of six wheat cultivars/lines varying in level of resistance were inoculated with F. graminearum or water. The spikelet disease severity was quantified, and the metabolic profiles were recorded using gas chromatography - mass spectrometry. A total of 214 metabolites were detected in spikelets and rachis, including 79 with acceptable treatment effects. Univariate analysis of variance identified 41 resistance-related (RR) metabolites and multivariate analysis identified 45 resistance function associated metabolites, including 28 RR metabolites. Highly resistant cultivar 'Wangshuibai' and line AW488 had the maximum numbers of constitutive (22) and induced (14) R...

Volatile organic compounds collected from the headspace of mango cv. Keitt inoculated with Lasiodiplodia theobromae (stem-end rot), Colletotrichum gloeosporioides (anthracnose), mock (as the first control) and non-wounded-non-inoculated mango (as the second control) were analyzed using GC/MS to investigate the feasibility of automatic detection and diagnosis of diseases of mango in stores. A total of 37 metabolites, relatively consistent in 8 replicates, were identified based on mass spectral match using NIST library. Several of these were specific to a disease/inoculation or when common to all treatments, they varied in their abundances. 1-Pentanol was specific to Lasiodiplodia-inoculated mangoes while thujol was detected only in Colletotrichum-inoculated mangoes. Discriminant analysis models based on normalized abundances of 35 consistent metabolites and normalized abundances of 150 mass ions correctly classified 67 and 75% of the observations, respectively, based on cross-validation. The study has shown for the first time that it is possible to detect and differentiate between anthracnose and stem-end rot diseases of mangoes (cv. Keitt) based on their volatile production patterns using GC/MS. The methods developed here have the potential applications to mango industry to detect and diagnose diseases of mango fruits, at relatively early stages of the disease progress, after validation under commercial conditions.

Metabolite profiles based on GC/MS were used to study the temporal dynamics of metabolites in potato leaves following pathogen inoculation. In the polar and non-polar plant extracts a total of 106 consistent peaks were detected, of which 95 metabolites were tentatively identified. Following pathogen inoculation, the abundances of 42 metabolites were significantly increased or decreased, and these metabolites were designated as Pathogenesis-Related (PR) Metabolites. Factor analysis of the abundance of 106 metabolites identified four plant–pathogen interaction functions: (i) homeostasis; (ii) primary defence; (iii) secondary defence; (iv) collapse of primary and secondary defence responses. During the primary and secondary defence phases, dramatic changes in the amino acids, known precursors of several plant defence-related metabolites, were observed. Plausible satellite-networks of metabolic pathways leading to the up-regulation of these families of amino acids and other secondary metabolites, and their potential application for the evaluation of horizontal resistance in potato against the late blight pathogen is discussed.

This study was carried out to evaluate the effect of pectin-based edible emulsion coating on activity and disease severity of Lasiodiplodia theobromae in avocados, and their subsequent influence on the fruit quality. In order to assess the influence of coating and disease, avocados were sorted and devided into four equal lots and all were incubated at 20 °C for up to 4 days. The first and second lots constituted samples which were stored as coated and uncoated, respectively, without fungal inoculation. The third and fourth lots were coated and un-coated fruits inoculated with the fungal disease. For coating, a previously standardized pectin-based emulsion was used. The incubated fruits were examined for the spread of disease, respiration rate and quality parameters, color and texture. As the incubation time increased, the volume of disease (VDS) increased, which in turn influenced the respiration rate (RR) in both coated and uncoated fruits. However, the coated fruits sustained a significantly slower rate of disease spread and RR. Similarly, the associated quality changes (texture and color) were much lower in coated fruits as compared with the control. Thus, the pectin based coating was effective in controlling the spread and severity of stem end rot in avocados. Changes in physical and physiological parameters of coated and uncoated fruits were well described by some form of semi-logarithmic models and were related to the VDS as well as case dependent incubation time.

