Interspecific genetic variation was examined in the genus Capsicum based on shared restriction fragments in Southern analyses. Four distinct clusters were delineated among 21 accessions of cultivated and wild pepper (C. annuum, C. baccatum, C. chacoense, C. chinense, and C. frutescens). Three tight clusters comprised of accessions belonging to C. annuum, C. frutescens, and C. baccatum, respectively, were formed, along with a fourth cluster comprised of one accession each of C. chinense and C. chacoense. All accessions were differentiated by this technique, and the clusters corresponded closely to previous morphology-based classification. Sufficient DNA polymorphism exists among these accessions that segregating populations useful for restriction fragment length polymorphism (RFLP) mapping could be constructed using any two pepper accessions as parents. Regression analysis indicates that genetic distance is a good predictor (R2 = 0.872) of the level of mappable DNA polymorphism in Capsicum. Intraspecific variability was examined among four C. annuum cultivars (NuMex R Naky, Jupiter, Perennial, and Criollo de Morelos 334) using both RFLPs and randomly amplified polymorphic DNA (RAPDs), allowing a comparative evaluation of the two techniques. Seventeen percent of the clones used singly in RFLP analyses were sufficient for the differentiation of these varieties, as were 12.5% of the RAPD PCR amplifications. Dendrograms constructed from RFLP and RAPD analyses of the intraspecific data are similar but not identical. Southern analysis and RAPD PCR should be useful for DNA fingerprinting and the discrimination of closely related C. annuum genotypes.

We have created a genetic map of Capsicum (pepper) from an interspecific F2 population consisting of 11 large (76.2–192.3 cM) and 2 small (19.1 and 12.5 cM) linkage groups that cover a total of 1245.7 cM. Many of the markers are tomato probes that were chosen to cover the tomato genome, allowing comparison of this pepper map to the genetic map of tomato. Hybridization of all tomato-derived probes included in this study to positions throughout the pepper map suggests that no major losses have occurred during the divergence of these genomes. Comparison of the pepper and tomato genetic maps showed that 18 homeologous linkage blocks cover 98.1% of the tomato genome and 95.0% of the pepper genome. Through these maps and the potato map, we determined the number and types of rearrangements that differentiate these species and reconstructed a hypothetical progenitor genome. We conclude there have been 30 breaks as part of 5 translocations, 10 paracentric inversions, 2 pericentric inversions, and 4 disassociations or associations of genomic regions that differentiate tomato, potato, and pepper, as well as an additional reciprocal translocation, nonreciprocal translocation, and a duplication or deletion that differentiate the two pepper mapping parents.

Two unlinked, recessive loci have been characterized in Capsicum spp. that independently confer distinct types of resistance to pepper mottle potyvirus (PepMoV). The first locus, from C. annuum cv. Avelar, affected the spread of PepMoV through the plant and had no discernible effect on tobacco etch potyvirus (HAT isolate; TEV-HAT) infection (J. F. Murphy and M. K. Kyle, Phytopathology 85:561-566, 1995). The second locus, found in C. chinense PI 159236 and PI 152225, interfered with PepMoV and TEV-HAT infection in plants and in isolated protoplasts. The resistant responses displayed by the C. chinense accessions to PepMoV and TEV-HAT appeared indistinguishable; however, these accessions were both susceptible to a second isolate of TEV, TEV-Mex21. We propose the symbols pvr1 for recessive PepMoV and TEV resistance from the C. chinense accessions and pvr3 for recessive PepMoV resistance from Avelar. pvr1 has been genetically mapped to a small linkage group with synteny to the short arm of tomato chromosome 3.

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A small-fruited pungent pepper accession, Capsicum frutescens ‘BG2814-6’, is resistant to several isolates of Cucumber mosaic virus (CMV). Resistance in BG2814-6 is incompletely penetrant and is controlled by at least two major recessive genes. The accession BG2814-6 and C. annuum ‘Perennial’, the leading source of CMV tolerance, appear to share one or more CMV resistance genes. CMV was detected in uninoculated leaves in a small percentage of both BG2814-6 and Perennial plants, indicating that resistance is not absolute in either genotype. Enzyme-linked immunosorbent assay absorbance values of samples taken from inoculated leaves corresponded well with visible viral symptoms for parental genotypes. While Perennial plants accumulated CMV antigen in inoculated leaves, CMV antigen was not detected in inoculated leaves of 73% of BG2814-6 plants, suggesting that there may be a mechanistic difference in resistance between the two genotypes.