An NB-LRR gene, TYNBS1, is responsible for resistance mediated by the Ty-2 Begomovirus resistance locus of tomato

Molecular breeding of tomato: Advances and challenges

The modern cultivated tomato (Solanum lycopersicum) was domesticated from Solanum pimpinellifolium native to the Andes Mountains of South America through a "two-step domestication" process. It was introduced to Europe in the 16th century and later widely cultivated worldwide. Since the late 19th century, breeders, guided by modern genetics, breeding science, and statistical theory, have improved tomatoes into an important fruit and vegetable crop that serves both fresh consumption and processing needs, satisfying diverse consumer demands. Over the past three decades, advancements in modern crop molecular breeding technologies, represented by molecular marker technology, genome sequencing, and genome editing, have significantly transformed tomato breeding paradigms. This article reviews the research progress in the field of tomato molecular breeding, encompassing genome sequencing of germplasm resources, the identification of functional genes for agronomic traits, and the development of key molecular breeding technologies. Based on these advancements, we also discuss the major challenges and perspectives in this field.

NLR-mediated antiviral immunity in plants

Plant viruses cause substantial agricultural devastation and economic losses worldwide. Plant nucleotide-binding domain leucine-rich repeat receptors (NLRs) play a pivotal role in detecting viral infection and activating robust immune responses. Recent advances, including the elucidation of the interaction mechanisms between NLRs and pathogen effectors, the discovery of helper NLRs, and the resolution of the ZAR1 resistosome structure, have significantly deepened our understanding of NLR-mediated immune responses, marking a new era in NLR research. In this scenario, significant progress has been made in the study of NLR-mediated antiviral immunity. This review comprehensively summarizes the progress made in plant antiviral NLR research over the past decades, with a focus on NLR recognition of viral pathogen effectors, NLR activation and regulation, downstream immune signaling, and the engineering of NLRs.

The tomato gene Ty-6, encoding DNA polymerase delta subunit 1, confers broad resistance to Geminiviruses

KEY MESSAGE

The tomato Ty-6 gene conferring resistance against begomoviruses has been cloned and shown to be a variant of DNA polymerase delta subunit 1. Ty-6 is a major resistance gene of tomato that provides resistance against monopartite and bipartite begomoviruses. The locus was previously mapped on chromosome 10, and in this study, we fine-mapped Ty-6 to a region of 47 kb, including four annotated candidate genes. Via whole-genome resequencing of Ty-6 breeding lines and several susceptible breeding lines, the polymorphisms in gene sequences were discovered and gene-associated markers were developed for marker-assistant breeding. Further, virus-induced gene silencing and candidate gene overexpressing in susceptible tomatoes revealed that Ty-6-mediated resistance is controlled by Solyc10g081250, encoding the DNA polymerase delta subunit 1, SlPOLD1. The single nucleotide polymorphism of Ty-6 results in an amino acid change that might influence the fidelity of virus DNA replication.

Marker assisted pyramiding of major resistance genes of tomato leaf curl and late blight diseases for stabilising tomato production

Globally, tomato leaf curl disease (ToLCD) caused by begomoviruses and late blight disease caused by Phytophthora infestans are important limiting factors for tomato production. Development of disease resistant cultivars is an important objective of tomato breeding programmes. Resistance genes such as Ty2 and Ty3 against ToLCD, and Ph2 and Ph3 resistant genes against late blight were utilized in this study to develop tomato lines with ToLCD and late blight resistance. Two F2 populations derived from the crosses viz., VRT4-20-18 × (LA3152 × LA4286) and LA3152 × VRT-78-2 were used as base material. Marker assisted selection was employed throughout the generation advancement programme to select plants with the targeted genes. Gene based molecular markers AW910upF2R3, Ty3-SCAR and Ph3SCAR were used to select genotypes containing the Ty2, Ty3 and Ph3 genes, respectively. The dTG-63/HinfI CAPS marker linked to Ph2 gene was used to select the Ph2 gene containing genotypes. Advanced lines with all the four genes and/ or in different combinations with desirable agronomic traits were developed. Further, these selected genotypes were also tested for resistance to both the diseases under natural epiphytotic and artificially inoculated conditions. Lines with the Ty-3 alone or in combination with the Ty-2 performed well against ToLCD with DSI < 1, whereas lines with both the Ph2 and Ph3 genes performed well against late blight with DSI < 1. Developed advanced lines in the study can play a greater role in stabilizing tomato production by minimizing the losses caused by these diseases.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-025-01548-8.

Cy-1, a major QTL for tomato leaf curl New Delhi virus resistance, harbors a gene encoding a DFDGD-Class RNA-dependent RNA polymerase in cucumber (Cucumis sativus)

BACKGROUND

Tomato leaf curl New Delhi virus (ToLCNDV) (family Geminiviridae, genus Begomovirus) is a significant threat to cucumber (Cucumis sativus) production in many regions. Previous studies have reported the genetic mapping of loci related to ToLCNDV resistance, but no resistance genes have been identified.

RESULTS

We conducted map-based cloning of the ToLCNDV resistance gene in cucumber accession No.44. Agroinfiltration and graft-inoculation analyses confirmed the resistance of No.44 to ToLCNDV isolates from the Mediterranean and Asian countries. Initial mapping involving two rounds of phenotyping with two independent F2 populations generated by crossing the begomovirus-susceptible cultivar SHF and No.44 consistently detected major quantitative trait loci (QTLs) on chromosomes 1 and 2 that confer resistance to ToLCNDV. Fine-mapping of Cy-1, the dominant QTL on chromosome 1, using F3 populations narrowed the candidate region to a 209-kb genomic segment harboring 24 predicted genes. Among these genes, DFDGD-class RNA-dependent RNA polymerase (CsRDR3), an ortholog of Ty-1/Ty-3 of tomato and Pepy-2 of capsicum, was found to be a strong candidate conferring ToLCNDV resistance. The CsRDR3 sequence of No.44 contained multiple amino acid substitutions; the promoter region of CsRDR3 in No.44 had a large deletion; and the CsRDR3 transcript levels were greater in No.44 than in SHF. Virus-induced gene silencing (VIGS) of CsRDR3 using two chromosome segment substitution lines harboring chromosome 1 segments derived from No.44 compromised resistance to ToLCNDV.

CONCLUSIONS

Forward and reverse genetic approaches identified CsRDR3, which encodes a DFDGD-class RNA-dependent RNA polymerase, as the gene responsible for ToLCNDV resistance at the major QTL Cy-1 on chromosome 1 in cucumber. Marker-assisted breeding of ToLCNDV resistance in cucumber will be expedited by using No.44 and the DNA markers developed in this study.

Geminiviruses and Food Security: A Molecular Genetics Perspective for Sustainable Agriculture in Africa

The African continent is vulnerable to food insecurity. Increased food costs, job losses, and climate change force Africans to chronic hunger. Biotechnology can be used to mitigate this by using techniques such as CRISPR/Cas9 systems, TALENs, and ZFNs. Biotechnology can utilize geminiviruses to deliver the necessary reagents for precise genome alteration. Additionally, plants infected with geminiviruses can withstand harsher weather conditions such as drought. Therefore, this article discusses geminivirus replication and its use as beneficial plant DNA viruses. It focuses explicitly on genome editing to increase plant resistance by manipulating plants' salicylic acid and jasmonic acid pathways.

A Coiled-Coil Nucleotide-Binding Domain Leucine-Rich Repeat Receptor Gene MeRPPL1 Plays a Role in the Replication of a Geminivirus in Cassava

Disease resistance gene (R gene)-encoded nucleotide-binding leucine-rich repeat proteins (NLRs) are critical players in plant host defence mechanisms because of their role as receptors that recognise pathogen effectors and trigger plant effector-triggered immunity (ETI). This study aimed to determine the putative role of a cassava coiled-coil (CC)-NLR (CNL) gene MeRPPL1 (Manes.12G091600) (single allele) located on chromosome 12 in the tolerance or susceptibility to South African cassava mosaic virus (SACMV), one of the causal agents of cassava mosaic disease (CMD). A transient protoplast system was used to knock down the expression of MeRPPL1 by clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9). The MeRPPL1-targeting CRISPR vectors and/or SACMV DNA A and DNA B infectious clones were used to transfect protoplasts isolated from leaf mesophyll cells from the SACMV-tolerant cassava (Manihot esculenta) cultivar TME3. The CRISPR/Cas9 silencing vector significantly reduced MeRPPL1 expression in protoplasts whether with or without SACMV co-infection. Notably, SACMV DNA A replication was higher in protoplasts with lower MeRPPL1 expression levels than in non-silenced protoplasts. Mutagenesis studies revealed that protoplast co-transfection with CRISPR-MeRPPL1 silencing vector + SACMV and transfection with only SACMV induced nucleotide substitution mutations that led to altered amino acids in the highly conserved MHD motif of the MeRPPL1-translated polypeptide. This may abolish or alter the regulatory role of the MHD motif in controlling R protein activity and could contribute to the increase in SACMV-DNA A accumulation observed in MeRPPL1-silenced protoplasts. The results herein demonstrate for the first time a role for a CNL gene in tolerance to a geminivirus in TME3.

