Fecha/hora: 09/06/2024 02:47:56

Biblioteca(s): | INIA Las Brujas.
Fecha corriente: | 04/10/2014
Fecha de la última actualización: | 10/02/2020
Autoria: | FORNI, S.; AGUILAR, I.; MISZTAL, I.
Afiliación: | IGNACIO AGUILAR GARCIA, Instituto Nacional de Investigación Agropecuaria (INIA), Uruguay.
Título: | Different genomic relationship matrices for single-step analysis using phenotypic, pedigree and genomic information.
Año de publicación: | 2011
Fuente/Imprenta: | Genetics Selection Evolution, 2011, v.43, no.1, p.443-447.
ISSN: | 0999-193X
DOI: | 10.1186/1297-9686-43-1
Idioma: | Inglés
Notas: | ARTICULO OPEN ACCESS.

Contenido:

BACKGROUND: 

The incorporation of genomic coefficients into the numerator relationship matrix allows estimation of breeding values using all phenotypic, pedigree and genomic information simultaneously. In such a single-step procedure, genomic and pedigree-based relationships have to be compatible. As there are many options to create genomic relationships, there is a question of which is optimal and what the effects of deviations from optimality are. Methods. Data of litter size (total number born per litter) for 338,346 sows were analyzed. Illumina PorcineSNP60 BeadChip genotypes were available for 1,989. Analyses were carried out with the complete data set and with a subset of genotyped animals and three generations pedigree (5,090 animals). A single-trait animal model was used to estimate variance components and breeding values. Genomic relationship matrices were constructed using allele frequencies equal to 0.5 (G05), equal to the average minor allele frequency (GMF), or equal to observed frequencies (GOF). A genomic matrix considering random ascertainment of allele frequencies was also used (GOF*). A normalized matrix (GN) was obtained to have average diagonal coefficients equal to 1. The genomic matrices were combined with the numerator relationship matrix creating H matrices. Results: In G05 and GMF, both diagonal and off-diagonal elements were on average greater than the pedigree-based coefficients. In GOF and GOF*, the average diagonal elements were smaller than pedigree-based coefficients. The mean of off-diagonal coefficients was zero in GOF and GOF*. Choices of G with average diagonal coefficients different from 1 led to greater estimates of additive variance in the smaller data set. The correlation between EBV and genomic EBV (n = 1,989) were: 0.79 using G05, 0.79 using GMF, 0.78 using GOF, 0.79 using GOF*, and 0.78 using GN. Accuracies calculated by inversion increased with all genomic matrices. The accuracies of genomic-assisted EBV were inflated in all cases except when GN was used. Conclusions: Parameter estimates may be biased if the genomic relationship coefficients are in a different scale than pedigree-based coefficients. A reasonable scaling may be obtained by using observed allele frequencies and re-scaling the genomic relationship matrix to obtain average diagonal elements of 1. 
© 2011 Forni et al; licensee BioMed Central Ltd.

Thesagro: | CERDOS; GENOTIPOS; MEJORAMIENTO GENÉTICO ANIMAL.
Categoría del tema: | L10 Genética y mejoramiento animal

URL:

http://www.ainfo.inia.uy/digital/bitstream/item/3441/1/Aguilar-I.-2011.-GSE-v.431-OPEN-ACCESS.pdf
http://www.biomedcentral.com/content/pdf/1297-9686-43-1.pdf

Registro original: | INIA Las Brujas (LB)
Ejemplares: | LB - (100166-1) - PXI - AP - DD - PP/GSE/2011 -  -  - DIS