Screening and Field Trials of Virus Resistant Sources in Capsicum spp

Current knowledge and breeding strategies for management of aphid-transmitted viruses of pepper (Capsicum spp.) in Africa

Aphid-transmitted viruses cause significant losses in pepper production worldwide, negatively affecting yield and quality. The emergence of new aphid-transmitted viruses or development of variants as well as the occurrence in mixed infections make management a challenge. Here, we overview the current status of the distribution, incidence and phylogeny of aphids and the viruses they transmit in pepper in Africa; outline the available genetic resources, including sources of resistance, resistance genes and molecular markers; and discuss the recent advances in understanding the genetic basis of resistance to the predominant African viruses infecting pepper. Pepper veinal mottle virus (PVMV; Potyvirus); Potato virus Y (PVY; Potyvirus), Chili veinal mottle virus (ChiVMV; Potyvirus), Cucumber mosaic virus (CMV; Cucumovirus) and Pepper veins yellow virus (PeVYV; Polerovirus) have been reported to be the most widespread and devastating aphid-transmitted viruses infecting pepper across Africa. Co-infection or mixed infection between aphid-transmitted viruses has been detected and the interrelationship between viruses that co-infect chili peppers is poorly understood. Establishing and evaluating existing and new diversity sets with more genetic diversity is an important component of developing host resistance and implementing integrated management strategies. However, more work needs to be done to characterize the aphid-transmitted viral strains across Africa and understand their phylogeny in order to develop more durable host resistance. In addition, a limited number of QTLs associated with resistance to the aphid-transmitted virus have been reported and QTL data are only available for PVY, ChiVMV and CMV mainly against European and Asian strains, although PVMV is likely the most important aphid-transmitted viral disease in Africa. There is a need to identify germplasm resources with resistance against various aphid-transmitted virus strains, and subsequent pyramiding of the resistance using marker-assisted selection could be an effective strategy. The recent advances in understanding the genetic basis of the resistance to the virus and the new breeding techniques that can be leveraged to accelerate breeding for aphid-transmitted virus in pepper are proposed as strategies to more efficiently develop resistant cultivars. The deployment of multi-genetic resistances in pepper is an effective and desirable method of managing viral-diseases in Africa and limit losses for farmers in a sustainable manner.

Transcriptional Comparison Reveals Differential Resistance Mechanisms between CMV-Resistant PBC688 and CMV-Susceptible G29

The Cucumber mosaic virus (CMV) presents a significant threat to pepper cultivation worldwide, leading to substantial yield losses. We conducted a transcriptional comparative study between CMV-resistant (PBC688) and -susceptible (G29) pepper accessions to understand the mechanisms of CMV resistance. PBC688 effectively suppressed CMV proliferation and spread, while G29 exhibited higher viral accumulation. A transcriptome analysis revealed substantial differences in gene expressions between the two genotypes, particularly in pathways related to plant-pathogen interactions, MAP kinase, ribosomes, and photosynthesis. In G29, the resistance to CMV involved key genes associated with calcium-binding proteins, pathogenesis-related proteins, and disease resistance. However, in PBC688, the crucial genes contributing to CMV resistance were ribosomal and chlorophyll a-b binding proteins. Hormone signal transduction pathways, such as ethylene (ET) and abscisic acid (ABA), displayed distinct expression patterns, suggesting that CMV resistance in peppers is associated with ET and ABA. These findings deepen our understanding of CMV resistance in peppers, facilitating future research and variety improvement.

