Characterization and molecular genetic mapping of microsatellite loci in pepper

Ecology, genetic diversity, and population structure among commercial varieties and local landraces of Capsicum spp. grown in northeastern states of India

Northeastern states of India are known for unique landraces of Capsicum spp. with geographical indications. However, little information is available about these valuable landraces of chillies. Surveys and collections were carried out in niche areas to find out their ecology and diversity through morphological traits and molecular analysis using microsatellite markers. Our result characterized the ecology of niche areas as cool (11.0°C-20.7°C) and humid (>60% relative humidity) climates for dalle-chilli (Capsicum annuum L.); mild-warm (12.2°C-28.6°C) and humid for king-chilli (C. chinense Jacq.); and cool to warm (11.3°C-33.1°C) and humid for bird's eye chilli (C. frutescens L.) during the crop period. The canonical correspondence analysis has shown the significant impact of temperature on the agro-morphological traits and distribution of the landraces in their niche areas. A wide variability was observed for different quantitative traits and yield attributing characters (fruit length, diameter, weight, and yield), showing high heritability (97.0%-99.0%), and genetic advance as a percentage of the mean (119.8%-434.0%). A total of 47 SSR markers used for the molecular analysis generated 230 alleles, ranging from 2 (HPMSE-7) to 10 (HPMSE-5), with an average of 4.89 alleles per locus. The average polymorphism information content was also high (0.61) and ranged from 0.20 (HPMSE-7) to 0.85 (CAMS-91). The observed average heterozygosity was lower than the expected value. Analysis of molecular variance has shown significant variation within (69%) and between (31%) of the populations of Capsicum spp. Based on Nei's genetic distance, bird's eye chilli and king-chilli were found to be closer to each other, whereas dalle-chilli, a tretraploid species, was closer to hot pepper (C. annuum). However, the flower size of dalle-chilli was large and found closer to king-chilli in color and differs from C. chinense due to the presence of calyx teeth. For quality traits, landraces king-chilli, dalle-chilli, and bird's eye chilli have shown 2.8, 2.0, and 1.4 times higher average capsaicin and 0.46, 0.25, and 0.22 times higher average oleoresin content over the hot pepper, respectively. The knowledge of ecology and diversity can be used in identifying new areas for production, selection of elite lines, conservation, and crop improvement.

The bs5 allele of the susceptibility gene Bs5 of pepper (Capsicum annuum L.) encoding a natural deletion variant of a CYSTM protein conditions resistance to bacterial spot disease caused by Xanthomonas species

KEY MESSAGE

The bs5 resistance gene against bacterial spot was identified by map-based cloning. The recessive bs5 gene of pepper (Capsicum annuum L.) conditions a non-hypersensitive resistance trait, characterized by a slightly swollen, pale green, photosynthetically active leaf tissue, following Xanthomonas euvesicatoria infection. The isolation of the bs5 gene by map-based cloning revealed that the bs5 protein was shorter by 2 amino acids as compared to the wild type Bs5 protein. The natural 2 amino acid deletion occurred in the cysteine-rich transmembrane domain of the tail-anchored (TA) protein, Ca_CYSTM1. The protein products of the wild type Bs5 and mutant bs5 genes were shown to be located in the cell membrane, indicating an unknown function in this membrane compartment. Successful infection of the Bs5 pepper lines was abolished by the 6 bp deletion in the TM encoding domain of the Ca_CYSTM1 gene in bs5 homozygotes, suggesting, that the resulting resistance might be explained by the lack of entry of the Xanthomonas specific effector molecules into the plant cells.

Chile Pepper (Capsicum) Breeding and Improvement in the "Multi-Omics" Era

Chile pepper (Capsicum spp.) is a major culinary, medicinal, and economic crop in most areas of the world. For more than hundreds of years, chile peppers have "defined" the state of New Mexico, USA. The official state question, "Red or Green?" refers to the preference for either red or the green stage of chile pepper, respectively, reflects the value of these important commodities. The presence of major diseases, low yields, decreased acreages, and costs associated with manual labor limit production in all growing regions of the world. The New Mexico State University (NMSU) Chile Pepper Breeding Program continues to serve as a key player in the development of improved chile pepper varieties for growers and in discoveries that assist plant breeders worldwide. Among the traits of interest for genetic improvement include yield, disease resistance, flavor, and mechanical harvestability. While progress has been made, the use of conventional breeding approaches has yet to fully address producer and consumer demand for these traits in available cultivars. Recent developments in "multi-omics," that is, the simultaneous application of multiple omics approaches to study biological systems, have allowed the genetic dissection of important phenotypes. Given the current needs and production constraints, and the availability of multi-omics tools, it would be relevant to examine the application of these approaches in chile pepper breeding and improvement. In this review, we summarize the major developments in chile pepper breeding and present novel tools that can be implemented to facilitate genetic improvement. In the future, chile pepper improvement is anticipated to be more data and multi-omics driven as more advanced genetics, breeding, and phenotyping tools are developed.

Oligo-FISH Can Identify Chromosomes and Distinguish Hippophaë rhamnoides L. Taxa

Oligo-fluorescence in situ hybridization (FISH) facilitates precise chromosome identification and comparative cytogenetic analysis. Detection of autosomal chromosomes of Hippophaë rhamnoides has not been achieved using oligonucleotide sequences. Here, the chromosomes of five H. rhamnoides taxa in the mitotic metaphase and mitotic metaphase to anaphase were detected using the oligo-FISH probes (AG3T3)3, 5S rDNA, and (TTG)6. In total, 24 small chromosomes were clearly observed in the mitotic metaphase (0.89–3.03 μm), whereas 24–48 small chromosomes were observed in the mitotic metaphase to anaphase (0.94–3.10 μm). The signal number and intensity of (AG3T3)3, 5S rDNA, and (TTG)6 in the mitotic metaphase to anaphase chromosomes were nearly consistent with those in the mitotic metaphase chromosomes when the two split chromosomes were integrated as one unit. Of note, 14 chromosomes (there is a high chance that sex chromosomes are included) were exclusively identified by (AG3T3)3, 5S rDNA, and (TTG)6. The other 10 also showed a terminal signal with (AG3T3)3. Moreover, these oligo-probes were able to distinguish one wild H. rhamnoides taxon from four H. rhamnoides taxa. These chromosome identification and taxa differentiation data will help in elucidating visual and elaborate physical mapping and guide breeders’ utilization of wild resources of H. rhamnoides.

