Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers

A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 landraces derived from natural interspecific crosses. Out of 106 SSR markers, 25 polymorphic SSR markers (24 %) detected a total of 76 alleles (average, 3.04; range, 2–5). The average polymorphic information content (PIC) was 0.69 (range, 0.29–0.92). Seventeen RAMPO markers produced 87 polymorphic fragments with average PIC of 0.63 (range, 0.44–0.81). Dendrograms based on SSRs and RAMPOs generated two clusters. All 38 Capsicum annuum genotypes and an interspecific landrace clustered together, whereas nine non-annuum (three Capsicum frutescens, one Capsicum chinense, one Capsicum baccatum and four interspecific landraces) genotypes clustered separately. Genetic variation within non-annuum genotypes was greater than the C. annuum genotypes. Distinctness of interspecific derivative landraces grown in northeast India was validated; natural crossing between sympatric Capsicum species has been proposed as the mechanism of their origin.     

Pepper Rootstock Graft Compatibility and Response to Meloidogyne javanica and M. incognita

Resistance of pepper species (Capsicum annuum, C. baccatum, C. chinense, C. chacoense, and C. frutescens), cultivars and accessions to the root-knot nematodes Meloidogyne incognita race 2 and M. javanica, and their graft compatibility with commercial pepper varieties as rootstocks were evaluated in growth chamber and greenhouse experiments. Most of the plants tested were highly resistant to M. javanica but susceptible to M. incognita. Capsicum annuum AR-96023 and C. frutescens accessions as rootstocks showed moderate and relatively high resistance to M. incognita, respectively. In M. incognita-infested soil in a greenhouse, AR-96023 supported approximately 6-fold less nematode eggs per gram root and produced about 2-fold greater yield compared to a nongrafted commercial variety. The commercial variety grafted on AR-96023 produced a yield as great as the non-grafted variety in the root-knot nematode-free greenhouse. Some resistant varieties and accessions used as rootstocks produced lower yields (P < 0.01) than that of the non-grafted variety in the noninfested greenhouse. Use of rootstocks with nematode-resistance and graft compatibility may be effective for control of root-knot nematodes on susceptible pepper.     

Root-knot nematode (Meloidogyne spp.) Me resistance genes in pepper (Capsicum annuum L.) are clustered on the P9 chromosome

The root-knot nematode (Meloidogyne spp.) is a major plant pathogen, affecting several solanaceous crops worldwide. In Capsicum annuum, resistance to this pathogen is controlled by several independent dominant genes—the Me genes. Six Me genes have previously been shown to be stable at high temperature in three highly resistant and genetically distant accessions: PI 322719, PI 201234, and CM334 (Criollo de Morelos 334). Some genes (Me4, Mech1, and Mech2) are specific to certain Meloidogyne species or populations, whereas others (Me1, Me3, and Me7) are effective against a wide range of Meloidogyne species, including M. arenaria, M. javanica, and M. incognita, the most common species in Mediterranean and tropical areas. These genes direct different response patterns in root cells depending on the pepper line and nematode species. Allelism tests and fine mapping using the BSA-AFLP approach showed these genes to be different but linked, with a recombination frequency of 0.02–0.18. Three of the PCR-based markers identified in several genetic backgrounds were common to the six Me genes. Comparative mapping with CarthaGene software indicated that these six genes clustered in a single genomic region within a 28 cM interval. Four markers were used to anchor this cluster on the P9 chromosome on an intraspecific reference map for peppers. Other disease resistance factors have earlier been mapped in the vicinity of this cluster. This genomic area is colinear to chromosome T12 of tomato and chromosome XII of potato. Four other nematode resistance genes have earlier been identified in this area, suggesting that these nematode resistance genes are located in orthologous genomic regions in Solanaceae.     

