Root transcriptional responses of two melongenotypes with contrasting resistance toMonosporascus 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.Roig Montaner, MC.; Fita, A.; Rios, G.; Hammond, JP.; Nuez Viñals, F.; Picó Sirvent, MB. (2012). 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Recuperación y conservación de cultivares tradicionales de melón castellano-manchego

Los trabajos realizados han sido financiados por el proyecto INIARF2008-00003-C02.Ribas, F.; Cabello, M.; Castellanos, MT.; Fita, A.; Roig Montaner, MC.; Nuez Viñals, F.; Picó Sirvent, MB. (2011). Recuperación y conservación de cultivares tradicionales de melón castellano-manchego. Agrícola Vergel. 347:206-213. http://hdl.handle.net/10251/49390S20621334

Transcriptome sequencing for SNP discovery across Cucumis melo

Background: Melon (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.Results: The 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.Conclusions: This 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. © 2012 Blanca et al.; licensee BioMed Central Ltd.This project was carried out in the frame of the MELONOMICS project (2009-2012) of the Fundacion Genoma Espana.Blanca Postigo, JM.; Esteras Gómez, C.; Ziarsolo Areitioaurtena, P.; Perez, D.; Fernández-Pedrosa, V.; Collado, C.; Rodríguez De Pablos, R.... (2012). Transcriptome sequencing for SNP discovery across Cucumis melo. BMC Genomics. 13(280):1-18. doi:10.1186/1471-2164-13-280S1181328

RICORS2040 : The need for collaborative research in chronic kidney disease

Chronic kidney disease (CKD) is a silent and poorly known killer. The current concept of CKD is relatively young and uptake by the public, physicians and health authorities is not widespread. Physicians still confuse CKD with chronic kidney insufficiency or failure. For the wider public and health authorities, CKD evokes kidney replacement therapy (KRT). In Spain, the prevalence of KRT is 0.13%. Thus health authorities may consider CKD a non-issue: very few persons eventually need KRT and, for those in whom kidneys fail, the problem is 'solved' by dialysis or kidney transplantation. However, KRT is the tip of the iceberg in the burden of CKD. The main burden of CKD is accelerated ageing and premature death. The cut-off points for kidney function and kidney damage indexes that define CKD also mark an increased risk for all-cause premature death. CKD is the most prevalent risk factor for lethal coronavirus disease 2019 (COVID-19) and the factor that most increases the risk of death in COVID-19, after old age. Men and women undergoing KRT still have an annual mortality that is 10- to 100-fold higher than similar-age peers, and life expectancy is shortened by ~40 years for young persons on dialysis and by 15 years for young persons with a functioning kidney graft. CKD is expected to become the fifth greatest global cause of death by 2040 and the second greatest cause of death in Spain before the end of the century, a time when one in four Spaniards will have CKD. However, by 2022, CKD will become the only top-15 global predicted cause of death that is not supported by a dedicated well-funded Centres for Biomedical Research (CIBER) network structure in Spain. Realizing the underestimation of the CKD burden of disease by health authorities, the Decade of the Kidney initiative for 2020-2030 was launched by the American Association of Kidney Patients and the European Kidney Health Alliance. Leading Spanish kidney researchers grouped in the kidney collaborative research network Red de Investigación Renal have now applied for the Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORS) call for collaborative research in Spain with the support of the Spanish Society of Nephrology, Federación Nacional de Asociaciones para la Lucha Contra las Enfermedades del Riñón and ONT: RICORS2040 aims to prevent the dire predictions for the global 2040 burden of CKD from becoming true

An analysis in the structure of a genetic characterized melon germplasm collection for climacteric-non climacteric ripening behaviour

[EN] Melon (Cucumis melo L. Cucurbitaceae) is considered one of the most variable species within the genus Cucumis as well as among the other cultivated plants. Moreover it represents a key species in order to study ethylene involvement in ripening because several climacteric and non climacteric accessions are available. In this study we used a core collection of 198 melon accessions including wild relatives, feral types, landraces, breeding lines and commercial cultivars from 54 countries. This collection established within the framework of a previous project, was selfed, genotyped with AFLP markers and extensively phenotyped for plant and fruit traits at COMAV. Furthermore deep transcriptome resequencing work was carried out on all the genotypes, thus providing the largest melon SNP collection generated to date. Taking advantage of this information we present here the preliminary analysis of the structure of this germplasm collection with the aim of selecting a group of melon varieties with great differences in ripening behavior and minimum genetic structure to be used for association studies.Leida, C.; Moser, C.; Esteras Gómez, C.; Roig Montaner, MC.; Picó Sirvent, MB.; Monforte Gilabert, AJ. (2015). An analysis in the structure of a genetic characterized melon germplasm collection for climacteric-non climacteric ripening behaviour. Acta Horticulturae. 1100:95-98. doi:10.17660/ActaHortic.2015.1100.12S9598110