A tremendous decline in cultivable land and resources and a huge increase in food demand calls for immediate attention to crop improvement. Though molecular plant breeding serves as a viable solution and is considered as "foundation for twenty-first century crop improvement", a major stumbling block for crop improvement is the availability of a limited functional gene pool for cereal crops. Advancement in the next generation sequencing (NGS) technologies integrated with tools like metabolomics, proteomics and association mapping studies have facilitated the identification of candidate genes, their allelic variants and opened new avenues to accelerate crop improvement through development and use of functional molecular markers (FMMs). The FMMs are developed from the sequence polymorphisms present within functional gene(s) which are associated with phenotypic trait variations. Since FMMs obviate the problems associated with random DNA markers, these are considered as "the holy grail" of plant breeders who employ targeted marker assisted selections (MAS) for crop improvement. This review article attempts to consider the current resources and novel methods such as metabolomics, proteomics and association studies for the identification of candidate genes and their validation through virus-induced gene silencing (VIGS) for the development of FMMs. A number of examples where the FMMs have been developed and used for the improvement of cereal crops for agronomic, food quality, disease resistance and abiotic stress tolerance traits have been considered.

The volatile metabolites from the headspace gas of containerised mango (Mangifera indica) cv. Tommy Atkins fruits, surface wounded and inoculated with the two fungal anamorphic pathogens Colletotrichum gloeosporioides and Lasiodiplodia theobromae, or non-inoculated (controls), were profiled using a portable gas chromatograph/mass spectrometer to discriminate diseases of mango. Thirty-four compounds were detected relatively consistently among replicates. Several of these were disease/inoculation-discriminatory and were classified into three groups: (i) compounds unique to only one treatment; (ii) compounds common to two or more treatments, but not to all; and (iii) compounds common to all treatments, but varying in their abundance. Two compounds, 1-pentanol and ethyl boronate, were detected in L. theobromae-inoculated mangoes alone, while thujol was observed only in C. gloeosporioides-inoculated mangoes. Discriminant analysis models based on the abundance of significant mass ions and consistent compounds correctly classified diseases/inoculations in up to 100% of cases. The disease-discriminatory compounds and discriminant analysis models developed here have the potential to be used in the early detection of postharvest diseases of mango fruits after validation under commercial conditions.

Gas chromatography and mass spectrometry was used to analyze volatiles in the headspace of 'Fortress' onion bulbs inoculated with Fusarium oxysporum, Botrytis allii, Erwinia carotovora subsp. carotovora, Aspergillus niger, or Penicillium aurantiogriseum. A total of 130 volatile metabolites were detected, of which 28 occurred more than four times in seven replicates and two incubation periods. Out of 28 relatively consistent compounds, 12 compounds were specific to one or more diseases or inoculations. Ethyl cyclobutane was specific to bulbs inoculated with F. oxysporum, while styrene was common to A. niger, E. carotovora subsp. carotovora, and F. oxysporum, with the highest abundance in the latter. N-3-Aminophenyl acetamide was common to E. carotovora subsp. carotovora, P. aurantiogriseum, and the water inoculated control. 2-Azabicyclo[3.2.0]hept-6-ene was detected in bulbs inoculated with A. niger, E. carotovora subsp. carotovora, and P. aurantiogriseum. Discriminant analysis models based on metabolic fi...

Metabolic profiles of spikelets of wheat cultivars, Roblin and Sumai3, respectively, susceptible and resistant to fusarium head blight (FHB) were analyzed using GC/MS to develop a technology to discriminate resistance. More than 700 peaks were detected and a total of 55 compounds were tentatively identified, of which 49 were induced/up-regulated following pathogen inoculation, including 23 in Roblin and 26 in Sumai3. However, only five metabolites were significantly different both between cultivars and inoculations. Metahydroxycinnamic acid, though was detected in all four treatments, exhibited a six-fold increase in abundance in Sumai3 following pathogen inoculation, with no corresponding change in Roblin. The abundance of myo-inositol in Sumai3 was higher than that in Roblin, and in both the abundance increased following pathogen inoculation. The compounds common to all treatments were subjected to factor analysis to identify groups of compounds, based on significant factor-loadings, associated with susceptibility or resistance against FHB. The treatment involving pathogen-inoculation of the resistant cv. Sumai3 was associated with the highest scores for the first and second factors that can be used for the discrimination of resistance against FHB. The first factor was associated with higher abundances of several fatty acids and aromatic compounds, while the second factor was associated with metabolites such as p- and m-coumaric acids, myo-inositol and other sugars, and malonic acid. The treatments involving pathogen-inoculation had higher factor scores for the third factor than the water inoculated, the highest being for the susceptible cultivar Roblin, and may be useful in explaining susceptibility/pathogenesis. The third factor had positive correlation with metabolites from different groups, mostly amino acids, fatty acids, and aromatics. The various compounds detected in this study are discussed, in terms of their possible roles in plant defense against pathogen-stress, their metabolic pathways of synthesis, and their potential application for screening cultivars of wheat for resistance to FHB.

