Root transcriptional responses of two melon genotypes with contrasting resistance to Monosporascus cannonballus (Pollack et Uecker) infection.

BACKGROUND: Monosporascus cannonballus is the main causal agent of melon vine decline disease. Several studies have been carried out mainly focused on the study of the penetration of this pathogen into melon roots, the evaluation of symptoms severity on infected roots, and screening assays for breeding programs. However, a detailed molecular view on the early interaction between M. cannonballus and melon roots in either susceptible or resistant genotypes is lacking. In the present study, we used a melon oligo-based microarray to investigate the gene expression responses of two melon genotypes, Cucumis melo 'Piel de sapo' ('PS') and C. melo 'Pat 81', with contrasting resistance to the disease. This study was carried out at 1 and 3 days after infection (DPI) by M. cannonballus. RESULTS: Our results indicate a dissimilar behavior of the susceptible vs. the resistant genotypes from 1 to 3 DPI. 'PS' responded with a more rapid infection response than 'Pat 81' at 1 DPI. At 3 DPI the total number of differentially expressed genes identified in 'PS' declined from 451 to 359, while the total number of differentially expressed transcripts in 'Pat 81' increased from 187 to 849. Several deregulated transcripts coded for components of Ca2+ and jasmonic acid (JA) signalling pathways, as well as for other proteins related to defence mechanisms. Transcriptional differences in the activation of the JA-mediated response in 'Pat 81' compared to 'PS' suggested that JA response might be partially responsible for their observed differences in resistance. CONCLUSIONS: As a result of this study we have identified for the first time a set of candidate genes involved in the root response to the infection of the pathogen causing melon vine decline. This information is useful for understanding the disease progression and resistance mechanisms few days after inoculation.

Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato.

Tomato, Solanum lycopersicum, is divided into two widely distributed varieties: the cultivated S. lycopersicum var. lycopersicum, and the weedy S. lycopersicum var. cerasiforme. Solanum pimpinellifolium is the most closely related wild species of tomato.The roles of S. pimpinellifolium and S. l. cerasiforme during the domestication of tomato are still under debate. Some authors consider S. l. cerasiforme to be the ancestor, whereas others think that S. l. cerasiforme is an admixture of S. pimpinellifolium and the cultivated S. l. lycopersicum. It is also not clear whether the domestication occurred in the Andean region or in Mesoamerica. We characterized 272 accessions (63 S. pimpinellifolium, 106 S. l. cerasiforme, 95 S. l. lycopersicum and 8 derived from hybridization processes) were morphologically and genetically using the SolCap platform (7,414 SNPs). The two species were distinguished in a PCA analysis and displayed a rich geographic structure. Solanum lycopersicum var. cerasiforme and S. l. lycopersicum were also differentiated in the PCA and Structure analyses, which supports maintaining them as different varieties. Solanum pimpinellifolium and the Andean S. l. cerasiforme were more diverse than the non-Andean S. lycopersicum. Solanum lycopersicum var. cerasiforme was morphologically and molecularly intermediate between S. pimpinellifolium and tomato. Solanum lycopersicum var. cerasiforme, with the exception of several Ecuadorian and Mexican accessions, is composed of the products of admixture processes according to the Structure analysis. The non-admixtured S. l. cerasiforme might be similar to the ancestral cultivars from which the cultivated tomato originated, and presents remarkable morphological diversity, including fruits of up to 6 cm in diameter. The data obtained would fit a model in which a pre-domestication took place in the Andean region, with the domestication being completed in Mesoamerica. Subsequently, the Spaniards took plants from Mesoamerica to Spain and from there they were exported to the rest of the world.

High efficiency joint CZE determination of sugars and acids in vegetables and fruits.

