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Review

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

1
Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA
2
Institut National de la Recherche Agronomique, UMR1388 GenPhySE, 31326 Castanet Tolosan, France
3
Instituto Nacional de Investigación Agropecuaria (INIA), 11500 Montevideo, Uruguay
*
Author to whom correspondence should be addressed.
Genes 2020, 11(7), 790; https://doi.org/10.3390/genes11070790
Received: 19 June 2020 / Revised: 3 July 2020 / Accepted: 6 July 2020 / Published: 14 July 2020
(This article belongs to the Special Issue Genomic Prediction Methods for Sequencing Data)
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 sequence data. View Full-Text
Keywords: genomic selection; genomic prediction; genome-wide association; single-step genomic BLUP genomic selection; genomic prediction; genome-wide association; single-step genomic BLUP
MDPI and ACS Style

Lourenco, D.; Legarra, A.; Tsuruta, S.; Masuda, Y.; Aguilar, I.; Misztal, I. Single-Step Genomic Evaluations from Theory to Practice: Using SNP Chips and Sequence Data in BLUPF90. Genes 2020, 11, 790. https://doi.org/10.3390/genes11070790

AMA Style

Lourenco D, Legarra A, Tsuruta S, Masuda Y, Aguilar I, Misztal I. Single-Step Genomic Evaluations from Theory to Practice: Using SNP Chips and Sequence Data in BLUPF90. Genes. 2020; 11(7):790. https://doi.org/10.3390/genes11070790

Chicago/Turabian Style

Lourenco, Daniela, Andres Legarra, Shogo Tsuruta, Yutaka Masuda, Ignacio Aguilar, and Ignacy Misztal. 2020. "Single-Step Genomic Evaluations from Theory to Practice: Using SNP Chips and Sequence Data in BLUPF90" Genes 11, no. 7: 790. https://doi.org/10.3390/genes11070790

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