Unilateral incompatibility in Capsicum (Solanaceae): occurrence and taxonomic distribution

Evolutionary relationships, hybridization and diversification under domestication of the locoto chile (Capsicum pubescens) and its wild relatives

Patterns of genetic variation in crops are the result of multiple processes that have occurred during their domestication and improvement, and are influenced by their wild progenitors that often remain understudied. The locoto chile, Capsicum pubescens, is a crop grown mainly in mid-highlands of South-Central America. This species is not known from the wild and exists only as a cultigen. The evolutionary affinities and exact origin of C. pubescens have still not been elucidated, with hypotheses suggesting its genetic relatedness and origin to two wild putative ancestral Capsicum species from the Central Andes, C. eximium and C. cardenasii. In the current study, RAD-sequencing was applied to obtain genome-wide data for 48 individuals of C. pubescens and its wild allies representing different geographical areas. Bayesian, Maximum Likelihood and coalescent-based analytical approaches were used to reconstruct population genetic patterns and phylogenetic relationships of the studied species. The results revealed that C. pubescens forms a well-defined monotypic lineage closely related to wild C. cardenasii and C. eximium, and also to C. eshbaughii. The primary lineages associated with the diversification under domestication of C. pubescens were also identified. Although direct ancestor-descendant relationship could not be inferred within this group of taxa, hybridization events were detected between C. pubescens and both C. cardenasii and C. eximium. Therefore, although hybrid origin of C. pubescens could not be inferred, gene flow involving its wild siblings was shown to be an important factor contributing to its contemporary genetic diversity. The data allowed for the inference of the center of origin of C. pubescens in central-western Bolivia highlands and for better understanding of the dynamics of its gene pool. The results of this study are essential for germplasm conservation and breeding purposes, and provide excellent basis for further research of the locoto chile and its wild relatives.

Genetic Cause of Hybrid Lethality Observed in Reciprocal Interspecific Crosses between Nicotiana simulans and N. tabacum

Hybrid lethality, a type of postzygotic reproductive isolation, is an obstacle to wide hybridization breeding. Here, we report the hybrid lethality that was observed in crosses between the cultivated tobacco, Nicotiana tabacum (section Nicotiana), and the wild tobacco species, Nicotiana simulans (section Suaveolentes). Reciprocal hybrid seedlings were inviable at 28 °C, and the lethality was characterized by browning of the hypocotyl and roots, suggesting that hybrid lethality is due to the interaction of nuclear genomes derived from each parental species, and not to a cytoplasmic effect. Hybrid lethality was temperature-sensitive and suppressed at 36 °C. However, when hybrid seedlings cultured at 36 °C were transferred to 28 °C, all of them showed hybrid lethality. After crossing between an N. tabacum monosomic line missing one copy of the Q chromosome and N. simulans, hybrid seedlings with or without the Q chromosome were inviable and viable, respectively. These results indicated that gene(s) on the Q chromosome are responsible for hybrid lethality and also suggested that N. simulans has the same allele at the Hybrid Lethality A1 (HLA1) locus responsible for hybrid lethality as other species in the section Suaveolentes. Haplotype analysis around the HLA1 locus suggested that there are at least six and two haplotypes containing Hla1-1 and hla1-2 alleles, respectively, in the section Suaveolentes.

Heterosis for capsacinoids accumulation in chili pepper hybrids is dependent on parent-of-origin effect

Heterosis for agronomic traits is a widespread phenomenon that underpins hybrid crop breeding. However, heterosis at the level of cellular metabolites has not yet been fully explored. Some metabolites are highly sought after, like capsaicinoids found in peppers of the Capsicum genus, which confer the characteristic pungent ('hot') flavour of the fruits. We analysed the metabolic profile of the fruit placenta and pericarp of inter- and intra-specific hybrids of two species of Capsicum peppers, C. chinense (cv. Habanero and cv. Biquinho) and C. annuum var. annuum (cv. Jalapeño and cv. Cascadura Ikeda) in complete diallel crosses with reciprocals. The parents and hybrids were grown in a glasshouse and the profile of primary metabolites (sugars, amino acids and organic acids) and capsaicinoids was generated via gas chromatography-time of flight-mass spectrometry (GC-TOF-MS) and ultra-performance liquid chromatography coupled to a mass spectrometer (UPLC-MS), respectively. We found considerable heterotic effects specifically for capsaicinoids accumulation in the fruit placenta of the hybrids, including those derived from non-pungent parents. Furthermore, a large fraction of fruit primary metabolism was influenced by the specific cross combination, with marked parent-of-origin effects, i.e. whether a specific genotype was used as the pistillate or pollen parent. The differences in metabolite levels between the hybrids and their parents provide a snapshot of heterosis for primary and secondary metabolites and may contribute to explain the manifestation of whole-plant heterotic phenotypes.