In this work, an improved CE method for the medium-throughput determination of main organic acids (oxalate, malate, citrate), the amino acid glutamate and the sugars fructose, glucose and sucrose in several food matrices is described. These compounds have been identified as key components in the taste intensity of fruit and vegetable crops. Using a running buffer with 20 mM 2,6-pyridine dicarboxylic acid pH 12.1 and 0.1% hexadimethrine bromide, replacing it every 5 h to avoid pH decrease, and optimizing capillary conditioning between runs with 58 mM SDS during 2 min at 20 psi, it is possible to effectively quantify these compounds while increasing medium throughput repeatability. This procedure resolves problems such as increases in migration time and reduction of resolution between problematic peaks (malate/citrate and fructose/glucose) detected in a previous method. The new procedure even considerably reduced time analysis down to 12 min. Under optimal conditions, a large number of injections (200) could be administered without any disturbances in the same capillary. The reliability of the proposed method was further investigated with several food matrix samples, including tomato, pepper, muskmelon, winter squash, and orange. This method is recommended for routine analysis of large number of samples typical of production quality systems or plant breeding programs.

The genome of melon (Cucumis melo L.).

We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication, and our data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber. A low number of nucleotide-binding site-leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. The use of the genome sequence in future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.

Diversity in expression of phosphorus (P) responsive genes in Cucumis melo L.

BACKGROUND: Phosphorus (P) is a major limiting nutrient for plant growth in many soils. Studies in model species have identified genes involved in plant adaptations to low soil P availability. However, little information is available on the genetic bases of these adaptations in vegetable crops. In this respect, sequence data for melon now makes it possible to identify melon orthologues of candidate P responsive genes, and the expression of these genes can be used to explain the diversity in the root system adaptation to low P availability, recently observed in this species. METHODOLOGY AND FINDINGS: Transcriptional responses to P starvation were studied in nine diverse melon accessions by comparing the expression of eight candidate genes (Cm-PAP10.1, Cm-PAP10.2, Cm-RNS1, Cm-PPCK1, Cm-transferase, Cm-SQD1, Cm-DGD1 and Cm-SPX2) under P replete and P starved conditions. Differences among melon accessions were observed in response to P starvation, including differences in plant morphology, P uptake, P use efficiency (PUE) and gene expression. All studied genes were up regulated under P starvation conditions. Differences in the expression of genes involved in P mobilization and remobilization (Cm-PAP10.1, Cm-PAP10.2 and Cm-RNS1) under P starvation conditions explained part of the differences in P uptake and PUE among melon accessions. The levels of expression of the other studied genes were diverse among melon accessions, but contributed less to the phenotypical response of the accessions. CONCLUSIONS: This is the first time that these genes have been described in the context of P starvation responses in melon. There exists significant diversity in gene expression levels and P use efficiency among melon accessions as well as significant correlations between gene expression levels and phenotypical measurements.

High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping.

BACKGROUND: Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species.The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL). RESULTS: We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. CONCLUSION: Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in the coding regions of genes involved in different physiological processes. The platform will also be useful for future mapping and diversity studies, and will be essential in order to accelerate the process of breeding new and better-adapted squash varieties.

Localization of QTLs for in vitro plant regeneration in tomato.

BACKGROUND: Low regeneration ability limits biotechnological breeding approaches. The influence of genotype in the regeneration response is high in both tomato and other important crops. Despite the various studies that have been carried out on regeneration genetics, little is known about the key genes involved in this process. The aim of this study was to localize the genetic factors affecting regeneration in tomato. RESULTS: We developed two mapping populations (F2 and BC1) derived from a previously selected tomato cultivar (cv. Anl27) with low regeneration ability and a high regeneration accession of the wild species Solanum pennellii (PE-47). The phenotypic assay indicated dominance for bud induction and additive effects for both the percentage of explants with shoots and the number of regenerated shoots per explant. Two linkage maps were developed and six QTLs were identified on five chromosomes (1, 3, 4, 7 and 8) in the BC1 population by means of the Interval Mapping and restricted Multiple QTL Mapping methods. These QTLs came from S. pennellii, with the exception of the minor QTL located on chromosome 8, which was provided by cv. Anl27. The main QTLs correspond to those detected on chromosomes 1 and 7. In the F2 population, a QTL on chromosome 7 was identified on a similar region as that detected in the BC1 population. Marker segregation distortion was observed in this population in those areas where the QTLs of BC1 were detected. Furthermore, we located two tomato candidate genes using a marker linked to the high regeneration gene: Rg-2 (a putative allele of Rg-1) and LESK1, which encodes a serine/threonine kinase and was proposed as a marker for regeneration competence. As a result, we located a putative allele of Rg-2 in the QTL detected on chromosome 3 that we named Rg-3. LESK1, which is also situated on chromosome 3, is outside Rg-3. In a preliminary exploration of the detected QTL peaks, we found several genes that may be related to regeneration. CONCLUSIONS: In this study we have identified new QTLs related to the complex process of regeneration from tissue culture. We have also located two candidate genes, discovering a putative allele of the high regeneration gene Rg-1 in the QTL on chromosome 3. The identified QTLs could represent a significant step toward the understanding of this process and the identification of other related candidate genes. It will also most likely facilitate the development of molecular markers for use in gene isolation.

