Unraveling the genetic basis of quantitative resistance to diseases in tomato: a meta-QTL analysis and mining of transcript profiles.

KEY MESSAGE: Whole-genome QTL mining and meta-analysis in tomato for resistance to bacterial and fungal diseases identified 73 meta-QTL regions with significantly refined/reduced confidence intervals. Tomato production is affected by a range of biotic stressors, causing yield losses and quality reductions. While sources of genetic resistance to many tomato diseases have been identified and characterized, stability of the resistance genes or quantitative trait loci (QTLs) across the resources has not been determined. Here, we examined 491 QTLs previously reported for resistance to tomato diseases in 40 independent studies and 54 unique mapping populations. We identified 29 meta-QTLs (MQTLs) for resistance to bacterial pathogens and 44 MQTLs for resistance to fungal pathogens, and were able to reduce the average confidence interval (CI) of the QTLs by 4.1-fold and 6.7-fold, respectively, compared to the average CI of the original QTLs. The corresponding physical length of the CIs of MQTLs ranged from 56 kb to 6.37 Mb, with a median of 921 kb, of which 27% had a CI lower than 500 kb and 53% had a CI lower than 1 Mb. Comparison of defense responses between tomato and Arabidopsis highlighted 73 orthologous genes in the MQTL regions, which were putatively determined to be involved in defense against bacterial and fungal diseases. Intriguingly, multiple genes were identified in some MQTL regions that are implicated in plant defense responses, including PR-P2, NDR1, PDF1.2, Pip1, SNI1, PTI5, NSL1, DND1, CAD1, SlACO, DAD1, SlPAL, Ph-3, EDS5/SID1, CHI-B/PR-3, Ph-5, ETR1, WRKY29, and WRKY25. Further, we identified a number of candidate resistance genes in the MQTL regions that can be useful for both marker/gene-assisted breeding as well as cloning and genetic transformation.

The full spectrum of MRI findings in 18 patients with Canavan disease: new insights into the areas of selective susceptibility.

INTRODUCTION: Canavan disease (CD) is a rare autosomal recessive neurodegenerative disorder caused by a deficiency of aspartoacylase A, an enzyme that degrades N-acetylaspartate (NAA). The disease is characterized by progressive white matter degeneration, leading to intellectual disability, seizures, and death. This retrospective study aims to describe the full spectrum of magnetic resonance imaging (MRI) findings in a large case series of CD patients. MATERIALS AND METHODS: MRI findings in 18 patients with confirmed CD were investigated, and the full spectrum of brain abnormalities was compared with the existing literature to provide new insights regarding the brain MRI findings in these patients. All the cases were proven based on genetic study or NAA evaluation in urine or brain. RESULTS: Imaging analysis showed involvement of the deep and subcortical white matter as well as the globus pallidus in all cases, with sparing of the putamen, caudate, and claustrum. The study provides updates on the imaging characteristics of CD and validates some underreported findings such as the involvement of the lateral thalamus with sparing of the pulvinar, involvement of the internal capsules and corpus callosum, and cystic formation during disease progression. CONCLUSION: To our knowledge, this is one of the largest case series of patients with CD which includes a detailed description of the brain MRI findings. The study confirmed many of the previously reported MRI findings but also identified abnormalities that were previously rarely or not described. We speculate that areas of ongoing myelination are particularly vulnerable to changes in CD.

On the Pin-Bearing Strength of Additively Manufactured Polymer Parts.

Due to the wide scope of applications of additive manufacturing (AM) in making final products, the mechanical strength of AM parts has become very important. Therefore, different tests are being developed to determine the structural integrity of three-dimensional printed components. In this respect, the pin-bearing test is designed to evaluate the response of a fastener, plate, and hole to stress. In this study, two different polymer materials were used to fabricate the samples utilizing the fused deposition modeling technique. Since the specimen width and hole diameter have effects on the pin-bearing strength and structural integrity of the parts, we prepared the specimens with four hole diameters to determine the influence of this ratio. A series of tensile tests were performed, and the stiffness and pin-bearing strength of additively manufactured specimens were determined. The preferred bearing failure mode was observed in several tested specimens. Subsequently, a scanning electron microscope investigation was conducted on the damaged area of the examined specimens to obtain insights into the damage mechanisms and failure behavior of the aforementioned specimens. We used digital image correlation technique to determine the strain field of dumbbell-shaped test coupons. The results of this research can be utilized for new designs of AM parts with a higher mechanical strength.

