Browsing by Author "Kevei, Zoltan"
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Item Open Access Application of Spatial Offset Raman Spectroscopy (SORS) and machine learning for sugar syrup adulteration detection in UK Honey(MDPI , 2024-07-31) Shehata, Mennatullah; Dodd, Sophie; Mosca, Sara; Matousek, Pavel; Parmar, Bhavna; Kevei, Zoltan; Anastasiadi, MariaHoney authentication is a complex process which traditionally requires costly and time-consuming analytical techniques not readily available to the producers. This study aimed to develop non-invasive sensor methods coupled with a multivariate data analysis to detect the type and percentage of exogenous sugar adulteration in UK honeys. Through-container spatial offset Raman spectroscopy (SORS) was employed on 17 different types of natural honeys produced in the UK over a season. These samples were then spiked with rice and sugar beet syrups at the levels of 10%, 20%, 30%, and 50% w/w. The data acquired were used to construct prediction models for 14 types of honey with similar Raman fingerprints using different algorithms, namely PLS-DA, XGBoost, and Random Forest, with the aim to detect the level of adulteration per type of sugar syrup. The best-performing algorithm for classification was Random Forest, with only 1% of the pure honeys misclassified as adulterated and <3.5% of adulterated honey samples misclassified as pure. Random Forest was further employed to create a classification model which successfully classified samples according to the type of adulterant (rice or sugar beet) and the adulteration level. In addition, SORS spectra were collected from 27 samples of heather honey (24 Calluna vulgaris and 3 Erica cinerea) produced in the UK and corresponding subsamples spiked with high fructose sugar cane syrup, and an exploratory data analysis with PCA and a classification with Random Forest were performed, both showing clear separation between the pure and adulterated samples at medium (40%) and high (60%) adulteration levels and a 90% success at low adulteration levels (20%). The results of this study demonstrate the potential of SORS in combination with machine learning to be applied for the authentication of honey samples and the detection of exogenous sugars in the form of sugar syrups. A major advantage of the SORS technique is that it is a rapid, non-invasive method deployable in the field with potential application at all stages of the supply chain.Item Open Access BIFURCATE FLOWER TRUSS: a novel locus controlling inflorescence branching in tomato contains a defective MAP kinase gene(Oxford University Press, 2018-03-02) Silva Ferreira, Demetryus; Kevei, Zoltan; Kurowski, Tomasz J.; de Noronha Fonseca, Maria Esther; Mohareb, Fady R.; Boiteux, Leonardo S.; Thompson, Andrew J.A mutant line, bifurcate flower truss (bif), was recovered from a tomato breeding program. Plants from the control line LAM183 produced a mean of 0.16 branches per truss, whereas the value for bif plants was 4.1. This increase in branching was accompanied by a 3.3-fold increase in flower number and showed a significant interaction with exposure to low temperature during truss development. The LAM183 and bif genomes were resequenced and the bif gene was mapped to a 2.01 Mbp interval on chromosome 12; all coding region polymorphisms in the interval were surveyed and five candidate genes displaying altered protein sequences were detected. One of these genes, SlMAPK1, encoding a MAP kinase, contained a leucine-to-stop codon mutation predicted to disrupt kinase function. SlMAPK1 is an excellent candidate for bif because knock-out mutations of an Arabidopsis orthologue MPK6 were reported to have increased flower number. An introgression browser was used to demonstrate that the origin of the bif genomic DNA at the BIF locus was Solanum galapagense and that the SlMAPK1 null mutant is a naturally occurring allele widespread only on the Galápagos Islands. This work strongly implicates SlMAPK1 as part of the network of genes controlling inflorescence branching in tomato.Item Open Access A chromosome-level genome assembly of Solanum chilense, a tomato wild relative associated with resistance to salinity and drought(Frontiers, 2024-03-08) Molitor, Corentin; Kurowski, Tomasz J.; Fidalgo de Almeida, Pedro M.; Kevei, Zoltan; Spindlow, Daniel J.; Chacko Kaitholil, Steffimol R.; Iheanyichi, Justice U.; Prasanna, H. C.; Thompson, Andrew J.; Mohareb, Fady R.Introduction: Solanum chilense is a wild relative of tomato reported to exhibit resistance to biotic and abiotic stresses. There is potential to improve tomato cultivars via breeding with wild relatives, a process greatly accelerated by suitable genomic and genetic resources. Methods: In this study we generated a high-quality, chromosome-level, de novo assembly for the S. chilense accession LA1972 using a hybrid assembly strategy with ~180 Gbp of Illumina short reads and ~50 Gbp long PacBio reads. Further scaffolding was performed using Bionano optical maps and 10x Chromium reads. Results: The resulting sequences were arranged into 12 pseudomolecules using Hi-C sequencing. This resulted in a 901 Mbp assembly, with a completeness of 95%, as determined by Benchmarking with Universal Single-Copy Orthologs (BUSCO). Sequencing of RNA from multiple tissues resulting in ~219 Gbp of reads was used to annotate the genome assembly with an RNA-Seq guided gene prediction, and for a de novo transcriptome assembly. This chromosome-level, high-quality reference genome for S. chilense accession LA1972 will support future breeding efforts for more sustainable tomato production. Discussion: Gene sequences related to drought and salt resistance were compared between S. chilense and S. lycopersicum to identify amino acid variations with high potential for functional impact. These variants were subsequently analysed in 84 resequenced tomato lines across 12 different related species to explore the variant distributions. We identified a set of 7 putative impactful amino acid variants some of which may also impact on fruit development for example the ethylene-responsive transcription factor WIN1 and ethylene-insensitive protein 2. These variants could be tested for their ability to confer functional phenotypes to cultivars that have lost these variants.Item Open Access Dataset "BIFURCATE FLOWER TRUSS: a novel locus controlling inflorescence branching in tomato contains a defective MAP kinase gene"(Cranfield University, 2024-05-22 08:52) Thompson, Andrew; Kevei, Zoltan; Silva ferreira, Demetryus; Mohareb, Fady; Kurowski, TomaszData underlying manuscript entitled: "Identification and characterisation of bifuricate, a novel locus on chromosome 12 controlling truss branching and flower number in tomato"Item Open Access Detection of sugar syrup adulteration in UK honey using DNA barcoding(Elsevier, 2025-01-01) Dodd, Sophie; Kevei, Zoltan; Karimi, Zahra; Parmar, Bhavna; Franklin, David; Koidis, Anastasios; Anastasiadi, MariaHoney is a valuable and nutritious food product, but it is at risk to fraudulent practices such as the addition of cheaper syrups including corn, rice, and sugar beet syrup. Honey authentication is of the utmost importance, but current methods are faced with challenges due to the large variations in natural honey composition (influenced by climate, seasons and bee foraging), or the incapability to detect certain types of plant syrups to confirm the adulterant used. Molecular methods such as DNA barcoding have shown great promise in identifying plant DNA sources in honey and could be applied to detect plant-based sugars used as adulterants. In this work DNA barcoding was successfully used to detect corn and rice syrup adulteration in spiked UK honey with novel DNA markers. Different levels of adulteration were simulated (1 – 30%) with a range of different syrup and honey types, where adulterated honey was clearly separated from natural honey even at 1% adulteration level. Moreover, the test was successful for multiple syrup types and effective on honeys with different compositions. These results demonstrated that DNA barcoding could be used as a sensitive and robust method to detect common sugar adulterants and confirm syrup species origin in honey, which can be applied alongside current screening methods to improve existing honey authentication tests.Item Open Access Genes involved in auxin biosynthesis, transport and signalling underlie the extreme adventitious root phenotype of the tomato aer mutant(Springer, 2024-03-03) Kevei, Zoltan; Larriba, Eduardo; Romero‑Bosquet, María Dolores; Nicolás‑Albujer, Miriam; Kurowski, Tomasz J.; Mohareb, Fady; Rickett, Daniel; Pérez‑Pérez, José Manuel; Thompson, Andrew J.The use of tomato rootstocks has helped to alleviate the soaring abiotic stresses provoked by the adverse effects of climate change. Lateral and adventitious roots can improve topsoil exploration and nutrient uptake, shoot biomass and resulting overall yield. It is essential to understand the genetic basis of root structure development and how lateral and adventitious roots are produced. Existing mutant lines with specific root phenotypes are an excellent resource to analyse and comprehend the molecular basis of root developmental traits. The tomato aerial roots (aer) mutant exhibits an extreme adventitious rooting phenotype on the primary stem. It is known that this phenotype is associated with restricted polar auxin transport from the juvenile to the more mature stem, but prior to this study, the genetic loci responsible for the aer phenotype were unknown. We used genomic approaches to define the polygenic nature of the aer phenotype and provide evidence that increased expression of specific auxin biosynthesis, transport and signalling genes in different loci causes the initiation of adventitious root primordia in tomato