An R Package for Bayesian Analysis of Multi-environment and Multi-trait Multi-environment Data for Genome-Based Prediction

G3 : Genes - Genomes - Genetics
Osval Montesinos-LópezJosé Crossa

Abstract

Evidence that genomic selection (GS) is a technology that is revolutionizing plant breeding continues to grow. However, it is very well documented that its success strongly depends on statistical models, which are used by GS to perform predictions of candidate genotypes that were not phenotyped. Because there is no universally better model for prediction and models for each type of response variable are needed (continuous, binary, ordinal, count, etc.), an active area of research aims to develop statistical models for the prediction of univariate and multivariate traits in GS. However, most of the models developed so far are for univariate and continuous (Gaussian) traits. Therefore, to overcome the lack of multivariate statistical models for genome-based prediction by improving the original version of the BMTME, we propose an improved Bayesian multi-trait and multi-environment (BMTME) R package for analyzing breeding data with multiple traits and multiple environments. We also introduce Bayesian multi-output regressor stacking (BMORS) functions that are considerably efficient in terms of computational resources. The package allows parameter estimation and evaluates the prediction performance of multi-trait and multi-environmen...Continue Reading

References

Apr 6, 2001·Genetics·T H MeuwissenM E Goddard
Oct 24, 2008·Journal of Dairy Science·P M VanRaden
Feb 12, 2009·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·T M VillumsenM S Lund
Nov 16, 2010·Genome Génome / Conseil National De Recherches Canada·Ben Hayes, Mike Goddard
May 11, 2012·PloS One·Satish KumarCharmaine Carlisle
Aug 25, 2012·Journal of Dairy Science·K M OlsonM E Tooker
Feb 7, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Frank Technow, Albrecht E Melchinger
Sep 21, 2013·BMC Genetics·Tobias WürschumYusheng Zhao
Jul 11, 2014·Genetics·Paulino Pérez, Gustavo de los Campos
Dec 30, 2014·G3 : Genes - Genomes - Genetics·Osval A Montesinos-LópezJosé Crossa
Feb 11, 2015·G3 : Genes - Genomes - Genetics·Marco Lopez-CruzGustavo de los Campos
Mar 15, 2015·BMC Genomics·Judith BurstinGérard Duc
Aug 21, 2015·G3 : Genes - Genomes - Genetics·Osval A Montesinos-LópezKent Eskridge
Dec 18, 2015·Nucleic Acids Research·Robert D FinnAlex Bateman
Jan 21, 2016·Scientific Reports·Eiji YamamotoHiroyuki Fukuoka
Jun 9, 2016·PloS One·Giovanny Covarrubias-Pazaran
Jun 28, 2016·G3 : Genes - Genomes - Genetics·Osval A Montesinos-LópezJessica Rutkoski
Jul 28, 2018·G3 : Genes - Genomes - Genetics·Italo GranatoRoberto Fritsche-Neto
Oct 7, 2018·G3 : Genes - Genomes - Genetics·Osval A Montesinos-LópezJavier Martín-Vallejo

❮ Previous
Next ❯

Citations

Aug 21, 2019·G3 : Genes - Genomes - Genetics·Osval A Montesinos-LópezRavi Singh
Oct 28, 2019·Bioinformatics·Alencar XavierKaty M Rainey
Oct 21, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Philomin JulianaRavi P Singh
May 31, 2020·Heredity·Amanda Avelar de OliveiraGabriel Rodrigues Alves Margarido
Nov 21, 2020·The Plant Genome·Maria Itria IbbaJesse Poland
May 4, 2021·Frontiers in Plant Science·Jose CrossaAlison R Bentley
Sep 8, 2021·Frontiers in Plant Science·Harsimardeep S GillSunish K Sehgal

❮ Previous
Next ❯

Methods Mentioned

BETA
genotyping
genome-based prediction

Software Mentioned

Windows
covModel
R package
ETA
XCode
Rtools
JAGS
Env
phenoMada
BMORS

Related Concepts

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.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

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.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.