Exploring the source of TYLCV resistance in Nicotiana benthamiana

Tomato Yellow Leaf Curl Virus (TYLCV) is one of the most devastating pathogens of tomato, worldwide. It is vectored by the globally prevalent whitefly, Bemisia tabaci, and is asymptomatic in a wide range of plant species that act as a virus reservoir. The most successful crop protection for tomato in the field has been from resistance genes, of which five loci have been introgressed fromwild relatives. Of these, the Ty-1/Ty-3 locus, which encodes an RNA-dependent RNA polymerase 3 (RDR3), has been the most effective. Nevertheless, several TYLCV strains that break this resistance are beginning to emerge, increasing the need for new sources of resistance. Here we use segregation analysis and CRISPR-mediated gene dysfunctionalisation to dissect the differential response of two isolates of Nicotiana benthamiana to TYLCV infection. Our study indicates the presence of a novel non-RDR3, but yet to be identified, TYLCV resistance gene in a wild accession of N. benthamiana. This gene has the potential to be incorporated into tomatoes.

Breakdown of Ty-1-Based Resistance to Tomato Yellow Leaf Curl Virus in Tomato Plants at High Temperatures

The global dissemination of the Israel (IL) and mild (Mld) strains of tomato yellow leaf curl virus (TYLCV) (family Geminiviridae, genus Begomovirus) is a major threat to tomato production in many regions worldwide. The use of resistant hybrid cultivars bearing the dominant resistance genes Ty-1, Ty-3, and Ty-3a has become a common practice for controlling tomato yellow leaf curl disease (TYLCD) caused by TYLCV. However, TYLCD symptoms have been sporadically observed in resistant cultivars grown in seasons when temperatures are high. In this study, we used TYLCV-resistant cultivars with confirmed presence of Ty-1, which were determined using newly developed allele-specific markers based on polymorphisms within the locus. These Ty-1-bearing resistant tomato plants and susceptible plants were infected with TYLCV and grown at moderate or high temperatures. Under high-temperature conditions, the Ty-1-bearing tomato cultivar Momotaro Hope (MH) infected with TYLCV-IL had severe TYLCD symptoms, which were almost equivalent to those of the susceptible cultivar. However, MH plants infected with TYLCV-Mld were symptomless or had slight symptoms under the same temperature condition. The quantitative analysis of the TYLCV-IL viral DNA content revealed a correlation between symptom development and viral DNA accumulation. Furthermore, under high-temperature conditions, TYLCV-IL caused severe symptoms in multiple commercial tomato cultivars with different genetic backgrounds. Our study provided the scientific evidence for the experientially known phenomenon by tomato growers, and it is anticipated that global warming, associated with climate change, could potentially disrupt the management of TYLCV in tomato plants mediated by the Ty-1 gene.

Transcriptional and epigenetic changes during tomato yellow leaf curl virus infection in tomato

BACKGROUND

Geminiviruses are DNA plant viruses that cause highly damaging diseases affecting crops worldwide. During the infection, geminiviruses hijack cellular processes, suppress plant defenses, and cause a massive reprogramming of the infected cells leading to major changes in the whole plant homeostasis. The advances in sequencing technologies allow the simultaneous analysis of multiple aspects of viral infection at a large scale, generating new insights into the molecular mechanisms underlying plant-virus interactions. However, an integrative study of the changes in the host transcriptome, small RNA profile and methylome during a geminivirus infection has not been performed yet. Using a time-scale approach, we aim to decipher the gene regulation in tomato in response to the infection with the geminivirus, tomato yellow leaf curl virus (TYLCV).

RESULTS

We showed that tomato undergoes substantial transcriptional and post-transcriptional changes upon TYLCV infection and identified the main altered regulatory pathways. Interestingly, although the principal plant defense-related processes, gene silencing and the immune response were induced, this cannot prevent the establishment of the infection. Moreover, we identified extra- and intracellular immune receptors as targets for the deregulated microRNAs (miRNAs) and established a network for those that also produced phased secondary small interfering RNAs (phasiRNAs). On the other hand, there were no significant genome-wide changes in tomato methylome at 14 days post infection, the time point at which the symptoms were general, and the amount of viral DNA had reached its maximum level, but we were able to identify differentially methylated regions that could be involved in the transcriptional regulation of some of the differentially expressed genes.

CONCLUSION

We have conducted a comprehensive and reliable study on the changes at transcriptional, post-transcriptional and epigenetic levels in tomato throughout TYLCV infection. The generated genomic information is substantial for understanding the genetic, molecular and physiological changes caused by TYLCV infection in tomato.

The amount and chemistry of acylsugars affects sweetpotato whitefly (Bemisia tabaci) oviposition and development, and tomato yellow leaf curl virus incidence, in field grown tomato plants

The objectives of this study were to ascertain the impact of endogenous production of trichome-exuded acylsugars on insects and insect transmitted virus by evaluating tomato lines and their hybrids bred for acylsugar production under field settings on whiteflies and the whitefly-transmitted tomato yellow leaf curl virus. Specifically, we utilized a diverse array of tomato lines and hybrids bred for changes in acylsugar amount or type, grown in three field trials under natural whitefly and virus pressure, to investigate whether the amount of accumulated acylsugars and or the chemical profile of the acylsugars were associated with greater resistance to whiteflies and reduced incidence of tomato yellow leaf curl virus. There was considerable variation in the abundance of whitefly eggs and nymphs and incidence of tomato yellow leaf curl virus across experiments and between entries. Increasing amount of acylsugars accumulated by the tomato entries was associated with a reduction in the abundance of whitefly eggs and nymphs and a reduction in the incidence of tomato yellow leaf curl virus. Additionally, we identified lines with changes in several acylsugar fatty acids that were associated with decreased abundance of whitefly eggs and nymphs and reduced incidence of tomato yellow leaf curl virus. These results inform the utility of acylsugars as a host plant defense system for improving resistance to whiteflies and their transmitted viruses, with potential for reducing insecticides as a control method for whiteflies and provide breeding targets for optimization of existing acylsugar tomato lines to create lines with the most efficacious amount and chemistry of acylsugars.

Advances and Prospects of Virus-Resistant Breeding in Tomatoes

Plant viruses are the main pathogens which cause significant quality and yield losses in tomato crops. The important viruses that infect tomatoes worldwide belong to five genera: Begomovirus, Orthotospovirus, Tobamovirus, Potyvirus, and Crinivirus. Tomato resistance genes against viruses, including Ty gene resistance against begomoviruses, Sw gene resistance against orthotospoviruses, Tm gene resistance against tobamoviruses, and Pot 1 gene resistance against potyviruses, have been identified from wild germplasm and introduced into cultivated cultivars via hybrid breeding. However, these resistance genes mainly exhibit qualitative resistance mediated by single genes, which cannot protect against virus mutations, recombination, mixed-infection, or emerging viruses, thus posing a great challenge to tomato antiviral breeding. Based on the epidemic characteristics of tomato viruses, we propose that future studies on tomato virus resistance breeding should focus on rapidly, safely, and efficiently creating broad-spectrum germplasm materials resistant to multiple viruses. Accordingly, we summarized and analyzed the advantages and characteristics of the three tomato antiviral breeding strategies, including marker-assisted selection (MAS)-based hybrid breeding, RNA interference (RNAi)-based transgenic breeding, and CRISPR/Cas-based gene editing. Finally, we highlighted the challenges and provided suggestions for improving tomato antiviral breeding in the future using the three breeding strategies.