stems. Our results allow the selection of different levels of adventitious rooting using molecular markers, potentially contributing to rootstock breeding strategies in grafted vegetable crops, especially in tomato. In crops vegetatively propagated as cuttings, such as fruit trees and cane fruits, orthologous genes may be useful for the selection of cultivars more amenable to propagation.Item Open Access Identification of novel stress-responsive biomarkers from gene expression datasets in tomato roots(CSIRO Publishing, 2016-05-17) Thompson, Andrew J.; Kevei, ZoltanAbiotic stresses such as heat, drought or salinity have been widely studied individually. Nevertheless, in the nature and in the field, plants and crops are commonly exposed to a different combination of stresses, which often result in a synergistic response mediated by the activation of several molecular pathways that cannot be inferred from the response to each individual stress. By screening microarray data obtained from different plant species and under different stresses, we identified several conserved stress-responsive genes whose expression was differentially regulated in tomato (Solanum lycopersicum L.) roots in response to one or several stresses. We validated 10 of these genes as reliable biomarkers whose expression levels are related to different signalling pathways involved in adaptive stress responses. In addition, the genes identified in this work could be used as general salt-stress biomarkers to rapidly evaluate the response of salt-tolerant cultivars and wild species for which sufficient genetic information is not yet available.Item Open Access Improving the tea withering process using ethylene or UV-C(American Chemical Society, 2021-11-05) Collings, Emma R.; Alamar, M. Carmen; Bogaerts Márquez, Maria; Kourmpetli, Sofia; Kevei, Zoltan; Thompson, Andrew J.; Mohareb, Fady; Terry, Leon A.Using a combination of biochemical, transcriptomic, and physiological analyses, we elucidated the mechanisms of physical and chemical withering of tea shoots subjected to UV-C and ethylene treatments. UV-C irradiation (15 kJ m–2) initiated oxidation of catechins into theaflavins, increasing theaflavin-3-monogallate and theaflavin digallate by 5- and 13.2–4.4-fold, respectively, at the end of withering. Concomitantly, a rapid change to brown/red, an increase in electrolyte leakage, and the upregulation of peroxidases (viz. Px2, Px4, and Px6) and polyphenol oxidases (PPO-1) occurred. Exogenous ethylene significantly increased the metabolic rate (40%) and moisture loss (30%) compared to control during simulated withering (12 h at 25 °C) and upregulated transcripts associated with responses to dehydration and abiotic stress, such as those in the ethylene signaling pathway (viz. EIN4-like, EIN3-FBox1, and ERFs). Incorporating ethylene during withering could shorten the tea manufacturing process, while UV-C could enhance the accumulation of flavor-related compounds.Item Open Access Improving the tea withering process using ethylene or UV-C(Cranfield University, 2021-12-13 11:24) del carmen Alamar Gavidia, Maria; Terry, Leon; Collings, Emma; Thompson, Andrew; Mohareb, Fady; Kourmpetli, Sofia; Kevei, Zoltan; Bogaerts Marquez, MariaThe data set contains objective colour, respiration rate, water loss data, as well as individual catechin and theobromine concentrations of Camellia sinensis shoots subjected to UV-C radiation and ethylene supplementation during simulated withering.Item Open Access Is it feasible to use mixed orchards to manage apple scab?(Maximum Academic Press, 2023-10-10) Stewart, Katie; Passey, Thomas; Verheecke-Vaessen, Carol; Kevei, Zoltan; Xu, XiangmingApple scab, caused by the fungus Venturia inaequalis, is one of the most damaging diseases of cultivated apples (Malus x domestica) worldwide. It results in huge losses as it diminishes fruit quality and impacts tree growth. Current management revolves around application of fungicides, however the number of sprays required per season is unsustainable and expensive. Further to this, populations of V. inaequalis have developed fungicide resistance. Breeding new cultivars with higher levels of resistance to scab is a priority, however, this process is long, so introducing mixed cultivar orchards may be a faster solution. We reviewed the general principles of using mixtures to manage plant diseases, and then considered specifically using mixed cultivars to manage apple scab in commercial production. Limited field studies have demonstrated the potential of using mixture to suppress apple scab development; but scab super-races that could emerge from mixture can pose a significant risk to in commercial production. However, recent research on population genetics of apple scab in monoculture and mixed orchards suggests that the risk of super-race emergence is probably over-stated because assortative mating among lesions on the same leaves