Genome-enabled prediction of genetic values using radial basis function neural networks

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Juan Manuel González-CamachoJosé Crossa

Abstract

The availability of high density panels of molecular markers has prompted the adoption of genomic selection (GS) methods in animal and plant breeding. In GS, parametric, semi-parametric and non-parametric regressions models are used for predicting quantitative traits. This article shows how to use neural networks with radial basis functions (RBFs) for prediction with dense molecular markers. We illustrate the use of the linear Bayesian LASSO regression model and of two non-linear regression models, reproducing kernel Hilbert spaces (RKHS) regression and radial basis function neural networks (RBFNN) on simulated data and real maize lines genotyped with 55,000 markers and evaluated for several trait-environment combinations. The empirical results of this study indicated that the three models showed similar overall prediction accuracy, with a slight and consistent superiority of RKHS and RBFNN over the additive Bayesian LASSO model. Results from the simulated data indicate that RKHS and RBFNN models captured epistatic effects; however, adding non-signal (redundant) predictors (interaction between markers) can adversely affect the predictive accuracy of the non-linear regression models.

References

Feb 19, 2004·Biometrics·Inyoung KimRaymond J Carroll
May 2, 2006·Genetics·Daniel GianolaAlessandra Stella
Jan 1, 1991·IEEE Transactions on Neural Networks·S ChenP M Grant
May 6, 2008·PLoS Genetics·William G HillPeter M Visscher
Oct 24, 2008·Journal of Dairy Science·P M VanRaden
Jan 24, 2009·Journal of Dairy Science·B J HayesM E Goddard
Feb 14, 2009·Journal of Animal Science·Gustavo de Los CamposGuilherme J M Rosa
Mar 19, 2009·Genetics·Gustavo de Los CamposJosé Miguel Cotes
Jul 30, 2010·Genetics Research·Nanye LongOscar González-Recio
Jun 16, 2011·Genetica·Nanye LongK A Weigel
Jul 1, 1991·Neural Computation·J Park, I W Sandberg