Monograph of wild and cultivated chili peppers (Capsicum L., Solanaceae)

Capsicum L. (tribe Capsiceae, Solanaceae) is an American genus distributed ranging from the southern United States of America to central Argentina and Brazil. The genus includes chili peppers, bell peppers, ajíes, habaneros, jalapeños, ulupicas and pimientos, well known for their economic importance around the globe. Within the Solanaceae, the genus can be recognised by its shrubby habit, actinomorphic flowers, distinctive truncate calyx with or without appendages, anthers opening by longitudinal slits, nectaries at the base of the ovary and the variously coloured and usually pungent fruits. The highest diversity of this genus is located along the northern and central Andes. Although Capsicum has been extensively studied and great advances have been made in the understanding of its taxonomy and the relationships amongst species, there is no monographic treatment of the genus as a whole. Based on morphological and molecular evidence studied from field and herbarium specimens, we present here a comprehensive taxonomic treatment for the genus, including updated information about morphology, anatomy, karyology, phylogeny and distribution. We recognise 43 species and five varieties, including C.mirum Barboza, sp. nov. from São Paulo State, Brazil and a new combination C.muticum (Sendtn.) Barboza, comb. nov.; five of these taxa are cultivated worldwide (C.annuumL.var.annuum, C.baccatumL.var.pendulum (Willd.) Eshbaugh, C.baccatumL.var.umbilicatum (Vell.) Hunz. & Barboza, C.chinense Jacq. and C.frutescens L.). Nomenclatural revision of the 265 names attributed to chili peppers resulted in 89 new lectotypifications and five new neotypifications. Identification keys and detailed descriptions, maps and illustrations for all taxa are provided.

Investigating the Mechanism of Unilateral Cross Incompatibility in Longan (Dimocarpus longan Lour.) Cultivars (Yiduo × Shixia)

Longan (Dimocarpus longan Lour.) is an important subtropical fruit tree in China. Nearly 90% of longan fruit imports from Thailand are from the cultivar Yiduo. However, we have observed that there exists a unilateral cross incompatibility (UCI) when Yiduo is used as a female parent and Shixia (a famous Chinese cultivar) as a male parent. Here, we performed a comparative transcriptome analysis coupled with microscopy of pistils from two reciprocal pollination combinations [Shixia♂ × Yiduo♀(SY) and Yiduo♀ × Shixia♂(YS)] 4, 8, 12, and 24 h after pollination. We also explored endogenous jasmonic acid (JA) and jasmonyl isoleucine (JA-Ile) levels in pistils of the crosses. The microscopic observations showed that the UCI was sporophytic. The endogenous JA and JA-Ile levels were higher in YS than in SY at the studied time points. We found 7,251 differentially expressed genes from the transcriptome analysis. Our results highlighted that genes associated with JA biosynthesis and signaling, pollen tube growth, cell wall modification, starch and sucrose biosynthesis, and protein processing in endoplasmic reticulum pathways were differentially regulated between SY and YS. We discussed transcriptomic changes in the above-mentioned pathways regarding the observed microscopic and/or endogenous hormone levels. This is the first report on the elaboration of transcriptomic changes in longan reciprocal pollination combination showing UCI. The results presented here will enable the longan breeding community to better understand the mechanisms of UCI.

The hybrid lethality of interspecific F1 hybrids of Nicotiana: a clue to understanding hybrid inviability-a major obstacle to wide hybridization and introgression breeding of plants

Reproductive isolation poses a major obstacle to wide hybridization and introgression breeding of plants. Hybrid inviability in the postzygotic isolation barrier inevitably reduces hybrid fitness, consequently causing hindrances in the establishment of novel genotypes from the hybrids among genetically divergent parents. The idea that the plant immune system is involved in the hybrid problem is applicable to the intra- and/or interspecific hybrids of many different taxa. The lethality characteristics and expression profile of genes associated with the hypersensitive response of the hybrids, along with the suppression of causative genes, support the deleterious epistatic interaction of parental NB-LRR protein genes, resulting in aberrant hyper-immunity reactions in the hybrid. Moreover, the cellular, physiological, and biochemical reactions observed in hybrid cells also corroborate this hypothesis. However, the difference in genetic backgrounds of the respective hybrids may contribute to variations in lethality phenotypes among the parental species combinations. The mixed state in parental components of the chaperone complex (HSP90-SGT1-RAR1) in the hybrid may also affect the hybrid inviability. This review article discusses the facts and hypothesis regarding hybrid inviability, alongside the findings of studies on the hybrid lethality of interspecific hybrids of the genus Nicotiana. A possible solution for averting the hybrid problem has also been scrutinized with the aim of improving the wide hybridization and introgression breeding program in plants.

Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions

This study provides a deep population genomic analysis of 10,000 Capsicum accessions held in genebanks and representing a frame of the global diversity of the genus. By combining single nucleotide polymorphisms (SNPs) based data and passport information, we investigated the genomic diversity and population structure of wild and domesticated peppers, tracing back to routes of evolution and providing a model of Capsicum annuum distribution, which reflects human trade and historical/cultural influences. Our results highlight west–east routes of expansion, shedding light on the links between South and Mesoamerica, Africa, and East/South Asia, the latter two constituting important diversification centers of pepper diversity. Finally, we outline a roadmap for genebank management and future direction for better exploitation of germplasm resources.

Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker–trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper (Capsicum spp.) accessions from worldwide genebanks and investigated the recent history of this iconic staple. Genomic data detected up to 1,618 duplicate accessions within and between genebanks and showed that taxonomic ambiguity and misclassification often involve interspecific hybrids that are difficult to classify morphologically. We deeply interrogated the genetic diversity of the commonly consumed Capsicum annuum to investigate its history, finding that the kinds of peppers collected in broad regions across the globe overlap considerably. The method ReMIXTURE—using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions—was developed to supplement traditional population genetic analyses. The results reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes. Marker associations and possible selective sweeps affecting traits such as pungency were observed, and these traits were shown to be distributed nonuniformly across the globe, suggesting that human preferences exerted a primary influence over domesticated pepper genetic structure.

Intraspecific crossability and compatibility within Solanum aethiopicum

Understanding hybridization barriers is relevant for germplasm conservation and utilization. The prezygotic barriers to hybridization include floral morphological differences like pistil and stamen length, pollen characteristics and pollen-pistil interactions. This study sought to elucidate the reproductive biology of Solanum aethiopicum; its mating systems and compatibility barriers. Eight genotypes of Solanum aethiopicum were examined for differences in floral morphology, phenology and cross compatibility in a full diallel mating design, with assessment of fruit set, seed set and seed viability. In-vivo pollen tube growth was observed for failed crosses at 24, 48 and 72 h after pollination. All genotypes had heterostyly flowers, with predominantly small white petals. Incompatibility was observed in five out of 39 combinations. All selfed genotypes displayed compatibility implying the genotypes are self-compatible. Pollen–pistil incompatibility, which was exhibited in four out of the five failed cross combinations, occurred on the stigma, upper style and lower style, a phenomenon typical in Solanaceae. Solanum aethiopicum is self-compatible and majorly self-pollinating but has features that support cross-pollination.

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.

De novo domestication of wild species to create crops with increased resilience and nutritional value

Creating crops with resistance to drought, soil salinity and insect damage, that simultaneously have higher nutritional quality, is challenging to conventional breeding due to the complex and diffuse genetic basis of those traits. Recent advances in gene editing technology, such as base editors and prime-editing, coupled with a deeper understanding of the genetic basis of domestication delivered by the analysis of crop 'pangenomes', open the exciting prospect of creating novel crops via manipulation of domestication-related genes in wild species. A de novo domestication platform may allow rapid and precise conversion of crop wild relatives into crops, while retaining many of the valuable resilience and nutritional traits left behind during domestication and breeding. Using the Solanaceae family as case in point, we discuss how such a knowledge-driven pipeline could be exploited to contribute to food security over the coming decades.

Reproductive compatibility in Capsicum is not necessarily reflected in genetic or phenotypic similarity between species complexes

Wild relatives of domesticated Capsicum represent substantial genetic diversity and thus sources of traits of potential interest. Furthermore, the hybridization compatibility between members of Capsicum species complexes remains unresolved. Improving our understanding of the relationship between Capsicum species relatedness and their ability to form hybrids is a highly pertinent issue. Through the development of novel interspecific hybrids in this study, we demonstrate interspecies compatibility is not necessarily reflected in relatedness according to established Capsicum genepool complexes. Based on a phylogeny constructed by genotyping using simple sequence repeat (SSR) markers and with a portion of the waxy locus, and through principal component analysis (PCA) of phenotypic data, we clarify the relationships among wild and domesticated Capsicum species. Together, the phylogeny and hybridization studies provide evidence for the misidentification of a number of species from the World Vegetable Center genebank included in this study. The World Vegetable Center holds the largest collection of Capsicum genetic material globally, therefore this may reflect a wider issue in the misidentification of Capsicum wild relatives. The findings presented here provide insight into an apparent disconnect between compatibility and relatedness in the Capsicum genus, which will be valuable in identifying candidates for future breeding programs.