The Hypersensitive Response to Plant Viruses

Plant proteins with domains rich in leucine repeats play important roles in detecting pathogens and triggering defense reactions, both at the cellular surface for pattern-triggered immunity and in the cell to ensure effector-triggered immunity. As intracellular parasites, viruses are mostly detected intracellularly by proteins with a nucleotide binding site and leucine-rich repeats but receptor-like kinases with leucine-rich repeats, known to localize at the cell surface, have also been involved in response to viruses. In the present review we report on the progress that has been achieved in the last decade on the role of these leucine-rich proteins in antiviral immunity, with a special focus on our current understanding of the hypersensitive response.

Signaling and Resistosome Formation in Plant Innate Immunity to Viruses: Is There a Common Mechanism of Antiviral Resistance Conserved across Kingdoms?

Virus-specific proteins, including coat proteins, movement proteins, replication proteins, and suppressors of RNA interference are capable of triggering the hypersensitive response (HR), which is a type of cell death in plants. The main cell death signaling pathway involves direct interaction of HR-inducing proteins with nucleotide-binding leucine-rich repeats (NLR) proteins encoded by plant resistance genes. Singleton NLR proteins act as both sensor and helper. In other cases, NLR proteins form an activation network leading to their oligomerization and formation of membrane-associated resistosomes, similar to metazoan inflammasomes and apoptosomes. In resistosomes, coiled-coil domains of NLR proteins form Ca2+ channels, while toll-like/interleukin-1 receptor-type (TIR) domains form oligomers that display NAD+ glycohydrolase (NADase) activity. This review is intended to highlight the current knowledge on plant innate antiviral defense signaling pathways in an attempt to define common features of antiviral resistance across the kingdoms of life.

A physical map of traits of agronomic importance based on potato and tomato genome sequences

Potato, tomato, pepper, and eggplant are worldwide important crop and vegetable species of the Solanaceae family. Molecular linkage maps of these plants have been constructed and used to map qualitative and quantitative traits of agronomic importance. This research has been undertaken with the vision to identify the molecular basis of agronomic characters on the one hand, and on the other hand, to assist the selection of improved varieties in breeding programs by providing DNA-based markers that are diagnostic for specific agronomic characters. Since 2011, whole genome sequences of tomato and potato became available in public databases. They were used to combine the results of several hundred mapping and map-based cloning studies of phenotypic characters between 1988 and 2022 in physical maps of the twelve tomato and potato chromosomes. The traits evaluated were qualitative and quantitative resistance to pathogenic oomycetes, fungi, bacteria, viruses, nematodes, and insects. Furthermore, quantitative trait loci for yield and sugar content of tomato fruits and potato tubers and maturity or earliness were physically mapped. Cloned genes for pathogen resistance, a few genes underlying quantitative trait loci for yield, sugar content, and maturity, and several hundred candidate genes for these traits were included in the physical maps. The comparison between the physical chromosome maps revealed, in addition to known intrachromosomal inversions, several additional inversions and translocations between the otherwise highly collinear tomato and potato genomes. The integration of the positional information from independent mapping studies revealed the colocalization of qualitative and quantitative loci for resistance to different types of pathogens, called resistance hotspots, suggesting a similar molecular basis. Synteny between potato and tomato with respect to genomic positions of quantitative trait loci was frequently observed, indicating eventual similarity between the underlying genes.

Crinivirus Tomato Chlorosis Virus Compromises the Control of Tomato Yellow Leaf Curl Virus in Tomato Plants by the Ty-1 Gene

Tomato yellow leaf curl disease (TYLCD) causes severe damage to tomato crops in warm regions of the world, and is associated with infections of several whitefly (Bemisia tabaci)-transmitted single-stranded (ss)DNA begomoviruses (genus Begomovirus, family Geminiviridae). The most widespread begomovirus isolates associated with TYLCD are those of the type strain of the Tomato yellow leaf curl virus species, known as Israel (TYLCV-IL). The Ty-1 gene is widely used in commercial tomato cultivars to control TYLCV-IL damage, providing resistance to the virus by restricting viral accumulation and tolerance to TYLCD by inhibiting disease symptoms. However, several reports suggest that TYLCV-IL-like isolates are adapting to the Ty-1 gene and are causes of concern for possibly overcoming the provided control. This is the case with TYLCV-IL IS76-like recombinants that have a small genome fragment acquired by genetic exchange from an isolate of Tomato yellow leaf curl Sardinia virus, another begomovirus species associated with TYLCD. Here we show that TYLCV-IL IS76-like isolates partially break down the TYLCD-tolerance provided by the Ty-1 gene and that virulence differences might exist between isolates. Interestingly, we demonstrate that mixed infections with an isolate of the crinivirus (genus Crinivirus, family Closteroviridae) species Tomato chlorosis virus (ToCV), an ssRNA virus also transmitted by B. tabaci and emerging worldwide in tomato crops, boosts the breakdown of the TYLCD-tolerance provided by the Ty-1 gene either with TYLCV-IL IS76-like or canonical TYLCV-IL isolates. Moreover, we demonstrate the incorporation of the Ty-2 gene in Ty-1-commercial tomatoes to restrict (no virus or virus traces, no symptoms) systemic infections of recombinant TYLCV-IL IS76-like and canonical TYLCV-IL isolates, even in the presence of ToCV infections, which provides more robust and durable control of TYLCD.

Transcriptome analysis during ToLCBaV disease development in contrasting tomato genotypes

Tomato leaf curl Bangalore virus (ToLCBaV) is one of the most important plant viruses. The infection causes substantial yield losses in tomato crop. The current viral disease management is based mainly on introgression of Ty locus into new tomato cultivars. Unfortunately, strains of the leaf curl virus have been evolving and are breaking Ty based tolerance in tomato. In this study, the defence response to ToLCBaV infection has been compared between contrasting tomato genotypes, resistant line (IIHR 2611; without any known Ty markers) and the susceptible line (IIHR 2843). We carried out comparative transcriptome profiling, and gene expression analysis in an effort to identify gene networks that are associated with a novel ToLCBaV resistance. A total of 22,320 genes were examined to identify differentially expressed genes (DEGs). We found that 329 genes of them were expressed significantly and differentially between ToLBaV-infected samples of both IIHR 2611 and IIHR 2843. A good number of DEGs were related to defence response, photosynthesis, response to wounding, toxin catabolic process, glutathione metabolic process, regulation of transcription DNA-template, transcription factor activity, and sequence-specific DNA binding. A few selected genes such as, nudix hydrolase 8, MIK 2-like, RING-H2 finger protein ATL2-like, MAPKKK 18-like, EDR-2, SAG 21 wound-induced basic protein, GRXC6 and P4 were validated using qPCR. The pattern of gene expression was significantly different in resistant and susceptible plants during disease progression. Both positive and negative regulators of virus resistance were found in the present study. These findings will facilitate breeding and genetic engineering efforts to incorporate novel sources of ToLCBaV resistance in tomatoes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03629-5.

Metabolic profiles of Sri Lankan cassava mosaic virus-infected and healthy cassava (Manihot esculenta Crantz) cultivars with tolerance and susceptibility phenotypes

BACKGROUND

Cassava mosaic disease (CMD) of cassava (Manihot esculenta Crantz) has expanded across many continents. Sri Lankan cassava mosaic virus (SLCMV; family Geminiviridae), which is the predominant cause of CMD in Thailand, has caused agricultural and economic damage in many Southeast Asia countries such as Vietnam, Loas, and Cambodia. The recent SLCMV epidemic in Thailand was commonly found in cassava plantations. Current understanding of plant-virus interactions for SLCMV and cassava is limited. Accordingly, this study explored the metabolic profiles of SLCMV-infected and healthy groups of tolerant (TME3 and KU50) and susceptible (R11) cultivars of cassava. Findings from the study may help to improve cassava breeding, particularly when combined with future transcriptomic and proteomic research.