Citations

Jul 25, 2013·Animal : an International Journal of Animal Bioscience·Llibertat TusellDaniel Gianola
Apr 11, 2013·Heredity·José CrossaK Mathews
Jun 19, 2013·Nature Reviews. Genetics·Naomi R WrayPeter M Visscher
Sep 12, 2013·G3 : Genes - Genomes - Genetics·José CrossaRaman Babu
Feb 6, 2014·Genetics, Selection, Evolution : GSE·Huiming LiuPeer Berg
Jan 16, 2014·Heredity·Leonardo OrnellaJosé Crossa
Sep 10, 2014·Nature Reviews. Genetics·Wen-Hua WeiChris S Haley
Jan 10, 2016·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Sang HeYong Jiang
Mar 10, 2016·BMC Genomics·Juan Manuel González-CamachoDaniel Gianola
Jan 9, 2014·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Llibertat TusellDaniel Gianola
Jun 28, 2014·Trends in Plant Science·Zeratsion Abera Desta, Rodomiro Ortiz
Apr 18, 2015·Genetics, Selection, Evolution : GSE·Huiming LiuPeer Berg
Apr 20, 2016·Genetics, Selection, Evolution : GSE·Yaodong HuDaniel Gianola
Nov 26, 2013·Current Opinion in Genetics & Development·K Christin FalkeGregor Schmitz
Nov 2, 2014·Frontiers in Genetics·Gota Morota, Daniel Gianola
Nov 5, 2014·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Julio IsidroMark E Sorrells
Oct 25, 2014·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Akio OnogiHiroyoshi Iwata
May 18, 2016·Biotechnology & Genetic Engineering Reviews·Elisabeth Jonas, Dirk Jan de Koning
Oct 8, 2016·The New Phytologist·Jennifer E Spindel, Susan R McCouch
Jun 18, 2016·Scientific Reports·C Saint PierreSukhwinder Singh
Sep 7, 2017·Genetica·Thammineni ChakradharPalakolanu Sudhakar Reddy
May 14, 2016·G3 : Genes - Genomes - Genetics·José CrossaSukhwinder Singh
Mar 29, 2018·G3 : Genes - Genomes - Genetics·Paulino Pérez-RodríguezJosé Crossa
Apr 6, 2019·Plant Biotechnology Journal·Xuehai HuShizhong Xu
Jan 1, 2013·G3 : Genes - Genomes - Genetics·Paulino Pérez-RodríguezSusanne Dreisigacker
May 10, 2013·Journal of Animal Science·Paulino Pérez-RodríguezJosé Crossa
Jun 7, 2019·G3 : Genes - Genomes - Genetics·Letícia A de C LaraAntonio Augusto F Garcia
Jul 3, 2019·G3 : Genes - Genomes - Genetics·Janeo Eustáquio de Almeida FilhoMarcio Fernando Ribeiro de Resende Júnior
Jun 19, 2016·G3 : Genes - Genomes - Genetics·Alencar XavierKaty Martin Rainey
Sep 20, 2019·G3 : Genes - Genomes - Genetics·Christina B AzodiShin-Han Shiu
Feb 6, 2020·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Fernando Brito LopesFernando Baldi
Mar 21, 2020·Perspectives on Psychological Science : a Journal of the Association for Psychological Science·Franzis PreckelFrank C Worrell
Dec 7, 2016·Frontiers in Plant Science·Manish RoorkiwalRajeev K Varshney
Jul 28, 2018·G3 : Genes - Genomes - Genetics·Italo GranatoRoberto Fritsche-Neto
Sep 2, 2018·Genetics·Pau BellotMiguel Pérez-Enciso
May 31, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Cathérine Pauline HerterThomas Miedaner
Feb 1, 2020·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Samaneh SolaymaniMehdi Momen
Mar 3, 2020·Frontiers in Plant Science·Laura M ZingarettiMiguel Pérez-Enciso
Nov 23, 2012·G3 : Genes - Genomes - Genetics·Vanessa S WindhausenAlbrecht E Melchinger
Dec 30, 2014·G3 : Genes - Genomes - Genetics·Osval Antonio Montesinos-LópezJosé Crossa
Jul 20, 2018·The Plant Genome·Juan Manuel González-CamachoJosé Crossa
Sep 30, 2020·International Journal of Molecular Sciences·Osvin ArriagadaAndrés R Schwember
Aug 21, 2015·G3 : Genes - Genomes - Genetics·Osval Antonio Montesinos-LópezKent Eskridge
Aug 27, 2014·G3 : Genes - Genomes - Genetics·Jaime CuevasJosé Crossa
Jun 3, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Amina AbedFrançois Belzile
Jul 11, 2019·G3 : Genes - Genomes - Genetics·Jaime CuevasJosé Crossa
Oct 6, 2020·The Plant Genome·Paulino Pérez-RodríguezJosé Crossa
Dec 16, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Cathérine Pauline HerterThomas Miedaner
Sep 17, 2020·G3 : Genes - Genomes - Genetics·Abelardo Montesinos-LópezJosé Crossa
Jan 2, 2021·Journal of Plant Physiology·Hao Tong, Zoran Nikoloski

Related Concepts

Bayesian Prediction
In Silico
Zea luxurians
Impacts, Environmental
Plant Diseases
Neural Network Simulation
Genome, Plant
Quantitative Trait, Heritable
Online Mendelian Inheritance In Man
Plant Carpals

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Synthetic Genetic Array Analysis

Synthetic genetic arrays allow the systematic examination of genetic interactions. Here is the latest research focusing on synthetic genetic arrays and their analyses.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Computational Methods for Protein Structures

Computational methods employing machine learning algorithms are powerful tools that can be used to predict the effect of mutations on protein structure. This is important in neurodegenerative disorders, where some mutations can cause the formation of toxic protein aggregations. This feed follows the latests insights into the relationships between mutation and protein structure leading to better understanding of disease.

Congenital Hyperinsulinism

Congenital hyperinsulinism is caused by genetic mutations resulting in excess insulin secretion from beta cells of the pancreas. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Epigenetic Memory

Epigenetic memory refers to the heritable genetic changes that are not explained by the DNA sequence. Find the latest research on epigenetic memory here.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Femoral Neoplasms

Femoral Neoplasms are bone tumors that arise in the femur. Discover the latest research on femoral neoplasms here.