Volatiles from the headspace of Russet Burbank potato tubers, non-wounded non-inoculated (N-control), wounded-inoculated-with sterile water (W-control), wounded-inoculated withPhytophthora infestans, Pythium ultimum orBotrytis cinerea, respectively, were sampled at 3 and 6 days after inoculation (dai), using gas chromatography/mass spectrometry (GC/MS).Botrytis inoculated tubers produced two specific volatiles: 2-2-propenyl-l,3-dioxolane and 3, 5-heptadiyn-2-one, while thePythium inoculated tubers produced three: 2-methyl-l-butanol, 2-butanone and 2-methyl-2-butanamine. Similarly, ethoxy-ethene was specific forPhytophthora inoculated tubers. 5-l-methylethylidene-l,3-cyclopentadiene was specific to W-control tubers. Discriminant analysis models based on metabolic fingerprints of metabolites or of mass ions correctly classified 80 to 100% of the observations into respective inoculations/diseases. However, a test-validation correctly classified only 44, 50, 44, 50 and 44% of the fingerprints based on consistent metabolites and 44, 63, 38, 75 and 31% of fingerprints based on mass ions, intoBotrytis, N-control,Phytophthora, Pythium and W-control, respectively. The disease discriminatory metabolite markers and the discriminant models developed here can be used to differentiate the three diseases of Russet Burbank potato tubers, after further validation under commercial conditions.

Volatile metabolites from ‘Russet Burbank’ potatoes inoculated withErwinia carotovora ssp.carotovora (ECC),Erwinia carotovora ssp.atroseptica (ECA), andFusarium sambucinum (FSA) were analyzed by sampling the headspace at 3 and 6 days after inoculation and then using a gas chromatograph/mass spectrometer (GC/MS) to identify the compounds. Non-wounded noninoculated and wounded non-inoculated tubers served as checks. Compounds with an abundance of ≥105 and with frequency of ≥3 out of 20 replicates (10 replicates × 2 incubation times) were subjected to further analysis. A total of 81 volatile metabolites were detected, of which 58 were specific to one or common to a few, but not to all inoculations/diseases. Acetic acid ethenyl ester was unique to ECA, while cyclohexene, diazene, and methoxy-(1,1-dimethyl-2-dihydroxy-ethyl)-amine were unique to ECC, and 2,5-norbornadiene and styrene were unique to FSA. Several metabolites were common only to tubers inoculated with ECC and ECA and were not detected in fungus-inoculated or in control tubers. High abundances of acetone and butane were detected in ECC- and ECA-inoculated tubers, respectively. The possible use of differences in volatile metabolic profiles to discriminate diseases of potato tubers in storage is discussed.