RESULTS

SLCMV-infected and healthy leaves were subjected to metabolite extraction followed by ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS/MS). The resulting data were analyzed using Compound Discoverer software, the mzCloud, mzVault, and ChemSpider databases, and published literature. Of the 85 differential compounds (SLCMV-infected vs healthy groups), 54 were differential compounds in all three cultivars. These compounds were analyzed using principal component analysis (PCA), hierarchical clustering dendrogram analysis, heatmap analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation. Chlorogenic acid, DL-carnitine, neochlorogenic acid, (E)-aconitic acid, and ascorbyl glucoside were differentially expressed only in TME3 and KU50, with chlorogenic acid, (E)-aconitic acid, and neochlorogenic acid being downregulated in both SLCMV-infected TME3 and KU50, DL-carnitine being upregulated in both SLCMV-infected TME3 and KU50, and ascorbyl glucoside being downregulated in SLCMV-infected TME3 but upregulated in SLCMV-infected KU50. Furthermore, 7-hydroxycoumarine was differentially expressed only in TME3 and R11, while quercitrin, guanine, N-acetylornithine, uridine, vorinostat, sucrose, and lotaustralin were differentially expressed only in KU50 and R11.

CONCLUSIONS

Metabolic profiling of three cassava landrace cultivars (TME3, KU50, and R11) was performed after SLCMV infection and the profiles were compared with those of healthy samples. Certain differential compounds (SLCMV-infected vs healthy groups) in different cultivars of cassava may be involved in plant-virus interactions and could underlie the tolerance and susceptible responses in this important crop.

Plant Defense and Viral Counter-Defense during Plant-Geminivirus Interactions

Geminiviruses are the largest family of plant viruses that cause severe diseases and devastating yield losses of economically important crops worldwide. In response to geminivirus infection, plants have evolved ingenious defense mechanisms to diminish or eliminate invading viral pathogens. However, increasing evidence shows that geminiviruses can interfere with plant defense response and create a suitable cell environment by hijacking host plant machinery to achieve successful infections. In this review, we discuss recent findings about plant defense and viral counter-defense during plant-geminivirus interactions.

Vegetable biology and breeding in the genomics era

Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize, thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.

An Effective Integrated Machine Learning Framework for Identifying Severity of Tomato Yellow Leaf Curl Virus and Their Experimental Validation

Tomato yellow leaf curl virus (TYLCV) dispersed across different countries, specifically to subtropical regions, associated with more severe symptoms. Since TYLCV was first isolated in 1931, it has been a menace to tomato industrial production worldwide over the past century. Three groups were newly isolated from TYLCV-resistant tomatoes in 2022; however, their functions are unknown. The development of machine learning (ML)-based models using characterized sequences and evaluating blind predictions is one of the major challenges in interdisciplinary research. The purpose of this study was to develop an integrated computational framework for the accurate identification of symptoms (mild or severe) based on TYLCV sequences (isolated in Korea). For the development of the framework, we first extracted 11 different feature encodings and hybrid features from the training data and then explored 8 different classifiers and developed their respective prediction models by using randomized 10-fold cross-validation. Subsequently, we carried out a systematic evaluation of these 96 developed models and selected the top 90 models, whose predicted class labels were combined and considered as reduced features. On the basis of these features, a multilayer perceptron was applied and developed the final prediction model (IML-TYLCVs). We conducted blind prediction on 3 groups using IML-TYLCVs, and the results indicated that 2 groups were severe and 1 group was mild. Furthermore, we confirmed the prediction with virus-challenging experiments of tomato plant phenotypes using infectious clones from 3 groups. Plant virologists and plant breeding professionals can access the user-friendly online IML-TYLCVs web server at https://balalab-skku.org/IML-TYLCVs, which can guide them in developing new protection strategies for newly emerging viruses.

Soaud S, Huang Q, M. Saleh A, A. S. Abourehab M, Wan L, Cheng GT, Liu J, Ihtisham M, Noor Z, Rouf Mir R, Zhao X, Yan K, Abbas M, Li J. Natural resistance of tomato plants to Tomato yellow leaf curl virus

Tomato yellow leaf curl virus (TYLCV) is one of the most harmful afflictions in the world that affects tomato growth and production. Six regular antagonistic genes (Ty-1, Ty-2, Ty-3, Ty-4, ty-5, and Ty-6) have been transferred from wild germplasms to commercial cultivars as TYLCV protections. With Ty-1 serving as an appropriate source of TYLCV resistance, only Ty-1, Ty-2, and Ty-3 displayed substantial levels of opposition in a few strains. It has been possible to clone three TYLCV opposition genes (Ty-1/Ty-3, Ty-2, and ty-5) that target three antiviral safety mechanisms. However, it significantly impacts obtaining permanent resistance to TYLCV, trying to maintain opposition whenever possible, and spreading opposition globally. Utilizing novel methods, such as using resistance genes and identifying new resistance resources, protects against TYLCV in tomato production. To facilitate the breeders make an informed decision and testing methods for TYLCV blockage, this study highlights the portrayal of typical obstruction genes, common opposition sources, and subatomic indicators. The main goal is to provide a fictitious starting point for the identification and application of resistance genes as well as the maturation of tomato varieties that are TYLCV-resistant.

Resistance genes on the verge of plant-virus interaction

Viruses are acellular pathogens that cause severe infections in plants, resulting in worldwide crop losses every year. The lack of chemical agents to control viral diseases exacerbates the situation. Thus, to devise proper management strategies, it is important that the defense mechanisms of plants against viruses are understood. Resistance (R) genes regulate plant defense against invading pathogens by eliciting a hypersensitive response (HR). Compatible interaction between plant R gene and viral avirulence (Avr) protein activates the necrotic cell death response at the site of infection, resulting in the cessation of disease. Here, we review different aspects of R gene-mediated dominant resistance against plant viruses in dicotyledonous plants and possible ways for developing crops with better disease resistance.

Analysis of Heat Shock Proteins Based on Amino Acids for the Tomato Genome

This research aimed to investigate heat shock proteins in the tomato genome through the analysis of amino acids. The highest length among sequences was found in seq19 with 3534 base pairs. This seq19 was reported and contained a family of proteins known as HsfA that have a domain of transcriptional activation for tolerance to heat and other abiotic stresses. The values of the codon adaptation index (CAI) ranged from 0.80 in Seq19 to 0.65 in Seq10, based on the mRNA of heat shock proteins for tomatoes. Asparagine (AAT, AAC), aspartic acid (GAT, GAC), phenylalanine (TTT, TTC), and tyrosine (TAT, TAC) have relative synonymous codon usage (RSCU) values bigger than 0.5. In modified relative codon bias (MRCBS), the high gene expressions of the amino acids under heat stress were histidine, tryptophan, asparagine, aspartic acid, lysine, phenylalanine, isoleucine, cysteine, and threonine. RSCU values that were less than 0.5 were considered rare codons that affected the rate of translation, and thus selection could be effective by reducing the frequency of expressed genes under heat stress. The normal distribution of RSCU shows about 68% of the values drawn from the standard normal distribution were within 0.22 and -0.22 standard deviations that tend to cluster around the mean. The most critical component based on principal component analysis (PCA) was the RSCU. These findings would help plant breeders in the development of growth habits for tomatoes during breeding programs.

ty-5 Confers Broad-Spectrum Resistance to Geminiviruses

The selection of resistant crops is an effective method for controlling geminivirus diseases. ty-5 encodes a messenger RNA surveillance factor Pelota with a single amino acid mutation (PelotaV16G), which confers effective resistance to tomato yellow leaf curl virus (TYLCV). No studies have investigated whether ty-5 confers resistance to other geminiviruses. Here, we demonstrate that the tomato ty-5 line exhibits effective resistance to various geminiviruses. It confers resistance to two representative begomoviruses, tomato yellow leaf curl China virus/tomato yellow leaf curl China betasatellite complex and tomato leaf curl Yunnan virus. The ty-5 line also exhibits partial resistance to a curtovirus beet curly top virus. Importantly, ty-5 confers resistance to TYLCV with a betasatellite. Southern blotting and quantitative polymerase chain reaction analyses showed that significantly less DNA of these geminiviruses accumulated in the ty-5 line than in the susceptible line. Moreover, knockdown of Pelota expression converted a Nicotiana benthamiana plant from a geminivirus-susceptible host to a geminivirus-resistant host. Overall, our findings suggest that ty-5 is an important resistance gene resource for crop breeding to control geminiviruses.