is likely to occur rather than commonly assumed random mating. Thus, we conclude that cultivar mixtures can contribute towards sustainable scab management, particularly in commercial cider apple production.Item Open Access A loss-of-function allele of a TAC1-like gene (SlTAC1) located on tomato chromosome 10 is a candidate for the Erectoid leaf (Erl) mutation(Springer Verlag, 2019-04-16) González-Arcos, Matías; de Noronha Fonseca, Maria Esther; Basílio Zandonadi, Daniel; Peres, Lázaro E. P.; Arruabarrena, Ana; Ferreira, Demetryus S.; Kevei, Zoltan; Mohareb, Fady R.; Thompson, Andrew J.; Boiteux, Leonardo S.The genetic basis of an erectoid leaf phenotype was investigated in distinct tomato breeding populations, including one derived from Solanum lycopersicum ‘LT05’ (with the erectoid leaf phenotype and uniform ripening, genotype uu) × S. pimpinellifollium ‘TO-937’ (with the wild-type leaf phenotype and green fruit shoulder, genotype UU). The erectoid leaf phenotype was inherited as a semi-dominant trait and it co-segregated with the u allele of gene SlGLK2 (Solyc10g008160). This genomic location coincides with a previously described semi-dominant mutation named as Erectoid leaf (Erl). The genomes of ‘LT05’, ‘TO-937’, and three other unrelated accessions (with the wild-type Erl+ allele) were resequenced with the aim of identifying candidate genes. Comparative genomic analyses, including the reference genome ‘Heinz 1706’ (Erl+ allele), identified an Erectoid leaf-specific single nucleotide polymorphism (SNP) in the gene Solyc10g009320. This SNP caused a change of a glutamine codon (present in all the wild-type genomes) to a TAA (= ochre stop-codon) in the Erl allele, resulting in a smaller version of the predicted mutant protein (221 vs. 279 amino acids). Solyc10g009320, previously annotated as an ‘unknown protein’, was identified as a TILLER ANGLE CONTROL1-like gene. Linkage between the Erl and Solyc10g009320 was confirmed via Sanger sequencing of the PCR amplicons of the two variant alleles. No recombinants were detected in 265 F2 individuals. Contrasting S7 near-isogenic lines were also homozygous for each of the alternate alleles, reinforcing Solyc10g009320 as a strong Erl candidate gene and opening the possibility for fine-tuning manipulation of tomato architecture in breeding programs.Item Open Access Missense mutation of a class B heat shock factor is responsible for the tomato bushy root-2 phenotype(Biomed Central, 2022-02-08) Kevei, Zoltan; Silva Ferreira, Demetryus; Perez Casenave, Cristina Maria; Kurowski, Tomasz J.; Mohareb, Fady; Rickett, Daniel; Stain, Chris; Thompson, Andrew J.The bushy root-2 (brt-2) tomato mutant has twisting roots, and slower plant development. Here we used whole genome resequencing and genetic mapping to show that brt-2 is caused by a serine to cysteine (S75C) substitution in the DNA binding domain (DBD) of a heat shock factor class B (HsfB) encoded by SolycHsfB4a. This gene is orthologous to the Arabidopsis SCHIZORIZA gene, also known as AtHsfB4. The brt-2 phenotype is very similar to Arabidopsis lines in which the function of AtHsfB4 is altered: a proliferation of lateral root cap and root meristematic tissues, and a tendency for lateral root cap cells to easily separate. The brt-2 S75C mutation is unusual because all other reported amino acid substitutions in the highly conserved DBD of eukaryotic heat shock factors are dominant negative mutations, but brt-2 is recessive. We further show through reciprocal grafting that brt-2 exerts its effects predominantly through the root genotype even through BRT-2 is expressed at similar levels in both root and shoot meristems. Since AtHsfB4 is induced by root knot nematodes (RKN), and loss-of-function mutants of this gene are resistant to RKNs, BRT-2 could be a target gene for RKN resistance, an important trait in tomato rootstock breeding.Item Open Access The ORGAN SIZE (ORG) locus modulates both vegetative and reproductive gigantism in domesticated tomato(Oxford University Press, 2023-10-11) Vicente, Mateus Henrique; MacLeod, Kyle; Zhu, Feng; Rafael, Diego D.; Figueira, Antonio; Fernie, Alisdair R.; Mohareb, Fady; Kevei, Zoltan; Thompson, Andrew J.; Zsögön, Agustin; Pereira Peres, Lázaro EustáquioBackground and Aims Gigantism is a key component of the domestication syndrome, a suite of traits that differentiates crops from their wild relatives. Allometric gigantism is strongly marked in horticultural crops, causing disproportionate increases in the size of edible parts such as stems, leaves or fruits. Tomato (Solanum lycopersicum) has attracted attention as a model for fruit gigantism, and many genes have been described controlling this trait. However, the genetic basis of a corresponding increase in size of vegetative organs contributing to isometric gigantism has remained relatively unexplored. Methods Here, we identified a 0.4-Mb region on chromosome 7 in introgression