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 versatile PCR marker for pungency in Capsicum spp.

Pungency in Capsicum spp. is an important quality trait for pepper breeding. The perception of pungency in pepper is due to the presence of a group of compounds named capsaicinoids, only found within the Capsicum genus. How pungency is controlled at genetic and molecular levels has not been completely elucidated. The use of molecular markers to assess pungency trait is required for molecular breeding, despite the difficulty of development of universal markers for this trait. In this work, a DNA sequence possibly related to pungency with a high similarity to Pun1 locus was studied, and sequence analysis of this homolog revealed a 15?bp deletion in non-pungent pepper accessions. An allele-specific pair of primers was designed and specific fragments of 479?bp from non-pungent and 494?bp from pungent accessions were obtained. Polymorphism of this marker, named MAP1, was tested in a wide range of accessions, belonging to several Capsicum species, including pungent and non-pungent accessions of C. annuum L., and pungent accessions of C. chinense, C. baccatum, C. frutescens, C. pubescens, C. galapagoense, C. eximium, C. tovarii, C. cardenasii, and C. chacoense. All these Capsicum accessions were correctly discriminated. The marker suitability to assess pungency in domesticated and wild Capsicum species was demonstrated, and therefore it will be very useful in marker assisted selection (MAS). Moreover, MAP1 was located in a saturated pepper linkage map and its possible relationship with the Pun1 locus has been discussed. Among the available markers for this complex quality trait, the marker developed in this study is the most universal so far.     

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.     

Identification,validation and survey of a single nucleotide polymorphism (SNP) associated with pungency in <Emphasis Type="Italic">Capsicum</Emphasis> spp.

A single nucleotide polymorphism (SNP) associated with pungency was detected within an expressed sequence tag (EST) of 307 bp. This fragment was identified after expression analysis of the EST clone SB2-66 in placenta tissue of Capsicum fruits. Sequence alignments corresponding to this new fragment allowed us to identify an SNP between pungent and non-pungent accessions. Two methods were chosen for the development of the SNP marker linked to pungency: tetra-primer amplification refractory mutation system-PCR (tetra-primer ARMS-PCR) and cleaved amplified polymorphic sequence. Results showed that both methods were successful in distinguishing genotypes. Nevertheless, tetra-primer ARMS-PCR was chosen for SNP genotyping because it was more rapid, reliable and less cost-effective. The utility of this SNP marker for pungency was demonstrated by the ability to distinguish between 29 pungent and non-pungent cultivars of Capsicum annuum. In addition, the SNP was also associated with phenotypic pungent character in the tested genotypes of C. chinense, C. baccatum, C. frutescens, C. galapagoense, C. eximium, C. tovarii and C. cardenasi. This SNP marker is a faster, cheaper and more reproducible method for identifying pungent peppers than other techniques such as panel tasting, and allows rapid screening of the trait in early growth stages.     

Screening Genetic Resources of Capsicum Peppers in Their Primary Center of Diversity in Bolivia and Peru

For most crops, like Capsicum, their diversity remains under-researched for traits of interest for food, nutrition and other purposes. A small investment in screening this diversity for a wide range of traits is likely to reveal many traditional varieties with distinguished values. One objective of this study was to demonstrate, with Capsicum as model crop, the application of indicators of phenotypic and geographic diversity as effective criteria for selecting promising genebank accessions for multiple uses from crop centers of diversity. A second objective was to evaluate the expression of biochemical and agromorphological properties of the selected Capsicum accessions in different conditions. Four steps were involved: 1) Develop the necessary diversity by expanding genebank collections in Bolivia and Peru; 2) Establish representative subsets of ~100 accessions for biochemical screening of Capsicum fruits; 3) Select promising accessions for different uses after screening; and 4) Examine how these promising accessions express biochemical and agromorphological properties when grown in different environmental conditions. The Peruvian Capsicum collection now contains 712 accessions encompassing all five domesticated species (C. annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens). The collection in Bolivia now contains 487 accessions, representing all five domesticates plus four wild taxa (C. baccatum var. baccatum, C. caballeroi, C. cardenasii, and C. eximium). Following the biochemical screening, 44 Bolivian and 39 Peruvian accessions were selected as promising, representing wide variation in levels of antioxidant capacity, capsaicinoids, fat, flavonoids, polyphenols, quercetins, tocopherols, and color. In Peru, 23 promising accessions performed well in different environments, while each of the promising Bolivian accessions only performed well in a certain environment. Differences in Capsicum diversity and local contexts led to distinct outcomes in each country. In Peru, mild landraces with high values in health-related attributes were of interest to entrepreneurs. In Bolivia, wild Capsicum have high commercial demand.     