Exploring Disease Resistance in Pepper (Capsicum spp.) Germplasm Collection Using Fluidigm SNP Genotyping

This study utilized a diverse Capsicum accessions (5658) sourced from various species and geographical regions, deposited at the National Agrobiodiversity Center, Genebank. We employed 19 SNP markers through a Fluidigm genotyping system and screened these accessions against eight prevalent diseases of pepper. This study revealed accessions resistant to individual diseases as well as those exhibiting resistance to multiple diseases, including bacterial spot, anthracnose, powdery mildew, phytophthora root rot, and potyvirus. The C. chacoense accessions were identified as resistant materials against bacterial spot, anthracnose, powdery mildew, and phytophthora root rot, underscoring the robust natural defense mechanisms inherent in the wild Capsicum species and its potential uses as sources of resistance for breeding. C. baccatum species also demonstrated to be a promising source of resistance to major pepper diseases. Generally, disease-resistant germplasm has been identified from various Capsicum species. Originating from diverse locations such as Argentina, Bolivia, and the United Kingdom, these accessions consistently demonstrated resistance, indicating the widespread prevalence of disease-resistant traits across varied environments. Additionally, we selected ten pepper accessions based on their resistance to multiple diseases, including CMV, Phytophthora root rot, potyviruses, and TSWV, sourced from diverse geographical regions like Hungary, Peru, the United States, and the Netherlands. This comprehensive analysis provides valuable insights into disease resistance in Capsicum, crucial for fostering sustainable agricultural practices and advancing crop improvement through breeding strategies.

A Survey of Main Pepper Crop Viruses in Different Cultivation Systems for the Selection of the Most Appropriate Resistance Genes in Sensitive Local Cultivars in Northern Spain

Viral diseases have become one of the main phytosanitary problems for pepper growers in the Basque Country (northern Spain). In 2014, a survey was carried out to determine the prevalence of the most common viruses found in Gernika pepper and Ibarra chili pepper landraces. A total of 97 plots were surveyed and classified according to the crop system. Within these plots, 1107 plants were sampled and tested for tobacco mosaic virus (TMV), tomato mosaic virus (ToMV), tobacco mild green mosaic virus (TMGMV), pepper mild mottle virus (PMMoV), paprika mild mottle virus (PaMMV), potato virus Y (PVY) and tomato spotted wilt virus (TSWV) applying a DAS-ELISA test. PaMMV was verified by the non-radioactive molecular hybridization technique and it was found to be negative. All viruses were detected, but the most prevalent viruses were PVY and TMGMV (19.8% and 10.6% of tested plants, respectively). Differences among cultivation systems were found for most of the tested viruses. PVY had a higher level of infection under open field conditions (27.3%) than under greenhouse conditions (12.3%). Inversely, the viruses belonging to the Tobamovirus genus and TSWV prevailed under greenhouse conditions (28.9% and 5.2%) when compared to open field (11.2% and 1.1%), respectively. Single (28%) and multiple infections (8.9%) were found. All PMMoV isolates were classified as pathotype P1.2. Survey results indicated that tobamovirus and PVY resistance genes would be the most appropriate to be included in breeding programs with these sensitive pepper landraces.

Pepper Crop Improvement Against Cucumber Mosaic Virus (CMV): A Review

Cucumber mosaic virus (CMV) is a prevalent virus affecting the quality and yield of pepper, resulting in yield losses of greater than 80% during severe local epidemics. Cultural practices and the heavy use of agrochemicals are the most common control measures for CMV. Sources of resistance provide a practical reference and a basis for breeding for CMV resistance. Genetic factors underlying CMV resistance have been studied and advanced breeding lines and cultivars with improved resistance have been developed by traditional breeding methods. Additionally, QTLs or genes for CMV resistance have been identified and can be utilized for marker-assisted resistance breeding. This review focuses on status and prospect of CMV against different virus strains, host resistance, and its applied genetics. With the advent of novel technologies, more useful markers and precise approaches can facilitate the progress for improving CMV resistance in Capsicum.