Molecular mapping of dominant gene responsible for leaf curl virus resistance in chilli pepper (Capsicum annuum L.)

A resistant source (S-343) having monogenic dominant resistance to chilli leaf curl virus disease (ChiLCVD) has been identified at Punjab Agricultural University (PAU), Ludhiana. The F₂ mapping population of 204 plants was derived from the cross MS-341 (susceptible) × S-343 (resistant) to identify the linked marker with the disease-resistant gene. Out of the 685 single-sequence repeats (SSRs) used, only 160 primers showed parental polymorphism. These 160 polymorphic primers were used for bulk segregant analysis and only eight SSR primers were able to differentiate the resistant and susceptible bulks. The linkage analysis revealed that the two markers CA 516044 and PAU-LC-343-1 were found linked with the disease-resistant gene covering a total distance of 15.7 centimorgan (cM). The two primers CA 516044 and PAU-LC-343-1 were found located on chromosome 6 of the pepper genome at a genetic distance of 6.8 cM and 8.9 cM, respectively, from the resistant gene. The validation of linked markers was performed using 26 resistant and susceptible genotypes developed at PAU, Ludhiana by former researchers. The validation of the primers revealed that there was a correlation between phenotypic and genotypic data of the used genotypes, and these markers can be used for the marker-assisted breeding procedures for transferring ChiLCVD resistance until the gene-based markers will be developed. The markers described in this study are the first-ever molecular markers identified as linked to the ChiLCVD-resistant gene.

Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties

BACKGROUND

The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; however, little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of 92 perfect single-nucleotide polymorphisms (SNPs) was identified using re-sequencing data from 35 different C. annuum lines. Based on this panel, a Target SNP-seq genotyping method was designed, which combined multiplex amplification of perfect SNPs with Illumina sequencing, to detect polymorphisms across 271 commercial pepper varieties.

RESULTS

The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content, observed heterozygosity, expected heterozygosity, and minor allele frequency, which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape as blocky-, long horn-, short horn-, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn-, linear-, and blocky-fruited populations. A set of 35 core SNPs were then used as kompetitive allele-specific PCR (KASPar) markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and F_st statistics. Nine loci, located on chromosomes 1, 2, 3, 4, 6, and 12, were identified to be significantly associated with the fruit shape index (p < 0.0001).

CONCLUSIONS

Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of Chinese pepper varieties is significantly influenced by breeding programs focused on fruit shape.

Development and Application of InDel Markers for Capsicum spp. Based on Whole-Genome Re-Sequencing

Genome-wide identification of Insertion/Deletion polymorphisms (InDels) in Capsicum spp. was performed through comparing whole-genome re-sequencing data from two Capsicum accessions, C. annuum cv. G29 and C. frutescens cv. PBC688, with the reference genome sequence of C. annuum cv. CM334. In total, we identified 1,664,770 InDels between CM334 and PBC688, 533,523 between CM334 and G29, and 1,651,856 between PBC688 and G29. From these InDels, 1605 markers of 3-49 bp in length difference between PBC688 and G29 were selected for experimental validation: 1262 (78.6%) showed polymorphisms, 90 (5.6%) failed to amplify, and 298 (18.6%) were monomorphic. For further validation of these InDels, 288 markers were screened across five accessions representing five domesticated species. Of these assayed markers, 194 (67.4%) were polymorphic, 87 (30.2%) monomorphic and 7 (2.4%) failed. We developed three interspecific InDels, which associated with three genes and showed specific amplification in five domesticated species and clearly differentiated the interspecific hybrids. Thus, our novel PCR-based InDel markers provide high application value in germplasm classification, genetic research and marker-assisted breeding in Capsicum species.

Detection of quantitative trait loci for capsanthin content in pepper (Capsicum annuum L.) at different fruit ripening stages

Capsanthin, the main carotenoid of red pepper fruits, is beneficial for human health. To breed pepper (Capsicum annuum L.) with high capsanthin content by marker-assisted selection, we constructed a linkage map of doubled-haploid (DH) lines derived from a cross of two pure lines of C. annuum ('S3586' × 'Kyoto-Manganji No. 2'). The map, designated as the SM-DH map, consisted of 15 linkage groups and the total map distance was 1403.8 cM. Mapping of quantitative trait loci (QTLs) for capsanthin content detected one QTL on linkage group (LG) 13 at 90 days after flowering (DAF) and one on LG 15 at 45 DAF; they were designated Cst13.1 and Cst15.1, respectively. Cst13.1 explained 17.0% of phenotypic variance and Cst15.1 explained 16.1%. We grouped DH lines according to the genotypes of markers adjacent to Cst13.1 and Cst15.1 on both sides. The DH lines with the alleles of both QTLs derived from 'S3586' showed higher capsanthin content at 45 and 90 DAF than the other lines. This is the first identification of QTLs for capsanthin content in any plant species. The data obtained here will be useful in marker-assisted selection for pepper breeding for high capsanthin content.

Allelic and epigenetic DNA variation in relation to F1 heterosis manifestation in F1 hybrids of Capsicum annuum L

Managing F1heterosis is one of the major objectives in hybrid crop breeding programs. The classical theory considers the heterozygosity in F1hybrids to be the main factor contributing to heterosis and therefore presumes a linear relationship between the value of genetic polymorphisms in parental lines and the heterotic response of their F1offspring. Therefore, the genetic diversity information is viewed as a tool for selection of promising cross-combinations, but results published by different researchers are inconsistent. In this work, we studied the contributions of structural and nonstructural DNA polymorphisms to F1heterosis manifestation. We used SSR and methyl-sensitive AFLP (MSAP with HpaII and MspI izoshisomers) protocols for obtaining specific patterns for heterotic and nonheterotic F1hybrids of sweet pepper (Capsicum annuum L.) from a Belarusian breeding program. We found out that a certain portion of heterosis for yield-related traits might be explained by the polymorphism revealed by SSR analysis. According to our data, the total number of polymorphic SSR loci and the ratio of polymorphic and nonpolymorphic loci demonstrate a significant predictive value and can serve as additional prognostic criteria for the selection of promising cross-combinations. From the MSAP assay, we found a relationship between heterosis and the numbers of methylated and nonmethylated DNA loci for yield traits. Our results indicate that cross-hybridization may favor epiallelic modifications in F1hybrids, presumably responsible for heterosis. Thus, epigenetic DNA variation may explain the absence of a linear relationship between the level of structural DNA divergence and F1heterosis, as well as the manifestation of heterosis in crosses of related (genetically similar) accessions.

