Using breed-origin-of-alleles in genomic prediction
Mario Calus
Claudia Sevillano
Pascal Duenk
Yvonne Wientjes
Piter Bijma
Jérémie Vandenplas
10.6084/m9.figshare.12145749.v1
https://tagc2020.figshare.com/articles/poster/Using_breed-origin-of-alleles_in_genomic_prediction/12145749
<p>Breeding is based on selecting the genetically
best individuals as parents of the next generation. Traditionally, selection relied
on breeding values estimated from phenotypic records of the individual itself
and its relatives, connected using pedigree information. In the last decade, many
livestock and plant breeding programs have adopted genomic selection, which estimates
breeding values based on genome-wide marker data. Genomic prediction enables
accurate selection early in life, leading to faster genetic improvement.</p><p><br></p>
<p>In pig and poultry breeding the production individuals
are crosses between three or four breeding lines. Similar strategies are used
in crops like maize, where the breeding lines are intentionally inbred, while in livestock breeding lines inbreeding
is restricted. In all these cases, the breeding goal is to improve crossbred
performance. Selection in pigs and poultry, however, takes place among individuals
within a breeding line, and selection decisions are often based on purebred
performance. The genetic correlation between purebred and crossbred performance
is generally lower than unity, which can limit the progress in crossbred
performance. This limitation can be removed by using a crossbred reference
population in genomic prediction. Crossbred individuals carry alleles from
several parental lines, which may affect genomic prediction. </p><p><br></p>
<p>We developed a method to derive the Breed-Origin-of-Alleles
(BOA) for individuals resulting from crossing non-inbred breeding lines, based
on phased genotype data and haplotype frequencies observed in the parental
lines. We were able to derive BOA for 92-95% of the alleles in crossbred
broilers and pigs. We hypothesized that using BOA in genomic prediction models
would increase genomic prediction accuracy for crossbred performance. Empirical
accuracies, however, were at best slightly improved, despite the observation
that allele frequencies and estimated allelic effects for crossbred performance
did differ among the parental lines. Using BOA, relationships with respect to a
focal breeding line are only based on alleles from this line, while alleles
from other lines are ignored. The limited benefit in accuracy when using BOA is
likely because alleles from other lines contribute little to variation in
relationships of the focal line. Nevertheless, the BOA methodology is
potentially beneficial in genomic prediction in admixed populations in other
species, especially if founder populations are very different.</p>
<p><br></p>
<a>The
most likely explanation for this limited benefit is that the alleles from other
breeding lines had little impact on variation in genomic relationships with
respect to the breeding line of interest, so that considering BOA hardly
affected the genomic estimated breeding values.</a><div><div><div>
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2020-04-20 23:15:50
Genomic prediction
Crossbred performance
Breed-origin-of-alleles
Animal Breeding