Agromorphological genetic diversity of Spanish traditional melons

[EN] The variability of 62 Spanish landraces (and two hybrids used as reference) was described by analysing 39 morphological traits and eight SSR makers. Results showed that 81% of the examined genetic pool belonged to the inodorus type. Spanish traditional melons presented fruits from flattened and globular shapes to elliptical. Rind colour varied from pale green, almost white and yellow to dark green and almost black. Rind texture varied from smooth to intensely wrinkled. Spanish landraces also had larger fruits (average fruit weight 2.6 kg) and longer vegetative cycles (117 days to maturity) compared to landraces from other geographical origins. Farmers seem to have focused on selection towards large fruits, which usually requires the longest production cycles. Fruit colour, size and shape seemed to have been determinant in varietal selection. Hierarchical clustering resulted in two main groups (climacteric and non-climacteric). The largest group was composed of 60 accessions of non-climacteric types, which includes the most demanded by national markets, 'Piel de Sapo', which fruits were characterized by an ovate or elliptical shape, a green rind, big spots and stains distributed over the whole fruit, a rounded blossom end shape and a very pointed stem end shape. The study demonstrates that the Spanish genetic pool is much more diverse. Wide variability was found in a geographical area with vast historical importance in melon farming. These evaluations has allowed the identification of several uniform groups of non-climacteric cultivars ('Piel de Sapo', 'Mochuelo', 'Tendral', Yellow/White, Winter and Black groups) and a set of highly variable climacteric ones. However, many accessions with singular properties remain unclassified, demonstrating the morphological variability of the studied collection. Melons in Spain have wide variability together with a vast historical importance on farms. Some fruit types, or at least some morphological characters reflected by painters during centuries, have reached the present. The present study confirmed the need to preserve these irreplaceable genetic resources and continue their study and evaluation for valuable traits which could enhance farmer's opportunities for entering new markets.The authors would like to thank Maria Jose Diez, the curator of the COMAV's Genebank for providing some of the melon varieties included in this study. Financial support was received from the Genome-Spain Foundation through the Project MELONOMICS (http://www.gen-es.org/es/melanomics.cfm). This study was partially supported by the Project AGL2014-53398-C2-R (funded by the Spanish Economy and Competitiveness Department, and the European Regional Development Fund).Lázaro, A.; Fernandez, I.; Borrero, M.; Cabello, F.; Lopez-Sese, A.; Gómez-Guillamon, M.; Picó Sirvent, MB. (2017). Agromorphological genetic diversity of Spanish traditional melons. 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Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

Background: We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15–20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases. Methods: We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded. Results: No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5–528.7, P = 1.1 × 10−4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3–8.2], P = 2.1 × 10−4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1–2635.4], P = 3.4 × 10−3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3–8.4], P = 7.7 × 10−8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10−5). Conclusions: Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

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