Gas chromatography-mass spectrometry (GC/MS) technology was used to profile volatile metabolites from the headspace gas of McIntosh apple (Malus domestica Borkh.), which were non- inoculated or inoculated with four different fungi, Botrytis cinerea Pers, Penicillium expansum Link, Mucor piriformis Fischer and Monilinia sp. The study yielded a total of 498 different volatile metabolites. Among them only 35 occurred relatively consistently in six replicates over three incubation periods. Of the consistent metabolites, 20 were specific to one or more inoculation agents/diseases, including seven that were unique to apples inoculated with different pathogens. Fluoroethene and 3,4-dimethyl-1-hexene were specific for Penicillium, while butanoic acid butyl ester, 4-methyl-1-hexene and 2-methyltetrazole were specific for Mucor. Similarly, acetic acid methyl ester and fluoroethane were specific to Botrytis and Monilinia, respectively. The method developed in this study can be used by storage managers to detect apple diseases at an early stage of disease progress and use this to manage apple diseases in storage, after further validation under commercial conditions.  2004 Society of Chemical Industry

The volatile metabolites of the headspace gas of onion bulbs inoculated with three different pathogens, Erwinia carotovora ssp. carotovora, Fusarium oxysporum and Botrytis allii, were profiled using gas chromatography/mass spectrometry. Differences in the number and amount of volatile metabolites were observed. Two hundred and fifty three volatile metabolites were detected in bulbs inoculated with three pathogens or sterile distilled water. On day three, 202 volatile metabolites were observed, compared to 166 on day six. Of the 253 compounds, however, only 59 occurred relatively consistently over replications, of which 25 compounds were specific to one or more pathogens, including 10 that were unique to a pathogen. Metabolites such as 1-Oxa-4,6-diazacyclooctane-5-thione and 4-mercapto-3-(methylthio)-ς-(thio-lactone)-crotonic acid were exclusive to onions inoculated with F. oxysporum. Acetone, acetic acid-hydrazide, propylcarbamate, 1-bromo-1-propene, thiirane, 1-(methylthio)-E-1-propene and 1-ethenyl-4-ethyl-benzene were specific to B. allii. 3-bromo-furan was specific to E. carotovora ssp. carotovora. Sterile water-inoculated bulbs produced 3,3′-dioxy-1,2-propanediol-tetranitrate. Highest amount of sulfurs was found in pathogen-inoculated, while highest amounts of terpenes, aromatics and aliphatics were found in sterile distilled water-inoculated bulbs. The possible use of these differences in the volatile metabolites for detecting and discriminating diseases of onion in storage is discussed.

Models were developed to predict the potential of leak development from factors influencing infection and lesion expansion. Such models could be used as a tool to manage leak in potato after harvest. Potato tubers, cv. Russet Burbank were wounded, inoculated with 20 μl of 104 sporangia per ml suspension of Pythium ultimum and incubated in mist chambers placed in growth chambers. Inoculated tubers were kept at 4, 8, 12, 16 and 20 °C. After 3, 6, 12, 24 and 48 h of incubation samples of five tubers were removed, stored at 12 °C and 95% RH. After 30 days of storage the disease severity was assessed to determine infection potential. Tubers were inoculated, incubated in mist chambers for 24 h, at 16 °C, to establish initial infections, and stored at 4, 8, 12, and 16 °C, for 15, 30, 45, 60, 75 and 90 days, at 95% RH to quantify lesion expansion potential. At the end of storage time, tubers were sliced, disease severity was assessed as volume diseased and the data were transformed into proportion of maximum volume diseased (PVD). The PVD was the least at the lowest temperature level tested and at the end of 12 h wet period at 12 °C, but it increased with increase in wetness duration and temperature. The maximum PVD was observed at 20 °C and 48 h wetness duration. Very little lesion expansion occurred at 4 °C, however, the lesions expanded rapidly with increase in temperature. A cubic model to predict infection potential from incubation temperature and duration of wetness explained 96.75% of the variation in PVD. A cubic model to predict lesion expansion potential as a function of storage temperature and duration explained of 99.2% of the variation in PVD. The potential application of these models to manage leak is discussed.