Development of sequence characterized amplified region (SCAR) primers for the detection of Phyto.5.2, a major QTL for resistance to Phytophthora capsici Leon. in pepper

Phytophthora capsici causes devastating disease on many crop species, including Capsicum. Resistance in Capsicum annuum is genetically and physiologically complex. A panel of Capsicum germplasm that included genotypes from both C. annuum and C. chinense showing highly resistant, highly susceptible and intermediate or tolerant responses to the pathogen, respectively, was screened with a series of randomly amplified polymorphic sequence primers to determine which genomic regions contribute to the highest level of resistance. One primer, OpD04, amplified a single band only in those C. annuum and C. chinense genotypes showing the highest level of resistance. The amplified product was cloned, sequenced and used to design longer primers in order to generate a sequence characterized amplified region marker which was then mapped in a reference mapping population and a screened population segregating for resistance to P. capsici. These primers were observed to define a locus on pepper chromosome 5 tightly linked to Phyto.5.2, one of six quantitative trait loci (QTL) previously reported to contribute to P. capsici resistance. These results indicate that the Phyto.5.2 QTL may be widely distributed in highly resistant germplasm and provide improved resolution for this QTL. This work also defines the first breeding tools for this system, allowing for the rapid selection of genotypes likely to be highly resistant to P. capsici.     

Diversity of genetic backgrounds modulating the durability of a major resistance gene. Analysis of a core collection of pepper landraces resistant to Potato virus Y

The evolution of resistance‐breaking capacity in pathogen populations has been shown to depend on the plant genetic background surrounding the resistance genes. We evaluated a core collection of pepper (Capsicum annuum) landraces, representing the worldwide genetic diversity, for its ability to modulate the breakdown frequency by Potato virus Y of major resistance alleles at the pvr2 locus encoding the eukaryotic initiation factor 4E (eIF4E). Depending on the pepper landrace, the breakdown frequency of a given resistance allele varied from 0% to 52.5%, attesting to their diversity and the availability of genetic backgrounds favourable to resistance durability in the plant germplasm. The mutations in the virus genome involved in resistance breakdown also differed between plant genotypes, indicating differential selection effects exerted on the virus population by the different genetic backgrounds. The breakdown frequency was positively correlated with the level of virus accumulation, confirming the impact of quantitative resistance loci on resistance durability. Among these loci, pvr6, encoding an isoform of eIF4E, was associated with a major effect on virus accumulation and on the breakdown frequency of the pvr2‐mediated resistance. This exploration of plant genetic diversity delivered new resources for the control of pathogen evolution and the increase in resistance durability.     

Metabolomics and molecular marker analysis to explore pepper (Capsicum sp.) biodiversity

An overview of the metabolic diversity in ripe fruits of a collection of 32 diverse pepper (Capsicum sp.) accessions was obtained by measuring the composition of both semi-polar and volatile metabolites in fruit pericarp, using untargeted LC–MS and headspace GC–MS platforms, respectively. Accessions represented C. annuum, C. chinense, C. frutescens and C. baccatum species, which were selected based on variation in morphological characters, pungency and geographic origin. Genotypic analysis using AFLP markers confirmed the phylogenetic clustering of accessions according to Capsicum species and separated C. baccatum from the C. annuum–C. chinense–C. frutescens complex. Species-specific clustering was also observed when accessions were grouped based on their semi-polar metabolite profiles. In total 88 semi-polar metabolites could be putatively identified. A large proportion of these metabolites represented conjugates of the main pepper flavonoids (quercetin, apigenin and luteolin) decorated with different sugar groups at different positions along the aglycone. In addition, a large group of acyclic diterpenoid glycosides, called capsianosides, was found to be highly abundant in all C. annuum genotypes. In contrast to the variation in semi-polar metabolites, the variation in volatiles corresponded well to the differences in pungency between the accessions. This was particularly true for branched fatty acid esters present in pungent accessions, which may reflect the activity through the acyl branch of the metabolic pathway leading to capsaicinoids. In addition, large genetic variation was observed for many well-established pepper aroma compounds. These profiling data can be used in breeding programs aimed at improving metabolite-based quality traits such as flavour and health-related metabolites in pepper fruits.     

