Single-Step Genomic Evaluations from Theory to Practice: Using SNP Chips and Sequence Data in BLUPF90 - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Accéder directement au contenu
Article Dans Une Revue (Article De Synthèse) Genes Année : 2020

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

Daniela Lourenco
  • Fonction : Auteur
Shogo Tsuruta
  • Fonction : Auteur
Yutaka Masuda
  • Fonction : Auteur
Ignacio Aguilar
  • Fonction : Auteur
Ignacy Misztal
  • Fonction : Auteur

Résumé

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.

Dates et versions

hal-03154325 , version 1 (28-02-2021)

Identifiants

Citer

Daniela Lourenco, Andres Legarra, Shogo Tsuruta, Yutaka Masuda, Ignacio Aguilar, et al.. Single-Step Genomic Evaluations from Theory to Practice: Using SNP Chips and Sequence Data in BLUPF90. Genes, 2020, 11 (7), pp.790. ⟨10.3390/genes11070790⟩. ⟨hal-03154325⟩
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