Overview of Biotic Stresses in Pepper (Capsicum spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics

Pepper (Capsicum spp.) is one of the major vegetable crops grown worldwide largely appreciated for its economic importance and nutritional value. This crop belongs to the large Solanaceae family, which, among more than 90 genera and 2500 species of flowering plants, includes commercially important vegetables such as tomato and eggplant. The genus includes over 30 species, five of which (C. annuum, C. frutescens, C. chinense, C. baccatum, and C. pubescens) are domesticated and mainly grown for consumption as food and for non-food purposes (e.g., cosmetics). The main challenges for vegetable crop improvement are linked to the sustainable development of agriculture, food security, the growing consumers' demand for food. Furthermore, demographic trends and changes to climate require more efficient use of plant genetic resources in breeding programs. Increases in pepper consumption have been observed in the past 20 years, and for maintaining this trend, the development of new resistant and high yielding varieties is demanded. The range of pathogens afflicting peppers is very broad and includes fungi, viruses, bacteria, and insects. In this context, the large number of accessions of domesticated and wild species stored in the world seed banks represents a valuable resource for breeding in order to transfer traits related to resistance mechanisms to various biotic stresses. In the present review, we report comprehensive information on sources of resistance to a broad range of pathogens in pepper, revisiting the classical genetic studies and showing the contribution of genomics for the understanding of the molecular basis of resistance.

Identification of Cucumber mosaic resistance 2 (cmr2) That Confers Resistance to a New Cucumber mosaic virus Isolate P1 (CMV-P1) in Pepper (Capsicum spp.)

Cucumber mosaic virus (CMV) is one of the most devastating phytopathogens of Capsicum. The single dominant resistance gene, Cucumber mosaic resistant 1 (Cmr1), that confers resistance to the CMV isolate P0 has been overcome by a new isolate (CMV-P1) after being deployed in pepper (Capsicum annuum) breeding for over 20 years. A recently identified Indian C. annuum cultivar, "Lam32," displays resistance to CMV-P1. In this study, we show that the resistance in "Lam32" is controlled by a single recessive gene, CMV resistance gene 2 (cmr2). We found that cmr2 conferred resistance to CMV strains including CMV-Korean, CMV-Fny, and CMV-P1, indicating that cmr2 provides a broad-spectrum type of resistance. We utilized two molecular mapping approaches to determine the chromosomal location of cmr2. Bulked segregant analysis (BSA) using amplified fragment-length polymorphism (AFLP) (BSA-AFLP) revealed one marker, cmvAFLP, located 16 cM from cmr2. BSA using the Affymetrix pepper array (BSA-Affy) identified a single-nucleotide polymorphism (SNP) marker (Affy4) located 2.3 cM from cmr2 on chromosome 8. We further screened a pepper germplasm collection of 4,197 accessions for additional CMV-P1 resistance sources and found that some accessions contained equivalent levels of resistance to that of "Lam32." Inheritance and allelism tests demonstrated that all the resistance sources examined contained cmr2. Our result thus provide genetic and molecular evidence that cmr2 is a single recessive gene that confers to pepper an unprecedented resistance to the dangerous new isolate CMV-P1 that had overcome Cmr1.

RNA-based vaccination of Bhut Jolokia pepper (Capsicum chinense Jacq.) against cucumber mosaic virus

Cucumber mosaic virus (CMV) causes great losses in Bhut Jolokia pepper (Capsicum chinense Jacq.) plantations in Assam, India. To investigate possible means to induce plant resistance against this virus, the crude extract of bacterially-expressed double-stranded (ds) RNA, derived from CMV-2b gene (dsRNA_CMV-2b), was exogenously applied along with CMV-G strain onto Bhut Jolokia plants. In this 'RNA-vaccination' bioassay, disease incidence, assessed by testing the plants at 21 days post inoculation by DAS-ELISA, ranged from 0 to 29% in case of dsRNA-treated plants, and from 55 to 92% when only CMV was applied. CMV-infected pepper plants became severely stunted, having dull light green foliage with leathery appearance, whereas plants receiving dsRNA_CMV-2b exhibited milder symptoms or remained healthy. The results obtained suggest that this non-transgenic approach has a considerable effect in protecting pepper against CMV.