Whole Genome Resequencing of Capsicum baccatum and Capsicum annuum to Discover Single Nucleotide Polymorphism Related to Powdery Mildew Resistance

The present study deals with genome wide identification of single-nucleotide polymorphism (SNP) markers related to powdery mildew (PM) resistance in two pepper varieties. Capsicum baccatum (PRH1- a PM resistant line) and Capsicum annuum (Saengryeg- a PM susceptible line), were resequenced to develop SNP markers. A total of 6,213,009 and 6,840,889 SNPs for PRH1 and Saengryeg respectively have been discovered. Among the SNPs, majority were classified as homozygous type SNPs, particularly in the resistant line. Moreover, the SNPs were differentially distributed among the chromosomes in both the resistant and susceptible lines. In total, 4,887,031 polymorphic SNP loci were identified between the two lines and 306,871 high-resolution melting (HRM) marker primer sets were designed. In order to understand the SNPs associated with the vital genes involved in diseases resistance and stress associated processes, chromosome-wise gene ontology analysis was performed. The results revealed the occurrence that SNPs related to diseases resistance genes were predominantly distributed in chromosome 4. In addition, 6281 SNPs associated with 46 resistance genes were identified. Among the lines, PRH1 consisted of maximum number of polymorphic SNPs related to NBS-LRR genes. The SNP markers were validated using HRM assay in 45 F4 populations and correlated with the phenotypic disease index.

Mapping of fruit length related QTLs in interspecific cross (Capsicum annuum L. × Capsicum galapagoense Hunz.) of chilli

Fruit length in chilli is quantitatively inherited trait and selection based on phenotypic performance is tedious and time consuming. To detect QTLs determining fruit length in Capsicum spp., an interspecific F₂ mapping population was developed from the cross of C. annuum L. cv. 'FL 201' with C. galapagoense Hunz. accession 'TC 07245'. Fruit length in this cross showed a quantitative inheritance with the population depicting a symmetric distribution in histogram. To map quantitative trait loci (QTLs) for fruit length 400 SSR markers were surveyed on the parental genotypes but only 28 markers were observed to be polymorphic indicating less genetic diversity between the two Capsicum species. Polymorphic markers were then analyzed in F₂ population consisting of 210 plants and 24 of these markers were mapped on to three linkage groups (LGs): LG 1, LG 2 and LG 3. Two fruit length determining QTLs designated as paufl2.1 and paufl2.2 were identified and both the QTLs were mapped on to LG 2. The two QTLs together explained 21.78 per cent of the phenotypic variation. Apart from the two QTLs, positive alleles were detected in the small fruited parent 'TC 07245' which might be of potential use in chilli breeding programs.

Conservation and Dispersion of Genes Conferring Resistance to Tomato Begomoviruses between Tomato and Pepper Genomes

In the present climate change scenario, controlling plant disease through exploitation of host plant resistance could contribute toward the sustainable crop production and global food security. In this respect, the identification of new sources of resistance and utilization of genetic diversity within the species may help in the generation of cultivars with improved disease resistance. Begomoviruses namely, Tomato yellow leaf curl virus (TYLCV) and Chilli leaf curl virus (ChLCV) are known to cause major yield losses in several economically important crop plants of the family Solanaceae. Though co-occurrence, association and synergistic interactions among these viruses in the host plants is reported, whether orthologous genetic loci in related host plants could be responsible for conferring resistance to these viruses has not been investigated yet. Several loci including Ty1, Ty2, Ty3, Ty4, and ty5 have been reported to confer resistance to leaf curl viruses in tomato. Here, we examined the pepper orthologous markers, corresponding to these QTL regions, for polymorphism between ChLCV susceptible and resistant genotypes of pepper. Further, to examine if the polymorphic markers are segregating with the disease resistance, Bulk Segregant Analysis (BSA) was performed on F₂ population derived from crosses between resistant and susceptible lines. However, none of the markers showed polymorphism in BSA suggesting that the tested markers are not linked to genes/QTLs responsible for conferring resistance to ChLCV in the selected genotypes. In silico analysis was performed to study the synteny and collinearity of genes located within these QTL regions in tomato and pepper genomes, which revealed that more than 60% genes located in Ty2 and Ty4, 13.71% genes in Ty1, 23.07% in Ty3, and 44.77% genes located within ty5 QTL region in tomato are conserved in pepper genome. However, despite such a high conservation in gene content, the linkage relationship in these regions seems to be greatly affected by gross rearrangements in both the species.

A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum

The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.

Construction of an interspecific genetic map based on InDel and SSR for mapping the QTLs affecting the initiation of flower primordia in pepper (Capsicum spp.)

Re-sequencing permits the mining of genome-wide variations on a large scale and provides excellent resources for the research community. To accelerate the development and application of molecular markers and identify the QTLs affecting the flowering time-related trait in pepper, a total of 1,038 pairs of InDel and 674 SSR primers from different sources were used for genetic mapping using the F2 population (n = 154) derived from a cross between BA3 (C. annuum) and YNXML (C. frutescens). Of these, a total of 224 simple PCR-based markers, including 129 InDels and 95 SSRs, were validated and integrated into a map, which was designated as the BY map. The BY map consisted of 13 linkage groups (LGs) and spanned a total genetic distance of 1,249.77 cM with an average marker distance of 5.60 cM. Comparative analysis of the genetic and physical map based on the anchored markers showed that the BY map covered nearly the whole pepper genome. Based on the BY map, one major and five minor QTLs affecting the number of leaves on the primary axis (Nle) were detected on chromosomes P2, P7, P10 and P11 in 2012. The major QTL on P2 was confirmed based on another subset of the same F2 population (n = 147) in 2014 with selective genotyping of markers from the BY map. With the accomplishment of pepper whole genome sequencing and annotations (release 2.0), 153 candidate genes were predicted to embed in the Nle2.2 region, of which 12 important flowering related genes were obtained. The InDel/SSR-based interspecific genetic map, QTLs and candidate genes obtained by the present study will be useful for the downstream isolation of flowering time-related gene and other genetic applications for pepper.