Analysis of Microsatellite Loci of the Chloroplast Genome in the Genus Capsicum (Pepper)

Six plastome microsatellites were examined in 43 accessions of the genus Capsicum. In total, 33 allelic variants were detected. A specific haplotype of chloroplast DNA was identified for eachCapsicum species. Species-specific allelic variants were found for most wild Capsicum species. The highest intraspecific variation was observed for the C. baccatum plastome. Low cpDNA polymorphism was characteristic of C. annuum:the cpSSRs were either monomorphic or dimorphic. The vast majority of C. annuum accessions each had alleles of one type. Another allele type was rare and occurred only in wild accessions. The results testified again to genetic conservation of C. anuum and especially its cultivated forms. The phylogenetic relationships established for the Capsicum species on the basis of plastome analysis were similar to those inferred from the morphological traits, isozyme patterns, and molecular analysis of the nuclear genome.     

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 (C_A), C. baccatum complex (C_B), C. pubescens complex (C_P), and C. chacoense accessions (C_A/_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 C_P; the accessions in C_B 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 C_A, C_B, and C_P.     

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.     

Resistance to three thrips species in Capsicum spp. depends on site conditions and geographic regions

Capsicum species are commercially grown for pepper production. This crop suffers severely from thrips damage and the identification of natural sources of thrips resistance is essential for the development of resistant cultivars. It is unclear whether resistance to Frankliniella occidentalis as assessed in a specific environment holds under different conditions. Additionally, other thrips species may respond differently to the plant genotypes. Screening for robust and general resistance to thrips encompasses testing different Capsicum accessions under various conditions and with different thrips species. We screened 11 Capsicum accessions (C. annuum and C. chinense) for resistance to F. occidentalis at three different locations in the Netherlands. Next, the same 11 accessions were screened for resistance to Thrips palmi and Scirtothrips dorsalis at two locations in Asia. This resulted in a unique analysis of thrips resistance in Capsicum at five different locations around the world. Finally, all accessions were also screened for resistance to F. occidentalis in the Netherlands using a leaf disc choice assay, allowing direct comparison of whole plant and leaf disc assays. Resistance to F. occidentalis was only partially consistent among the three sites in the Netherlands. The most susceptible accessions were consistently susceptible, but which accession was the most resistant differed among sites. In Asia, one C. chinense accession was particularly resistant to S. dorsalis and T. palmi, but this was not the most resistant accession to F. occidentalis. Overall, resistance to F. occidentalis correlated with S. dorsalis but not with T. palmi resistance in the C. annuum accessions. Damage inflicted on leaf discs reflected damage on the whole plant level. Our study showed that identifying broad spectrum resistance to thrips in Capsicum may prove to be challenging. Breeding programmes should focus on developing cultivars suitable for growing in defined geographic regions with specific thrips species and abiotic conditions.     

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.     

Successful Wide Hybridization and Introgression Breeding in a Diverse Set of Common Peppers (Capsicum annuum) Using Different Cultivated Ají (C. baccatum) Accessions as Donor Parents

Capsicum baccatum, commonly known as ají, has been reported as a source of variation for many different traits to improve common pepper (C. annuum), one of the most important vegetables in the world. However, strong interspecific hybridization barriers exist between them. A comparative study of two wide hybridization approaches for introgressing C. baccatum genes into C. annuum was performed: i) genetic bridge (GB) using C. chinense and C. frutescens as bridge species; and, ii) direct cross between C. annuum and C. baccatum combined with in vitro embryo rescue (ER). A diverse and representative collection of 18 accessions from four cultivated species of Capsicum was used, including C. annuum (12), C. baccatum (3), C. chinense (2), and C. frutescens (1). More than 5000 crosses were made and over 1000 embryos were rescued in the present study. C. chinense performed as a good bridge species between C. annuum and C. baccatum, with the best results being obtained with the cross combination [C. baccatum (♀) × C. chinense (♂)] (♀) × C. annuum (♂), while C. frutescens gave poor results as bridge species due to strong prezygotic and postzygotic barriers. Virus-like-syndrome or dwarfism was observed in F₁ hybrids when both C. chinense and C. frutescens were used as female parents. Regarding the ER strategy, the best response was found in C. annuum (♀) × C. baccatum (♂) crosses. First backcrosses to C. annuum (BC₁s) were obtained according to the crossing scheme [C. annuum (♀) × C. baccatum (♂)] (♀) × C. annuum (♂) using ER. Advantages and disadvantages of each strategy are discussed in relation to their application to breeding programmes. These results provide breeders with useful practical information for the regular utilization of the C. baccatum gene pool in C. annuum breeding.     