Impact Fatigue Life of Adhesively Bonded Composite-Steel Joints Enhanced with the Bi-Adhesive Technique.

One of the most common loading conditions that bonded joints experience in service is repeated impact. Despite the destructive effects of impact fatigue, the behavior of metal-composite bonded joints subjected to repeated impact loads has rarely been studied in the literature. Therefore, it is of utmost importance to pay attention to this phenomenon on the one hand and to find solutions to improve the impact fatigue life of bonded composite metal components on the other hand. Accordingly, in this study, the use of the bi-adhesive technique is proposed to improve the durability of composite-metal single-lap joints (SLJs) under impact fatigue loading conditions. J-N (energy-life) method is also used to analyze the experimental data obtained. Accordingly, in the present study, the impact fatigue behavior of single adhesive metal to composite joints was analyzed experimentally based on the J-N method and also numerically using the finite element method (FEM). By using two adhesives along a single overlap, the impact fatigue life of joints between dissimilar composite and metal joints was also analyzed experimentally. The results show that the double adhesives technique can significantly improve the impact fatigue life of the tested joints. It was also found that the optimum length ratio of the adhesives (the length covered by the ductile adhesive relative to the total overlap size) is a function of the stiffness of the joint and is more pronounced for less stiff bonded joints. A linear elastic numerical analysis was also conducted to evaluate the stress state along the bloodline of the bonded joints. Results show that the compressive peel stress made at the boundary of the two adhesives can be a possible reason behind the different results observed.

Physiological genetic variation in tomato fruit chilling tolerance during postharvest storage.

Storage at low temperatures is a common practice to prolong postharvest life of fruit and vegetables with a minimal negative impact on human/environmental health. Storage at low temperatures, however, can be restricted due to produce susceptibility to non-freezing chilling temperatures, when injuries such as physiological disorders and decays may result in unmarketable produce. We have investigated tomato fruit response to postharvest chilling stress in a recombinant inbred line (RIL) population developed from a cross between a chilling-sensitive cultivated tomato (Solanum lycopersicum L.) breeding line and a chilling-tolerant inbred accession of the tomato wild species S. pimpinellifolium L. Screening of the fruit of 148 RILs under cold storage (1.5°C) indicated presence of significant variations in chilling tolerance, manifested by varying degrees of fruit injury. Two extremely contrasting groups of RILs were identified, chilling-tolerant and chilling-sensitive RILs. The RILs in the two groups were further investigated under chilling stress conditions, and several physiological parameters, including weight loss, chlorophyll fluorescence parameters Fv/Fm, and Performance Index (PI), were determined to be efficient markers for identifying response to chilling stress in postharvest fruit. The Fv/Fm values reflected the physiological damages endured by the fruit after cold storage, and PI was a sensitive marker for early changes in photosystem II function. These two parameters were early indicators of chilling response before occurrence of visible chilling injuries. Antioxidant activities and ascorbic acid content were significantly higher in the chilling-tolerant than the chilling-sensitive lines. Further, the expression of C-repeat/DREB binding factors (CBFs) genes swiftly changed within 1-hr of fruit exposure to the chilling temperature, and the SlCBF1 transcript level was generally higher in the chilling-tolerant than chilling-sensitive lines after 2-hr exposure to the low temperature. This research demonstrates the presence of potential genetic variation in fruit chilling tolerance in the tomato RIL population. Further investigation of the RIL population is underway to better understand the genetic, physiological, and biochemical mechanisms involved in postharvest fruit chilling tolerance in tomato.

Identification of late blight resistance quantitative trait loci in Solanum pimpinellifolium accession PI 270441.