PepYLCIV and PepYLCAV resistance gene Pepy-2 encodes DFDGD-Class RNA-dependent RNA polymerase in Capsicum

A begomovirus resistance gene Pepy-2 encoding the DFDGD-Class RNA-dependent RNA polymerase 3a was identified in pepper (C. annuum) through the forward and reverse genetic analyses. In several countries throughout the world, the whitefly-transmitted begomovirus causes massive yield losses in pepper (Capsicum spp.) production. Although introgression of the genetic resistance against begomovirus to commercial cultivars is strongly required, the recently discovered recessive resistance gene pepy-1, which encodes the messenger RNA surveillance factor Pelota, is the only begomovirus resistance gene identified in Capsicum so far. In this study, we fine-mapped another begomovirus resistance gene from PG1-1 (C. annuum), which is resistant to pepper yellow leaf curl Indonesia virus (PepYLCIV) and pepper yellow leaf curl Aceh virus (PepYLCAV), to further speed up the marker-assisted breeding of begomovirus resistance in peppers. A single dominant locus, Pepy-2, conferring resistance against PepYLCIV in PG1-1 was identified on chromosome 7 by screening recombinants from the F₂ and F₃ segregating populations derived from a cross between PG1-1 and begomovirus susceptible SCM334. In the target region spanning 722 kb, a strong candidate gene, the RNA-dependent RNA polymerase 3a (CaRDR3a), was identified. The whole-genome and transcriptome sequences of PG1-1 and SCM334 revealed a single Guanine (G) deletion in CaRDR3a first exon, causing a frameshift resulting in loss-of-function in SCM334. In addition, multiple loss-of-function alleles of CaRDR3a were identified in the reference sequences of C. annuum, C. chinense, and C. baccatum in the public database. Furthermore, virus-induced gene silencing of CaRDR3a in PG1-1 resulted in the loss of resistance against PepYLCIV. PG1-1 and the DNA marker developed in this study will be useful to breeders using Pepy-2 in their breeding programs.

Genotyping-by-sequencing-based QTL mapping reveals novel loci for Pepper yellow leaf curl virus (PepYLCV) resistance in Capsicum annuum

Disease caused by Pepper yellow leaf curl virus (PepYLCV) is one of the greatest threats to pepper (Capsicum spp.) cultivation in the tropics and subtropics. Resistance to PepYLCV was previously identified in a few Capsicum accessions, but no resistance QTLs have been mapped. This study aimed to elucidate the genetics of PepYLCV resistance in C. annuum L. Augmented inoculation by the viruliferous whitefly Bemisia tabaci was used to evaluate parental lines and an F₂ segregating population derived from a cross between resistant C. annuum line LP97 and susceptible C. annuum line ECW30R. Final evaluation was performed six weeks after inoculation using a standardized 5-point scale (0 = no symptoms to 4 = very severe symptoms). A high-density linkage map was constructed using genotyping-by-sequencing (GBS) to identify single-nucleotide polymorphism (SNP) markers associated with PepYLCV resistance in the F₂ population. QTL analysis revealed three QTLs, peplcv-1, peplcv-7, and peplcv-12, on chromosomes P1, P7, and P12, respectively. Candidate genes associated with PepYLCV resistance in the QTL regions were inferred. In addition, single markers Chr7-LCV-7 and Chr12-LCV-12 derived from the QTLs were developed and validated in another F₂ population and in commercial varieties. This work thus provides not only information for mapping PepYLCV resistance loci in pepper but also forms the basis for future molecular analysis of genes involved in PepYLCV resistance.

Transcriptome Profiling Unravels the Involvement of Phytohormones in Tomato Resistance to the Tomato Yellow Leaf Curl Virus (TYLCV)

Tomato yellow leaf curl virus (TYLCV) is a serious pathogen transmitted by the whitefly (Bemisia tabaci). Due to the quick spread of the virus, which is assisted by its vector, tomato yield and quality have suffered a crushing blow. Resistance to TYLCV has been intensively investigated in transmission, yet the mechanism of anti-TYLCV remains elusive. Herein, we conducted transcriptome profiling with a TYLCV-resistant cultivar (CLN2777A) and a susceptible line (Moneymaker) to identify the potential mechanism of resistance to TYLCV. Compared to the susceptible line, CLN2777A maintained a lower level of lipid peroxidation (LPO) after TYLCV infection. Through RNA-seq, over 1000 differentially expressed genes related to the metabolic process, cellular process, response to stimulus, biological regulation, and signaling were identified, indicating that the defense response was activated after the virus attack. Further analysis showed that TYLCV infection could induce the expression of the genes involved in salicylic and jasmonic acid biosynthesis and the signal transduction of phytohormones, which illustrated that phytohormones were essential for tomatoes to defend against TYLCV. These findings provide greater insight into the effective source of resistance for TYLCV control, indicating a potential molecular tool for the design of TYLCV-resistant tomatoes.

Development of a Gene-Based High Resolution Melting (HRM) Marker for Selecting the Gene ty-5 Conferring Resistance to Tomato Yellow Leaf Curl Virus

Tomato yellow leaf curl virus (TYLCV) causes serious yield reductions in China. The use of certain resistance genes in tomato varieties has alleviated the impact of the virus to a certain extent. Recently, varieties with the Ty-1, Ty-2, or Ty-3 genes lost their resistance to TYLCV in some areas in China. New genes should be introduced into tomato to maintain the resistance to TYLCV. Tomato line AVTO1227 has excellent resistance to disease due to the resistance gene ty-5. In this study, we screened different types of markers in a tomato F2 population to compare their accuracy and efficiency. The sequencing analysis results were consistent with the high resolution melting (HRM) marker genotype and field identification results. The result confirmed that the functional marker of ty-5 was accurate and reliable. The single nucleotide polymorphism-based HRM genotyping method established in this study can be used for the selection of breeding parent material, gene correlation analysis, and molecular marker-assisted breeding.

A recessive gene pepy-1 encoding Pelota confers resistance to begomovirus isolates of PepYLCIV and PepYLCAV in Capsicum annuum

A begomovirus resistance gene pepy-1, which encodes the messenger RNA surveillance factor Pelota, was identified in pepper (C. annuum) through map-based cloning and functional characterization. Pepper yellow leaf curl disease caused by begomoviruses seriously affects pepper (Capsicum spp.) production in a number of regions around the world. Ty genes of tomato, which confer resistance to the tomato yellow leaf curl virus, are the only begomovirus resistance genes cloned to date. In this study, we focused on the identification of begomovirus resistance genes in Capsicum annuum. BaPep-5 was identified as a novel source of resistance against pepper yellow leaf curl Indonesia virus (PepYLCIV) and pepper yellow leaf curl Aceh virus (PepYLCAV). A single recessive locus, which we named as pepper yellow leaf curl disease virus resistance 1 (pepy-1), responsible for PepYLCAV resistance in BaPep-5 was identified on chromosome 5 in an F₂ population derived from a cross between BaPep-5 and the begomovirus susceptible accession BaPep-4. In the target region spanning 34 kb, a single candidate gene, the messenger RNA surveillance factor Pelota, was identified. Whole-genome resequencing of BaPep-4 and BaPep-5 and comparison of their genomic DNA sequences revealed a single nucleotide polymorphism (A to G) located at the splice site of the 9th intron of CaPelota in BaPep-5, which caused the insertion of the 9th intron into the transcript, resulting in the addition of 28 amino acids to CaPelota protein without causing a frameshift. Virus-induced gene silencing of CaPelota in the begomovirus susceptible pepper No.218 resulted in the gain of resistance against PepYLCIV, a phenotype consistent with BaPep-5. The DNA marker developed in this study will greatly facilitate marker-assisted breeding of begomovirus resistance in peppers.

Plant responses to geminivirus infection: guardians of the plant immunity

BACKGROUND

Geminiviruses are circular, single-stranded viruses responsible for enormous crop loss worldwide. Rapid expansion of geminivirus diversity outweighs the continuous effort to control its spread. Geminiviruses channelize the host cell machinery in their favour by manipulating the gene expression, cell signalling, protein turnover, and metabolic reprogramming of plants. As a response to viral infection, plants have evolved to deploy various strategies to subvert the virus invasion and reinstate cellular homeostasis.