An InDel-based linkage map of hot pepper (Capsicum annuum)

Two independent pepper (Capsicum annuum) genomes were published recently, opening a new era of molecular genetics research on pepper. However, pepper molecular marker technologies are still mainly focusing on the simple sequence repeats derived from public database or genomic library. The development and application of the third generation marker system such as single nucleotide polymorphisms, structure variations as well as insertion/deletion polymorphisms (InDels) is still in its infancy. In the present study, we developed InDel markers for pepper genetic mapping with the convenience of two whole-genome re-sequenced inbred lines BA3 (C. annuum) and B702 (C. annuum). A total of 154,519 and 149,755 InDel (1-5 bp) sites were identified for BA3 and B702, respectively, by the alignment of re-sequencing reads to Zunla-1 reference genome. Then, 14,498 InDel sites (only 4 and 5 bp) that are different between BA3 and B702 were predicted. Finally, within a random set of 1,000 primer pairs, 251 InDel markers were validated and mapped onto a linkage map using F₂ population derived from the intraspecific cross BA3 × B702. The first InDel-based map, named as BB-InDel map, consisted of 12 linkage groups, covered a genetic distance of 1,178.01 cM and the average distance between bin markers was 5.01 cM. Compared to the Zunla-1 reference physical map, high consistency was observed on all 12 chromosomes, and the total length of scaffold anchored and physical distance covered by this map was 299.66 and 2,558.68 Mb, respectively, which accounted for 8.95 and 76.38 % of the Zunla-1 reference genome (3.35 Gb), respectively. Furthermore, 37 scaffolds (total length of 36.21 Mb) from the pseudo-chromosome (P0) of the current genome assembly were newly assigned to the corresponding chromosomes by 40 InDel markers. Thus, this map provided good genome coverage and would be useful for basic and applied research in pepper.

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.

Multiple lines of evidence for the origin of domesticated chili pepper, Capsicum annuum, in Mexico

The study of crop origins has traditionally involved identifying geographic areas of high morphological diversity, sampling populations of wild progenitor species, and the archaeological retrieval of macroremains. Recent investigations have added identification of plant microremains (phytoliths, pollen, and starch grains), biochemical and molecular genetic approaches, and dating through (14)C accelerator mass spectrometry. We investigate the origin of domesticated chili pepper, Capsicum annuum, by combining two approaches, species distribution modeling and paleobiolinguistics, with microsatellite genetic data and archaeobotanical data. The combination of these four lines of evidence yields consensus models indicating that domestication of C. annuum could have occurred in one or both of two areas of Mexico: northeastern Mexico and central-east Mexico. Genetic evidence shows more support for the more northern location, but jointly all four lines of evidence support central-east Mexico, where preceramic macroremains of chili pepper have been recovered in the Valley of Tehuacán. Located just to the east of this valley is the center of phylogenetic diversity of Proto-Otomanguean, a language spoken in mid-Holocene times and the oldest protolanguage for which a word for chili pepper reconstructs based on historical linguistics. For many crops, especially those that do not have a strong archaeobotanical record or phylogeographic pattern, it is difficult to precisely identify the time and place of their origin. Our results for chili pepper show that expressing all data in similar distance terms allows for combining contrasting lines of evidence and locating the region(s) where cultivation and domestication of a crop began.

Mining secreted proteins that function in pepper fruit development and ripening using a yeast secretion trap (YST)

Plant cells secrete diverse sets of constitutively- and conditionally-expressed proteins under various environmental and developmental states. Secreted protein populations, or secretomes have multiple functions, including defense responses, signaling, metabolic processes, and developmental regulation. To identify genes encoding secreted proteins that function in fruit development and ripening, a yeast secretion trap (YST) screen was employed using pepper (Capsicum annuum) fruit cDNAs. The YST screen revealed 80 pepper fruit-related genes (CaPFRs) encoding secreted proteins including cell wall proteins, several of which have not been previously described. Transient GFP-fusion assay and an in planta secretion trap were used to validate the secretion of proteins encoded by selected YST clones. In addition, RNA gel blot analyses provided further insights into their expression and regulation during fruit development and ripening. Integrating our data, we conclude that the YST provides a valuable functional genomics tool for the identification of substantial numbers of novel secreted plant proteins that are associated with biological processes, including fruit development and ripening.

Quantitative trait loci from the host genetic background modulate the durability of a resistance gene: a rational basis for sustainable resistance breeding in plants

The combination of major resistance genes with quantitative resistance factors is hypothesized as a promising breeding strategy to preserve the durability of resistant cultivar, as recently observed in different pathosystems. Using the pepper (Capsicum annuum)/Potato virus Y (PVY, genus Potyvirus) pathosystem, we aimed at identifying plant genetic factors directly affecting the frequency of virus adaptation to the major resistance gene pvr2(3) and at comparing them with genetic factors affecting quantitative resistance. The resistance breakdown frequency was a highly heritable trait (h(2)=0.87). Four loci including additive quantitative trait loci (QTLs) and epistatic interactions explained together 70% of the variance of pvr2(3) breakdown frequency. Three of the four QTLs controlling pvr2(3) breakdown frequency were also involved in quantitative resistance, strongly suggesting that QTLs controlling quantitative resistance have a pleiotropic effect on the durability of the major resistance gene. With the first mapping of QTLs directly affecting resistance durability, this study provides a rationale for sustainable resistance breeding. Surprisingly, a genetic trade-off was observed between the durability of PVY resistance controlled by pvr2(3) and the spectrum of the resistance against different potyviruses. This trade-off seemed to have been resolved by the combination of minor-effect durability QTLs under long-term farmer selection.

