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Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches.

ABSTRACT: The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genomewide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long-term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness: (i) Pedigree 1, using observation-derived maternal links and microsatellite-derived paternal links; (ii) Pedigree 2, using SNP-derived assignment of both maternity and paternity; and (iii) whole-genome relatedness at 37 037 autosomal SNPs. In initial analyses, heritability estimates were strikingly similar for all three methods, while standard errors were systematically lower in analyses based on Pedigree 2 and genomic relatedness. Genetic correlations were generally strong, differed little between the three estimates of relatedness and the standard errors declined only very slightly with improved relatedness information. When partitioning maternal effects into separate genetic and environmental components, maternal genetic effects found in juvenile traits increased substantially across the three relatedness estimates. Heritability declined compared to parallel models where only a maternal environment effect was fitted, suggesting that maternal genetic effects are confounded with direct genetic effects and that more accurate estimates of relatedness were better able to separate maternal genetic effects from direct genetic effects. We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics studies in natural populations.

SUBMITTER: Berenos C

PROVIDER: S-EPMC4149785 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

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Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches.

Bérénos Camillo C Ellis Philip A PA Pilkington Jill G JG Pemberton Josephine M JM

Molecular ecology 20140626 14

The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genomewide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long-term study population of Soay sheep on St Kilda using three increasingly complete and a ...[more]

PMID: 24917482

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Project description:BackgroundIn pig and poultry breeding programs, the breeding goal is to improve crossbred (CB) performance, whereas selection in the purebred (PB) lines is often based on PB performance. Thus, response to selection may be suboptimal, because the genetic correlation between PB and CB performance ([Formula: see text]) is generally lower than 1. Accurate estimates of the [Formula: see text] are needed, so that breeders can decide if they should collect data from CB animals. [Formula: see text] can be estimated either from pedigree or genomic relationships, which may produce different results. With genomic relationships, the [Formula: see text] estimate could be improved when relationships between purebred and crossbred animals are based only on the alleles that originate from the PB line of interest. This work presents the first comparison of estimated [Formula: see text] and variance components of body weight in broilers, using pedigree-based or genotype-based models, where the breed-of-origin of alleles was either ignored or considered. We used genotypes and body weight measurements of PB and CB animals that have a common sire line.ResultsOur results showed that the [Formula: see text] estimates depended on the relationship matrix used. Estimates were 5 to 25% larger with genotype-based models than with pedigree-based models. Moreover, [Formula: see text] estimates were similar (max. 7% difference) regardless of whether the model considered breed-of-origin of alleles or not. Standard errors of [Formula: see text] estimates were smaller with genotype-based than with pedigree-based methods, and smaller with models that ignored breed-of-origin than with models that considered breed-of-origin.ConclusionsWe conclude that genotype-based models can be useful for estimating [Formula: see text], even when the PB and CB animals that have phenotypes are closely related. Considering breed-of-origin of alleles did not yield different estimates of [Formula: see text], probably because the parental breeds of the CB animals were distantly related.

Dataset Information

Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches.

Publications

Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches.

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