Double mutations in eIF4E and eIFiso4E confer recessive resistance to <Emphasis Type="Italic">Chilli veinal mottle virus</Emphasis> in pepper

To evaluate the involvement of translation initiation factors eIF4E and eIFiso4E in Chilli veinai mottle virus (ChiVMV) infection in pepper, we conducted a genetic analysis using a segregating population derived from a cross between Capsicum annuum ‘Dempsey’ containing an eIF4E mutation (pvr1 ² ) and C. annuum ‘Perennial’ containing an eIFiso4E mutation (pvr6). C. annuum ‘Dempsey’ was susceptible and C. annuum ‘Perennial’ was resistant to ChiVMV. All F₁ plants showed resistance, and F₂ individuals segregated in a resistant-susceptible ratio of 166:21, indicating that many resistance loci were involved. Seventy-five F₂ and 329 F₃ plants of 17 families were genotyped with pvr1 ² and pvr6 allele-specific markers, and the genotype data were compared with observed resistance to viral infection. All plants containing homozygous genotypes of both pvr1 ² and pvr6 were resistant to ChiVMV, demonstrating that simultaneous mutations in eIF4E and eIFiso4E confer resistance to ChiVMV in pepper. Genotype analysis of F2 plants revealed that all plants containing homozygous genotypes of both pvr1 ² and pvr6 showed resistance to ChiVMV. In protein-protein interaction experiments, ChiVMV viral genome-linked protein (VPg) interacted with both eIF4E and eIFiso4E. Silencing of eIF4E and eIFiso4E in the VIGS experiment showed reduction in ChiVMV accumulation. These results demonstrated that ChiVMV can use both eIF4E and eIFiso4E for replication, making simultaneous mutations in eIF4E and eIFiso4E necessary to prevent ChiVMV infection in pepper. These authors contributed equally to this work.     

New Insights into Capsicum spp Relatedness and the Diversification Process of Capsicum annuum in Spain

The successful exploitation of germplasm banks, harbouring plant genetic resources indispensable for plant breeding, will depend on our ability to characterize their genetic diversity. The Vegetable Germplasm Bank of Zaragoza (BGHZ) (Spain) holds an important Capsicum annuum collection, where most of the Spanish pepper variability is represented, as well as several accessions of other domesticated and non-domesticated Capsicum spp from all over the five continents. In the present work, a total of 51 C. annuum landraces (mainly from Spain) and 51 accessions from nine Capsicum species maintained at the BGHZ were evaluated using 39 microsatellite (SSR) markers spanning the whole genome. The 39 polymorphic markers allowed the detection of 381 alleles, with an average of 9.8 alleles per locus. A sizeable proportion of alleles (41.2%) were recorded as specific alleles and the majority of these were present at very low frequencies (rare alleles). Multivariate and model-based analyses partitioned the collection in seven clusters comprising the ten different Capsicum spp analysed: C. annuum, C. chinense, C. frutescens, C. pubescens, C. bacatum, C. chacoense and C. eximium. The data clearly showed the close relationships between C. chinense and C. frutescens. C. cardenasii and C. eximium were indistinguishable as a single, morphologically variable species. Moreover, C. chacoense was placed between C. baccatum and C. pubescens complexes. The C. annuum group was structured into three main clusters, mostly according to the pepper fruit shape, size and potential pungency. Results suggest that the diversification of C. annuum in Spain may occur from a rather limited gene pool, still represented by few landraces with ancestral traits. This ancient population would suffer from local selection at the distinct geographical regions of Spain, giving way to pungent and elongated fruited peppers in the South and Center, while sweet blocky and triangular types in Northern Spain.     

