Paul W. Bosland

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

Significance The two pepper genomes together with 20 resequencing accessions, including 3 accessions that are classified as semiwild/wild, provide a better understanding of the evolution, domestication, and divergence of various pepper species and ultimately, will enhance future genetic improvement of this important worldwide crop. 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.

Evaluation of genotype, environment, and genotype-by-environment interaction for capsaicinoids in Capsicum annuum L.

The response, in terms of capsaicinoid content, of chile (Capsicum annuum L.) genotypes to different environments was studied. Double haploidlines, an F1 hybrid, and an open-pollinated cultivar estimated the genotype, environment, and genotype-by-environment interaction effect on the total capsaicinoids and on individual capsaicinoids. Significant differences were observed among the genotypes and among genotype-by-environment interactions over the environments. Among the genotypes in an environment, the within-genotype variances were also significantly different. The double haploid line, HDA 207, had low within-genotype variance for individual and total capsaicinoids, with the exception of the isomer of dihydrocapsaicin. Also for HDA 270, the genotype-by-environment interaction was negligible for individual and total capsaicinoids, Indicating stability across environments.

Capsaicinoid profiles are not good chemotaxonomic indicators for Capsicum species.

Capsaicinoids have been suggested as an aid in identifying Capsicum species. The distribution of seven capsaicinoids and their chemotaxonomic significance were examined within nearly 200 accessions of six Capsicum species. The seven capsaicinoids were separated and quantified using high-performance liquid chromatography. The capsaicinoid profiles were not consistent when examined within a species, therefore they have limited use as a chemotaxonomic indicator. In addition, the generalization that capsaicin and dihydrocapsaicin are always the major capsaicinoids was not true, exceptions were found for some of the accessions studied.

Recombinant Inbred Line Differential Identifies Race-Specific Resistance to Phytophthora Root Rot in Capsicum annuum

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.

Establishing a core collection of Capsicum using a cluster analysis with enlightened selection of accessions

A core collection represents the genetic diversity of a crop with minimal redundancy. A technique is proposed for establishing a representative core collection of Capsicum annuum L., C. chinense Jacq., and C. baccatum L. from the collection maintained at the Southern Plant Genetic Resources Conservation Unit, Griffin, GA, U.S.A. The accessions were stratified by species, and then cluster analyses were performed on the GRIN data for morphological descriptors of a given species. Three selection methods to form a core collection of approximately 10% of the collections were compared. Selecting one accession (equal number) from each cluster using either a random or a systematic selection procedure did not include all the existing morphological diversity. However, a third method, where selecting systematically a number of accessions per cluster based on the presence of unique traits allowed 100% of the known morphological diversity to be retained in the core collections of the three species.

Genetic Diversity of Chile (Capsicum Annuum Var. Annuum L.) Landraces from Northern New Mexico, Colorado, and Mexico

Four hundred years of chile(Capsicum annuum var.annuum) cultivation, together with concerns about losing genetic resources in their native agrohabitats, provide the pretext for collecting and preserving landraces of this species in New Mexico. The molecular analysis of these accessions provided a powerful means by which their genetic structures were characterized. Random amplified polymorphic DNA (RAPD) molecular markers were used to compare the relative genetic diversity of native chile landraces to the genetic diversity found in commercially available cultivars in the United States as well as landraces from Mexico.

Genetic diversity and similarity revealed via molecular analysis among and within an in situ population and ex situ accessions of chiltepín (Capsicum annuum var. glabriusculum)

Molecular analysis of genetic diversity amongand within phenotypically similar wild Capsicum annuum var. glabriusculum(chile) populations revealed geneticdifferences among accessions spread over abroad geographic range. These chiles areregionally known as chiltepíns and are a 50metric ton per year wild harvest for the spiceindustry, as well as a genetic resource forcrop improvement. Understanding geneticvariability in this species providesinformation related to conservation efforts. The objective of this research was to surveygenetic diversity among and within an insitu population and ex situ accessionsof chiltepíns. Random AmplifiedPolymorphic DNA (RAPD) molecular markers wereused to study the genetic structure of an in situ population found at the nothernmostrange of this species and ex situaccessions collected from Mexico and Guatemala. Novel genetic variation was found in both thein situ northern disjunct population, aswell as some ex situ accessions, thussupporting conservation of this species viaboth in situ and ex situ strategies The evidence presented here supports effortsto conserve outlier populations via insitu management practices.

Capsicum tovarii, a new member of the Capsicum baccatum complex

Interspecific hybrid performance and meiotic chromosome behavior of F1 hybrids were studied to elucidate the genetic relationship between C. tovarii and the other Capsicum species. C. tovarii was hybridized, as a female and a male parent, to C. annuum, C. chinense, C. frutescens, C. chacoense, C. galapogense, C. baccatum, C. praetermissum, C. cardenasii, C. eximium and C. pubescens. When the hybridization of C. baccatum × C. tovarii was performed, F1, F2 and backcross progenies were successfully obtained. In addition, a successful hybridization of C. praetermissum × C. tovarii was also obtained. A cytological investigation of F1 hybrids of C. baccatum × C. tovarii revealed that most meiotic chromosomes paired as bivalents. However, multivalents, chromosome bridges, and chromosome lags were observed. These results suggest that C. baccatum differs from C. tovarii by at least a chromosomal reciprocal translocation. Crosses of C. tovarii to C. chinense and C. frutescens produced plump seeds, but none of the seeds germinated. Hybridizations of C. tovarii to C. pubescens, C. eximium and C. cardenasii did not produce seed. These hybridization results indicate that C. tovarii is genetically more closely related to the C. baccatum complex than to the C. annuum complex or the C. pubescens complex.

Fruit cuticle lipid composition and water loss in a diverse collection of pepper (Capsicum)

Pepper (Capsicum spp.) fruits are covered by a relatively thick coating of cuticle that limits fruit water loss, a trait previously associated with maintenance of postharvest fruit quality during commercial marketing. To shed light on the chemical-compositional diversity of cuticles in pepper, the fruit cuticles from 50 diverse pepper genotypes from a world collection were screened for both wax and cutin monomer amount and composition. These same genotypes were also screened for fruit water loss rate and this was tested for associations with cuticle composition. Our results revealed an unexpectedly large amount of variation for the fruit cuticle lipids, with a more than 14-fold range for total wax amounts and a more than 16-fold range for cutin monomer amounts between the most extreme accessions. Within the major wax constituents fatty acids varied from 1 to 46%, primary alcohols from 2 to 19%, n-alkanes from 13 to 74% and triterpenoids and sterols from 10 to 77%. Within the cutin monomers, total hexadecanoic acids ranged from 54 to 87%, total octadecanoic acids ranged from 10 to 38% and coumaric acids ranged from 0.2 to 8% of the total. We also observed considerable differences in water loss among the accessions, and unique correlations between water loss and cuticle constituents. The resources described here will be valuable for future studies of the physiological function of fruit cuticle, for the identification of genes and QTLs associated with fruit cuticle synthesis in pepper fruit, and as a starting point for breeding improved fruit quality in pepper.