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As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.de novo genome sequence | genome expansion | Solanaceae evolution

An improved high-performance liquid chromatography (HPLC) method for analysis of capsaicinoids in dried Capsicum fruit powder, involving changes in extraction, mobile phase, flow rate, and excitation and emission spectra and resulting in reduced analysis time, increased sensitivity, and safety, is reported. Extraction of Capsicum fruit powder using acetonitrile proved to be the best capsaicinoid extractor in the shortest time interval. Solvents used for HPLC separation and quantification of capsaicinoids include methanol and water at 1 ml·min–1 flow rate. Instrument sensitivity is enhanced by altering the fluorescence detector excitation and emission wavelengths. Two analytical methods have been developed. One method determines total amount of heat units in 7 minutes, while the other provides total amount of heat units as well as separation of all present major and minor capsaicinoids in 20 minutes. These improved techniques provide inexpensive and rapid methods for quantitative and qualitative analysis of capsaicinoids in Capsicum fruit samples along with good sensitivity and no interference or confounding peaks.

Pepper, Capsicum spp., is a worldwide crop valued for heat, nutrition, and rich pigment content. Carotenoids, the largest group of plant pigments, function as antioxidants and as vitamin A precursors. The most abundant carotenoids in ripe pepper fruits are β-carotene, capsanthin, and capsorubin. In this study, the carotenoid composition of orange fruited Capsicum lines was defined along with the allelic variability of the biosynthetic enzymes. The carotenoid chemical profiles present in seven orange pepper varieties were determined using a novel UPLC method. The orange appearance of the fruit was due either to the accumulation of β-carotene, or in two cases, due to only the accumulation of red and yellow carotenoids. Four carotenoid biosynthetic genes, Psy, Lcyb, CrtZ-2, and Ccs were cloned and sequenced from these cultivars. This data tested the hypothesis that different alleles for specific carotenoid biosynthetic enzymes are associated with specific carotenoid profiles in orange peppers. While the coding regions within Psy and CrtZ-2 did not change in any of the lines, the genomic sequence contained introns not previously reported. Lcyb and Ccs contained no introns but did exhibit polymorphisms resulting in amino acid changes; a new Ccs variant was found. When selectively breeding for high provitamin A levels, phenotypic recurrent selection based on fruit color is not sufficient, carotenoid chemical composition should also be conducted. Based on these results, specific alleles are candidate molecular markers for selection of orange pepper lines with high β-carotene and therefore high pro-vitamin A levels.

Despite extensive breeding efforts, no pepper (Capsicum annuum L. var. annuum) cultivars with universal resistance to phytophthora root rot and foliar blight (Phytophthora capsici Leon) have been commercially released. A reason for this limitation may be that physiological races exist within P. capsici, the causal agent of phytophthora root rot and phytophthora foliar blight. Physiological races are classified by the pathogen's reactions to a set of cultivars (host differential). In this study, 18 varieties of peppers were inoculated with 10 isolates of P. capsici for phytophthora root rot, and four isolates of P. capsici for phytophthora foliar blight. The isolates originated from pepper plants growing in New Mexico, New Jersey, Italy, Korea, and Turkey. For phytophthora root rot, nine of the 10 isolates were identified as different physiological races. The four isolates used in the phytophthora foliar blight study were all determined to be different races. The identification of physiological races within P. capsici has significant implication in breeding for phytophthora root rot and phytophthora foliar blight resistance.

A differential series is the normal method for identification of races within a plant pathogen and a host interaction. A host differential is extremely useful for phytopathological as well as breeding purposes. A set of recombinant inbred lines (RILs) were developed and characterized for race differentiation of Phytophthora root rot caused by Phytophthora capsici. The highly resistant Capsicum annuum accession Criollo de Morelos-334 was hybridized to a susceptible cultivar, Early Jalapeno, to generate the RIL population. The host differential characterized 17 isolates of P. capsici into 13 races. The establishment of a stable host differential for the P. capsici and C. annuum interaction will assist researchers in understanding the complex inheritance of resistance to Phytophthora root rot and to develop resistant cultivars.

A global collection of 123 putative isolates of Fusarium oxysporum from crucifers was examined for pathogenicity, isozyme polymorphism, and vegetative compatibility. Of these isolates, 103 were found to be pathogenic on one or more of six differential crucifer cultivars. Three patterns of isozyme polymorphism (electrophoretic types) were found and by means of a nitrate reductase complementation test, three major vegetative compatibility groups were identified that could differentiate among the F. oxysporum pathotypes. Complete correspondence was found among pathotype, electrophoretic type, and vegetative compatibility. It seems appropriate to classify isolates from the Cruciferae into the subspecific taxa, F. oxysporum f.sp. conglutinans, F. oxysporum f.sp. raphani, and F. oxysporum f.sp. matthioli, based on their naturally infected host species, Brassica oleracea, Raphanus sativus, and Matthiola incana, and on estimates of genetic identity. Within formae speciales, races can be identified based on intraspecific host specialization. Geographic origin was not found to be associated with the vegetative compatibility, isozyme phenotype, or pathotype. Isozyme polymorphisms also differentiated among four F. oxysporum formae speciales from other host families and among various Fusarium species.

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