Genomic-assisted prediction of genetic value with semiparametric procedures.

Genetics
Daniel GianolaAlessandra Stella

Abstract

Semiparametric procedures for prediction of total genetic value for quantitative traits, which make use of phenotypic and genomic data simultaneously, are presented. The methods focus on the treatment of massive information provided by, e.g., single-nucleotide polymorphisms. It is argued that standard parametric methods for quantitative genetic analysis cannot handle the multiplicity of potential interactions arising in models with, e.g., hundreds of thousands of markers, and that most of the assumptions required for an orthogonal decomposition of variance are violated in artificial and natural populations. This makes nonparametric procedures attractive. Kernel regression and reproducing kernel Hilbert spaces regression procedures are embedded into standard mixed-effects linear models, retaining additive genetic effects under multivariate normality for operational reasons. Inferential procedures are presented, and some extensions are suggested. An example is presented, illustrating the potential of the methodology. Implementations can be carried out after modification of standard software developed by animal breeders for likelihood-based or Bayesian analysis.

References

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Citations

Jun 18, 2011·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Wenxin LiuJochen Christoph Reif
Jul 9, 2011·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Nanye LongKent A Weigel
Jul 21, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Nina HofheinzMatthias Frisch
Jan 7, 2009·Genetics Research·Daniel Gianola, Gustavo de los Campos
Feb 4, 2010·Genetics Research·M Graziano UsaiBen J Hayes
Mar 25, 2011·Genetics Research·Michael E GoddardTheo H E Meuwissen
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Jul 25, 2013·Animal : an International Journal of Animal Bioscience·L TusellD Gianola
Nov 15, 2012·Heredity·C-L WangQ Zhang
Nov 4, 2010·Nature Reviews. Genetics·Gustavo de los CamposDavid B Allison
Feb 2, 2002·Nature Reviews. Genetics·Jack C M Dekkers, Frédéric Hospital
Nov 16, 2010·Genome Génome / Conseil National De Recherches Canada·Ben Hayes, Mike Goddard
Mar 17, 2009·Genetics, Selection, Evolution : GSE·Nanye LongSantiago Avendaño
Mar 17, 2009·Genetics, Selection, Evolution : GSE·Jörn BennewitzTheo Meuwissen
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Jan 15, 2014·PloS One·Motohide Nishio, Masahiro Satoh
Apr 12, 2014·PloS One·Daniel GianolaChris-Carolin Schön
Sep 12, 2013·G3 : Genes - Genomes - Genetics·José CrossaRaman Babu
May 2, 2006·Genetics·Daniel GianolaAlessandra Stella
Sep 2, 2008·Genetics·Andrés LegarraJean-Michel Elsen
Jul 22, 2009·Genetics·Daniel GianolaRohan Fernando

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