Late blight (LB), caused by the oomycete Phytophthora infestans, is one of the most destructive diseases of the cultivated tomato (Solanum lycopersicum L.) and potato (Solanum tuberosum L.) worldwide. Genetic changes in the pathogen have resulted in the emergence of new genotypes, overcoming formerly effective fungicides or host resistance genes. We previously reported the identification of a LB-resistant accession (PI 270441) of the wild tomato species S. pimpinellifolium L. and the high heritability of its resistance. In the present study, an F2 population (n = 1,209), derived from a cross between PI 270441 and a LB-susceptible tomato breeding line (Fla. 8059), was screened for response to LB infection. Extreme resistant (n = 44) and susceptible (n = 39) F2 individuals were selected and used in a trait-based marker analysis (TBA; a.k.a selective genotyping) to identify and map quantitative trait loci (QTLs) conferring LB resistance. Reduced representation libraries (RRLs) of Fla. 8059 and PI 270441 were constructed, sequenced, and mapped to the tomato genome. A total of 13,054 single-nucleotide polymorphisms (SNPs) were identified, of which, 200 were used to construct a genetic linkage map and locate QTLs. Four LB resistance QTLs were identified on chromosomes 1, 10, and 11 of PI 270441. The markers associated with these QTLs can be used to transfer LB resistance from PI 270441 into new tomato cultivars and to develop near-isogenic lines for fine mapping of the QTL.

Beneficial Effect of Repetitive Transcranial Magnetic Stimulation Combined With Physiotherapy After Cervical Spondylotic Myelopathy Surgery.

PURPOSE: Cervical spondylotic myelopathy (CSM) is one of the most notable causes of spinal cord impairment among elderly people worldwide. Little is written about the influence of postoperative rehabilitation on recovery of function in patients with CSM. In this study, we assessed the combined effects of repetitive transcranial magnetic stimulation (rTMS) combined with physiotherapy and physiotherapy alone on motor and sensory improvement assessed after spinal cord decompression in patients with CSM. METHODS: This prospective study comprised 52 patients with CSM; they were divided into two randomized groups after spinal cord decompression. The first group (group Ι) includes 26 patients, received a combination of rTMS and physiotherapy. The second group (group ΙΙ) of 26 patients underwent only physiotherapy. The neurologic assessment measures, including American Spinal Cord Injury Association score, modified Japanese Orthopaedic Association score, Ashworth scale, and Nurick grade, were recorded before and after rehabilitation interventions for each patient. RESULTS: According to the neurologic assessment measures, physiotherapy with/without rTMS after surgical decompression corresponded to significant improvement of motor function (P < 0. 01) without significant restoration of sensory function (P > 0. 01). Recovery rates of motor function were significantly better in group Ι than in group ΙΙ (P < 0. 01). There was no significant difference between two groups with respect to age (P = 0.162) and sex (P = 1.00). CONCLUSIONS: Although physiotherapy with/without rTMS improves motor function recovery after CSM surgery, rTMS in combination with physiotherapy leads to a more rapid motor function recovery than physiotherapy alone.

Characterization of 3D-printed PLA parts with different raster orientations and printing speeds.

Fabrication based on additive manufacturing (AM) process from a three-dimensional (3D) model has received significant attention in the past few years. Although 3D printing was introduced for production of prototypes, it has been currently used for fabrication of end-use products. Therefore, the mechanical behavior and strength of additively manufactured parts has become of significant importance. 3D printing has been affected by different parameters during preparation, printing, and post-printing processes, which have influence on quality and behavior of the additively manufactured components. This paper discusses the effects of two printing parameters on the mechanical behavior of additively manufactured components. In detail, polylactic acid material was used to print test coupons based on fused deposition modeling process. The specimens with five different raster orientations were printed with different printing speeds. Later, a series of tensile tests was performed under static loading conditions. Based on the results, strength and stiffness of the examined specimens have been determined. Moreover, dependency of the strength and elastic modulus of 3D-printed parts on the raster orientation has been documented. In the current study, fractured specimens were visually investigated by a free-angle observation system. The experimental findings can be used for the development of computational models and next design of structural components.