A SNP-based genetic linkage map of <Emphasis Type="Italic">Capsicum baccatum</Emphasis> and its comparison to the <Emphasis Type="Italic">Capsicum annuum</Emphasis> reference physical map

Capsicum baccatum L., one of five domesticated species of Capsicum, is a valuable species in chili pepper breeding. In particular, it is a source of disease resistance against anthracnose and powdery mildew. Genetic maps and molecular markers are important to improve the efficiency of crop breeding programs. Recently, using genetic maps several researchers have identified quantitative trait loci (QTLs) for important horticultural traits and have cloned genes of interest. In this study, we constructed a genetic map of C. baccatum in an intraspecific population from a cross between ‘Golden-aji’ and ‘PI594137.’ A total of 395 high-resolution melting markers were developed based on single-nucleotide polymorphisms identified by comparing genome sequences generated through next-generation resequencing of the parents, ‘Golden-aji’ and ‘PI594137.’ The genetic linkage map contained 12 linkage groups, covered a total distance of 1056.2 cM, and had an average distance of 2.67 cM between markers. In addition, the final map was compared to the reference physical map of C. annuum ‘CM334.’ Interestingly, two major reciprocal translocations between chromosomes 3 and 5 and between chromosomes 3 and 9 were found, suggesting that these translocations might act as a genetic barrier between C. annuum and C. baccatum. Translocations between chromosomes 1 and 8 were also observed, as were previously reported in C. chinense, C. frutescens, and wild C. annuum. The synteny of other chromosomes was maintained, on the whole, except for several small inversions. The information on this genetic map will be helpful to analyze QTLs for important traits such as anthracnose resistance in C. baccatum and to study the causes of genetic barriers between C. annuum and C. baccatum.     

Conservation of floral,fruit and chromosomal diversity: a review on diploid and polyploid Capsicum annuum complex in India

Capsicum as a spice crop, has wild and cultivated forms admired globally, including Indian subcontinent with vast climatic ranges. Systematic representation of the Indian Capsicum is required to address species relationships and sustainable agriculture, in face of unpredictable climatic conditions. We have updated the catalogue of Indian ‘C. annuum complex’ with 28 landraces and populations from different agro-climatic regions. The agro-climatic influence on the origin of stable chili landraces in India is remarkable, especially in the North East. The floral and fruit morphotype standards and chromosomal attributes have been considered for four distinct ‘C. annuum complex’ members under three species. The highlights of study are: (1) comparative profiling of Indian Capsicum species revealing less infraspecific variation within C. frutescens and C. chinense than C. annuum, at par with cultivation status, (2) karyotype analysis of some unique diploid landraces of C. annuum, (3) karyotypic confirmation of the polyploid Dalle Khursani landraces exclusive to India. To obtain more information, we attempted to correlate diversity of fruit and floral morphotype with chromosomal diversity. Existence of elite and rare germplasm found in the regional pockets offer great scope for enriching the agricultural tradition. The present dataset may serve as a template to be continuously upgraded by taxonomists, genomicists and breeders.

     

Comparison of resistance to potyviruses within Solanaceae: infection of potatoes with tobacco etch potyvirus and peppers with potato A and Y potyviruses

The reaction of several cultivated potato varieties (Solarium tuberosum L.) to three strains of tobacco etch potyvirus (TEV-F, TEV-Mex21 and TEV-ATCC) and the reaction of several pepper lines (Capsicum annuum L. and C. chinense L.) to two strains of potato Y potyvirus (PVY^O and PVY^N) and one strain of potato A potyvirus (PVA-M) was tested. The potato varieties included in this study carried resistance genes against PVY, PVA and potato V potyvirus, but all were susceptible to TEV and developed mottle and mosaic symptoms. TEV was readily transmitted by mechanical inoculation from tobacco and potato to potato, whereas transmission from pepper to potato occurred infrequently. TEV was transmitted through potato tubers, and from pepper to potato plants by aphids. Lack of detectable systemic infection following graft-inoculation indicated extreme resistance to PVY^O and PVA in several pepper lines. No pepper line was systemically infected with PVY^N following mechanical inoculation (graft-inoculation was not carried out with PVY^N). The development of necrotic lesions following mechanical and graft-inoculation indicated hypersensitive response to PVY^O in several pepper lines which resembled the resistance responses to these potyvirus strains in potato. Results of this study together with previous work indicate that C. annuum cv. Avelar is resistant to four potyviruses [PVY, PVA, pepper mottle potyvirus (PepMoV) and some isolates of TEV]; C. annuum cv. Criollo de Morelos and C. chinense PI 152225 and PI 159236 are resistant to three potyviruses (PVY, PepMoV and PVA; and PVY, PepMoV and TEV, respectively); C. annuum 9093–1 and 92016–1 are resistant to PVY and PepMoV; and C. annuum cv. Jupiter and C. annuum cv. RNaky are resistant to PVY^N and PVA.     

