Web of Science: 52 citas, Scopus: 57 citas, Google Scholar: citas,
Sequence- vs. chip-assisted genomic selection : accurate biological information is advised
Pérez-Enciso, Miguel (Centre de Recerca en Agrigenòmica)
Rincón, Juan C. (Centre de Recerca en Agrigenòmica)
Legarra, Andres (Institut national de la recherche agronomique)

Fecha: 2015
Resumen: Background: the development of next-generation sequencing technologies (NGS) has made the use of whole-genome sequence data for routine genetic evaluations possible, which has triggered a considerable interest in animal and plant breeding fields. Here, we investigated whether complete or partial sequence data can improve upon existing SNP (single nucleotide polymorphism) array-based selection strategies by simulation using a mixed coalescence - gene-dropping approach. - Results: we simulated 20 or 100 causal mutations (quantitative trait nucleotides, QTN) within 65 predefined 'gene' regions, each 10 kb long, within a genome composed of ten 3-Mb chromosomes. We compared prediction accuracy by cross-validation using a medium-density chip (7. 5 k SNPs), a high-density (HD, 17 k) and sequence data (335 k). Genetic evaluation was based on a GBLUP method. The simulations showed: (1) a law of diminishing returns with increasing number of SNPs; (2) a modest effect of SNP ascertainment bias in arrays; (3) a small advantage of using whole-genome sequence data vs. HD arrays i. e. ~4%; (4) a minor effect of NGS errors except when imputation error rates are high (≥20%); and (5) if QTN were known, prediction accuracy approached 1. Since this is obviously unrealistic, we explored milder assumptions. We showed that, if all SNPs within causal genes were included in the prediction model, accuracy could also dramatically increase by ~40%. However, this criterion was highly sensitive to either misspecification (including wrong genes) or to the use of an incomplete gene list; in these cases, accuracy fell rapidly towards that reached when all SNPs from sequence data were blindly included in the model. - Conclusions: our study shows that, unless an accurate prior estimate on the functionality of SNPs can be included in the predictor, there is a law of diminishing returns with increasing SNP density. As a result, use of whole-genome sequence data may not result in a highly increased selection response over high-density genotyping.
Nota: Número d'acord de subvenció MICINN/AGL2010-14822
Nota: Número d'acord de subvenció MINECO/AGL2013-41834-R
Derechos: Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original. Creative Commons
Lengua: Anglès.
Documento: article ; recerca ; publishedVersion
Publicado en: Genetics selection evolution, Vol. 47, no. 1 (May 2015) , art. 53, ISSN 0999-193X

DOI: 10.1186/s12711-015-0117-5
PMID: 25956961


14 p, 1.0 MB

El registro aparece en las colecciones:
Documentos de investigación > Documentos de los grupos de investigación de la UAB > Centros y grupos de investigación (producción científica) > Ciencias > CRAG (Centro de Investigación en Agrigenómica)
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 Registro creado el 2017-10-31, última modificación el 2019-07-21



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