Construction of a high-density genetic map and identification of QTLs for cucumber mosaic virus resistance in pepper (Capsicum annuum L.) using specific length amplified fragment sequencing (SLAF-seq)

Pepper (Capsicum) is one of the most important vegetable and spice crops. Aphid-transmitted cucumber mosaic virus (CMV) causes significant damage to pepper crops across the world. The genetic basis of CMV resistance in pepper is complex, and the mechanisms underlying resistance remain largely unknown. Here, we employed a SLAF-seq approach to generate a high-density genetic map of pepper. The map spanned 1,785.46 cM, containing 12,727 markers on 12 chromosomes, with a mean marker distance of 0.16 cM between adjacent markers. We used this map and the interval mapping (IM) and multiple QTL mapping (MQM) procedures to detect genetic regions associated with quantitative trait for CMV resistance. Three QTLs, qcmv11.1, qcmv11.2 and qcmv12.1, conferred resistance to CMV and showed trait variation of 10.2%, 19.2% and 7.3% respectively. Our results will help to develop markers linked to CMV-resistant QTLs to improve pepper resistance to CMV.

Next-Generation Sequencing Approaches in Genome-Wide Discovery of Single Nucleotide Polymorphism Markers Associated with Pungency and Disease Resistance in Pepper

Pepper is an economically important horticultural plant that has been widely used for its pungency and spicy taste in worldwide cuisines. Therefore, the domestication of pepper has been carried out since antiquity. Owing to meet the growing demand for pepper with high quality, organoleptic property, nutraceutical contents, and disease tolerance, genomics assisted breeding techniques can be incorporated to develop novel pepper varieties with desired traits. The application of next-generation sequencing (NGS) approaches has reformed the plant breeding technology especially in the area of molecular marker assisted breeding. The availability of genomic information aids in the deeper understanding of several molecular mechanisms behind the vital physiological processes. In addition, the NGS methods facilitate the genome-wide discovery of DNA based markers linked to key genes involved in important biological phenomenon. Among the molecular markers, single nucleotide polymorphism (SNP) indulges various benefits in comparison with other existing DNA based markers. The present review concentrates on the impact of NGS approaches in the discovery of useful SNP markers associated with pungency and disease resistance in pepper. The information provided in the current endeavor can be utilized for the betterment of pepper breeding in future.

Rapid identification of QTLs underlying resistance to Cucumber mosaic virus in pepper (Capsicum frutescens)

Next-generation sequencing enabled a fast discovery of QTLs controlling CMV resistant in pepper. The gene CA02g19570 as a possible candidate gene of qCmr2.1 was identified for resistance to CMV in pepper. Cucumber mosaic virus (CMV) is one of the most important viruses infecting pepper, but the genetic basis of CMV resistance in pepper is elusive. In this study, we identified a candidate gene for CMV resistance QTL, qCmr2.1 through SLAF-seq. Segregation analysis in F₂, BC₁ and F_2:3 populations derived from a cross between two inbred lines 'PBC688' (CMV-resistant) and 'G29' (CMV-susceptible) suggested quantitative inheritance of resistance to CMV in pepper. Genome-wide comparison of SNP profiles between the CMV-resistant and CMV-susceptible bulks constructed from an F₂ population identified two QTLs, designated as qCmr2.1 on chromosome 2 and qCmr11.1 on chromosome 11 for resistance to CMV in PBC688, which were confirmed by InDel marker-based classical QTL mapping in the F₂ population. As a major QTL, joint SLAF-seq and traditional QTL analysis delimited qCmr2.1 to a 330 kb genomic region. Two pepper genes, CA02g19570 and CA02g19600, were identified in this region, which are homologous with the genes LOC104113703, LOC104248995, LOC102603934 and LOC101248357, which were predicted to encode N-like protein associated with TMV-resistant in Solanum crops. Quantitative RT-PCR revealed higher expression levels of CA02g19570 in CMV resistance genotypes. The CA02g19600 did not exhibit obvious regularity in expression patterns. Higher relative expression levels of CA02g19570 in PBC688 and F₁ were compared with those in G29 during days after inoculation. These results provide support for CA02g19570 as a possible candidate gene of qCmr2.1 for resistance to CMV in pepper.