MAIN BODY

Numerous reports exploring various aspects of plant-geminivirus interaction portray the subtlety and flexibility of the host-pathogen dynamics. To leverage this pool of knowledge towards raising antiviral resistance in host plants, a comprehensive account of plant's defence response against geminiviruses is required. This review discusses the current knowledge of plant's antiviral responses exerted to geminivirus in the light of resistance mechanisms and the innate genetic factors contributing to the defence. We have revisited the defence pathways involving transcriptional and post-transcriptional gene silencing, ubiquitin-proteasomal degradation pathway, protein kinase signalling cascades, autophagy, and hypersensitive responses. In addition, geminivirus-induced phytohormonal fluctuations, the subsequent alterations in primary and secondary metabolites, and their impact on pathogenesis along with the recent advancements of CRISPR-Cas9 technique in generating the geminivirus resistance in plants have been discussed.

CONCLUSIONS

Considering the rapid development in the field of plant-virus interaction, this review provides a timely and comprehensive account of molecular nuances that define the course of geminivirus infection and can be exploited in generating virus-resistant plants to control global agricultural damage.

Geminivirus-Host Interactions: Action and Reaction in Receptor-Mediated Antiviral Immunity

In plant−virus interactions, the plant immune system and virulence strategies are under constant pressure for dominance, and the balance of these opposing selection pressures can result in disease or resistance. The naturally evolving plant antiviral immune defense consists of a multilayered perception system represented by pattern recognition receptors (PRR) and resistance (R) proteins similarly to the nonviral pathogen innate defenses. Another layer of antiviral immunity, signaling via a cell surface receptor-like kinase to inhibit host and viral mRNA translation, has been identified as a virulence target of the geminivirus nuclear shuttle protein. The Geminiviridae family comprises broad-host range viruses that cause devastating plant diseases in a large variety of relevant crops and vegetables and hence have evolved a repertoire of immune-suppressing functions. In this review, we discuss the primary layers of the receptor-mediated antiviral immune system, focusing on the mechanisms developed by geminiviruses to overcome plant immunity.

Resistant Sources and Genetic Control of Resistance to ToLCNDV in Cucumber

Tomato leaf curl New Delhi virus (ToLCNDV) is a severe threat for cucurbit production worldwide. Resistance has been reported in several crops, but at present, there are no described accessions with resistance to ToLCNDV in cucumber (Cucumis sativus). C. sativus var. sativus accessions were mechanically inoculated with ToLCNDV and screened for resistance, by scoring symptom severity, tissue printing, and PCR (conventional and quantitative). Severe symptoms and high load of viral DNA were found in plants of a nuclear collection of Spanish landraces and in accessions of C. sativus from different geographical origins. Three Indian accessions (CGN23089, CGN23423, and CGN23633) were highly resistant to the mechanical inoculation, as well as all plants of their progenies obtained by selfing. To study the inheritance of the resistance to ToLCNDV, plants of the CGN23089 accession were crossed with the susceptible accession BGV011742, and F₁ hybrids were used to construct segregating populations (F₂ and backcrosses), which were mechanically inoculated and evaluated for symptom development and viral load by qPCR. The analysis of the genetic control fit with a recessive monogenic inheritance model, and after genotyping with SNPs distributed along the C. sativus genome, a QTL associated with ToLCNDV resistance was identified in chromosome 2 of cucumber.

Geminiviral Triggers and Suppressors of Plant Antiviral Immunity

Geminiviruses are circular single-stranded DNA plant viruses encapsidated into geminate virion particles, which infect many crops and vegetables and, hence, represent significant agricultural constraints worldwide. To maintain their broad-range host spectrum and establish productive infection, the geminiviruses must circumvent a potent plant antiviral immune system, which consists of a multilayered perception system represented by RNA interference sensors and effectors, pattern recognition receptors (PRR), and resistance (R) proteins. This recognition system leads to the activation of conserved defense responses that protect plants against different co-existing viral and nonviral pathogens in nature. Furthermore, a specific antiviral cell surface receptor signaling is activated at the onset of geminivirus infection to suppress global translation. This review highlighted these layers of virus perception and host defenses and the mechanisms developed by geminiviruses to overcome the plant antiviral immunity mechanisms.

The Global Dimension of Tomato Yellow Leaf Curl Disease: Current Status and Breeding Perspectives

Tomato yellow leaf curl disease (TYLCD) caused by tomato yellow leaf curl virus (TYLCV) and a group of related begomoviruses is an important disease which in recent years has caused serious economic problems in tomato (Solanum lycopersicum) production worldwide. Spreading of the vectors, whiteflies of the Bemisia tabaci complex, has been responsible for many TYLCD outbreaks. In this review, we summarize the current knowledge of TYLCV and TYLV-like begomoviruses and the driving forces of the increasing global significance through rapid evolution of begomovirus variants, mixed infection in the field, association with betasatellites and host range expansion. Breeding for host plant resistance is considered as one of the most promising and sustainable methods in controlling TYLCD. Resistance to TYLCD was found in several wild relatives of tomato from which six TYLCV resistance genes (Ty-1 to Ty-6) have been identified. Currently, Ty-1 and Ty-3 are the primary resistance genes widely used in tomato breeding programs. Ty-2 is also exploited commercially either alone or in combination with other Ty-genes (i.e., Ty-1, Ty-3 or ty-5). Additionally, screening of a large collection of wild tomato species has resulted in the identification of novel TYLCD resistance sources. In this review, we focus on genetic resources used to date in breeding for TYLCVD resistance. For future breeding strategies, we discuss several leads in order to make full use of the naturally occurring and engineered resistance to mount a broad-spectrum and sustainable begomovirus resistance.

Advances in Understanding Defense Mechanisms in Persea americana Against Phytophthora cinnamomi

Avocado (Persea americana) is an economically important fruit crop world-wide, the production of which is challenged by notable root pathogens such as Phytophthora cinnamomi and Rosellinia necatrix. Arguably the most prevalent, P. cinnamomi, is a hemibiotrophic oomycete which causes Phytophthora root rot, leading to reduced yields and eventual tree death. Despite its' importance, the development of molecular tools and resources have been historically limited, prohibiting significant progress toward understanding this important host-pathogen interaction. The development of a nested qPCR assay capable of quantifying P. cinnamomi during avocado infection has enabled us to distinguish avocado rootstocks as either resistant or tolerant - an important distinction when unraveling the defense response. This review will provide an overview of our current knowledge on the molecular defense pathways utilized in resistant avocado rootstock against P. cinnamomi. Notably, avocado demonstrates a biphasic phytohormone profile in response to P. cinnamomi infection which allows for the timely expression of pathogenesis-related genes via the NPR1 defense response pathway. Cell wall modification via callose deposition and lignification have also been implicated in the resistant response. Recent advances such as composite plant transformation, single nucleotide polymorphism (SNP) analyses as well as genomics and transcriptomics will complement existing molecular, histological, and biochemical assay studies and further elucidate avocado defense mechanisms.

The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies

Tomato (Solanum lycopersicum L.) is a model system for studying the molecular basis of resistance in plants. The investigation of evolutionary dynamics of tomato resistance (R)-loci provides unique opportunities for identifying factors that promote or constrain genome evolution. Nucleotide-binding domain and leucine-rich repeat (NB-LRR) receptors belong to one of the most plastic and diversified families. The vast amount of genomic data available for Solanaceae and wild tomato relatives provides unprecedented insights into the patterns and mechanisms of evolution of NB-LRR genes. Comparative analysis remarked a reshuffling of R-islands on chromosomes and a high degree of adaptive diversification in key R-loci induced by species-specific pathogen pressure. Unveiling NB-LRR natural variation in tomato and in other Solanaceae species offers the opportunity to effectively exploit genetic diversity in genomic-driven breeding programs with the aim of identifying and introducing new resistances in tomato cultivars. Within this motivating context, we reviewed the repertoire of NB-LRR genes available for tomato improvement with a special focus on signatures of adaptive processes. This issue is still relevant and not thoroughly investigated. We believe that the discovery of mechanisms involved in the generation of a gene with new resistance functions will bring great benefits to future breeding strategies.

