Estimation of variance components and prediction of breeding values based on group records from varying group sizes

Mahmoud Shirali,Just Jensen,Bjarne Nielsen,Guosheng Su,Ole F. Christensen,Tage Ostersen,Per Madsen

doi:10.1186/s12711-018-0413-y

Mahmoud Shirali, Just Jensen

Open Access

https://doi.org/10.1186/s12711-018-0413-y

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Abstract

BackgroundRecords on groups of individuals rather than on single individuals could be valuable for predicting breeding values (BV) of the traits that are difficult or costly to measure individually, such as feed intake in pigs or beef cattle. Here, we present a model, which handles group records from varying group sizes and involves multiple fixed and random effects, for estimating variance components and predicting BV. Moreover, using simulation, we investigated the efficiency of group records for predicting BV in situations with various group sizes and structures, and factors that affect the trait.ResultsThe results show that the presented model for group records worked well and that variances estimated from group records with varying group sizes were consistent with those estimated from individual records, but with larger standard errors. Ignoring litter and pen effects had very little or no influence on the accuracy of estimated BV (EBV) obtained from group records. However, ignoring litter effects resulted in biased estimates of additive genetic variance and EBV. The presence of litter and pen effects on phenotypes decreased the accuracy of EBV although the prediction model fitted both effects. Having more littermates in the same pen led to a higher accuracy of EBV. The decay of EBV accuracy with increasing group size was more marked for scenarios with litter and pen effects than without. When litters of six individuals were divided into two pens, accuracies of EBV obtained from group records with a size up to 12 (average 9.6) and up to 24 (average 19.2) were 66.6 and 57.6% of those estimated from individual records in the scenario with litter and pen effects on phenotypes. These percentages reached 77.0 and 68.4% in the scenario without litter and pen effects on phenotypes.ConclusionsOur results indicate that the model works appropriately for the analysis of group records from varying group sizes. Using group records for genetic evaluation of traits such as feed intake in pig is feasible and the efficiency of the resulting estimates depends on the size and structure of the groups and on the magnitude of the variances for litter and pen effects.

Highlights

Records on groups of individuals rather than on single individuals could be valuable for predicting breeding values (BV) of the traits that are difficult or costly to measure individually, such as feed intake in pigs or beef cattle
The objectives of this study were to (1) model group records from varying group sizes, considering both additive genetic and non-genetic random effects; (2) interpret variance components at the group level; (3) assess the variances estimated from group records; and (4) compare prediction accuracy based on group and individual records in different scenarios
Methods first we describe the model used to fit group records with unequal group sizes; second, we illustrate variances at the group level and variance components estimated from group records; third, we present the simulation of data for various scenarios by mimicking feed intake in pigs; and we describe the analysis of data to compare the efficiency of using group versus individual records for predicting BV in different scenarios and with different models

Summary

Introduction

Records on groups of individuals rather than on single individuals could be valuable for predicting breeding values (BV) of the traits that are difficult or costly to measure individually, such as feed intake in pigs or beef cattle. We present a model, which handles group records from varying group sizes and involves multiple fixed and random effects, for estimating variance components and predicting BV. Alternatives to measuring individual feed intake are required in order to improve the accuracy of genetic evaluation of feed efficiency. Many studies have reported the estimation of variance components [4,5,6] and prediction of BV using group records [5,6,7,8] In all these studies only additive genetic and residual effects were considered as random effects in the model, and they analyzed data of equal group sizes or set a constant group size to model the residual variance when analyzing data of varying group sizes [8]. It is necessary to extend these approaches to handle multiple fixed and random effects, such as litter and pen effects on feed intake in pigs, and investigate the efficiency of using group records for predicting BV in different scenarios

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