lines (ILs) from the wild species Solanum pennellii in two different tomato genetic backgrounds (cv. ‘M82’ and cv. ‘Micro-Tom’) that controls vegetative and reproductive organ size in tomato. The locus, named ORGAN SIZE (ORG), was fine-mapped using genotype-by-sequencing. A survey of the literature revealed that ORG overlaps with previously mapped quantitative trait loci controlling tomato fruit weight during domestication. Key Results Alleles from the wild species led to lower cell number in different organs, which was partially compensated by greater cell expansion in leaves, but not in fruits. The result was a proportional reduction in leaf, flower and fruit size in the ILs harbouring the alleles from the wild species. Conclusions Our findings suggest that selection for large fruit during domestication also tends to select for increases in leaf size by influencing cell division. Since leaf size is relevant for both source–sink balance and crop adaptation to different environments, the discovery of ORG could allow fine-tuning of these parameters.Item Open Access Overproduction of ABA in rootstocks alleviates salinity stress in tomato shoots(Wiley, 2021-05-30) Martínez-Andújar, Cristina; Martínez-Pérez, Ascensión; Albacete, Alfonso; Martínez-Melgarejo, Purificación A.; Dodd, Ian C.; Thompson, Andrew J.; Mohareb, Fady; Estelles-Lopez, Lucia; Kevei, Zoltan; Ferrández-Ayela, Almudena; Pérez-Pérez, José Manuel; Gifford, Miriam L.; Pérez-Alfocea, FranciscoTo determine whether root-supplied ABA alleviates saline stress, tomato (Solanum lycopersicum L. cv. Sugar Drop) was grafted onto two independent lines (NCED OE) overexpressing the SlNCED1 gene (9-cis-epoxycarotenoid dioxygenase) and wild type rootstocks. After 200 days of saline irrigation (EC = 3.5 dS m−1), plants with NCED OE rootstocks had 30% higher fruit yield, but decreased root biomass and lateral root development. Although NCED OE rootstocks upregulated ABA-signalling (AREB, ATHB12), ethylene-related (ACCs, ERFs), aquaporin (PIPs) and stress-related (TAS14, KIN, LEA) genes, downregulation of PYL ABA receptors and signalling components (WRKYs), ethylene synthesis (ACOs) and auxin-responsive factors occurred. Elevated SlNCED1 expression enhanced ABA levels in reproductive tissue while ABA catabolites accumulated in leaf and xylem sap suggesting homeostatic mechanisms. NCED OE also reduced xylem cytokinin transport to the shoot and stimulated foliar 2-isopentenyl adenine (iP) accumulation and phloem transport. Moreover, increased xylem GA3 levels in growing fruit trusses were associated with enhanced reproductive growth. Improved photosynthesis without changes in stomatal conductance was consistent with reduced stress sensitivity and hormone-mediated alteration of leaf growth and mesophyll structure. Combined with increases in leaf nutrients and flavonoids, systemic changes in hormone balance could explain enhanced vigour, reproductive growth and yield under saline stress.Item Open Access Resequencing at ≥ 40-fold depth of the parental genomes of a Solanum lycopersicum × S. pimpinellifolium recombinant inbred line population and characterisation of frame-shift InDels that are highly likely to perturb protein function(Genetics Society of America, 2015-03-24) Kevei, Zoltan; King, Robert C.; Mohareb, Fady R.; Sergeant, Martin J.; Awan, Sajjad Z.; Thompson, Andrew J.A recombinant in-bred line population derived from a cross between Solanum lycopersicum var. cerasiforme (E9) and S. pimpinellifolium (L5) has been used extensively to discover quantitative trait loci (QTL), including those that act via rootstock genotype, however, high-resolution single-nucleotide polymorphism genotyping data for this population are not yet publically available. Next-generation resequencing of parental lines allows the vast majority of polymorphisms to be characterized and used to progress from QTL to causative gene. We sequenced E9 and L5 genomes to 40- and 44-fold depth, respectively, and reads were mapped to the reference Heinz 1706 genome. In L5 there were three clear regions on chromosome 1, chromosome 4, and chromosome 8 with increased rates of polymorphism. Two other regions were highly polymorphic when we compared Heinz 1706 with both E9 and L5 on chromosome 1 and chromosome 10, suggesting that the reference sequence contains a divergent introgression in these locations. We also identified a region on chromosome 4 consistent with an introgression from S. pimpinellifolium into Heinz 1706. A large dataset of polymorphisms for the use in fine-mapping QTL in a specific tomato recombinant in-bred line population was created, including a high density of InDels validated as simple size-based polymerase chain reaction markers. By careful filtering and interpreting the SnpEff prediction tool, we have created a list of genes that are predicted to have highly perturbed protein functions in the E9 and L5 parental lines.