De novo transcriptome assembly and novel microsatellite marker information in Capsicum annuum varieties Saengryeg 211 and Saengryeg 213

BACKGROUND

Pepper, Capsicum annuum L., Solanaceae, is a major staple economically important vegetable crop worldwide. Limited functional genomics resources and whole genome association studies could be substantially improved through the application of molecular approach for the characterization of gene content and identification of molecular markers. The massive parallel pyrosequencing of two pepper varieties, the highly pungent, Saengryeg 211, and the non-pungent, Saengryeg 213, including de novo transcriptome assembly, functional annotation, and in silico discovery of potential molecular markers is described. We performed 454 GS-FLX Titanium sequencing of polyA-selected and normalized cDNA libraries generated from a single pool of transcripts obtained from mature fruits of two pepper varieties.

RESULTS

A single 454 pyrosequencing run generated 361,671 and 274,269 reads totaling 164.49 and 124.60 Mb of sequence data (average read length of 454 nucleotides), which assembled into 23,821 and 17,813 isotigs and 18,147 and 15,129 singletons for both varieties, respectively. These reads were organized into 20,352 and 15,781 'isogroups' for both varieties. Assembled sequences were functionally annotated based on homology to genes in multiple public databases and assigned with Gene Ontology (GO) terms. Sequence variants analyses identified a total of 3,766 and 2,431 potential (Simple Sequence Repeat) SSR motifs for microsatellite analysis for both varieties, where trinucleotide was the most common repeat unit (84%), followed by di (9.9%), hexa (4.1%) and pentanucleotide repeats (2.1%). GAA repeat (8.6%) was the most frequent repeat motif, followed by TGG (7.2%), TTC (6.5%), and CAG (6.2%).

CONCLUSIONS

High-throughput transcriptome assembly, annotation and large scale of SSR marker discovery has been achieved using next generation sequencing (NGS) of two pepper varieties. These valuable informations for functional genomics resource shall help to further improve the pepper breeding efforts with respect to genetic linkage maps, QTL mapping and marker-assisted trait selection.

Temperature-sensitive phenotype caused by natural mutation in Capsicum latescent in two tropical regions

Plants in tropical regions experience temperature fluctuation only in non-extreme ambient temperatures. Thus, moderate changes in temperatures, which they never experience in their local environments, might be sufficient to manifest the locally hidden phenotype caused by natural mutation. To validate this hypothesis, temperature-treating experiments were performed on Capsicum accessions collected from tropical regions. Thirty-six Capsicum accessions, collected from Caribbean countries, were screened for temperature sensitivity. Similarities in their temperature sensitivities were compared with Sy-2 (C. chinense) from Seychelles, which was previously found to be a temperature-sensitive accession. Tr-13 from Trinidad & Tobago exhibited developmental abnormalities at temperatures below 24 °C. Expression of defense-related genes was induced, and salicylic acid, which is a key molecule in the plant's defense response, accumulated in Tr-13 at temperatures below 24 °C. Tr-13 and Sy-2 appeared normal when they were grown at temperatures simulating those in Trinidad and Seychelles, respectively. Crossing Tr-13 with No. 3341 or Sy-2 revealed that the temperature-sensitive phenotype of Tr-13 was caused by a genetic mutation in the same locus as Sy-2. Plants having a temperature-sensitive phenotype that is caused by natural mutations evade artificial selection and exist as crops in specific environments, such as tropical regions.

RAPD, SCAR and conserved 18S rDNA markers for a red-listed and endemic medicinal plant species, Knema andamanica (Myristicaceae)

Knema andamanica is a red-listed endemic medicinal species of Myristicaceae restricted to Andaman and Nicobar (A&N) Islands, India. This species is used in tribal medicines and has immense bioprospective potential. With a view to generate suitable genomic markers for classification and identification, we have generated RAPD, SCAR and conserved 18S rDNA markers from K. andamanica. A unique 585 bp fragment, that distinguished it from seven other related species of Myristicaceae was first amplified using the random primer OPE 06 and converted to SCAR marker (GenBank accession # JN228256). The conserved sequences of 18S rDNA loci from K. andamanica were also amplified and sequenced (GenBank accession #JN228265). The sequence revealed deviations including 18 variable regions and 15 indels that were unique to K. andamanica. These markers can help in definite identification of K. andamanica even at the juvenile stages.

Three EST-SSR markers associated with QTL for the growth of the clam Meretrix meretrix revealed by selective genotyping

The clam Meretrix meretrix is a member of widely cultured, commercially important clams. A marker-trait association analysis was performed using expressed sequence tag (EST) simple sequence repeat (SSR) markers for marker-assisted selection in M. meretrix. Three markers, MM1272, MM2034, and MM7721, were found to be significantly associated with quantitative trait loci (QTLs) controlling shell length (P < 0.0001) in clams of a fast-growing population (JSF) and a control population (JSC). The 144-bp allele of MM1272, the 154-bp allele of MM2034, and the 152- and 165-bp alleles of MM7721 showed a significantly higher frequency in the JSF population (17.65, 36.41, 28.67, and 29.33 %) than in the JSC population (4.65, 8.33, 3.47, and 5.56 %). The three markers showed lower values for the number of alleles and observed heterozygosity as well as a higher proportion of homozygotes in JSF than in JSC population. The three markers have been further confirmed in the high and low tails of another population (09G₃SPSB); similarly, lower values for the number of alleles and observed heterozygosity as well as a higher proportion of homozygotes were found in 09G₃SPSB(H). The putative functions of the three gene fragments containing MM1272, MM2034, and MM7721 also suggested that the three SSR-containing genes might be involved in growth of M. meretrix. All the results suggest that the three EST-SSR markers associated with growth QTLs would be useful for marker-assisted selection in M. meretrix breeding.