Molecular characterization of the 5S rDNA non-transcribed spacer and reconstruction of phylogenetic relationships in Capsicum

Abstract Capsicum includes ca. 41 species of chili peppers. In this original report we PCR amplified, cloned, sequenced and characterized the 5S rDNA non-transcribed spacer -NTS- in 23 taxa of nine clades of Capsicum, divergent at geographical origin and fruit and chromosome traits, and compared the NTS features throughout Solanaceae. According to GC content, inner variability and regulatory elements, the NTS organizes into three distinct structural regions; genetic variability at the NTS in Capsicum and related genus clusters into defined taxa hierarchies. Based on the reconstruction of a maximum-likelihood phylogenetic tree and phylogenetic networks, NTS sequences of Capsicum and related taxa grouped into well recognized categories -genus, section, clade, species, variety-. An evolutionary scenario arose from combined genetic and phylogenetic NTS data, in which monophyly and lineage diversification over time of Capsicum are addressed. Our analysis is original to include all domesticated species of Capsicum prevailing in germplasm collections and breeding programs, together with a large group of wild taxa that demanded further genetic characterization. The NTS set up as a double purpose marker in Capsicum, to directly evaluate genetic variability and reconstruct phylogenetic relationships to a broad extent, and constitutes a valuable tool for germplasm characterization and evolutionary studies within Solanaceae.

A step towards Balkan Capsicum annuum L. core collection: Phenotypic and biochemical characterization of 180 accessions for agronomic, fruit quality, and virus resistance traits

Region-specific local landraces represent a germplasm diversity adapted and acclimatized to local conditions, and are ideal to breed for targeted market niches while maintaining the variability of heirloom traits. A collection of 180 pepper accessions, collected from 62 diverse locations across six Balkan countries, were characterized and evaluated for phenotypic and biochemical variation during a multi-year environment. An assortment of 32 agro-morphological, fruit quality, and virus resistance traits were evaluated, and the top 10% accessions were identified. A wide range of trait variation concerning plant architecture, inflorescence and fruit traits, yield and fruit quality was observed, and appreciable variation was noticed. According to hierarchical clustering, six distinct clusters were established based on pre-defined varietal groups. Divergence among accessions for phenotypic and fruit compositional variability was analyzed, and eight principal components were identified that contributed ~71% of the variation, with fruit shape, width, wall thickness, weight, and fruit quality traits being the most discriminant. Evaluation of the response to tobacco mosaic virus (TMV) and pepper mild mottle mosaic virus (PMMoV) showed that 24 and 1 accession were resistant, respectively while no tomato spotted wilt virus (TSWV) resistance was found. Considerable diversity for agro-bio-morphological traits indicates the Balkan pepper collection as good gene sources for pre-breeding and cultivar development that are locally adapted.

Phytochemical Assessment of Native Ecuadorian Peppers (Capsicum spp.) and Correlation Analysis to Fruit Phenomics

In this work, the impact of pepper (Capsicum spp.) fruits morphology on their composition for health-promoting compounds was investigated. For that purpose, pepper accessions from Ecuador, one of the hotspots in Capsicum's origin, were analyzed for ascorbic acid, polyphenols, capsaicinoids, and prevention of cholesterol oxidation. Plant and fruit phenomics were assessed with conventional descriptors and Tomato Analyzer digital traits. Significant differences among accessions and species revealed a large diversity within the collection. The Capsicum frutescens group displayed the highest levels of capsaicinoids, whereas the polyphenols shortly varied among the five domesticated species. Capsicum pubescens exhibited the lowest content of ascorbic acid. The conventional descriptors describing the magnitude of plants and fruits, as well as digital attributes under the categories of size, shape index, and latitudinal section, mostly explained the variance among Capsicum groups. Correlation test revealed that phytochemical components were negatively correlated with the morphometric fruit attributes, suggesting that huge fruits contained lower amounts of nutraceutical compounds. Multivariate analysis showed that parameters related to fruit size, shape, and nutraceutical composition primarily contribute to the arrangement of pepper accessions. Such results suggested that those traits have been subjected to higher selection pressures imposed by humans.

Production and characterization of intersectional hybrids between Tricyrtis sect. Brachycyrtis and sect. Hirtae via ovule culture

The liliaceous perennial plants, Tricyrtis spp., have recently become popular as ornamental plants for pot and garden uses. In order to broaden the variability in plant form, flower form and flower color of Tricyrtis spp., intersectional hybridization was examined between four T. formosana cultivars or T. hirta var. albescens (sect. Hirtae) and T. macranthopsis (sect. Brachycyrtis). After cross-pollination, ovary enlargement was observed only when T. macranthopsis was used as a pollen parent. Ovules with placental tissues were excised from enlarged ovaries and cultured on half-strength MS medium without plant growth regulators. From five cross-combinations, 31 ovule culture-derived plantlets were obtained and 20 of them were confirmed to be intersectional hybrids by flow cytometry and inter-simple sequence repeat analyses. Almost all hybrids grew well and produced flowers 1-2 years after transplantation to the greenhouse. Hybrids had semi-cascade-type shoots, which was intermediate between T. formosana cultivars and T. hirta var. albescens (erect-type shoots) and T. macranthopsis (cascade-type shoots). They produced flowers with novel forms and colors compared with the corresponding parents, and some were horticulturally attractive. The results obtained in the present study indicate the validity of intersectional hybridization via ovule culture for breeding of Tricyrtis spp.

Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species

Pepper species (Capsicum spp.) are widely used as food, spice, decoration, and medicine. Despite the recent old-world culinary impact, more than 50 commercially recognized pod types have been recorded worldwide from three taxonomic complexes (A, B, and P). The current study aimed to apply a pan-plastome approach to resolve the plastomic boundaries among those complexes and identify effective loci for the taxonomical resolution and molecular identification of the studied species/varieties. High-resolution pan-plastomes of five species and two varieties were assembled and compared from 321 accessions. Phyloplastomic and network analyses clarified the taxonomic position of the studied species/varieties and revealed a pronounced number of accessions to be the rare and endemic species, C. galapagoense, that were mistakenly labeled as C. annuum var. glabriusculum among others. Similarly, some NCBI-deposited plastomes were clustered differently from their labels. The rpl23-trnI intergenic spacer contained a 44 bp tandem repeat that, in addition to other InDels, was capable of discriminating the investigated Capsicum species/varieties. The rps16-trnQ/rbcL-accD/ycf3-trnS gene set was determined to be sufficiently polymorphic to retrieve the complete phyloplastomic signal among the studied Capsicum spp. The pan-plastome approach was shown to be useful in resolving the taxonomical complexes, settling the incomplete lineage sorting conflict and developing a molecular marker set for Capsicum spp. identification.

Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites

Capsicum is one of the major vegetable crops grown worldwide. Current subdivision in clades and species is based on morphological traits and coarse sets of genetic markers. Broad variability of fruits has been driven by breeding programs and has been mainly studied by linkage analysis. We discovered 746k variable sites by sequencing 1.8% of the genome in a collection of 373 accessions belonging to 11 Capsicum species from 51 countries. We describe genomic variation at population-level, confirm major subdivision in clades and species, and show that the known major subdivision of C. annuum separates large and bulky fruits from small ones. In C. annuum, we identify four novel loci associated with phenotypes determining the fruit shape, including a non-synonymous mutation in the gene Longifolia 1-like (CA03g16080). Our collection covers all the economically important species of Capsicum widely used in breeding programs and represent the widest and largest study so far in terms of the number of species and number of genetic variants analyzed. We identified a large set of markers that can be used for population genetic studies and genetic association analyses. Our results provide a comprehensive and precise perspective on genomic variability in Capsicum at population-level and suggest that future fine genetic association studies will yield useful results for breeding.

Capsaicinoids: Pungency beyond Capsicum

Capsaicinoids are metabolites responsible for the appealing pungency of Capsicum (chili pepper) species. The completion of the Capsicum annuum genome has sparked new interest into the development of biotechnological applications involving the manipulation of pungency levels. Pungent dishes are already part of the traditional cuisine in many countries, and numerous health benefits and industrial applications are associated to capsaicinoids. This raises the question of how to successfully produce more capsaicinoids, whose biosynthesis is strongly influenced by genotype-environment interactions in fruits of Capsicum. In this Opinion article we propose that activating the capsaicinoid biosynthetic pathway in a more amenable species such as tomato could be the next step in the fascinating story of pungent crops.

Genetic diversity, population structure, and relationships in a collection of pepper (Capsicum spp.) landraces from the Spanish centre of diversity revealed by genotyping-by-sequencing (GBS)

Pepper (Capsicum spp.) is one of the most important vegetable crops; however, pepper genomic studies lag behind those of other important Solanaceae. Here we present the results of a high-throughput genotyping-by-sequencing (GBS) study of a collection of 190 Capsicum spp. accessions, including 183 of five cultivated species (C. annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens) and seven of the wild form C. annuum var. glabriusculum. Sequencing generated 6,766,231 high-quality read tags, of which 40.7% were successfully aligned to the reference genome. SNP calling yielded 4083 highly informative segregating SNPs. Genetic diversity and relationships of a subset of 148 accessions, of which a complete passport information was available, was studied using principal components analysis (PCA), discriminant analysis of principal components (DAPC), and phylogeny approaches. C. annuum, C. baccatum, and C. chinense were successfully separated by all methods. Our population was divided into seven clusters by DAPC, where C. frutescens accessions were clustered together with C. chinense. C. annuum var. glabriusculum accessions were spread into two distinct genetic pools, while European accessions were admixed and closely related. Separation of accessions was mainly associated to differences in fruit characteristics and origin. Phylogeny studies showed a close relation between Spanish and Mexican accessions, supporting the hypothesis that the first arose from a main genetic flow from the latter. Tajima's D statistic values were consistent with positive selection in the C. annuum clusters, possibly related to domestication or selection towards traits of interest. This work provides comprehensive and relevant information on the origin and relationships of Spanish landraces and for future association mapping studies in pepper.