Predicting COVID-19 Vaccine Efficacy from Neutralizing Antibody Levels

Recent studies using data accrued from global SARS-CoV-2 vaccination efforts have demonstrated that breakthrough infections are correlated with levels of neutralizing antibodies. The decrease in neutralizing antibody titers of vaccinated individuals over time, combined with the emergence of more infectious variants of concern has resulted in waning vaccine efficacy against infection and a rise in breakthrough infections. Here we use a combination of neutralizing antibody measurements determined by a high throughput surrogate viral neutralization test (sVNT) together with published data from vaccine clinical trials and comparative plaque reduction neutralization test (PRNT) between SARS-CoV-2 variants to develop a model for vaccine efficacy (VE) against symptomatic infection. Vaccine efficacy estimates using this model show good concordance with real world data from the US and Israel. Our work demonstrates that appropriately calibrated neutralizing antibody measurements determined by high throughput sVNT can be used to provide a semi-quantitative estimate of protection against infection. Given the highly variable antibody levels among the vaccinated population, this model may be of use in identification of individuals with an elevated risk of breakthrough infections.

Inhibition of Activin A suppressed tumor necrosis factor-α secretion and improved histopathological conditions in malarial mice.

Malaria infection still remains as one of the most prominent parasitic diseases afflicting mankind in tropical and subtropical regions. The severity of malaria infection has often been associated to exuberant host immune inflammatory responses that could possibly lead to severe immunopathological conditions and subsequent death of host tissues. Activin A is a protein belonging to the transforming growth factor-beta (TGF-ß) family that regulates multiple physiological processes and pathological-associated diseases. The biological roles of activin A have been associated with manipulation of inflammation-related processes and modulation of host immune responses. This implies that activin A protein could play a role in malaria pathogenesis since malaria infection has been closely linked to severe immune responses leading to death, However, the actual in vivo role of activin A in malaria infection remains elusive. Hence, this study was undertaken to investigate the involvement of activin A in malaria infection as well as to assess the modulating effects of activin A on the cytokine releases (TNF-α, IFN-γ and IL-10) and histopathological changes in major affected organs (kidney, liver, lung, brain and spleen) in malarial mice infected with Plasmodium berghei ANKA. Our results showed that the concentrations of plasma activin A were significantly increased in malarial mice throughout the study periods. Also. the systemic activin A level was positively correlated with malaria parasitemia. This indicates that activin A could play a role in malaria pathogenesis and malaria parasitemia development. Plasma TNF-α, IFN-γ and IL-10 cytokine levels were significantly increased in malarial mice at day-5 post infection, suggesting that these cytokines attributed to severe malaria pathogenesis. Histopathological features such as sequestration of parasitized red blood cells (pRBCs) and hemozoin formation were amongst the most common pathological conditions observed in tissues of major affected organs (kidney, liver, lung, brain and spleen) in malarial mice. Neutralization of activin A production via recombinant mouse activin RIIA Fc chimera (rmActivin RIIA Fc chimera) had significantly reduced the parasitemia levels in malarial mice. The release of TNF-α cytokine was significantly reduced as well as the sequestration of parasitized pRBCs and hemozoin formation in major affected organs in malarial mice were also alleviated following inhibition of activin A production. Overall, this preliminary study suggests that activin A could play an immune modulation role in malaria pathogenesis through modulation of TNF-α release that benefits host from severe pathological destructions provoked by intensified inflammatory responses. Further studies are warranted to elucidate the precise mechanism of immune modulation mediated by activin A and its associated immune-modulation mediators in regulating the inflammatory responses elicited during the course of malaria infection.

Inhibition of Activin A suppressed tumor necrosis factor-α secretion and improved histopathological conditions in malarial mice