Genetic diversity of Spanish Cucurbita pepo landraces: an unexploited resource for summer squash breeding

[EN] Cucurbita pepo is a worldwide cultivated vegetable of American origin. Most of the widely grown commercial types are known as summer squashes and belong to the elongated forms of C. pepo ssp. pepo (Cocozelle, Vegetable marrow and Zucchini groups). These forms were developed in Europe after the arrival of the first American landraces through a process of selection and fixation that led to a loss of genetic diversity. Part of the genetic variability of the first American cultigens remains intact in diverse landraces that are still cultivated for self-consumption and sale in local markets. Using the first collection of genomic and EST-derived microsatellites that has just become available for the species, we compared the natural variation present in a collection of Spanish landraces with that of a set of commercial varieties and hybrids, representing current summer squash market offerings. A total of 194 alleles allowed us to distinguish all the genotypes, even those that were closely related. In general, Cocozelle and Vegetable marrow, groups with considerably long histories, were more variable than the Zucchini group, of more recent origin. We found significant genetic diversity among landraces. The variation present among landraces belonging to the Zucchini group was larger than that of the commercial cultivars. Cluster, principal coordinate and population structure results suggested that the variation of the Spanish landraces has not been extensively used in breeding. Commercial summer squashes can therefore benefit from this underexploited variability, especially from certain landraces that already display favourable commercial traits.This research was funded by Projects INIA (RTA2008-00035-C02-02 and RTA2011-00044-C02-2) of the Spanish Instituto Nacional de Investigacion y Tecnologia Agraria. G. Formisano was supported by the Italian Doctorate School in Agrobiology and Agrochemistry of the University of Naples "Federico II". Authors want to thank E. Martinez Perez her technical assistance for fruit characterization.Formisano, G.; Roig Montaner, MC.; Esteras Gómez, C.; Ercolano, MR.; Nuez Viñals, F.; Monforte Gilabert, AJ.; Picó Sirvent, MB. (2012). Genetic diversity of Spanish Cucurbita pepo landraces: an unexploited resource for summer squash breeding. Genetic Resources and Crop Evolution. 59(6):1169-1184. https://doi.org/10.1007/s10722-011-9753-yS1169118459

SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium

Novel sequencing technologies were recently used to generate sequences from multiple melon (Cucumis melo L.) genotypes, enabling the in silico identification of large single nucleotide polymorphism (SNP) collections. In order to optimize the use of these markers, SNP validation and large-scale genotyping are necessary. In this paper, we present the first validated design for a genotyping array with 768 SNPs that are evenly distributed throughout the melon genome. This customized Illumina GoldenGate assay was used to genotype a collection of 74 accessions, representing most of the botanical groups of the species. Of the assayed loci, 91 % were successfully genotyped. The array provided a large number of polymorphic SNPs within and across accessions. This set of SNPs detected high levels of variation in accessions from this crop s center of origin as well as from several other areas of melon diversification. Allele distribution throughout the genome revealed regions that distinguished between the two main groups of cultivated accessions (inodorus and cantalupensis). Population structure analysis showed a subdivision into five subpopulations, reflecting the history of the crop. A considerably low level of LD was detected, which decayed rapidly within a few kilobases. Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in melon. Since many of the genotyped accessions are currently being used as the parents of breeding populations in various programs, this set of mapped markers could be used for future mapping and breeding efforts.This project was carried out in the frame of the MELONOMICS project (2009-2012) of the Fundacion Genoma Espana and with the contributions of the PLAT KKBE project PIM2010PKB-00691.Esteras Gómez, C.; Formisano, G.; Roig Montaner, MC.; Díaz Bermúdez, A.; Blanca Postigo, JM.; Garcia-Mas, J.; Gomez-Guillamon, M.... (2013). SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium. TAG Theoretical and Applied Genetics. 126(5):1285-1303. https://doi.org/10.1007/s00122-013-2053-5S12851303126