Bacterial soft rot, caused by Erwinia carotovora ssp. carotovora (Ecc), is a major disease in stored potatoes. The pathogen causes different physical, physiological and chemical changes in potatoes, which may affect the acceptability of raw and processed products. This study was carried out to evaluate the effect of disease severity on different physico-chemical and physiological properties of raw and cooked potatoes and to select the parameters most responsive to disease severity. Potatoes were inoculated with bacteria and incubated at 20C for different lengths of time to produce different levels of disease. As incubation time increased the volume of disease (VDS) increased, which in turn influenced the respiration rate (RR). In both raw and cooked potatoes, the physical changes (texture and color) associated with the progress of disease were reduced hardness, firmness and L value, and increased a and b values and total color difference (ΔE). The chemical changes were reduced ascorbic acid and pH, and increased reducing sugars, total sugars and titrable acidity along with the activities of peroxidase and polyphenol oxidase. The changes in physical and chemical parameters of raw and cooked potatoes during storage were described by fractional conversion equation models. All parameters were quite sensitive to disease except reducing sugars, peroxidase and PPO activity. The correlation matrix indicated that several of the quality parameters were related and thus most of them could be successfully used to predict tuber quality from disease.

Volatiles from Russet Burbank potatoes inoculated with Erwinia carotovora subsp. carotovora, E. carotovora subsp. atroseptica, Pythium ultimum, Phytophthora infestans, or Fusarium sambucinum were monitored by sampling the head space 3, 4, and 5 days after inoculation, using a solid phase microextraction (SPME) fiber to trap and gas chromatography with flame ionization detector (GC-FID) to fingerprint volatiles. Noninoculated (NON) potatoes served as the control. Volatile fingerprints varied among diseases. Within a disease, the fingerprints varied with time since inoculation and among blocks. In general, more volatiles were observed on the fourth and fifth day after inoculation than on the third day. The amount of volatile compounds produced (peak area) within a disease group increased with incubation time; however, the variation among blocks was much higher. The amount of volatiles produced, in general, was associated with disease severity. Disease-specific volatiles were observed. The F. sambucinum chromatogram had two unique peaks at retention time (RT) = 14.1 and 17.3 min. P. infestans produced few peaks and the profile was quite similar to NON. In contrast, E. carotovora subsp. carotovora, E. carotovora subsp. atroseptica, and Pythium ultimum produced many peaks, and the P. ultimum was different from the bacteria, in that the chromatogram peaks at RT = 4.04 and 8.76 min were absent. Instead, it produced a distinct peak at RT = 1.71 min. E. carotovora subsp. carotovora and E. carotovora subsp. atroseptica couldn't be discriminated based on unique peaks; however, they varied in concentration of volatiles produced. E. carotovora subsp. carotovora produced more of RT = 2.0 min and less of RT = 2.3 and 2.44 min than E. carotovora subsp. atroseptica. A back-propagation network (using neural networks) was developed to classify volatile profiles into six disease-groups. Cross-validation classification probabilities were NON = 71, E. carotovora subsp. carotovora = 71, E. carotovora subsp. atroseptica = 71, P. ultimum = 67, Phytophthora infestans = 46, and F. sambucinum = 75%.

A forecasting system was developed to predict risk levels of downy mildew of lettuce ( Bremia lactucae ). The criteria for the forecasting system were derived from the relationships of weather variables to sporulation, dissemination and infection processes of B. lactucae . In addition the presence of inoculumsource, or the disease, in the field was taken into consideration. User-friendly software (BREMCAST) for use within the Windows (Microsoft Corp.) operating system was developed to calculate sporulation, infection, disease severity and cumulative disease severity values. The system predicted the occurrence of downy mildew on 84 and 80% of the days, under commercial and field plot conditions, respectively. The potential of the system for use as an intelligent decision tool in managing downy mildew is discussed.

Sprouting of tubers and spoilage due to invasion by bacterial and fungal pathogens are problems of potato storage that are usually dealt with by specialized chemicals. This study was aimed at determining whether both problems could rather be solved by a single thermal treatment without affecting the quality. The applicability to short-term storage conditions in cool climates and tropical climates was investigated. This study demonstrates that potato tubers can be safely stored for 12 weeks at either 8 or 18°C without sprouting, if dipped in a 57.5°C hot water bath for 20–30 min. Neither electron microscopy of starch granules, puncture tests nor chromacity analysis provided evidence of damage due to the thermal treatment.