Towards a TILLING platform for functional genomics in Piel de Sapo melons.

BACKGROUND: The availability of genetic and genomic resources for melon has increased significantly, but functional genomics resources are still limited for this crop. TILLING is a powerful reverse genetics approach that can be utilized to generate novel mutations in candidate genes. A TILLING resource is available for cantalupensis melons, but not for inodorus melons, the other main commercial group. RESULTS: A new ethyl methanesulfonate-mutagenized (EMS) melon population was generated for the first time in an andromonoecious non-climacteric inodorus Piel de Sapo genetic background. Diverse mutant phenotypes in seedlings, vines and fruits were observed, some of which were of possible commercial interest. The population was first screened for mutations in three target genes involved in disease resistance and fruit quality (Cm-PDS, Cm-eIF4E and Cm-eIFI(iso)4E). The same genes were also tilled in the available monoecious and climacteric cantalupensis EMS melon population. The overall mutation density in this first Piel de Sapo TILLING platform was estimated to be 1 mutation/1.5 Mb by screening four additional genes (Cm-ACO1, Cm-NOR, Cm-DET1 and Cm-DHS). Thirty-three point mutations were found for the seven gene targets, six of which were predicted to have an impact on the function of the protein. The genotype/phenotype correlation was demonstrated for a loss-of-function mutation in the Phytoene desaturase gene, which is involved in carotenoid biosynthesis. CONCLUSIONS: The TILLING approach was successful at providing new mutations in the genetic background of Piel de Sapo in most of the analyzed genes, even in genes for which natural variation is extremely low. This new resource will facilitate reverse genetics studies in non-climacteric melons, contributing materially to future genomic and breeding studies.

ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using next generation sequence.

BACKGROUND: The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application. RESULTS: The ngs_backbone software is a parallel pipeline capable of analyzing Sanger, 454, Illumina and SOLiD (Sequencing by Oligonucleotide Ligation and Detection) sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping and single nucleotide polymorphism (SNP) calling and selection. In order to build a truly useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism in tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina. 23,360 single nucleotide variations (SNVs) were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real. CONCLUSIONS: ngs_backbone is a new software package capable of analyzing sequences produced by NGS technologies and predicting SNVs with great accuracy. In our tomato example, we created a highly polymorphic collection of SNVs that will be a useful resource for tomato researchers and breeders. The software developed along with its documentation is freely available under the AGPL license and can be downloaded from http://bioinf.comav.upv.es/ngs_backbone/ or http://github.com/JoseBlanca/franklin.

Volatile and capsaicinoid composition of ají (Capsicum baccatum) and rocoto (Capsicum pubescens), two Andean species of chile peppers.