Development of Capsicum EST-SSR markers for species identification and in silico mapping onto the tomato genome sequence

Capsicum spp. are widely cultivated for use as vegetables and spices. The Kihara Institute for Biological Research, Yokohama City University, Japan, has stocks of approximately 800 lines of Capsicum spp. collected from various regions of Central and South America, the regions of origin for Capsicum spp. In this study, 5,751 primer pairs for simple sequence repeat markers, based on 118,060 publicly available sequences of expressed sequence tags of Capsicum annuum, were designed and subjected to a similarity search against the genomic sequence of tomato, a model Solanaceae species. Nucleotide sequences spanning 2,245 C. annuum markers were successfully mapped onto the tomato genome, and 96 of these, which spanned the entire tomato genome, were selected for further analysis. In genotyping analysis, 60 out of the 77 markers that produced specific DNA amplicons showed polymorphism among the Capsicum lines examined. On the basis of the resulting data, the 192 tested lines were grouped into five main clusters. The additional sequencing analysis of the plastid genes, matK and rbcL, divided the resources into three groups. As a result, 19 marker loci exhibited genotypes specific to species and cluster, suggesting that the DNA markers are useful for species identification. Information on the DNA markers will contribute to Capsicum genetics, genomics, and breeding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-012-9774-z) contains supplementary material, which is available to authorized users.

An SSR-based genetic map of pepper (Capsicum annuum L.) serves as an anchor for the alignment of major pepper maps

Of the Capsicum peppers (Capsicum spp.), cultivated C. annuum is the most commercially important, but has lacked an intraspecific linkage map based on sequence-specific PCR markers in accord with haploid chromosome numbers. We constructed a linkage map of pepper using a doubled haploid (DH) population derived from a cross between two C. annuum genotypes, a bell-type cultivar 'California Wonder' and a Malaysian small-fruited cultivar 'LS2341 (JP187992)', which is used as a source of resistance to bacterial wilt (Ralstonia solanacearum). A set of 253 markers (151 SSRs, 90 AFLPs, 10 CAPSs and 2 sequence-tagged sites) was on the map which we constructed, spanning 1,336 cM. This is the first SSR-based map to consist of 12 linkage groups, corresponding to the haploid chromosome number in an intraspecific cross of C. annuum. As this map has a lot of PCR-based anchor markers, it is easy to compare it to other pepper genetic maps. Therefore, this map and the newly developed markers will be useful for cultivated C. annuum breeding.

Identification and development of polymorphic EST-SSR markers by sequence alignment in pepper, Capsicum annuum (Solanaceae)

PREMISE OF THE STUDY

The redundancies in expressed sequence tags (ESTs) in the National Center for Biotechnology Information sequence database were used to identify and develop polymorphic simple sequence repeat (SSR) markers for pepper (Capsicum annuum).

METHODS AND RESULTS

Sixty-eight polymorphic SSR loci were identified in the contigs (containing redundant ESTs) generated by assembling 118060 pepper ESTs from the public sequence database. Thirty-three SSR markers exhibited polymorphism among 31 pepper varieties, with alleles per SSR marker ranging from two to six. The mean observed and expected heterozygosity were 0.28 and 0.39, respectively. There were 18 SSR markers with a motif repeat number of less than five, accounting for 55% of the total.

CONCLUSIONS

We demonstrated the value of mining the redundant sequences in public sequence databases for the development of polymorphic SSR markers, which can be used for marker-assisted breeding in pepper.

Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68

Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) using 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of expressed sequence tag (EST) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by raw reads assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. All unigenes have an approximately equal distribution on chromosomes by aligning with tomato (Solanum lycopersicum) pseudomolecules. Furthermore, 1,536 high quality single nucleotide discrepancies were discovered using the Bukang mature fruit cDNA collection (dbEST ID: 23667) as a reference. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from 614 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research.

Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements

Background

Among the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is not known. To determine the causes for the expansion of pepper euchromatic regions, we compared the pepper genome to that of tomato.

Results

For sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila) were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation.

Conclusions

Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family.

Efficiency of DNA typing methods for detection of smoked paprika "pimenton de la vera" adulteration used in the elaboration of dry-cured Iberian pork sausages

The purpose of this work was to develop a PCR method for the identification of smoked paprika "Pimentón de la Vera" adulteration with paprika elaborated from varieties of pepper foreign to the la Vera region, in central western Spain. Three autochthonous varieties of pepper, Jaranda, Jariza, and Bola, and the varieties Papri Queen, Papri King, Sonora, PS9794, and Papri Ace, foreign to the La Vera region, were used in the study. Analyses of the ITS and 5.8S rDNA, RAPD-PCR, SSR, and ISSR were tested. RAPD-PCR, SSR, and ISSR analyses allowed differentiation among the varieties of paprika analyzed. There was no difference in the sequence of ITS1-5.8S rDNA-ITS2. In addition, with the RAPD-PCR primers S13 and S22, two molecular markers were obtained of 641 and 704 bp, respectively, which allowed all of the smoked paprika varieties to be differentiated from paprikas elaborated with the five foreign varieties. These two molecular markers were investigated as a basis for detecting the adulteration of smoked paprika with paprika elaborated from foreign varieties of pepper.

A COSII genetic map of the pepper genome provides a detailed picture of synteny with tomato and new insights into recent chromosome evolution in the genus Capsicum

We report herein the development of a pepper genetic linkage map which comprises 299 orthologous markers between the pepper and tomato genomes (including 263 conserved ortholog set II or COSII markers). The expected position of additional 288 COSII markers was inferred in the pepper map via pepper-tomato synteny, bringing the total orthologous markers in the pepper genome to 587. While pepper maps have been previously reported, this is the first complete map in the sense that all markers could be placed in 12 linkage groups corresponding to the 12 chromosomes. The map presented herein is relevant to the genomes of cultivated C. annuum and wild C. annuum (as well as related Capsicum species) which differ by a reciprocal chromosome translocation. This map is also unique in that it is largely based on COSII markers, which permits the inference of a detailed syntenic relationship between the pepper and tomato genomes-shedding new light on chromosome evolution in the Solanaceae. Since divergence from their last common ancestor is approximately 20 million years ago, the two genomes have become differentiated by a minimum number of 19 inversions and 6 chromosome translocations, as well as numerous putative single gene transpositions. Nevertheless, the two genomes share 35 conserved syntenic segments (CSSs) within which gene/marker order is well preserved. The high resolution COSII synteny map described herein provides a platform for cross-reference of genetic and genomic information (including the tomato genome sequence) between pepper and tomato and therefore will facilitate both applied and basic research in pepper.