@#Malaria infection still remains as one of the most prominent parasitic diseases afflicting mankind in tropical and subtropical regions. The severity of malaria infection has often been associated to exuberant host immune inflammatory responses that could possibly lead to severe immunopathological conditions and subsequent death of host tissues. Activin A is a protein belonging to the transforming growth factor-beta (TGF-β) family that regulates multiple physiological processes and pathological-associated diseases. The biological roles of activin A have been associated with manipulation of inflammation-related processes and modulation of host immune responses. This implies that activin A protein could play a role in malaria pathogenesis since malaria infection has been closely linked to severe immune responses leading to death, However, the actual in vivo role of activin A in malaria infection remains elusive. Hence, this study was undertaken to investigate the involvement of activin A in malaria infection as well as to assess the modulating effects of activin A on the cytokine releases (TNF-α, IFN-γ and IL-10) and histopathological changes in major affected organs (kidney, liver, lung, brain and spleen) in malarial mice infected with Plasmodium berghei ANKA. Our results showed that the concentrations of plasma activin A were significantly increased in malarial mice throughout the study periods. Also. the systemic activin A level was positively correlated with malaria parasitemia. This indicates that activin A could play a role in malaria pathogenesis and malaria parasitemia development. Plasma TNF-α, IFN-γ and IL-10 cytokine levels were significantly increased in malarial mice at day-5 post infection, suggesting that these cytokines attributed to severe malaria pathogenesis. Histopathological features such as sequestration of parasitized red blood cells (pRBCs) and hemozoin formation were amongst the most common pathological conditions observed in tissues of major affected organs (kidney, liver, lung, brain and spleen) in malarial mice. Neutralization of activin A production via recombinant mouse activin RIIA Fc chimera (rmActivin RIIA Fc chimera) had significantly reduced the parasitemia levels in malarial mice. The release of TNF-α cytokine was significantly reduced as well as the sequestration of parasitized pRBCs and hemozoin formation in major affected organs in malarial mice were also alleviated following inhibition of activin A production. Overall, this preliminary study suggests that activin A could play an immune modulation role in malaria pathogenesis through modulation of TNF-α release that benefits host from severe pathological destructions provoked by intensified inflammatory responses. Further studies are warranted to elucidate the precise mechanism of immune modulation mediated by activin A and its associated immune-modulation mediators in regulating the inflammatory responses elicited during the course of malaria infection.

Nucleotide substitution rates of diatom plastid encoded protein genes are positively correlated with genome architecture.

Diatoms are the largest group of heterokont algae with more than 100,000 species. As one of the single-celled photosynthetic organisms that inhabit marine, aquatic and terrestrial ecosystems, diatoms contribute ~ 45% of global primary production. Despite their ubiquity and environmental significance, very few diatom plastid genomes (plastomes) have been sequenced and studied. This study explored patterns of nucleotide substitution rates of diatom plastids across the entire suite of plastome protein-coding genes for 40 taxa representing the major clades. The highest substitution rate was lineage-specific within the araphid 2 taxon Astrosyne radiata and radial 2 taxon Proboscia sp. Rate heterogeneity was also evident in different functional classes and individual genes. Similar to land plants, proteins genes involved in photosynthetic metabolism have lower synonymous and nonsynonymous substitutions rates than those involved in transcription and translation. Significant positive correlations were identified between substitution rates and measures of genomic rearrangements, including indels and inversions, which is a similar result to what was found in legume plants. This work advances the understanding of the molecular evolution of diatom plastomes and provides a foundation for future studies.

Experimental and theoretical fracture analyses for three biomaterials with dental applications.

Dental materials are known as efficient tools to revive the functionality and integrity of decayed/missing tooth structure. Being frequently subjected to different mixtures of tensile and shear loads accompanied by temperature changes and suffering from pre-existing voids and imperfect interfaces at the same time, dental restorations and prostheses are found to be susceptible to crack initiation and growth. In this paper, fracture properties of three dental biomaterials namely polymethylmethacrylate (PMMA), 75Sr and 75Sr10 undergoing mixed tensile-shear loads are investigated. The PMMA used in this study has application as a cold-cured acrylic resin for repairing dental prostheses, while 75Sr and 75Sr10 are dental restorative materials. Fracture growth angle and onset of crack propagation are evaluated experimentally using shortened semi-circular bend specimens made from PMMA. In addition, the generalized maximum tangential strain (GMTSN) criterion is applied to theoretically predict the fracture behavior of the tested PMMA, as well as two other dental bio-composites reported in the literature viz 75Sr and 75Sr10. Good agreement is met between theory and practice when comparing fracture curves extracted from the GMTSN criterion and the experimental data points. Further, it is found that conventional stress- and strain-based fracture models fail to provide suitable estimates of crack growth behavior.

Progression of malaria induced pathogenicity during chloroquine therapy.