BACKGROUND: Ají (Capsicum baccatum L. var. pendulum) and rocoto (Capsicum pubescens R. & P.) are two species of chile pepper used for millennia in Andean cuisine. The introduction of these relatively unknown Capsicum species to new markets requires an understanding of their flavour-related compounds. Thus both heat level (Scoville method and gas chromatography/mass spectrometry (GC/MS)) and, particularly, aroma (headspace solid phase microextraction and GC/MS/olfactometry) were studied in different accessions of ají and rocoto and a C. chinense control. RESULTS: Ajíes and rocotos are mildly pungent compared with C. chinense (13-352 vs 1605 mg kg(-1) total capsaicinoids). More than 200 volatiles were detected and marked differences in volatile pattern were found between the studied accessions. The powerful fruity/exotic aroma of the C. chinense control is due to esters such as ethyl 4-methylpentanoate, norcarotenoids such as ß-ionone and the hydrocarbon ectocarpene. In contrast, the Andean peppers had more earthy/vegetable/bell pepper-like aromas. Rocotos also exhibited a distinct additional cucumber odour, while one of the ajíes had a distinctive sweet/fruity note. The aroma of C. pubescens fruits is mainly due to substituted 2-methoxypyrazines and lipoxygenase cleavage products (e.g. 2-nonenals, 2,6-nonadienal). 2-Heptanethiol, 3-isobutyl-2-methoxypyrazine and several phenols (e.g. guaiacol) and terpenoids (e.g. α-pinene, 1,8-cineol, linalool) are the basis of C. baccatum aroma, with some 3-methyl-2-butyl esters contributing to fruity notes. CONCLUSION: In this study the compounds responsible for heat and aroma in the Andean peppers C. baccatum and C. pubescens were identified. The results will be of use to inspire future studies aimed at improving the flavour of these species.

Evaluation of the genotype, environment and their interaction on carotenoid and ascorbic acid accumulation in tomato germplasm.

BACKGROUND: Tomatoes are an important source of antioxidants (carotenoids, vitamin C, etc.) owing to their high level of consumption. There is great interest in developing cultivars with increased levels of lycopene, ß-carotene or L-ascorbic acid. There is necessary to survey new sources of variation. In this study, the potential of improvement for each character in tomato breeding programmes, in a single or joint approach, and the nature of genotype (G), environment (E) and G × E interaction effects in the expression of these characters were investigated. RESULTS: The content of lycopene, ß-carotene and ascorbic acid determined was very high in some phenotypes (up to 281, 35 and 346 mg kg(-1) respectively). The important differences in the three environments studied (with some stressing conditions in several situations) had a remarkable influence in the phenotypic expression of the functional characters evaluated. Nevertheless, the major contribution came from the genotypic effect along with a considerable G × E interaction. CONCLUSION: The joint accumulation of lycopene and ß-carotene has a high genetic component. It is possible to select elite genotypes with high content of both carotenoids in tomato breeding programmes but multi-environment trials are recommended. The improvement of ascorbic acid content is more difficult because the interference of uncontrolled factors mask the real genetic potential. Among the accessions evaluated, there are four accessions with an amazing genetic potential for functional properties that can be used as donor parents in tomato breeding programmes or for direct consumption in quality markets.

Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae).

BACKGROUND: Cucurbita pepo belongs to the Cucurbitaceae family. The "Zucchini" types rank among the highest-valued vegetables worldwide, and other C. pepo and related Cucurbita spp., are food staples and rich sources of fat and vitamins. A broad range of genomic tools are today available for other cucurbits that have become models for the study of different metabolic processes. However, these tools are still lacking in the Cucurbita genus, thus limiting gene discovery and the process of breeding. RESULTS: We report the generation of a total of 512,751 C. pepo EST sequences, using 454 GS FLX Titanium technology. ESTs were obtained from normalized cDNA libraries (root, leaves, and flower tissue) prepared using two varieties with contrasting phenotypes for plant, flowering and fruit traits, representing the two C. pepo subspecies: subsp. pepo cv. Zucchini and subsp. ovifera cv Scallop. De novo assembling was performed to generate a collection of 49,610 Cucurbita unigenes (average length of 626 bp) that represent the first transcriptome of the species. Over 60% of the unigenes were functionally annotated and assigned to one or more Gene Ontology terms. The distributions of Cucurbita unigenes followed similar tendencies than that reported for Arabidopsis or melon, suggesting that the dataset may represent the whole Cucurbita transcriptome. About 34% unigenes were detected to have known orthologs of Arabidopsis or melon, including genes potentially involved in disease resistance, flowering and fruit quality. Furthermore, a set of 1,882 unigenes with SSR motifs and 9,043 high confidence SNPs between Zucchini and Scallop were identified, of which 3,538 SNPs met criteria for use with high throughput genotyping platforms, and 144 could be detected as CAPS. A set of markers were validated, being 80% of them polymorphic in a set of variable C. pepo and C. moschata accessions. CONCLUSION: We present the first broad survey of gene sequences and allelic variation in C. pepo, where limited prior genomic information existed. The transcriptome provides an invaluable new tool for biological research. The developed molecular markers are the basis for future genetic linkage and quantitative trait loci analysis, and will be essential to speed up the process of breeding new and better adapted squash varieties.