Construction of an integrated pepper map using RFLP, SSR, CAPS, AFLP, WRKY, rRAMP, and BAC end sequences

Map-based cloning to find genes of interest, markerassisted selection (MAS), and marker-assisted breeding (MAB) all require good genetic maps with high reproducible markers. For map construction as well as chromosome assignment, development of single copy PCR-based markers and map integration process are necessary. In this study, the 132 markers (57 STS from BAC-end sequences, 13 STS from RFLP, and 62 SSR) were newly developed as single copy type PCR-based markers. They were used together with 1830 markers previously developed in our lab to construct an integrated map with the Joinmap 3.0 program. This integrated map contained 169 SSR, 354 RFLP, 23 STS from BAC-end sequences, 6 STS from RFLP, 152 AFLP, 51 WRKY, and 99 rRAMP markers on 12 chromosomes. The integrated map contained four genetic maps of two interspecific (Capsicum annuum 'TF68' and C. chinense 'Habanero') and two intraspecific (C. annuum 'CM334' and C. annuum 'Chilsungcho') populations of peppers. This constructed integrated map consisted of 805 markers (map distance of 1858 cM) in interspecific populations and 745 markers (map distance of 1892 cM) in intraspecific populations. The used pepper STS were first developed from end sequences of BAC clones from Capsicum annuum 'CM334'. This integrated map will provide useful information for construction of future pepper genetic maps and for assignment of linkage groups to pepper chromosomes.

Isolation of microsatellites from Catharanthus roseus (L.) G. Don using enriched libraries

Catharanthus roseus is an indispensable source of the anticancerous alkaloids-vincristine and vinblastine, even though they are produced in trace amounts in vivo. In order to increase the yield of alkaloids, in vitro tissue culture studies are carried out which result in a large number of lines/cultures. For identification and characterization of the in vitro cultures, microsatellites in the form of STMS (Sequenced Tagged Microsatellite Sites) markers are used for identification of genetic polymorphism. STMS markers are also used for assessment of genetic diversity within natural populations as well as for construction of genetic linkage maps. Isolation of microsatellites and development of STMS markers typically involves library construction and screening, DNA sequencing, polymerase chain reaction (PCR) primer design, and PCR optimization. This chapter details two approaches for the isolation of microsatellite loci. The first approach is based on PCR using microsatellite containing primers which also have degenerate bases at the 5 cent-end that act as anchors preventing the primers from slippage to the 3 cent-end and the subsequent loss of polymorphism. The multi-locus PCR amplified product is cloned and sequenced. Though this method generates a large number of microsatellites, the major drawback is the high redundancy observed in this method. The second approach described in this chapter is based on the construction of a microsatellite enriched library which involves preferential cloning of the microsatellite enriched fraction of genomic DNA. This method therefore necessitates the isolation of microsatellites through hybridization with biotin labeled oligoprobe followed by their capture with streptavidin-coated magnetic beads. In comparison to the first approach, this approach yields less redundant clones with high microsatellite enrichment. Moreover enriched libraries are 40-60 times more efficient than the conventional small insert genomic libraries.

BAC-derived markers converted from RFLP linked to Phytophthora capsici resistance in pepper (Capsicum annuum L.)

Phytophthora capsici Leonian, an oomycete pathogen, is a serious problem in pepper worldwide. Its resistance in pepper is controlled by quantitative trait loci (QTL). To detect QTL associated with P. capsici resistance, a molecular linkage map was constructed using 100 F(2) individuals from a cross between Capsicum annuum 'CM334' and C. annuum 'Chilsungcho'. This linkage map consisted of 202 restriction fragment length polymorphisms (RFLPs), 6 WRKYs and 1 simple sequence repeat (SSR) covering 1482.3 cM, with an average interval marker distance of 7.09 cM. QTL mapping of Phytophthora root rot and damping-off resistance was performed in F(2:3) originated from a cross between resistant Mexican landrace C. annuum 'CM334' and susceptible Korean landrace C. annuum 'Chilsungcho' using composite interval mapping (CIM) analysis. Four QTL explained 66.3% of the total phenotypic variations for root rot resistance and three 44.9% for damping-off resistance. Of these QTL loci, two were located close to RFLP markers CDI25 on chromosome 5 (P5) and CT211A on P9. A bacterial artificial chromosome (BAC) library from C. annuum 'CM334' was screened with these two RFLP probes to obtain sequence information around the RFLP marker loci for development of PCR-based markers. CDI25 and CT211 probes identified seven and eight BAC clones, respectively. Nine positive BAC clones containing probe regions were sequenced and used for cytogenetic analysis. One single-nucleotide amplified polymorphism (SNAP) for the CDI25 locus, and two SSRs and cleaved amplified polymorphic sequence (CAPS) for CT211 were developed using sequences of the positive BAC clones. These markers will be valuable for rapid selection of genotypes and map-based cloning for resistance genes against P. capsici.

