Sparse single-step method for genomic evaluation in pigs.

Tage Ostersen,Ole F Christensen,Mark Henryon,Per Madsen

doi:10.1186/s12711-016-0227-8

Tage Ostersen, Ole F Christensen + Show 2 more

Open Access

https://doi.org/10.1186/s12711-016-0227-8

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Abstract

BackgroundIn many animal breeding programs, with the increasing number of genotyped animals, estimation of genomic breeding values by the single-step method is becoming limited by excessive computing requirements. A recently proposed algorithm for proven and young animals (APY) is an approximation that reduces computing time drastically by dividing genotyped animals into core and non-core animals, with only computations for core animals being time-consuming. We hypothesized that choosing core animals based on representing all generations, minimizing the relatedness within the core group, or maximizing the number of genotyped offspring, would result in greater accuracies of estimated breeding values (EBV).MethodsWe compared eight different core groups for the three pig breeds DanAvl Duroc, DanAvl Landrace and DanAvl Yorkshire. These eight sparse approximations of the single-step method were evaluated based on correlations of EBV for genotyped animals obtained from the sparse methods with those obtained from the usual version of the single-step method. We used a single-trait model with daily gain as trait.ResultsFor core groups that distributed animals across generations, correlations for genotyped animals (from 0.977 to 0.989) were higher than for those that did not distribute core animals across generations (from 0.934 to 0.956). For core groups that maximized the number of genotyped offspring, correlations for genotyped animals (from 0.983 to 0.989) were higher than for other core groups (from 0.934 to 0.981). There was no clear association between low relatedness within the core group and accuracy of approximations.ConclusionsWe found that for core groups that represent all generations and that maximize the number of genotyped offspring, accurate approximations of EBV were obtained. However, we did not find a clear association between accuracy and relatedness within the core group. For the APY method, this is the first study that reports systematic criteria for the creation of core groups that result in more accurate EBV than a similar-sized random core group. Random core groups only ensure across-generation representation. Therefore, we recommend choosing a core group that represents all generations and that maximizes the number of genotyped offspring for single-step genomic evaluation using the APY method.

Highlights

In many animal breeding programs, with the increasing number of genotyped animals, estimation of genomic breeding values by the single-step method is becoming limited by excessive computing requirements
Other ways of choosing core animals have been proposed [6, 9], no study has reported a formal choice of the core animals that results in more accurate approximations than choosing them at random while keeping the size of the core group constant [5–11]
This suggests that approximations of estimated breeding values (EBV) obtained with APY could be more accurate by choosing core animals that represent the most independent chromosome segments

Summary

Introduction

In many animal breeding programs, with the increasing number of genotyped animals, estimation of genomic breeding values by the single-step method is becoming limited by excessive computing requirements. We hypothesized that choosing core animals based on representing all generations, minimizing the relatedness within the core group, or maximizing the number of genotyped offspring, would result in greater accuracies of estimated breeding values (EBV). Other ways of choosing core animals have been proposed [6, 9], no study has reported a formal choice of the core animals that results in more accurate approximations than choosing them at random while keeping the size of the core group constant [5–11] This is surprising because based on [12], the accuracy of APY is related to how well the animals in the core group represent the independent chromosome segments that are present in the population. We tested this hypothesis by estimating accuracies of approximations of EBV for daily gain for three Danish pig breeds

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Discussion

Conclusion