Evaluation of genotype and environment effects on taste and aroma flavor components of Spanish fresh tomato varieties.

Taste and aroma related compounds have been analyzed in a collection of four traditional varieties and two tomato hybrids, representing a wide variability in fruit shape and color, grown in different environments: screenhouse and open field. Protected cultivation tended to show lower sugar concentration (fructose and glucose) but similar acid contents (citric, malic, and glutamic acids). The decreased levels of sucrose equivalents and the similar ratios of sucrose equivalents to citric or glutamic acid contents indicated that protected cultivation, despite being useful to reduce the incidence of pests and viral diseases, reduces the organoleptic quality. Additionally, it doubles the interaccession variability and increased the level of intra-accession variability. In the case of aroma, the genotypic effect was considerably higher than the environmental component on the 12 main volatiles analyzed. Only hexanal and methyl salicylate were significantly affected by environment, while 10 out of 12 volatiles were affected by the genotype. Biplot analysis showed that, even in considerably different environments, it is possible to identify genotype-dependent main aroma profiles. In the case of 13 background volatiles, the environment showed no significant effects and the genotypic effect was lower, though it is possible to identify genotypic trends in background notes.

Evolutionary analysis of tomato Sw-5 resistance-breaking isolates of Tomato spotted wilt virus.

Tomato spotted wilt virus (TSWV) causes severe economic losses in many crops worldwide and often overcomes resistant cultivars used for disease control. Comparison of nucleotide and amino acid sequences suggested that tomato resistance conferred by the gene Sw-5 can be overcome by the amino acid substitution C to Y at position 118 (C118Y) or T120N in the TSWV movement protein, NSm. Phylogenetic analysis revealed that substitution C118Y has occurred independently three times in the studied isolates by convergent evolution, whereas the substitution T120N was a unique event. Analysis of rates of non-synonymous and synonymous changes at individual codons showed that substitution C118Y was positively selected.

EcoTILLING in Capsicum species: searching for new virus resistances.

BACKGROUND: The EcoTILLING technique allows polymorphisms in target genes of natural populations to be quickly analysed or identified and facilitates the screening of genebank collections for desired traits. We have developed an EcoTILLING platform to exploit Capsicum genetic resources. A perfect example of the utility of this EcoTILLING platform is its application in searching for new virus-resistant alleles in Capsicum genus. Mutations in translation initiation factors (eIF4E, eIF(iso)4E, eIF4G and eIF(iso)4G) break the cycle of several RNA viruses without affecting the plant life cycle, which makes these genes potential targets to screen for resistant germplasm. RESULTS: We developed and assayed a cDNA-based EcoTILLING platform with 233 cultivated accessions of the genus Capsicum. High variability in the coding sequences of the eIF4E and eIF(iso)4E genes was detected using the cDNA platform. After sequencing, 36 nucleotide changes were detected in the CDS of eIF4E and 26 in eIF(iso)4E. A total of 21 eIF4E haplotypes and 15 eIF(iso)4E haplotypes were identified. To evaluate the functional relevance of this variability, 31 possible eIF4E/eIF(iso)4E combinations were tested against Potato virus Y. The results showed that five new eIF4E variants (pvr2(10), pvr2(11), pvr2(12), pvr2(13) and pvr2(14)) were related to PVY-resistance responses. CONCLUSIONS: EcoTILLING was optimised in different Capsicum species to detect allelic variants of target genes. This work is the first to use cDNA instead of genomic DNA in EcoTILLING. This approach avoids intronic sequence problems and reduces the number of reactions. A high level of polymorphism has been identified for initiation factors, showing the high genetic variability present in our collection and its potential use for other traits, such as genes related to biotic or abiotic stresses, quality or production. Moreover, the new eIF4E and eIF(iso)4E alleles are an excellent collection for searching for new resistance against other RNA viruses.