Virus diseases of peppers (Capsicum spp.) and their control

The number of virus species infecting pepper (Capsicum spp.) crops and their incidences has increased considerably over the past 30 years, particularly in tropical and subtropical pepper production systems. This is probably due to a combination of factors, including the expansion and intensification of pepper cultivation in these regions, the increased volume and speed of global trade of fresh produce (including peppers) carrying viruses and vectors to new locations, and perhaps climate change expanding the geographic range suitable for the viruses and vectors. With the increased incidences of diverse virus species comes increased incidences of coinfection with two or more virus species in the same plant. There is then greater chance of synergistic interactions between virus species, increasing symptom severity and weakening host resistance, as well as the opportunity for genetic recombination and component exchange and a possible increase in aggressiveness, virulence, and transmissibility. The main virus groups infecting peppers are transmitted by aphids, whiteflies, or thrips, and a feature of many populations of these vector groups is that they can develop resistance to some of the commonly used insecticides relatively quickly. This, coupled with the increasing concern over the impact of over- or misuse of insecticides on the environment, growers, and consumers, means that there should be less reliance on insecticides to control the vectors of viruses infecting pepper crops. To improve the durability of pepper crop protection measures, there should be a shift away from the broadscale use of insecticides and the use of single, major gene resistance to viruses. Instead, integrated and pragmatic virus control measures should be sought that combine (1) cultural practices that reduce sources of virus inoculum and decrease the rate of spread of viruliferous vectors into the pepper crop, (2) synthetic insecticides, which should be used judiciously and only when the plants are young and most susceptible to infection, (3) appropriate natural products and biocontrol agents to induce resistance in the plants, affect the behavior of the vector insects, or augment the local populations of parasites or predators of the virus vectors, and (4) polygenic resistances against viruses and vector insects with pyramided single-gene virus resistances to improve resistance durability.

Vegetable crops in the Mediterranean basin with an overview of virus resistance

The Mediterranean area (MA) produces about 12% of the world vegetables both for local consumption and for export. With an average consumption of 242 kg per person and per year (and almost 400 kg in Turkey), vegetables are an important part of the Mediterranean diet. Vegetables are cultivated using different cultivation techniques (for instance, open field or protected), and the importance of viruses varies greatly between these growing conditions. Breeding virus-resistant cultivars is a key component of an integrated pest management strategy. The origin and the diversity of the main vegetables are presented with the sources of virus resistance. The center of origin of most vegetables is not in the MA: for instance, tomato, potato, pepper, bean, squash and pumpkin, and sweetpotato have been introduced from the American continent. Very few original sources of resistance against viruses have been described in local landraces from the MA.

Molecular mapping and characterization of a single dominant gene controlling CMV resistance in peppers (Capsicum annuum L.)

Cucumber mosaic virus (CMV) is one of the most destructive viruses in the Solanaceae family. Simple inheritance of CMV resistance in peppers has not previously been documented; all previous studies have reported that resistance to this virus is mediated by several partially dominant and recessive genes. In this study, we showed that the Capsicum annuum cultivar 'Bukang' contains a single dominant resistance gene against CMV(Korean) and CMV(FNY) strains. We named this resistance gene Cmr1 (Cucumber mosaic resistance 1). Analysis of the cellular localization of CMV using a CMV green fluorescent protein construct showed that in 'Bukang,' systemic movement of the virus from the epidermal cell layer to mesophyll cells is inhibited. Genetic mapping and FISH analysis revealed that the Cmr1 gene is located at the centromeric region of LG2, a position syntenic to the ToMV resistance locus (Tm-1) in tomatoes. Three SNP markers were developed by comparative genetic mapping: one intron-based marker using a pepper homolog of Tm-1, and two SNP markers using tomato and pepper BAC sequences mapped near Cmr1. We expect that the SNP markers developed in this study will be useful for developing CMV-resistant cultivars and for fine mapping the Cmr1 gene.