Treatment Failure with chloroquine is one of the challenges that faced the dedicated efforts to eradicate malaria This study aims at investigating the impact of treatment failure with chloroquine on the progression of the disease-induced histo-pathogenic and immunogenic outcomes. To achieve this, Rane's protocol with modifications was applied on a model of Plasmodium berghei ANKA infected ICR mice to determine the dose response curve of chloroquine and to screen the treatment impact on the disease progression. Chloroquine was given at 1, 5, 10, 15 and 20 mg/kg once the parasitemia reached to 20-30% (the experimental initiation point). During the subsequent days, the mice were monitored for changes in the clinical signs, hematology parameters and the progress of the parasitemia until the parasitemia reached to 60-70% (the experimental termination point) or up to 10 days after chloroquine administration in case of achieving a complete eradication of the parasite. At the end, the mice were exsanguinated and their blood and organs were collected for the biochemistry and the histology study. A complete eradication of the parasite was achieved at 20 mg/kg while recrudescence was observed at the lower doses. At 1 mg/kg, the parasite growth was comparable to that of the positive control. The histo-pathogenic and immunogenic changes were stronger in the groups that experienced recrudescence (at 5 and 10 mg/kg). All in all, the study highlights the possibility of having a worsened clinical condition when chloroquine is given at its sub-therapeutic doses during malaria treatment.

Progression of malaria induced pathogenicity during chloroquine therapy

@#Treatment Failure with chloroquine is one of the challenges that faced the dedicated efforts to eradicate malaria This study aims at investigating the impact of treatment failure with chloroquine on the progression of the disease-induced histo-pathogenic and immunogenic outcomes. To achieve this, Rane’s protocol with modifications was applied on a model of Plasmodium berghei ANKA infected ICR mice to determine the dose response curve of chloroquine and to screen the treatment impact on the disease progression. Chloroquine was given at 1, 5, 10, 15 and 20 mg/kg once the parasitemia reached to 20-30% (the experimental initiation point). During the subsequent days, the mice were monitored for changes in the clinical signs, hematology parameters and the progress of the parasitemia until the parasitemia reached to 60-70% (the experimental termination point) or up to 10 days after chloroquine administration in case of achieving a complete eradication of the parasite. At the end, the mice were exsanguinated and their blood and organs were collected for the biochemistry and the histology study. A complete eradication of the parasite was achieved at 20 mg/kg while recrudescence was observed at the lower doses. At 1 mg/kg, the parasite growth was comparable to that of the positive control. The histo-pathogenic and immunogenic changes were stronger in the groups that experienced recrudescence (at 5 and 10 mg/kg). All in all, the study highlights the possibility of having a worsened clinical condition when chloroquine is given at its sub-therapeutic doses during malaria treatment.

Molecular evolution of cytochrome C oxidase-I protein of insects living in Saudi Arabia.

The study underpins barcode characterization of insect species collected from Saudi Arabia and explored functional constraints during evolution at the DNA and protein levels to expect the possible mechanisms of protein evolution in insects. Codon structure designated AT-biased insect barcode of the cytochrome C oxidase I (COI). In addition, the predicted 3D structure of COI protein indicated tyrosine in close proximity with the heme ligand, depicted substitution to phenylalanine in two Hymenopteran species. This change resulted in the loss of chemical bonding with the heme ligand. The estimated nucleotide substitution matrices in insect COI barcode generally showed a higher probability of transversion compared with the transition. Computations of codon-by-codon nonsynonymous substitutions in Hymenopteran and Hemipteran species indicated that almost half of the codons are under positive evolution. Nevertheless, codons of COI barcode of Coleoptera, Lepidoptera and Diptera are mostly under purifying selection. The results reinforce that codons in helices 2, 5 and 6 and those in loops 2-3 and 5-6 are mostly conserved and approach strong purifying selection. The overall results argue the possible evolutionary position of Hymenopteran species among those of other insects.

Induced Plant Defenses Against Herbivory in Cultivated and Wild Tomato.