Development and Application of Gene-Specific Markers for Tomato Yellow Leaf Curl Virus Resistance in Both Field and Artificial Infections

Tomato yellow leaf curl virus (TYLCV) is a disease that is damaging to tomato production worldwide. Resistance to TYLCV has been intensively investigated, and single resistance genes such as Ty-1 have been widely deployed in breeding programs. However, resistance-breaking incidences are frequently reported, and achieving durable resistance against TYLCV in the field is important. In this study, gene-specific markers for Ty-2 and ty-5, and closely-linked markers for Ty-4 were developed and applied to distinguish TYLCV resistance in various tomato genotypes. Quantitative infectivity assays using both natural infection in the field and artificial inoculation utilizing infectious TYLCV clones in a growth chamber were optimized and performed to investigate the individual and cumulative levels of resistance. We confirmed that Ty-2 could also be an effective source of resistance for TYLCV control, together with Ty-1. Improvement of resistance as a result of gene-pyramiding was speculated, and breeding lines including both Ty-1 and Ty-2 showed the strongest resistance in both field and artificial infections.

Ty-2 and Ty-3a Conferred Resistance are Insufficient Against Tomato Yellow Leaf Curl Kanchanaburi Virus from Southeast Asia in Single or Mixed Infections of Tomato

Tomato yellow leaf curl virus (TYLCV), a monopartite begomovirus that originated in the eastern Mediterranean, has spread worldwide, becoming a serious threat to tomato (Solanum lycopersicum L.) production. Southeast Asia is considered one of the hotspots for begomovirus diversity, and a wide variety of local begomovirus species distinct from TYLCV have been identified. In this study, the protection effect of introgressions of single TYLCV Ty resistance genes, Ty-2 and Ty-3a, in tomato was examined against inoculations of the bipartite begomoviruses Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV) and Pepper yellow leaf curl Indonesia virus (PepYLCIV) isolated from Indonesia. Our findings suggest that Ty-2 in the heterozygous state was found to be ineffective against PepYLCIV and TYLCKaV, whereas Ty-3a in the heterozygous state was effective against PepYLCIV and partially effective against TYLCKaV. Quantification of viral DNAs showed correlation between symptom expression and viral DNA accumulation. Moreover, mixed infections of TYLCKaV and PepYLCIV caused notably severe symptoms in tomato plants harboring Ty-3a. In cases of mixed infection, quantifying viral DNAs showed a relatively high accumulation of PepYLCIV, indicating that Ty-3a loses its effectiveness against PepYLCIV when TYLCKaV is also present. This study demonstrates the lack of effectiveness of Ty resistance genes against single and mixed infections of distinct local begomoviruses from Southeast Asia.

The NLR Protein Encoded by the Resistance Gene Ty-2 Is Triggered by the Replication-Associated Protein Rep/C1 of Tomato Yellow Leaf Curl Virus

The whitefly-transmitted tomato yellow leaf curl virus (TYLCV) is one of the most destructive viral pathogens of cultivated tomato. To combat TYLCV, resistance gene Ty-2 has been introduced into cultivated tomato (Solanum lycopersicum) from wild tomato species Solanum habrochaites by interspecific crossing. Introgression lines with Ty-2 contain a large inversion compared with S. lycopersicum, which causes severe suppression of recombination and has hampered the cloning of Ty-2 so far. Here, we report the fine-mapping and cloning of Ty-2 using crosses between a Ty-2 introgression line and several susceptible S. habrochaites accessions. Ty-2 was shown to encode a nucleotide-binding leucine-rich repeat (NLR) protein. For breeding purposes, a highly specific DNA marker tightly linked to the Ty-2 gene was developed permitting marker-assisted selection. The resistance mediated by Ty-2 was effective against the Israel strain of TYLCV (TYLCV-IL) and tomato yellow leaf curl virus-[China : Shanghai2] (TYLCV-[CN : SH2]), but not against tomato yellow leaf curl Sardinia virus (TYLCSV) and leafhopper-transmitted beet curly top virus (BCTV). By co-infiltration experiments we showed that transient expression of the Rep/C1 protein of TYLCV, but not of TYLCSV triggered a hypersensitive response (HR) in Nicotiana benthamiana plants co-expressing the Ty-2 gene. Our results indicate that the Rep/C1 gene of TYLCV-IL presents the avirulence determinant of Ty-2-mediated resistance.

Tomato Yellow Leaf Curl Virus: Impact, Challenges, and Management

Tomato yellow leaf curl virus (TYLCV) is one of the most studied plant viral pathogens because it is the most damaging virus for global tomato production. In order to combat this global threat, it is important that we understand the biology of TYLCV and devise management approaches. The prime objective of this review is to highlight management strategies for efficiently tackling TYLCV epidemics and global spread. For that purpose, we focus on the impact TYLCV has on worldwide agriculture and the role of recent advances for our understanding of TYLCV interaction with its host and vector. Another important focus is the role of recombination and mutations in shaping the evolution of TYLCV genome and geographical distribution.

Recent advances on the plant manipulation by geminiviruses

As intracellular parasites, viruses co-opt the molecular machinery of the cells they infect in order to multiply and spread, and the extensiveness and effectiveness of this manipulation ultimately determine the outcome of the interaction between virus and host. Members of the Geminiviridae family, causal agents of devastating diseases in crops, encode only a handful of multifunctional, fast-evolving proteins, which efficiently target host proteins to re-wire plant development and physiology and enable replication and spread of the viral genome. In this review, we offer an overview of the different steps in the geminiviral invasion of the host plant, and explore the knowns and unknowns in geminivirus biology.

Geminivirus Resistance: A Minireview

A continuing challenge to crop production worldwide is the spectrum of diseases caused by geminiviruses, a large family of small circular single-stranded DNA viruses. These viruses are quite diverse, some containing mono- or bi-partite genomes, and infecting a multitude of monocot and dicot plants. There are currently many efforts directed at controlling these diseases. While some of the methods include controlling the insect vector using pesticides or genetic insect resistance (Rodríguez-López et al., 2011), this review will focus on the generation of plants that are resistant to geminiviruses themselves. Genetic resistance was traditionally found by surveying the wild relatives of modern crops for resistance loci; this method is still widely used and successful. However, the quick rate of virus evolution demands a rapid turnover of resistance genes. With better information about virus-host interactions, scientists are now able to target early stages of geminivirus infection in the host, preventing symptom development and viral DNA accumulation.

Identification of Tomato Proteins That Interact With Replication Initiator Protein (Rep) of the Geminivirus TYLCV

Geminiviruses are plant-infecting DNA viruses that reshape the intracellular environment of their host in order to create favorable conditions for viral replication and propagation. Viral manipulation is largely mediated via interactions between viral and host proteins. Identification of this protein network helps us to understand how these viruses manipulate their host and therefore provides us potentially with novel leads for resistance against this class of pathogens, as genetic variation in the corresponding plant genes could subvert viral manipulation. Different studies have already yielded a list of host proteins that interact with one of the geminiviral proteins. Here, we use affinity purification followed by mass spectrometry (AP-MS) to further expand this list of interacting proteins, focusing on an important host (tomato) and the Replication initiator protein (Rep, AL1, C1) from Tomato yellow leaf curl virus (TYLCV). Rep is the only geminiviral protein proven to be essential for geminiviral replication and it forms an integral part of viral replisomes, a protein complex that consists of plant and viral proteins that allows for viral DNA replication. Using AP-MS, fifty-four 'high confidence' tomato proteins were identified that specifically co-purified with Rep. For two of them, an unknown EWS-like RNA-binding protein (called Geminivirus Rep interacting EWS-like protein 1 or GRIEP1) and an isoform of the THO complex subunit 4A (ALY1), we were able to confirm this interaction with Rep in planta using a second method, bimolecular fluorescence complementation (BiFC). The THO subunit 4 is part of the THO/TREX (TRanscription-EXport) complex, which controls RNA splicing and nuclear export of mRNA to the cytoplasm and is also connected to plant disease resistance. This work represents the first step towards characterization of novel host factors with a putative role in the life cycle of TYLCV and possibly other geminiviruses.