Carotenoid composition and vitamin A value in ají (Capsicum baccatum L.) and rocoto (C. pubescens R. & P.), 2 pepper species from the Andean region.

The carotenoid patterns of fully ripe fruits from 12 Bolivian accessions of the Andean peppers Capsicum baccatum (ají) and C. pubescens (rocoto) were determined by high-performance liquid chromatography (HPLC)-photodiode array detector (PDA)-mass spectrometry (MS). We include 2 California Wonder cultivars as C. annuum controls. A total of 16 carotenoids were identified and differences among species were mostly found at the quantitative level. Among red-fruited genotypes, capsanthin was the main carotenoid in the 3 species (25% to 50% contribution to carotenoid fraction), although ajíes contained the lowest contribution of this carotenoid. In addition, the contribution of capsanthin 5,6-epoxide to total carotenoids in this species was high (11% to 27%) in comparison to rocotos and red C. annuum. Antheraxanthin and violaxanthin were, in general, the next most relevant carotenoids in the red Andean peppers (6.1% to 10.6%). Violaxanthin was the major carotenoid in yellow-/orange-fruited genotypes of the 3 species (37% to 68% total carotenoids), although yellow rocotos were characterized by lower levels (<45%). Cis-violaxanthin, antheraxanthin, and lutein were the next most relevant carotenoids in the yellow/orange Andean peppers (5% to 14%). As a whole, rocotos showed the highest contributions of provitamin A carotenoids to the carotenoid fraction. In terms of nutritional contribution, both ajíes and rocotos provide a remarkable provitamin A activity, with several accessions showing a content in retinol equivalents higher than California Wonder controls. Furthermore, levels of lutein in yellow/orange ajíes and rocotos were clearly higher than California Wonder pepper (≥1000 µg·100/g). Finally, the Andean peppers, particularly red ajíes, can be also considered as a noticeable source of capsanthin, the most powerful antioxidant compound among pepper carotenoids. Practical Application: Capsicum peppers are known for their content in carotenoids, although there is no information about 2 species with Andean origin: ajíes and rocotos. Due to their relevance for the Andean cuisine and increasing importance in ethnic restaurants in Europe, we studied their carotenoid pattern and vitamin A contribution.

An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.).

BACKGROUND: Melon (Cucumis melo) is a horticultural specie of significant nutritional value, which belongs to the Cucurbitaceae family, whose economic importance is second only to the Solanaceae. Its small genome of approx. 450 Mb coupled to the high genetic diversity has prompted the development of genetic tools in the last decade. However, the unprecedented existence of a transcriptomic approaches in melon, highlight the importance of designing new tools for high-throughput analysis of gene expression. RESULTS: We report the construction of an oligo-based microarray using a total of 17,510 unigenes derived from 33,418 high-quality melon ESTs. This chip is particularly enriched with genes that are expressed in fruit and during interaction with pathogens. Hybridizations for three independent experiments allowed the characterization of global gene expression profiles during fruit ripening, as well as in response to viral and fungal infections in plant cotyledons and roots, respectively. Microarray construction, statistical analyses and validation together with functional-enrichment analysis are presented in this study. CONCLUSION: The platform validation and enrichment analyses shown in our study indicate that this oligo-based microarray is amenable for future genetic and functional genomic studies of a wide range of experimental conditions in melon.

A set of EST-SNPs for map saturation and cultivar identification in melon.