Interspecific reproductive barriers between sympatric populations of wild tomato species (Solanum section Lycopersicon)

PREMISE OF THE STUDY

Interspecific reproductive barriers (IRBs) often prevent hybridization between closely related species in sympatry. In the tomato clade (Solanum section Lycopersicon), interspecific interactions between natural sympatric populations have not been evaluated previously. In this study, we assessed IRBs between members of the tomato clade from nine sympatric sites in Peru.

METHODS

Coflowering was assessed at sympatric sites in Peru. Using previously collected seeds from sympatric sites in Peru, we evaluated premating prezygotic (floral morphology), postmating prezygotic (pollen-tube growth), and postzygotic barriers (fruit and seed development) between sympatric species in common gardens. Pollen-tube growth and seed development were examined in reciprocal crosses between sympatric species.

KEY RESULTS

We confirmed coflowering of sympatric species at five sites in Peru. We found three types of postmating prezygotic IRBs during pollen-pistil interactions: (1) unilateral pollen-tube rejection between pistils of self-incompatible species and pollen of self-compatible species; (2) potential conspecific pollen precedence in a cross between two self-incompatible species; and (3) failure of pollen tubes to target ovules. In addition, we found strong postzygotic IRBs that prevented normal seed development in 11 interspecific crosses, resulting in seed-like structures containing globular embryos and aborted endosperm and, in some cases, overgrown endothelium. Viable seed and F₁ hybrid plants were recovered from three of 19 interspecific crosses.

CONCLUSIONS

We have identified diverse prezygotic and postzygotic IRBs that would prevent hybridization between sympatric wild tomato species, but interspecific hybridization is possible in a few cases.

Phylogenetic relationships, diversification and expansion of chili peppers (Capsicum, Solanaceae)

BACKGROUND AND AIMS

Capsicum (Solanaceae), native to the tropical and temperate Americas, comprises the well-known sweet and hot chili peppers and several wild species. So far, only partial taxonomic and phylogenetic analyses have been done for the genus. Here, the phylogenetic relationships between nearly all taxa of Capsicum were explored to test the monophyly of the genus and to obtain a better knowledge of species relationships, diversification and expansion.

METHODS

Thirty-four of approximately 35 Capsicum species were sampled. Maximum parsimony and Bayesian inference analyses were performed using two plastid markers (matK and psbA-trnH) and one single-copy nuclear gene (waxy). The evolutionary changes of nine key features were reconstructed following the parsimony ancestral states method. Ancestral areas were reconstructed through a Bayesian Markov chain Monte Carlo analysis.

KEY RESULTS

Capsicum forms a monophyletic clade, with Lycianthes as a sister group, following both phylogenetic approaches. Eleven well-supported clades (four of them monotypic) can be recognized within Capsicum, although some interspecific relationships need further analysis. A few features are useful to characterize different clades (e.g. fruit anatomy, chromosome base number), whereas some others are highly homoplastic (e.g. seed colour). The origin of Capsicum is postulated in an area along the Andes of western to north-western South America. The expansion of the genus has followed a clockwise direction around the Amazon basin, towards central and south-eastern Brazil, then back to western South America, and finally northwards to Central America.

CONCLUSIONS

New insights are provided regarding interspecific relationships, character evolution, and geographical origin and expansion of Capsicum A clearly distinct early-diverging clade can be distinguished, centred in western-north-western South America. Subsequent rapid speciation has led to the origin of the remaining clades. The diversification of Capsicum has culminated in the origin of the main cultivated species in several regions of South to Central America.

Genomics-based strategies for the use of natural variation in the improvement of crop metabolism

Next-generation genomics holds great potential in the study of plant phenotypic variation. With several crop reference genomes now available, the affordable costs of de novo genome assembly or target resequencing offer the opportunity to mine the enormous amount of genetic diversity hidden in crop wild relatives. Wide introgressions from these wild ancestors species or land races represent a possible strategy to improve cultivated varieties. In this review, we discuss the mechanisms underlying metabolic diversity within plant species and the possible strategies (and barriers) to introgress novel metabolic traits into cultivated varieties. We show how deep genomic surveys uncover various types of structural variants from extended gene pools of major crops and highlight how this variation may be used for the improvement of crop metabolism.