Evaluation of rice and sugarcane SSR markers for phylogenetic and genetic diversity analyses in bamboo

Simple sequence repeat (SSR) markers are valuable tools for many purposes such as phylogenetic, fingerprinting, and molecular breeding studies. However, only a few SSR markers are known and available in bamboo species of the tropics (Bambusa spp.). Considering that grass genomes have co-evolved and share large-scale synteny, theoretically it should be possible to use the genome sequence based SSR markers of field crops such as rice (Oryza sativa) and sugarcane (Saccharum spp.) for genome analysis in bamboo. To test this, 98 mapped SSR primers representing 12 linkage groups of rice and 20 EST-derived sugarcane SSR primers were evaluated for transferability to 23 bamboo species. Of the tested markers, 44 (44.9%) rice and 15 (75%) sugarcane SSR primers showed repeatable amplification in at least one species of bamboo and thus were successfully utilized for phylogenetic and genetic diversity analyses. Transferred SSR primers revealed complex amplification patterns in bamboo, with an average of 9.62 fragments per primer, indicating a high level of polyploidy and genetic variability in bamboo. Forty-two of these primers (34 rice and 8 sugarcane SSR primers) detected an average of 2.12 unique fragments per primer and thus could be exploited for species identification. Six bamboo SSR primers exhibited cross transferability, to varying degrees, to different bamboo species. The genetic similarity coefficient indicated a high level of divergence at the species level (73%). However, a relatively low level of diversity was observed within species (25% in 20 accessions of Dendrocalamus hamiltonii). Further, cluster analysis revealed that the major grouping was in accordance with the taxonomical classification of bamboo. Thus, the rice and sugarcane SSRs can be utilized for phylogenetic and genetic diversity studies in bamboo.

Development, characterization, and transferability to other Solanaceae of microsatellite markers in pepper (Capsicum annuum L.)

A novel set of informative microsatellite markers for pepper (Capsicum annuum L.) is provided. Screening of approximately 168 000 genomic clones and 23 174 public database entries resulted in a total of 411 microsatellite-containing sequences that could be used for primer design and functional testing. A set of 154 microsatellite markers originated from short-insert genomic libraries and 257 markers originated from database sequences. Of those markers, 147 (61 from genomic libraries and 86 from database sequences) showed specific and scoreable amplification products and detected polymorphisms between at least 2 of the 33 lines of a test panel consisting of cultivated and wild Capsicum genotypes. These informative markers were subsequently surveyed for allelic variation and information content. The usefulness of the new markers for diversity and taxonomic studies was demonstrated by the construction of consistent phylogenetic trees based on the microsatellite polymorphisms. Conservation of a subset of microsatellite loci in pepper, tomato, and potato was proven by cross-species amplification and sequence comparisons. For several informative pepper microsatellite markers, homologous expressed sequence tag (EST) counterparts could be identified in these related species that also carry microsatellite motifs. Such orthologs can potentially be used as reference markers and common anchoring points on the genetic maps of different solanaceous species.

A high-resolution, intraspecific linkage map of pepper (Capsicum annuum L.) and selection of reduced recombinant inbred line subsets for fast mapping

A high-resolution, intraspecific linkage map of pepper (Capsicum annuum L.) was constructed from a population of 297 recombinant inbred lines. The parents were the large-fruited inbred cultivar 'Yolo Wonder' and the hot pepper line 'Criollo de Morelos 334', which is heavily used as a source of resistance to a number of diseases. A set of 587 markers (507 amplified fragment length polymorphisms, 40 simple sequence repeats, 19 restriction fragment length polymorphisms, 17 sequence-specific amplified polymorphisms, and 4 sequence tagged sites) were used to generate the map; of these, 489 were assembled into 49 linkage groups (LGs), including 14 LGs with 10 to 60 markers per LG and 35 with 2 to 9 markers per LG. The framework map covered 1857 cM with an average intermarker distance of 5.71 cM. Twenty-three LGs, composed of 69% of the markers and covering 1553 cM, were assigned to 1 of the 12 haploid pepper chromosomes, leaving 26 LGs (304 cM) unassigned. The chromosome framework map built with 250 markers led to a high level of mapping confidence and an average intermarker distance of 6.54 cM. By applying MapPop software, it was possible to select smaller subsets of 141 or 93 most informative individuals with a view to reducing the time and cost of further mapping and phenotyping. To define the smallest number of individuals sufficient for assigning any new marker to a chromosome, subsets from 12 to 45 individuals and a set of 13 markers distributed over all 12 chromosomes were screened. In most cases, the markers were correctly assigned to their expected chromosome, but the accuracy of the map position decreased as the number of individuals was reduced.

Are the polygenic architectures of resistance to Phytophthora capsici and P. parasitica independent in pepper?

The pepper accession Criollo de Morelos 334 is the most efficient source of resistance currently known to Phytophthora capsici and P. parasitica. To investigate whether genetic controls of resistance to two Phytophthora species are independent, we compared the genetic architecture of resistance of CM334 to both Phytophthora species. The RIL population F5YC used to construct the high-resolution genetic linkage map of pepper was assessed for resistance to one isolate of each Phytophthora species. Inheritance of the P. capsici and P. parasitica resistance was polygenic. Twelve additive QTLs involved in the P. capsici resistance and 14 additive QTLs involved in the P. parasitica resistance were detected. The QTLs identified in this progeny were specific to these Phytophthora species. Comparative mapping analysis with literature data identified three colocations between resistance QTLs to P. parasitica and P. capsici in pepper. Whereas this result suggests presence of common resistance factors to the two Phytophthora species in pepper, which possibly derive from common ancestral genes, calculation of the colocation probability indicates that these colocations could occur by chance.

Isolation and characterization of the cytoplasmic male sterility-associated orf456 gene of chili pepper (Capsicum annuum L.)

Cytoplasmic male sterility (CMS) in plants is known to be associated with novel open reading frames (ORFs) that result from recombination events in the mitochondrial genome. In this study Southern and Northern blot analyses using several mitochondrial DNA probes were conducted to detect the presence of differing band patterns between male fertile and CMS lines of chili pepper (Capsicum annuum L.). In the CMS pepper, a novel ORF, termed orf456, was found at the 3'-end of the coxll gene. Western blot analysis revealed the expression of an approximately 17-kDa product in the CMS line, and the intensity of expression of this protein was severely reduced in the restorer pepper line. To investigate the functional role of the ORF456 protein in plant mitochondria, we carried out two independent experiments to transform Arabidopsis with a mitochondrion-targeted orf456 gene construct by Agrobacterium-mediated transformation. About 45 % of the T1 transgenic population showed the male-sterile phenotype and no seed set. Pollen grains from semi-sterile T1 plants were observed to have defects on the exine layer and vacuolated pollen phenotypes. It is concluded that this newly discovered orf456 may represent a strong candidate gene--from among the many CMS-associated mitochondrial genes--for determining the male-sterile phenotype of CMS in chili pepper.