Single-Step Genomic Evaluations from Theory to Practice: Using SNP Chips and Sequence Data in BLUPF90.

Genes
D A L LourencoI Misztal

Abstract

Single-step genomic evaluation became a standard procedure in livestock breeding, and the main reason is the ability to combine all pedigree, phenotypes, and genotypes available into one single evaluation, without the need of post-analysis processing. Therefore, the incorporation of data on genotyped and non-genotyped animals in this method is straightforward. Since 2009, two main implementations of single-step were proposed. One is called single-step genomic best linear unbiased prediction (ssGBLUP) and uses single nucleotide polymorphism (SNP) to construct the genomic relationship matrix; the other is the single-step Bayesian regression (ssBR), which is a marker effect model. Under the same assumptions, both models are equivalent. In this review, we focus solely on ssGBLUP. The implementation of ssGBLUP into the BLUPF90 software suite was done in 2009, and since then, several changes were made to make ssGBLUP flexible to any model, number of traits, number of phenotypes, and number of genotyped animals. Single-step GBLUP from the BLUPF90 software suite has been used for genomic evaluations worldwide. In this review, we will show theoretical developments and numerical examples of ssGBLUP using SNP data from regular chips to se...Continue Reading

References

Nov 1, 1991·Journal of Dairy Science·B W Kennedy
Oct 20, 1998·Journal of Dairy Science·C S Haley, P M Visscher
Nov 15, 2000·Clinical Genetics·N J SchorkJ S Lanchbury
Mar 10, 2001·Nature·R SachidanandamUNKNOWN International SNP Map Working Group
Sep 25, 2002·Genetics, Selection, Evolution : GSE·Jean-Jacques Colleau
Aug 6, 2003·American Journal of Human Genetics·Anne-Louise LeuteneggerElizabeth A Thompson
Oct 24, 2008·Journal of Dairy Science·P M VanRaden
Jan 30, 2009·Bioinformatics·Mehdi Sargolzaei, Flavio S Schenkel
Aug 25, 2009·Journal of Dairy Science·A LegarraI Misztal
Jan 29, 2010·Genetics, Selection, Evolution : GSE·Ole F Christensen, Mogens S Lund
Apr 22, 2010·Genetics·Hans D DaetwylerJohn A Woolliams
Dec 21, 2010·American Journal of Human Genetics·Jian YangPeter M Visscher
Jan 25, 2011·Journal of Dairy Science·C Patry, V Ducrocq
Mar 4, 2011·Genetics, Selection, Evolution : GSE·Paul M VanRadenKent A Weigel
Apr 2, 2011·Journal of Animal Science·C Y ChenW M Muir
Jul 20, 2011·Genetics Research·Z G VitezicaA Legarra
Nov 9, 2011·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·I AguilarS Tsuruta
Jun 22, 2012·Animal : an International Journal of Animal Bioscience·O F ChristensenG Su
Aug 1, 2012·Genetics, Selection, Evolution : GSE·Kent A GrayChristian Maltecca
Jul 17, 2013·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·I MisztalA A Swan
Nov 1, 1983·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·M Soller, J S Beckmann
Dec 10, 2013·Journal of Dairy Science·G BalocheF Barillet
Apr 1, 2014·Journal of Dairy Science·I MisztalI Aguilar
Jul 21, 2014·BMC Bioinformatics·Jose L Gualdrón DuarteJuan P Steibel
Apr 18, 2015·Genetics, Selection, Evolution : GSE·Francesco Tiezzi, Christian Maltecca
Jun 27, 2015·Journal of Animal Science·D A L LourencoI Misztal
Jul 3, 2015·Genetics, Selection, Evolution : GSE·Daniela A L LourencoIgnacy Misztal

❮ Previous
Next ❯

Citations

Nov 25, 2020·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Rafaela MartinsVictor B Pedrosa
Jan 26, 2021·Journal of Animal Science·Yutaka MasudaIgnacy Misztal
Apr 6, 2021·Frontiers in Genetics·Fernanda M RezendeRaluca G Mateescu
Mar 28, 2021·Journal of Animal Science·Ignacy MisztalMiguel Toro
Jun 3, 2021·Animals : an Open Access Journal From MDPI·Ekaterina MelnikovaNatalia Zinovieva
Sep 10, 2021·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Ryota KomiyaMasahiro Satoh

❮ Previous
Next ❯

Methods Mentioned

BETA
genotyping
chips

Software Mentioned

BLUPF90
TauOmegaQ2
Linux
GEBV
pregsf90
GCTA
postGSf90
Mix99
gammaf90
renf90

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.