Genomic prediction with special weight of major genes is a valuable tool to populate bio-digital resource centers.
AbstractPhenotypic information of crop genetic resources is a prerequisite for an informed selection that aims to broaden the genetic base of the elite breeding pools. We investigated the potential of genomic prediction based on historical screening data of plant responses against the Barley yellow mosaic viruses for populating the bio-digital resource center of barley. Our study includes dense marker data for 3838 accessions of winter barley, and historical screening data of 1751 accessions for Barley yellow mosaic virus (BaYMV) and of 1771 accessions for Barley mild mosaic virus (BaMMV). Linear mixed models were fitted by considering combinations for the effects of genotypes, years, and locations. The best linear unbiased estimations displayed a broad spectrum of plant responses against BaYMV and BaMMV. Prediction abilities, computed as correlations between predictions and observed phenotypes of accessions, were low for the marker-assisted selection approach amounting to 0.42. In contrast, prediction abilities of genomic best linear unbiased predictions were high, with values of 0.62 for BaYMV and 0.64 for BaMMV. Prediction abilities of genomic prediction were improved by up to\uffe2\uff80\uff89~\uffe2\uff80\uff895% using W-BLUP, in which more weight is given to markers with significant major effects found by association mapping. Our results outline the utility of historical screening data and W-BLUP model to predict the performance of the non-phenotyped individuals in genebank collections. The presented strategy can be considered as part of the different approaches used in genebank genomics to valorize genetic resources for their usage in disease resistance breeding and research.
", "keywords": ["Genetic Markers", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Genotype", "Chromosome Mapping", "Genetic Variation", "Hordeum", "Genomics", "Potyviridae", "Linkage Disequilibrium", "Plant Breeding", "03 medical and health sciences", "Phenotype", "Databases", " Genetic", "Original Article", "Genetic Association Studies", "Disease Resistance", "Plant Diseases"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s00122-021-03815-0.pdf"}, {"href": "https://doi.org/10.1007/s00122-021-03815-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Theoretical%20and%20Applied%20Genetics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00122-021-03815-0", "name": "item", "description": "10.1007/s00122-021-03815-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00122-021-03815-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-25T00:00:00Z"}}, {"id": "10.1038/s41438-020-00353-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:17:47Z", "type": "Journal Article", "created": "2020-09-01", "title": "ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean \u2018da serbo\u2019 type long shelf-life germplasm", "description": "AbstractDouble digest restriction-site associated sequencing (ddRAD-seq) is a flexible and cost-effective strategy for providing in-depth insights into the genetic architecture of germplasm collections. Using this methodology, we investigated the genomic diversity of a panel of 288 diverse tomato (Solanum lycopersicumL.) accessions enriched in \uffe2\uff80\uff98da serbo\uffe2\uff80\uff99 (called \uffe2\uff80\uff98de penjar\uffe2\uff80\uff99 in Spain) long shelf life (LSL) materials (152 accessions) mostly originating from Italy and Spain. The rest of the materials originate from different countries and include landraces for fresh consumption, elite cultivars, heirlooms, and breeding lines. Apart from their LSL trait, \uffe2\uff80\uff98da serbo\uffe2\uff80\uff99 landraces are of remarkable interest for their resilience. We identified 32,799 high-quality SNPs, which were used for model ancestry population structure and non-parametric hierarchical clustering. Six genetic subgroups were revealed, clearly separating most \uffe2\uff80\uff98da serbo\uffe2\uff80\uff99 landraces, but also the Spanish germplasm, suggesting a subdivision of the population based on type and geographical provenance. Linkage disequilibrium (LD) in the collection decayed very rapidly within <5\uffe2\uff80\uff89kb. We then investigated SNPs showing contrasted minor frequency allele (MAF) in \uffe2\uff80\uff98da serbo\uffe2\uff80\uff99 materials, resulting in the identification of high frequencies in this germplasm of several mutations in genes related to stress tolerance and fruit maturation such asCTR1andJAR1. Finally, a mini-core collection of 58 accessions encompassing most of the diversity was selected for further exploitation of key traits. Our findings suggest the presence of a genetic footprint of the \uffe2\uff80\uff98da serbo\uffe2\uff80\uff99 germplasm selected in the Mediterranean basin. Moreover, we provide novel insights on LSL \uffe2\uff80\uff98da serbo\uffe2\uff80\uff99 germplasm as a promising source of alleles for tolerance to stresses.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "GENETICA", "0303 health sciences", "03 medical and health sciences", "Genetic markers", "Genomics", "Plant breeding", "Article", "02.- Poner fin al hambre", " conseguir la seguridad alimentaria y una mejor nutrici\u00f3n", " y promover la agricultura sostenible"]}, "links": [{"href": "https://iris.cnr.it/bitstream/20.500.14243/451962/1/41438_2020_article_353.pdf"}, {"href": "https://www.nature.com/articles/s41438-020-00353-6.pdf"}, {"href": "https://doi.org/10.1038/s41438-020-00353-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Horticulture%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41438-020-00353-6", "name": "item", "description": "10.1038/s41438-020-00353-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41438-020-00353-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-01T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Genetic+Markers&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Genetic+Markers&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Genetic+Markers&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Genetic+Markers&offset=2", "hreflang": "en-US"}], "numberMatched": 2, "numberReturned": 2, "distributedFeatures": [], "timeStamp": "2026-05-30T08:15:10.901621Z"}