Belén Picó

Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers

Cucurbita pepo is a highly polymorphic species. The cultivars can be grouped into eight morphotypes in two subspecies, ssp. pepo and ssp. ovifera. A collection of 69 accessions representative of the morphotypes and some unclassified types was used for analysing the morphological and molecular diversity of this species. This collection includes commercial cultivars and Spanish landraces, which represent the great diversification of types that have arisen in Europe after this species arrived from America. For the molecular variability studies, two PCR-based systems were employed, AFLP and SRAP, which preferentially amplify ORFs. Principal coordinates analysis and cluster analysis using the UPGMA method clearly separate the accessions into the two subspecies through the use of both markers. However, the gene diversity and the genetic identity values among morphotypes and subspecies varied between the two marker systems. The information given by SRAP markers was more concordant to the morphological variability and to the evolutionary history of the morphotypes than that of AFLP markers. In ssp. ovifera, the accessions of the different morphotypes were basically grouped according to the fruit colour. This may indicate different times of development and also the extent of breeding in the accessions used. This study has allowed identification of new types that can be employed for the development of new cultivars. The landraces of the spp. ovifera, used as ornamental in Europe, have proved to be of great interest for preserving the diversity of C. pepo.

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.

Application of genomic tools in plant breeding.

Plant breeding has been very successful in developing improved varieties using conventional tools and methodologies. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information. The analysis of NGS data by means of bioinformatics developments allows discovering new genes and regulatory sequences and their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Genomic approaches include TILLING and EcoTILLING, which make possible to screen mutant and germplasm collections for allelic variants in target genes. Re-sequencing of genomes is very useful for the genome-wide discovery of markers amenable for high-throughput genotyping platforms, like SSRs and SNPs, or the construction of high density genetic maps. All these tools and resources facilitate studying the genetic diversity, which is important for germplasm management, enhancement and use. Also, they allow the identification of markers linked to genes and QTLs, using a diversity of techniques like bulked segregant analysis (BSA), fine genetic mapping, or association mapping. These new markers are used for marker assisted selection, including marker assisted backcross selection, ‘breeding by design’, or new strategies, like genomic selection. In conclusion, advances in genomics are providing breeders with new tools and methodologies that allow a great leap forward in plant breeding, including the ‘superdomestication’ of crops and the genetic dissection and breeding for complex traits.

MELOGEN: an EST database for melon functional genomics

BackgroundMelon (Cucumis melo L.) is one of the most important fleshy fruits for fresh consumption. Despite this, few genomic resources exist for this species. To facilitate the discovery of genes involved in essential traits, such as fruit development, fruit maturation and disease resistance, and to speed up the process of breeding new and better adapted melon varieties, we have produced a large collection of expressed sequence tags (ESTs) from eight normalized cDNA libraries from different tissues in different physiological conditions.ResultsWe determined over 30,000 ESTs that were clustered into 16,637 non-redundant sequences or unigenes, comprising 6,023 tentative consensus sequences (contigs) and 10,614 unclustered sequences (singletons). Many potential molecular markers were identified in the melon dataset: 1,052 potential simple sequence repeats (SSRs) and 356 single nucleotide polymorphisms (SNPs) were found. Sixty-nine percent of the melon unigenes showed a significant similarity with proteins in databases. Functional classification of the unigenes was carried out following the Gene Ontology scheme. In total, 9,402 unigenes were mapped to one or more ontology. Remarkably, the distributions of melon and Arabidopsis unigenes followed similar tendencies, suggesting that the melon dataset is representative of the whole melon transcriptome. Bioinformatic analyses primarily focused on potential precursors of melon micro RNAs (miRNAs) in the melon dataset, but many other genes potentially controlling disease resistance and fruit quality traits were also identified. Patterns of transcript accumulation were characterised by Real-Time-qPCR for 20 of these genes.ConclusionThe collection of ESTs characterised here represents a substantial increase on the genetic information available for melon. A database (MELOGEN) which contains all EST sequences, contig images and several tools for analysis and data mining has been created. This set of sequences constitutes also the basis for an oligo-based microarray for melon that is being used in experiments to further analyse the melon transcriptome.