Exploring natural variation of photosynthetic, primary metabolism and growth parameters in a large panel of Capsicum chinense accessions

Collectively, the results presented improve upon the utility of an important genetic resource and attest to a complex genetic basis for differences in both leaf metabolism and fruit morphology between natural populations. Diversity of accessions within the same species provides an alternative method to identify physiological and metabolic traits that have large effects on growth regulation, biomass and fruit production. Here, we investigated physiological and metabolic traits as well as parameters related to plant growth and fruit production of 49 phenotypically diverse pepper accessions of Capsicum chinense grown ex situ under controlled conditions. Although single-trait analysis identified up to seven distinct groups of accessions, working with the whole data set by multivariate analyses allowed the separation of the 49 accessions in three clusters. Using all 23 measured parameters and data from the geographic origin for these accessions, positive correlations between the combined phenotypes and geographic origin were observed, supporting a robust pattern of isolation-by-distance. In addition, we found that fruit set was positively correlated with photosynthesis-related parameters, which, however, do not explain alone the differences in accession susceptibility to fruit abortion. Our results demonstrated that, although the accessions belong to the same species, they exhibit considerable natural intraspecific variation with respect to physiological and metabolic parameters, presenting diverse adaptation mechanisms and being a highly interesting source of information for plant breeders. This study also represents the first study combining photosynthetic, primary metabolism and growth parameters for Capsicum to date.

Testing the SI × SC rule: Pollen-pistil interactions in interspecific crosses between members of the tomato clade (Solanum section Lycopersicon, Solanaceae)

PREMISE OF THE STUDY

Interspecific reproductive barriers (IRBs) act to ensure species integrity by preventing hybridization. Previous studies on interspecific crosses in the tomato clade have focused on the success of fruit and seed set. The SI × SC rule (SI species × SC species crosses are incompatible, but the reciprocal crosses are compatible) often applies to interspecific crosses. Because SI systems in the Solanaceae affect pollen tube growth, we focused on this process in a comprehensive study of interspecific crosses in the tomato clade to test whether the SI × SC rule was always followed.

METHODS

Pollen tube growth was assessed in reciprocal crosses between all 13 species of the tomato clade using fluorescence microscopy.

KEY RESULTS

In crosses between SC and SI species, pollen tube growth follows the SI × SC rule: interspecific pollen tube rejection occurs when SI species are pollinated by SC species, but in the reciprocal crosses (SC × SI), pollen tubes reach ovaries. However, pollen tube rejection occurred in some crosses between pairs of SC species, demonstrating that a fully functional SI system is not necessary for pollen tube rejection in interspecific crosses. Further, gradations in the strength of both pistil and pollen IRBs were revealed in interspecific crosses using SC populations of generally SI species.

CONCLUSION

The SI × SC rule explains many of the compatibility relations in the tomato clade, but exceptions occur with more recently evolved SC species and accessions, revealing differences in strength of both pistil and pollen IRBs.

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.

Interactions of hybridization and mating systems: a case study in Leptosiphon (Polemoniaceae)

PREMISE OF THE STUDY

The roles of hybridization and mating systems in the evolution of angiosperms have been well studied, but less work has focused on their interactions. Self-incompatible and self-compatible species often show asymmetry in heterospecific pollen rejection. Self-fertilization can preempt ovules before opportunities for hybridization. In turn, hybridization might affect mating system evolution through selection for selfing to avoid production of low fitness hybrids. •

METHODS

AFLP and morphological analyses were used to test for hybrids in a contact zone between species with contrasting breeding systems. Crossing experiments examined the relative contributions to reproductive isolation of pollen-pistil interactions, timing of self-fertilization, and F1 viability and fertility. A diallel cross of siblings tested for an association between heterospecific incompatibility and S-genotype in the self-incompatible species. •

KEY RESULTS

A low frequency of hybrids was detected in the contact zone. Pollen-pistil interactions were partially consistent with the SI × SC rule; some individuals of the self-incompatible species rejected heterospecific pollen, whereas the self-compatible species was fully receptive to it. In the selfing species, individuals with early selfing produced fewer hybrid progeny than did those with delayed self-compatibility when heterospecific pollen was applied after self-pollen. Viability of F1s was high but fertility was low. Variability in heterospecific pollen rejection was not related to S-genotype. •

CONCLUSIONS

Both self-fertilization and self-incompatibility are associated with limits to hybridization at this site. The strong effect of timing of selfing on production of low fitness F1s suggests that hybridization might select for early selfing in this population.

Efficient sweet pepper transformation mediated by the BABY BOOM transcription factor

Pepper (Capsicum L.) is a nutritionally and economically important crop that is cultivated throughout the world as a vegetable, condiment, and food additive. Genetic transformation using Agrobacterium tumefaciens (agrobacterium) is a powerful biotechnology tool that could be used in pepper to develop community-based functional genomics resources and to introduce important agronomic traits. However, pepper is considered to be highly recalcitrant for agrobacterium-mediated transformation, and current transformation protocols are either inefficient, cumbersome or highly genotype dependent. The main bottleneck in pepper transformation is the inability to generate cells that are competent for both regeneration and transformation. Here, we report that ectopic expression of the Brassica napus BABY BOOM AP2/ERF transcription factor overcomes this bottleneck and can be used to efficiently regenerate transgenic plants from otherwise recalcitrant sweet pepper (C. annuum) varieties. Transient activation of BABY BOOM in the progeny plants induced prolific cell regeneration and was used to produce a large number of somatic embryos that could be converted readily to seedlings. The data highlight the utility of combining biotechnology and classical plant tissue culture approaches to develop an efficient transformation and regeneration system for a highly recalcitrant vegetable crop.

