Single-step genomic BLUP with genetic groups and automatic adjustment for allele coding.
Journal
Genetics, selection, evolution : GSE
ISSN: 1297-9686
Titre abrégé: Genet Sel Evol
Pays: France
ID NLM: 9114088
Informations de publication
Date de publication:
02 Jun 2022
02 Jun 2022
Historique:
received:
15
09
2021
accepted:
13
04
2022
entrez:
2
6
2022
pubmed:
3
6
2022
medline:
7
6
2022
Statut:
epublish
Résumé
Genomic estimated breeding values (GEBV) by single-step genomic BLUP (ssGBLUP) are affected by the centering of marker information used. The use of a fixed effect called J factor will lead to GEBV that are unaffected by the centering used. We extended the use of a single J factor to a group of J factors. J factor(s) are usually included in mixed model equations (MME) as regression effects but a transformation similar to that regularly used for genetic groups can be applied to obtain a simpler MME, which is sparser than the original MME and does not need computation of the J factors. When the J factor is based on the same structure as the genetic groups, then MME can be transformed such that coefficients for the genetic groups no longer include information from the genomic relationship matrix. We illustrate the use of J factors in the analysis of a Red dairy cattle data set for fertility. The GEBV from these analyses confirmed the theoretical derivations that show that the resulting GEBV are allele coding independent when a J factor is used. Transformed MME led to faster computing time than the original regression-based MME.
Sections du résumé
BACKGROUND
BACKGROUND
Genomic estimated breeding values (GEBV) by single-step genomic BLUP (ssGBLUP) are affected by the centering of marker information used. The use of a fixed effect called J factor will lead to GEBV that are unaffected by the centering used. We extended the use of a single J factor to a group of J factors.
RESULTS
RESULTS
J factor(s) are usually included in mixed model equations (MME) as regression effects but a transformation similar to that regularly used for genetic groups can be applied to obtain a simpler MME, which is sparser than the original MME and does not need computation of the J factors. When the J factor is based on the same structure as the genetic groups, then MME can be transformed such that coefficients for the genetic groups no longer include information from the genomic relationship matrix. We illustrate the use of J factors in the analysis of a Red dairy cattle data set for fertility.
CONCLUSIONS
CONCLUSIONS
The GEBV from these analyses confirmed the theoretical derivations that show that the resulting GEBV are allele coding independent when a J factor is used. Transformed MME led to faster computing time than the original regression-based MME.
Identifiants
pubmed: 35655157
doi: 10.1186/s12711-022-00721-x
pii: 10.1186/s12711-022-00721-x
pmc: PMC9164359
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
38Informations de copyright
© 2022. The Author(s).
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