Evaluation of whitefly-mediated inoculation techniques to screen Lycopersicon esculentum and wild relatives for resistance to Tomato yellow leaf curl virus

For two consecutive years nine hybrids and three varieties of tomato, four Lycopersicon peruvianum and four Lycopersicon chilense accessions were screened for Tomato yellow leaf curl virus (TYLCV) resistance. Three inoculation techniques using Bemisia tabaci, the vector of TYLCV, were compared: (1) artificial mass inoculation-simultaneous infection of cultivated and wild material in greenhouses; (2) artificial cage inoculation-individual infection in insect-proof cages; (3) natural field infection. Artificial inoculations led to higher levels of infection, but different patterns of response to each inoculation technique were found depending on the resistance level.Tomato varieties showed an important fruit set reduction after both artificial and natural inoculations. In contrast, field infection was milder in tomato hybrids, in which yield was barely affected. These hybrids showed a wide range of reactions with the two artificial inoculation techniques, but infection was always more severe after mass inoculation. Extreme severity of mass infection made it difficult to differentiate among variable degrees of resistance that were more reliably detected with cage inoculation. The hybrids F3524, F3522, Fiona, and Tyking showed the highest level of resistance. F3524 and F3522 had an acceptable yield in field and cage assays, but their resistance collapsed under massive conditions of infection. Tyking and Fiona exhibited the best response in all conditions, although their yield was moderately reduced in mass assays. Mass inoculation was not adequate for the screening of wild Lycopersicon. Some susceptible plants escaped infection, probably as a consequence of non-preference mechanisms and loss of vector infectivity. Individual inoculation in cages prevented the risk of non-infection, ensuring 100% disease incidence. This technique allowed the selection of highly resistant wild sources. L. chilense LA 1969 and LA 1963 had the highest level of resistance with the three inoculation techniques. L. peruvianum PI-126944 and L. chilense LA 1932, which were only tested in mass and field conditions, also exhibited a promising response.The results proved that the inoculation technique influences the response of tomato and wild Lycopersicon spp to TYLCV. It is concluded that artificial cage inoculation, although more time-consuming, is the most efficient, adequate, and reliable technique to screen both cultivated and wild Lycopersicon species for resistance to TYLCV.

Transcriptome sequencing for SNP discovery across Cucumis melo

BackgroundMelon (Cucumis melo L.) is a highly diverse species that is cultivated worldwide. Recent advances in massively parallel sequencing have begun to allow the study of nucleotide diversity in this species. The Sanger method combined with medium-throughput 454 technology were used in a previous study to analyze the genetic diversity of germplasm representing 3 botanical varieties, yielding a collection of about 40,000 SNPs distributed in 14,000 unigenes. However, the usefulness of this resource is limited as the sequenced genotypes do not represent the whole diversity of the species, which is divided into two subspecies with many botanical varieties variable in plant, flowering, and fruit traits, as well as in stress response. As a first step to extensively document levels and patterns of nucleotide variability across the species, we used the high-throughput SOLiD™ system to resequence the transcriptomes of a set of 67 genotypes that had previously been selected from a core collection representing the extant variation of the entire species.ResultsThe deep transcriptome resequencing of all of the genotypes, grouped into 8 pools (wild African agrestis, Asian agrestis and acidulus, exotic Far Eastern conomon, Indian momordica and Asian dudaim and flexuosus, commercial cantalupensis, subsp. melo Asian and European landraces, Spanish inodorus landraces, and Piel de Sapo breeding lines) yielded about 300 M reads. Short reads were mapped to the recently generated draft genome assembly of the DHL line Piel de Sapo (inodorus) x Songwhan Charmi (conomon) and to a new version of melon transcriptome. Regions with at least 6X coverage were used in SNV calling, generating a melon collection with 303,883 variants. These SNVs were dispersed across the entire C. melo genome, and distributed in 15,064 annotated genes. The number and variability of in silico SNVs differed considerably between pools. Our finding of higher genomic diversity in wild and exotic agrestis melons from India and Africa as compared to commercial cultivars, cultigens and landraces from Eastern Europe, Western Asia and the Mediterranean basin is consistent with the evolutionary history proposed for the species. Group-specific SNVs that will be useful in introgression programs were also detected. In a sample of 143 selected putative SNPs, we verified 93% of the polymorphisms in a panel of 78 genotypes.ConclusionsThis study provides the first comprehensive resequencing data for wild, exotic, and cultivated (landraces and commercial) melon transcriptomes, yielding the largest melon SNP collection available to date and representing a notable sample of the species diversity. This data provides a valuable resource for creating a catalog of allelic variants of melon genes and it will aid in future in-depth studies of population genetics, marker-assisted breeding, and gene identification aimed at developing improved varieties.

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

BackgroundThe 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.ResultsA 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.ConclusionsThe 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.