Genetic relationships within and between Capsicum species

Genetic relationships were estimated among 24 accessions belonging to 11 species of Capsicum, using 2,760 RAPD markers based on touch-down polymerase chain reactions (Td-RAPD-PCR). These markers were implemented in analyses of principal coordinates, unweighted pair group mean average, and 2,000 bootstrap replications. The accessions were divided into four groups, corresponding to previously described Capsicum complexes: C. annuum complex (CA), C. baccatum complex (CB), C. pubescens complex (CP), and C. chacoense accessions (CA/B). Their overall mean genetic similarity index was 0.487 +/- 0.082, ranging from 0.88 to 0.32, based on Jaccard's coefficient. The highest genetic variation was observed among the accessions in CP; the accessions in CB had a low level of variation as judged from the standard deviations of the genetic similarity indices. Based on the Td-RAPD-PCR markers, the 24 accessions were divided into four major groups, three of which corresponded to the three distinct Capsicum complexes. Accessions of C. chacoense were found to be equally related to complexes CA, CB, and CP.

LTR-retrotransposons Tnt1 and T135 markers reveal genetic diversity and evolutionary relationships of domesticated peppers

Plant genetic resources often constitute the foundation of successful breeding programs. Pepper (Capsicum annuum L.) is one of the most economically important and diversely utilized Solanaceous crop species worldwide, but less studied compared to tomato and potato. We developed and used molecular markers based on two copia-type retrotransposons, Tnt1 and T135, in a set of Capsicum species and wild relatives from diverse geographical origins. Results showed that Tnt1 and T135 insertion polymorphisms are very useful for studying genetic diversity and relationships within and among pepper species. Clusters of accessions correspond to cultivar types based on fruit shape, pungency, geographic origin and pedigree. Genetic diversity values, normally reflective of past transposition activity and population dynamics, showed positive correlation with the average number of insertions per accession. Similar evolutionary relationships are observed to that inferred by previous karyosystematics studies. These observations support the possibility that retrotransposons have contributed to genome inflation during Capsicum evolution.

Development of a real-time PCR method for the differential detection and quantification of four solanaceae in GMO analysis: potato (Solanum tuberosum), tomato (Solanum lycopersicum), eggplant (Solanum melongena), and pepper (Capsicum annuum)

The labeling of products containing genetically modified organisms (GMO) is linked to their quantification since a threshold for the presence of fortuitous GMOs in food has been established. This threshold is calculated from a combination of two absolute quantification values: one for the specific GMO target and the second for an endogenous reference gene specific to the taxon. Thus, the development of reliable methods to quantify GMOs using endogenous reference genes in complex matrixes such as food and feed is needed. Plant identification can be difficult in the case of closely related taxa, which moreover are subject to introgression events. Based on the homology of beta-fructosidase sequences obtained from public databases, two couples of consensus primers were designed for the detection, quantification, and differentiation of four Solanaceae: potato (Solanum tuberosum), tomato (Solanum lycopersicum), pepper (Capsicum annuum), and eggplant (Solanum melongena). Sequence variability was studied first using lines and cultivars (intraspecies sequence variability), then using taxa involved in gene introgressions, and finally, using taxonomically close taxa (interspecies sequence variability). This study allowed us to design four highly specific TaqMan-MGB probes. A duplex real time PCR assay was developed for simultaneous quantification of tomato and potato. For eggplant and pepper, only simplex real time PCR tests were developed. The results demonstrated the high specificity and sensitivity of the assays. We therefore conclude that beta-fructosidase can be used as an endogenous reference gene for GMO analysis.

Precolumbian use of chili peppers in the Valley of Oaxaca, Mexico

Excavations at Guilá Naquitz and Silvia's Cave, two dry rockshelters near Mitla, Oaxaca, Mexico, yielded the remains of 122 chili peppers dating to the period A.D. 600-1521. The chilies can be assigned to at least 10 cultivars, all belonging to the species Capsicum annuum or Capsicum frutescens. The specimens are well enough preserved to permit an evaluation of the criteria used to separate wild and domestic chilies and to distinguish among cultivated races. In addition, they provide the opportunity to assess the reliability of starch grains for documenting the presence of chilies in archaeological sites where no macrobotanical remains are preserved.