BACKGROUND: There are few genomic tools available in melon (Cucumis melo L.), a member of the Cucurbitaceae, despite its importance as a crop. Among these tools, genetic maps have been constructed mainly using marker types such as simple sequence repeats (SSR), restriction fragment length polymorphisms (RFLP) and amplified fragment length polymorphisms (AFLP) in different mapping populations. There is a growing need for saturating the genetic map with single nucleotide polymorphisms (SNP), more amenable for high throughput analysis, especially if these markers are located in gene coding regions, to provide functional markers. Expressed sequence tags (ESTs) from melon are available in public databases, and resequencing ESTs or validating SNPs detected in silico are excellent ways to discover SNPs. RESULTS: EST-based SNPs were discovered after resequencing ESTs between the parental lines of the PI 161375 (SC) x 'Piel de sapo' (PS) genetic map or using in silico SNP information from EST databases. In total 200 EST-based SNPs were mapped in the melon genetic map using a bin-mapping strategy, increasing the map density to 2.35 cM/marker. A subset of 45 SNPs was used to study variation in a panel of 48 melon accessions covering a wide range of the genetic diversity of the species. SNP analysis correctly reflected the genetic relationships compared with other marker systems, being able to distinguish all the accessions and cultivars. CONCLUSION: This is the first example of a genetic map in a cucurbit species that includes a major set of SNP markers discovered using ESTs. The PI 161375 x 'Piel de sapo' melon genetic map has around 700 markers, of which more than 500 are gene-based markers (SNP, RFLP and SSR). This genetic map will be a central tool for the construction of the melon physical map, the step prior to sequencing the complete genome. Using the set of SNP markers, it was possible to define the genetic relationships within a collection of forty-eight melon accessions as efficiently as with SSR markers, and these markers may also be useful for cultivar identification in Occidental melon varieties.

How microspores transform into haploid embryos: changes associated with embryogenesis induction and microspore-derived embryogenesis.

Microspore embryogenesis is the most powerful androgenic pathway to produce haploid and doubled haploid plants. To deviate a microspore toward embryogenesis, a number of factors, different for each species, must concur at the same time and place. Once induced, the microspore undergoes numerous changes at different levels, from overall morphology to gene expression. Induction of microspore embryogenesis not only implies the expression of an embryogenic program, but also a stress-related cellular response and a repression of the gametophytic program to revert the microspore to a totipotent status. In this review, we compile the most recent advances in the understanding of the changes undergone by the induced microspore to readapt to the new developmental scenario. We devote special attention to the efforts made to uncover changes in the transcriptome of the induced microspore and microspore-derived embryo (MDE). Finally, we discuss the influence that an in vitro environment exerts over the MDE, as compared with its zygotic counterpart.

EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration.

BACKGROUND: Expressed sequence tag (EST) collections are composed of a high number of single-pass, redundant, partial sequences, which need to be processed, clustered, and annotated to remove low-quality and vector regions, eliminate redundancy and sequencing errors, and provide biologically relevant information. In order to provide a suitable way of performing the different steps in the analysis of the ESTs, flexible computation pipelines adapted to the local needs of specific EST projects have to be developed. Furthermore, EST collections must be stored in highly structured relational databases available to researchers through user-friendly interfaces which allow efficient and complex data mining, thus offering maximum capabilities for their full exploitation. RESULTS: We have created EST2uni, an integrated, highly-configurable EST analysis pipeline and data mining software package that automates the pre-processing, clustering, annotation, database creation, and data mining of EST collections. The pipeline uses standard EST analysis tools and the software has a modular design to facilitate the addition of new analytical methods and their configuration. Currently implemented analyses include functional and structural annotation, SNP and microsatellite discovery, integration of previously known genetic marker data and gene expression results, and assistance in cDNA microarray design. It can be run in parallel in a PC cluster in order to reduce the time necessary for the analysis. It also creates a web site linked to the database, showing collection statistics, with complex query capabilities and tools for data mining and retrieval. CONCLUSION: The software package presented here provides an efficient and complete bioinformatics tool for the management of EST collections which is very easy to adapt to the local needs of different EST projects. The code is freely available under the GPL license and can be obtained at http://bioinf.comav.upv.es/est2uni. This site also provides detailed instructions for installation and configuration of the software package. The code is under active development to incorporate new analyses, methods, and algorithms as they are released by the bioinformatics community.