Development of simple sequence repeat markers and construction of a high-density linkage map of Capsicum annuum

To facilitate marker-assisted breeding and genetic analyses of pepper (Capsicum annuum), we developed non-redundant 2- or 3-base simple sequence repeat (SSR) markers from enriched C. annuum genomic libraries and from C. annuum cDNA sequences in public databases. The SSR-enriched libraries were constructed using combinations of three restriction enzymes (AluI, HaeIII, and RsaI) and two biotinylated oligonucleotides [b(GA)₁₅ and b(CA)₁₅]. Ultimately, we obtained 1,736 genomic SSR markers and 1,344 cDNA-derived SSR markers from 6,528 clones and 13,003 sequences, respectively. We mapped 597 markers, including 265 of the newly developed SSR markers, onto a linkage map by using doubled-haploid (DH) lines derived from an intraspecific cross of two pure lines of C. annuum (K9-11 × MZC-180). The map, designated as the KL-DH map, consisted of 12 linkage groups. The map covered a genetic distance of 2,028 cM, and the average distance between markers was less than 4 cM. The frame structure of the KL-DH map was compared with the published standard conserved ortholog set II (COSII) map, which was derived from an interspecific F₂ population (C. frutescens × C. annuum), by using tomato (Solanum lycopersicum) chromosomal sequences to bridge the two maps. The intraspecific KL-DH map constructed in this study and the interspecific COSII map were similar in map length and marker distribution, suggesting that the KL-DH map covers nearly the whole genome of C. annuum.     

An SSR-based linkage map of Capsicum annuum

There are five cultivated species of pepper, of which Capsicum annuum is the most widely cultivated as a vegetable or spice and the main experimental material of most pepper breeding programs. However, the number of simple sequence-repeat (SSR) markers known for C. annuum is limited. To develop SSR markers for Capsicum species, we constructed four SSR-enriched libraries from the genomic DNA of C.␣annuum, sequenced 1873 clones, and isolated 626 unique SSR clones. A higher percentage of these SSR markers were taken from dinucleotide motif libraries than from trinucleotide motif libraries. Primer pairs for the 626 SSR clones were synthesized and tested for polymorphisms; 594 amplified products were detected with the expected size. However, only 153 products were polymorphic between the parents of our mapping population. Using 106 highly reproducible pairs from the primer pairs, we constructed a linkage map of C. annuum in an intraspecific doubled haploid population (n=117) that contains nine previously reported SSRs as well as AFLP, CAPS, and RAPD markers and the trait of fruit pungency. The map contains 374 markers, including 106 new SSR markers distributed across all 13 linkage groups, and covers 1042 cM. The polymorphism information content (PIC) of these new SSR markers was calculated using 14 lines of Capsicum species. The average number of alleles per locus was 2.9 and the average PIC value was 0.46, even within C. annuum. The SSR markers developed in this study will be useful for mapping and marker-assisted selection in pepper breeding, and the linkage map provides a reference genetic map for Capsicum species.     

Genome-wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding

In this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping-by-sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome-wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability.     