A CHEMOSYSTEMATIC STUDY OF SELECTED TAXA OF CAPSICUM

Six taxa of Capsicum were chosen for a comparative chemosystematic study. A “key” individual from each taxon was selected for intensive chemical investigation. Thirteen flavonoids were isolated from leaf material and characterized by paper chromatography and absorption spectroscopy. The C-glycosylflavones vitexin and isovitexin, and orientin and iso-orientin, as well as O-glycosides of the flavones apigenin, luteolin, and chrysoeriol, were isolated from the key individuals. Chromatographic analysis of collections from various regions of South America, Central America, and Mexico showed in general that flavonoid variability is more common in cultivated taxa than in wild. Three groups of Capsicum were recognized and the main systematic conclusions were: (1) The white-flowered taxa in Group I, C. baccatum var. baccatum and C. baccatum var. pendulum, have identical flavonoids, corroborating previous conclusions that they are one species. The absence of chrysoeriol in this group separates it from Groups II and III. (2) The purple-to-white-flowered C. eximium var. eximium and C. eximium var. lomenlosum, Group II, have a complex flavonoid chemistry which appears to link Groups I and III. (3) Two purple-flowered species, C. cardenasii and C. pubescens, Group III, are chemically distinct from the other taxa examined.     

Variation among and within Capsicum species revealed by RAPD markers

 Germplasm characterization is an important link between the conservation and utilization of plant genetic resources. A total of 134 accessions from six Capsicumspecies maintained at the Asian Vegetable Research and Development Center were characterized using 110 randomly amplified polymorphic DNA (RAPD) markers. Ten pairs of potentially duplicated accessions were identified. Multidimensional scaling analysis of the genetic distances among accessions resulted in clustering corresponding to a previous species assignment except for six accessions. Diagnostic RAPDs were identified which discriminate among the Capsicumspecies. The diagnostic markers were employed for improved taxonomic identification of accessions since many morphological traits used in the identification of Capsicumare difficult to score. Three Capsicumaccessions, misclassified based on morphological traits, were reassigned species status based on diagnostic RAPDs. Three accessions, not previously classified, were assigned to a species based on diagnostic RAPDs. Definitive conclusions about the species assignment of three other accessions were not possible. The level of diversity between Capsicum annuumaccessions from the genebank and the breeding program were compared and no differences were observed either for RAPD variation or diversity. The utilization of genetic resources as a source of variance for useful traits in the breeding program may be the reason for the similarity of these two groups. Received: 1 September 1998 / Accepted: 28 December 1998     

Genetic analysis of stunted growth by nuclear-cytoplasmic interaction in interspecific hybrids of Capsicum by using RAPD markers

When eight cultivars of Capsicum annuum were used as female parents in interspecific crosses with two accessions of C. chinense, dwarfism occurred in hybrids originating from 10 out of 16 combinations, while hybrids of the remaining 6 combinations grew normally. In contrast, when C. chinense was used as female parent, all of the hybrids showed severely stunted growth as if affected by a virus. These results suggested that the stunted growth expressed in the cross of C. chinense x C. annuum is caused by an interaction between nuclear gene(s) from C. annuum and the cytoplasm of C. chinense. To examine the number of nuclear gene(s) which cause(s) the stunted growth, we backcrossed F₁ hybrids of C. annuum x C. chinense to C. chinense. About one-quarter of the progeny in the backcrossed hybrids of C. chinense x (C. annuum x C. chinense) showed the same stunted growth shown by the f₁ hybrids of C. chinense x C. annuum, suggesting that two complementary genes of C. annuum cause the stunted growth. However, the higher abortion rates of ovules and lower germination percentage of seeds in C. chinense x C. annuum than in the selfed C. chinense implied that the genetic ratio of the stunted type would have been higher than that observed in the C. chinense x (C. annuum x C. chinense) progeny. We then attempted a linkage analysis between the stunted growth and randomly amplified polymorphic DNA (RAPD) of C. chinense x (C. annuum x C. chinense) progeny. A RAPD marker that associated with 94% of the stunted plants but not with 94% of the normal one was identified. This confirmed that a single nuclear gene of C. annuum which is linked to the RAPD marker with a recombination value of 6% causes the stunted growth in an interaction with the cytoplasm of C. chinense.     