Crop domestication and selective breeding have altered plant defense mechanisms, influencing insect-plant interactions. A reduction in plant resistance/tolerance against herbivory is generally expected in domesticated species, however, limited efforts have been made to compare inducibility of plant defenses between wild and domesticated genotypes. In the present study, the inducibility of several plant defense mechanisms (e.g. defensive chemicals, trichomes, plant volatiles) were investigated, and the performance and preference of the herbivore Helicoverpa zea were measured in three different tomato genotypes; a) wild tomato, Solanum pimpinellifolium L. (accession LA 2093), b) cherry tomato, S. lycopersicum L. var. cerasiforme (accession Matts Wild Cherry), and c) cultivated tomato, S. lycopersicum L. var. Better Boy). Enhanced inducibility of defensive chemicals, trichomes, and plant volatiles in the cultivated tomato, and a higher level of constitutive plant resistance against herbivory in the wild genotype was observed. When comparing the responses of damaged vs. undamaged leaves, the percent reduction in larval growth was higher on damaged leaves from cultivated tomato, suggesting a higher induced resistance compared to other two genotypes. While all tomato genotypes exhibited increased volatile organic compound (VOCs) emissions in response to herbivory, the cultivated variety responded with generally higher levels of VOCs. Differences in VOC patterns may have influenced the ovipositional preferences, as H. zea female moths significantly preferred laying eggs on the cultivated versus the wild tomato genotypes. Selection of traits during domestication and selective breeding could alter allocation of resources, where plants selected for higher yield performance would allocate resources to defense only when attacked.

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor.

Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in the TomLoxC promoter selected against during domestication. Quantitative trait locus mapping and analysis of transgenic plants reveal a role for TomLoxC in apocarotenoid production, which contributes to desirable tomato flavor. In orange-stage fruit, accessions harboring both the rare and common TomLoxC alleles (heterozygotes) have higher TomLoxC expression than those homozygous for either and are resurgent in modern tomatoes. The tomato pan-genome adds depth and completeness to the reference genome, and is useful for future biological discovery and breeding.

Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection.

Genotyping-by-sequencing (GBS) was employed to construct a highly saturated genetic linkage map of a tomato ( L.) recombinant inbred line (RIL) population, derived from a cross between cultivar NC EBR-1 and the wild tomato L. accession LA2093. A pipeline was developed to convert single nucleotide polymorphism (SNP) data into genomic bins, which could be used for fine mapping of quantitative trait loci (QTL) and identification of candidate genes. The pipeline, implemented in a python script named SNPbinner, adopts a hidden Markov model approach for calculation of recombination breakpoints followed by genomic bins construction. The total length of the newly developed high-resolution genetic map was 1.2-fold larger than previously estimated based on restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR)-based markers. The map was used to verify and refine QTL previously identified for two fruit quality traits in the RIL population, fruit weight (FW) and fruit lycopene content (LYC). Two well-described FW QTL ( and ) were localized precisely at their known underlying causative genes, and the QTL intervals were decreased by two- to tenfold. A major QTL for LYC content () was verified at high resolution and its underlying causative gene was determined to be ζ (). The RIL population, the high resolution genetic map, and the easy-to-use genotyping pipeline, SNPbinner, are made publicly available.

Identification and Mapping of Late Blight Resistance Quantitative Trait Loci in Tomato Accession PI 163245.

Late blight (LB), caused by the oomycete (Mont.) de Bary, is one of the most devastating diseases of tomato ( L.) and potato ( tuberosum L. worldwide. The importance of LB on tomato has increased due to the occurrence of aggressive and fungicide-resistant clonal lineages of . Consequently, identification and characterization of new sources of genetic resistance to LB has become a priority in tomato breeding. Previously, we reported accession PI 163245 as a promising source of highly heritable LB resistance for tomato breeding. The purpose of this study was to identify and map quantitative trait loci (QTLs) associated with LB resistance in this accession using a trait-based marker analysis (a.k.a. selective genotyping). An F mapping population ( = 560) derived from a cross between a LB-susceptible tomato breeding line (Fla. 8059) and PI 163245 was screened for LB resistance, and the most resistant ( = 39) and susceptible ( = 35) individuals were selected for genotyping. Sequencing and comparison of the reduced representation libraries (RRLs) derived from genomic DNA of the two parents resulted in the identification of 33,541 putative single nucleotide polymorphism (SNP) markers, of which, 233 genome-wide markers were used to genotype the 74 selected F individuals. The marker analysis resulted in the identification of four LB resistance QTLs conferred by PI 163245, located on chromosomes 2, 3, 10, and 11. Research is underway to develop near-isogenic lines (NILs) for fine mapping the QTLs and develop tomato breeding lines with LB resistance introduced from PI 163245.