Polymorphic Microsatellite Markers Transferable Across <Emphasis Type="Italic">Capsicum</Emphasis> Species

Pepper (Capsicum annuum L.) is one of the most important crops in the family Solanaceae. However, the number of polymorphic molecular loci detected in this important crop is far behind that of other cultivated plant species. In the present study, a total of 45 microsatellite primer pairs were developed using Capsicum expressed sequence tags databases. Microsatellite primer pairs were tested using several species of Capsicum and several genera in the family Solanaceae including tomato, potato, eggplant, and tobacco. Results indicated that microsatellite primer pairs amplified genomic targets of C. annuum L., Capsicum baccatum L., Capsicum chacoense L., Capsicum chinense L., Capsicum frutescens L., and Capsicum pubescens Ruiz et Pavon, indicating species transferability within Capsicum. Further analyses revealed that amplicons of these primer pairs segregated 1:2:1 or 3:1 Mendelian fashions in 38 F₂ individuals of pepper. It was also noted that markers derived from sequences containing dinucleotide repeats were generally more polymorphic at the intraspecific level than sequences containing trinucleotide repeats. All the microsatellite primer pairs developed in this study will be useful for marker-assisted selection and mapping studies in pepper.     

Genetic Variability in Pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis> L.) Estimated by Morphological Data and Amplified Fragment Length Polymorphism Markers

Data on genetic similarity among crop cultivars is of vital importance for the plant breeder. The objectives of this study were to group pepper (Capsicum annuum L.) genotypes into clusters according to their distances as estimated by morphological traits and amplified fragment length polymorphism (AFLP) markers and to assess the relationships between the two. Thirty-nine pepper genotypes obtained from different countries were grown in the greenhouse at University of the Free State, South Africa, during 2001 and 2002 in a randomized complete block design with three replications. A total of 20 different morphological traits were measured and six AFLP primer pairs were used to estimate pairwise genetic distances. Both datasets showed high genetic distances among the different genotypes, indicating high genetic diversity among them. The mean genetic distance among Ethiopian pungent elongated-fruit genotypes, was lower than that between them and the introduced ones. Morphological and AFLP distance estimations generally clustered together genotypes with similar fruit sizes. Significant, positive correlation was observed between morphological and AFLP diversity estimations. The narrow genetic basis among the Ethiopian pungent elongated-fruit cultivars suggests that the pepper breeding program of Ethiopia should focus on enriching its germplasm through local collection and introductions from other parts of the world.     

Construction of an integrated pepper map using RFLP,SSR, CAPS,AFLP, WRKY,rRAMP, and BAC end sequences

Map-based cloning to find genes of interest, markerassisted selection (MAS), and marker-assisted breeding (MAB) all require good genetic maps with high reproducible markers. For map construction as well as chromosome assignment, development of single copy PCR-based markers and map integration process are necessary. In this study, the 132 markers (57 STS from BAC-end sequences, 13 STS from RFLP, and 62 SSR) were newly developed as single copy type PCR-based markers. They were used together with 1830 markers previously developed in our lab to construct an integrated map with the Joinmap 3.0 program. This integrated map contained 169 SSR, 354 RFLP, 23 STS from BAC-end sequences, 6 STS from RFLP, 152 AFLP, 51 WRKY, and 99 rRAMP markers on 12 chromosomes. The integrated map contained four genetic maps of two interspecific (Capsicum annuum ‘TF68’ and C. chinense ‘Habanero’) and two intraspecific (C. annuum ‘CM334’ and C. annuum ‘Chilsungcho’) populations of peppers. This constructed integrated map consisted of 805 markers (map distance of 1858 cM) in interspecific populations and 745 markers (map distance of 1892 cM) in intraspecific populations. The used pepper STS were first developed from end sequences of BAC clones from Capsicum annuum ‘CM334’. This integrated map will provide useful information for construction of future pepper genetic maps and for assignment of linkage groups to pepper chromosomes.     