Localization of 5S and 25S rRNA genes on Somatic and meiotic chromosomes in <Emphasis Type="Italic">Capsicum</Emphasis> species of chili pepper

The loci of the 5S and 45S rRNA genes were localized on chromosomes in five species of Capsicum, namely, an-nuum, chacoense, frutescens, baccatum, and chinense by FISH. The 5S rDNA was localized to the distal region of one chromosome in all species observed. The number of 45S rDNA loci varied among species; one in annuum, two in chacoense, frutescens, and chinense, and four in baccatum, with the exceptions that ‘CM334’ of annuum had three loci and ‘tabasco’ of frutescens had one locus. ‘CM334’-derived BAC clones, 384B09 and 365P05, were screened with 5S rDNA as a probe, and BACs 278M03 and 262A23 were screened with 25S rDNA as a probe. Both ends of these BAC clones were sequenced. FISH with these BAC probes on pachytenes from ‘CM334’ plant showed one 5S rDNA locus and three 45S rDNA loci, consistent with the patterns on the somatic chromosomes. The 5S rDNA probe was also applied on extended DNA fibers to reveal that its coverage measured as long as 0.439 Mb in the pepper genome. FISH techniques applied on somatic and meiotic chromosomes and fibers have been established for chili to provide valuable information about the copy number variation of 45S rDNA and the actual physical size of the 5S rDNA in chili.     

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.     

Analyses of genetic relationships in Nelumbo nucifera using nuclear ribosomal ITS sequence data,ISSR and RAPD markers

Despite the economic importance of Nelumbo nucifera, there have been no molecular studies on genetic relationships among cultivars in the species. In the present study 38 accessions were sampled including 37 accessions of N. nucifera or hybrids between N. nucifera and Nelumbo lutea and a single accession of N. lutea. In the ITS analyses, Chinese and Japanese lotus comprise a single cluster with a moderate bootstrap support 68% indicating there is very high similarity between them. Moreover, these ISSR and RAPD results also indicate that there is very close genetic relationship between Chinese and Japanese lotus. In the ISSR and RAPD analyses, although 38 accessions all are distinctly separately into two groups, viz. N. nucifera and N. lutea, there is a high Jaccard similarity coefficient (0.785 and 0.656) between the two species. In N. nucifera the two different groups of the species, viz. flower lotus and rhizome lotus accessions show clear genetic variations. Seed lotus accessions do not form a distinct cluster but are interspersed among the flower accessions indicating that seed lotus is phylogenetically close to flower lotus and they might originate from close wild lotus in genetic relationship. In flower lotus, big-flower type accessions and medium-small type accessions have obvious genetic variation, indicating height is an important criterion in the classification system of flower lotus.     

Patterns of genetic variation of the genusCapsicum (Solanaceae) in Mexico

The evolutionary relationships of 186 accessions ofCapsicum from Mexico were studied through enzyme electrophoresis. A total of 76 alleles representing 20 genetic loci coding for nine enzyme systems were observed and the allelic variations of enzymes were studied for geographical distribution. Allele frequencies were used to estimate the apportionment of gene diversity within and between populations and to construct a dendrogram based on a similarity matrix containingNei genetic distances. — The gene diversity estimates suggest that the structure ofCapsicum populations in Mexico consists of predominantly homozygous genotypes presumably due to a self-pollinated breeding system and population bottlenecks. Significant genetic differentiation was found mainly between populations of differing geographical regions.—Based on the results of this study, three species of domesticatedCapsicum can be identified in Mexico,C. annuum var.annuum, C. chinense, andC. pubescens. Semidomesticated and wild forms include two species,C. frutescens andC. annuum var.glabriusculum. A sharp geographical division results between the latter species;C. frutescens was collected exclusively in the southeastern states of Oaxaca, Chiapas, and Tabasco; whereas wild and semidomesticated forms from the rest of the country areC. annuum. Based upon the similarity of enzyme genotypes of semidomesticated and wild forms, the primary center of domestication of cultivatedC. annuum was estimated to be the region comprising the states of Tamaulipas, Nuevo Leon, San Luis Potosi, Veracruz, and Hidalgo in eastern Mexico. A possible second center of domestication is suggested to be localized in the state of Nayarit, western Mexico.     

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.

     

Single-base cytosine methylation analysis in fruits of three Capsicum species

Single-base cytosine methylation analysis across fruits of Capsicum annuum, C. chinense and C. frutescens showed global average methylation ranging from 82.8–89.1%, 77.6–83.9%, and 22.4–25% at CG, CHG and CHH contexts, respectively. High gene-body methylation at CG and CHG was observed across Capsicum species. The C. annuum showed the highest proportion (>80%) of mCs at different genomic regions compared to C. chinense and C. frutescens. Cytosine methylation for transposable-elements were lower in C. frutescens compared to C. annuum and C. chinense. A total of 510,165 CG, 583112 CHG and 277,897 CHH DMRs were identified across three Capsicum species. The differentially methylated regions (DMRs) distribution analysis revealed C. frutescens as more hypo-methylated compared to C. annuum and C. chinense, and also the presence of more intergenic DMRs in Capsicum genome. At CG and CHG context, gene expression and promoter methylation showed inverse correlations. Furthermore, the observed correlation between methylation and expression of genes suggested the potential role of methylation in Capsicum fruit development/ripening.