Improved Diagnostic Techniques for Tomato Yellow Leaf Curl Virus in Tomato Breeding Programs

Breeding for tomatoes resistant to tomato yellow leaf curl geminivirus (TYLCV) is difficult, mainly due to the lack of an accurate system for selecting resistant plants. The variable nature of the genotypes used (wild or wild-derived genotypes and advanced breeding lines) makes the development of a reproducible selection procedure necessary during the breeding program. Serological and nucleic acid-based diagnostic techniques for detecting TYLCV were evaluated for their sensitivity, reliability, and possibility of quantification in order to select the combination of techniques that provides the most rapid and accurate characterization of the resistance level of each item. Squash blot followed by the more sensitive polymerase chain reaction (PCR) detection of inconclusive samples is recommended for the screening of new resistant sources among asymptomatic Lycopersicon spp., as they accumulate extremely low viral concentrations that cannot be detected by serological methods. A triple antibody sandwich-enzyme-linked immunosorbent assay (TAS-ELISA), modified to reduce the background, can be used in large-scale field screening of advanced breeding lines if combined with the more sensitive squash blot, which is less affected by the age and state of the tissue. Hybridization methods were also more appropriate to assess viral distribution throughout the plant than TAS-ELISA or even PCR, which fails to reliably detect TYLCV in tissues like roots.

Widening the genetic basis of virus resistance in tomato

Abstract New and old accessions of Lycopersicon chilense (LA 1932, LA 1938 and LA 1963), L. peruvianum (PI-143679 and PI-126944), and L. hirsutum (UPV-16910) recently reported as resistant to TSWV, TYLCV and PepMV, viral agents responsible for the most severe economic losses in tomato crop in Spain, were selected as male parents for crosses with L. esculentum in order to widen the genetic basis of virus resistance in tomato. After the analysis of the nature and severity of the barriers found in each case, crossability barriers between wild and cultivated species were circumvented by using several techniques. Crosses with pollen mixture (1:1, wild:cultivated) were successful in obtaining interspecific hybrids with the two L. chilense accessions (LA 1932 and LA 1963) that exhibited more relaxed post-cigotic barriers. Embryo rescue was also successful in crosses with these accessions and also in crosses with L. peruvianum accessions in which embryos beyond the globular stage were found (PI-143679). However, a combination of two or more strategies was necessary in crosses with those accessions exhibiting more severe crossability barriers. Mixture pollen crosses (10:1, wild:cultivated), combined with embryo rescue, allowed for the recovery of hybrids with LA 1938. Stigma and pistil complementation with H 3 BO 3 and GA 3 , followed by immature seed culture was found to be an effective method for the production of novel interspecific hybrids with PI-126944, the accession with the highest level of resistance to TSWV and TYLCV. By using the best combination of techniques we also backcrossed these interspecific hybrids to tomato to generate the BC1 progeny. The new genes introgressed will be useful to obtain new tomato varieties resistant to TSWV, TYLCV and PepMV.

Involvement of ethylene biosynthesis and signalling in fruit set and early fruit development in zucchini squash ( Cucurbita pepo L.)

BackgroundWe have identified a kind of parthenocarpy in zucchini squash which is associated with an incomplete andromonoecy, i.e. a partial conversion of female into bisexual flowers. Given that andromonoecy in this and other cucurbit species is caused by a reduction of ethylene production in the female flower, the associated parthenocarpic development of the fruit suggested the involvement of ethylene in fruit set and early fruit development.ResultsWe have compared the production of ethylene as well as the expression of 13 ethylene biosynthesis and signalling genes in pollinated and unpollinated ovaries/fruits of two cultivars, one of which is parthenocarpic (Cavili), while the other is non-parthenocarpic (Tosca). In the latter, unpollinated ovaries show an induction of ethylene biosynthesis and ethylene signal transduction pathway genes three days after anthesis, which is concomitant with the initiation of fruit abortion and senescence. Fruit set and early fruit development in pollinated flowers of both cultivars and unpollinated flowers of Cavili is coupled with low ethylene biosynthesis and signalling, which would also explain the partial andromonoecy in the parthenocarpic genotype. The reduction of ethylene production in the ovary cosegregates with parthenocarpy and partial andromonoecy in the selfing progeny of Cavili. Moreover, the induction of ethylene in anthesis (by ethephon treatments) reduced the percentage of bisexual parthenocarpic flowers in Cavili, while the inhibition of ethylene biosynthesis or response (by AVG and STS treatments) induces not only andromonoecy but also the parthenocarpic development of the fruit in both cultivars.ConclusionsResults demonstrate that a reduction of ethylene production or signalling in the zucchini flower is able to induce fruit set and early fruit development, and therefore that ethylene is actively involved in fruit set and early fruit development. Auxin and TIBA treatments, inducing fruit set and early fruit development in this species, also inhibit ethylene production and the expression of ethylene biosynthesis and response genes. A model is presented that discusses the crosstalk between ethylene and auxin in the control of fruit set and early fruit development in zucchini squash.