Selection, biological properties and fitness of resistance-breaking strains of Tomato spotted wilt virus in pepper

In glasshouse tests, infective sap from plants infected with 17 different isolates of Tomato spotted wilt virus (TSWV) from four Australian states was inoculated to three Capsicum chinense accessions (PI 152225, PI 159236 and C00943) carrying single genes that confer hypersensitive resistance to TSWV. The normal response to inoculation was development of necrotic (hypersensitive) local lesions in inoculated leaves without systemic invasion, but 3/1386 infected plants also developed systemic susceptible reactions in addition to hypersensitive ones. Similarly when two isolates were inoculated to C. chinense backcross progeny plants, 1/72 developed systemic susceptible reactions in addition to localised hypersensitive ones. Using cultures from the four plants with susceptible reactions and following three to five further cycles of serial subculture in TSWV‐resistant C. chinense plants, four isolates were obtained that gave systemic susceptible type reactions in the three TSWV‐resistant accessions, and in TSWV‐resistant cultivated pepper (C. annuum). When three of these isolates were inoculated to tomato (Lycopersicon esculentum) breeding lines with single gene resistance to TSWV, resistance was not overcome. Similarly, none of the four isolates overcame partial resistance to TSWV in Lactuca virosa. When TSWV isolates were inoculated to tomato breeding lines carrying partial resistance from L. chilense, systemic infection developed which was sometimes followed by ‘recovery’. After four successive cycles of serial passage in susceptible cultivated pepper of a mixed culture of a resistance‐breaking isolate with the non resistance‐breaking isolate from which it came, the resistance‐breaking isolate remained competitive as both were still found. However, when the same resistance‐ breaking isolate was cultured alone, evidence of partial reversion to wild‐type behaviour was eventually obtained after five but not four cycles of long term serial subculture in susceptible pepper, as by then the culture had become a mixture of both types of strain. This work suggests that resistance‐breaking strains of TSWV that overcome single gene hypersensitive resistance in pepper are relatively stable. The findings have important implications for situations where resistant pepper cultivars are deployed widely in the field without taking other control measures as part of an integrated TSWV management strategy.     

Physical mapping of NBS-coding resistance genes to the <Emphasis Type="Italic">Me</Emphasis>-gene cluster on chromosome P9 reveals markers tightly linked to the <Emphasis Type="Italic">N</Emphasis> gene for root-knot nematode resistance in pepper

Natural root-knot nematode resistance genes are unique resources to control this major pest in pepper (Capsicum annuum). Although four genes (Me1, Me3, Me7 and N) conferring broad-spectrum resistance were mapped to a cluster in a 28-cm interval on chromosome P9, limited markers targeting this region were available. In the present study, the Me-gene cluster was structurally annotated for resistance genes to develop markers targeting the N gene. As a result, the Me-gene cluster (4.07 Mb in size) was found to contain three resistance gene hotspots. In addition, a SSR maker tightly linked to the N gene (0.8 cM away) was developed for marker-assisted selection in pepper.     

Responses of pepper to waterlogging stress

One of the effective ways to address the effects of abnormal climate change on plant is to find germplasms that have better resistance to adverse environments. In this paper, we studied the responses of 5 pepper species Capsicum annuum L. (CA), C. baccatum L. (CB), C. chinense Jacquin. (CC), C. frutescens L. (CF) and C. pubescens Ruiz & Pavon (CP) as well as a wild pepper C. baccatum var. baccatum (CBY) to waterlogging stress. The results showed that warterlogging treatment greatly decreases photosynthetic pigment content, net photosynthetic rate (P _N) and stomatal conductance (g _s), and dramatically increases proline content and water-use efficiency (WUE) in all tested pepper, suggesting that pepper has weak resistance to waterlogging stress. The results also showed that changes of the above parameters vary in different species. CP had the smallest decreases in photosynthetic pigment content, P _N, and g _s and greatest increases in proline content and WUE. By contrast, CC had the greatest decreases in photosynthetic pigment content, P _N, and g _s and smallest increases in proline content and WUE, indicating that different species had different resistance to adverse environment and species CP and CC had the strongest and the weakest resistances, respectively. In addition, the study also demonstrated that wild pepper CBY had better resistance to adverse environment than all the tested species, indicating loss of the stress resistance genes during the process of domestication. Taking together, our study strongly suggests that pepper species should crossbreed with other species and wild pepper to expand genetic diversity, enlarge genetic distance, promote production, and improve the resistance to adverse environments.