Tomato contrasting genotypes responses under combined salinity and viral stresses

Tomato yellow leaf curl disease (TYLCD) and salinity stress adversely affect tomato production worldwide by causing extensive damages. In Tunisia, identifying TYLCD resistant cultivars selected in different environments is useful to devise counter-measures. To this end, 20 tomato commercial cultivars were screened for different Ty gene alleles' combinations and evaluated either for TYLCD incidence or salinity constraint. We built a biological multi-layer network for integrating, visualizing and modelling generated data. It is a simple representation view linking allelic combinations to tomato cultivars behaviour under viral and salt stresses. In addition, we analyzed differential expression of transcriptions factors (TFs) belonging to WRKY and ERF families in selected resistant (R) and susceptible (S) tomato cultivars. Gene expression was evaluated for short- and long stress exposure to either TYLCSV infection or to both viral and salinity stresses. Evidence is that TFs promote resistance to abiotic and biotic stresses through a complex regulatory network.

Tomato yellow leaf curl virus (TYLCV)-resistant tomatoes share molecular mechanisms sustaining resistance with their wild progenitor Solanum habrochaites but not with TYLCV-susceptible tomatoes

The wild tomato species Solanum habrochaites (Sh) has been used as a source for tomato yellow leaf curl virus (TYLCV) resistance in a breeding program to generate a TYLCV-resistant tomato line. Susceptible (S) and resistant (R) lines have been developed through this program. We compared the behavior of R, S and Sh tomato plants upon infection to find out whether the resistant phenotype of R plants originated from Sh. Results showed that mechanisms involving sugar-signaling (i.e., LIN6/HT1), water channels (i.e., TIP1;1), hormone homeostasis (i.e., ABA and SA) and urea accumulation were shared by S. habrochaites and R plants, but not by S. habrochaites and S tomatoes. This finding supports the hypothesis that these mechanisms were introgressed in the R genotype from the wild tomato progenitor during breeding for TYLCV resistance. Hence, identification of genes contributing to resistance to biotic stress from wild tomato species and their introgression into domestic plants ensures tomato supply and food security.

Dissection of complex traits of tomato in the post-genome era

We present the main advances of dissection of complex traits in tomato by omics, the genes identified to control complex traits and the application of CRISPR/Cas9 in tomato breeding. Complex traits are believed to be under the control of multiple genes, each with different effects and interaction with environmental factors. Advance development of sequencing and molecular technologies has enabled the recognition of the genomic structure of most organisms and the identification of a nearly limitless number of markers that have made it to accelerate the speed of QTL identification and gene cloning. Meanwhile, multiomics have been used to identify the genetic variations among different tomato species, determine the expression profiles of genes in different tissues and at distinct developmental stages, and detect metabolites in different pathways and processes. The combination of these data facilitates to reveal mechanism underlying complex traits. Moreover, mutants generated by mutagens and genome editing provide relatively rich genetic variation for deciphering the complex traits and exploiting them in tomato breeding. In this article, we present the main advances of complex trait dissection in tomato by omics since the release of the tomato genome sequence in 2012. We provide further insight into some tomato complex traits because of the causal genetic variations discovered so far and explore the utilization of CRISPR/Cas9 for the modification of tomato complex traits.

Ty-1, a universal resistance gene against geminiviruses that is compromised by co-replication of a betasatellite

Tomato yellow leaf curl virus (TYLCV), a begomovirus, causes large yield losses and breeding for resistance is an effective way to combat this viral disease. The resistance gene Ty-1 codes for an RNA-dependent RNA polymerase and has recently been shown to enhance transcriptional gene silencing of TYLCV. Whereas Ty-1 was earlier shown to also confer resistance to a bipartite begomovirus, here it is shown that Ty-1 is probably generic to all geminiviruses. A tomato Ty-1 introgression line, but also stable transformants of susceptible tomato cv. Moneymaker and Nicotiana benthamiana (N. benthamiana) expressing the Ty-1 gene, exhibited resistance to begomoviruses as well as to the distinct, leafhopper-transmitted beet curly top virus, a curtovirus. Stable Ty-1 transformants of N. benthamiana and tomato showed fewer symptoms and reduced viral titres on infection compared to wild-type plants. TYLCV infections in wild-type N. benthamiana plants in the additional presence of a betasatellite led to increased symptom severity and a consistent, slightly lowered virus titre relative to the high averaged levels seen in the absence of the betasatellite. On the contrary, in Ty-1 transformed N. benthamiana viral titres increased in the presence of the betasatellite. The same was observed when these Ty-1-encoding plants were challenged with TYLCV and a potato virus X construct expressing the RNA interference suppressor protein βC1 encoded by the betasatellite. The resistance spectrum of Ty-1 and the durability of the resistance are discussed in light of antiviral RNA interference and viral counter defence strategies.

Tomato Yellow Leaf Curl Virus-Resistant and -Susceptible Tomato Genotypes Similarly Impact the Virus Population Genetics

Tomato yellow leaf curl virus is a species in the genus Begomovirus and family Geminiviridae. Tomato yellow leaf curl virus (TYLCV) infection induces severe symptoms on tomato plants and causes serious yield losses worldwide. TYLCV is persistently transmitted by the sweetpotato whitefly, Bemisia tabaci (Gennadius). Cultivars and hybrids with a single or few genes conferring resistance against TYLCV are often planted to mitigate TYLCV-induced losses. These resistant genotypes (cultivars or hybrids) are not immune to TYLCV. They typically develop systemic infection, display mild symptoms, and produce more marketable tomatoes than susceptible genotypes under TYLCV pressure. In several pathosystems, extensive use of resistant cultivars with single dominant resistance-conferring gene has led to intense selection pressure on the virus, development of highly virulent strains, and resistance breakdown. This study assessed differences in TYLCV genomes isolated from susceptible and resistant genotypes in Florida and Georgia. Phylogenetic analyses indicated that Florida and Georgia isolates were distinct from each other. Population genetics analyses with genomes field-collected from resistant and susceptible genotypes from Florida and/or Georgia provided no evidence of a genetic structure between the resistant and susceptible genotypes. No codons in TYLCV genomes from TYLCV-resistant or susceptible genotypes were under positive selection, suggesting that highly virulent or resistance-breaking TYLCV strains might not be common in tomato farmscapes in Florida and Georgia. With TYLCV-resistant genotypes usage increasing recently and multiple tomato crops being planted during a calendar year, host resistance-induced selection pressure on the virus remains a critical issue. To address the same, a greenhouse selection experiment with one TYLCV-resistant and susceptible genotype was conducted. Each genotype was challenged with TYLCV through whitefly-mediated transmission serially 10 times (T₁-T₁₀). Population genetics parameters at the genome level were assessed at T₁, T₅, and T₁₀. Results indicated that genomes from resistant and susceptible genotypes did not differentiate with increasing transmission number, no specific mutations were repeatedly observed, and no positive selection was detected. These results reiterate that resistance in tomato might not be exerting selection pressure against TYLCV to facilitate development of resistance-breaking strains. TYLCV populations rather seem to be shaped by purifying selection and/or population expansion.

Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars

Background

Cassava is an important food crop in tropical and sub-tropical regions worldwide. In Africa, cassava production is widely affected by cassava mosaic disease (CMD), which is caused by the African cassava mosaic geminivirus that is transmitted by whiteflies. Cassava breeders often use a single locus, CMD2, for introducing CMD resistance into susceptible cultivars. The CMD2 locus has been genetically mapped to a 10-Mbp region, but its organization and genes as well as their functions are unknown.

Results

We report haplotype-resolved de novo assemblies and annotations of the genomes for the African cassava cultivar TME (tropical Manihot esculenta), which is the origin of CMD2, and the CMD-susceptible cultivar 60444. The assemblies provide phased haplotype information for over 80% of the genomes. Haplotype comparison identified novel features previously hidden in collapsed and fragmented cassava genomes, including thousands of allelic variants, inter-haplotype diversity in coding regions, and patterns of diversification through allele-specific expression. Reconstruction of the CMD2 locus revealed a highly complex region with nearly identical gene sets but limited microsynteny between the two cultivars.

Conclusions

The genome maps of the CMD2 locus in both 60444 and TME3, together with the newly annotated genes, will help the identification of the causal genetic basis of CMD2 resistance to geminiviruses. Our de novo cassava genome assemblies will also facilitate genetic mapping approaches to narrow the large CMD2 region to a few candidate genes for better informed strategies to develop robust geminivirus resistance in susceptible cassava cultivars.

Electronic supplementary material

The online version of this article (10.1186/s12915-019-0697-6) contains supplementary material, which is available to authorized users.