Abstract
BackgroundRecently, there has been a growing interest in the genetic improvement of body measurement traits in farm animals. They are widely used as predictors of performance, longevity, and production traits, and it is worthwhile to investigate the prediction accuracies of genomic selection for these traits. In genomic prediction, the single-step genomic best linear unbiased prediction (ssGBLUP) method allows the inclusion of information from genotyped and non-genotyped relatives in the analysis. Hence, we aimed to compare the prediction accuracy obtained from a pedigree-based BLUP only on genotyped animals (PBLUP-G), a traditional pedigree-based BLUP (PBLUP), a genomic BLUP (GBLUP), and a single-step genomic BLUP (ssGBLUP) method for the following 10 body measurement traits at yearling age of Hanwoo cattle: body height (BH), body length (BL), chest depth (CD), chest girth (CG), chest width (CW), hip height (HH), hip width (HW), rump length (RL), rump width (RW), and thurl width (TW). The data set comprised 13,067 phenotypic records for body measurement traits and 1523 genotyped animals with 34,460 single-nucleotide polymorphisms. The accuracy for each trait and model was estimated only for genotyped animals using five-fold cross-validations.ResultsThe accuracies ranged from 0.02 to 0.19, 0.22 to 0.42, 0.21 to 0.44, and from 0.36 to 0.55 as assessed using the PBLUP-G, PBLUP, GBLUP, and ssGBLUP methods, respectively. The average predictive accuracies across traits were 0.13 for PBLUP-G, 0.34 for PBLUP, 0.33 for GBLUP, and 0.45 for ssGBLUP methods. Our results demonstrated that averaged across all traits, ssGBLUP outperformed PBLUP and GBLUP by 33 and 43%, respectively, in terms of prediction accuracy. Moreover, the least root of mean square error was obtained by ssGBLUP method.ConclusionsOur findings suggest that considering the ssGBLUP model may be a promising way to ensure acceptable accuracy of predictions for body measurement traits, especially for improving the prediction accuracy of selection candidates in ongoing Hanwoo breeding programs.
Highlights
There has been a growing interest in the genetic improvement of body measurement traits in farm animals
We investigated the accuracy of the breeding values for linear body measurement traits using four models, pedigree-based BLUP only on genotyped animals (PBLUP-G), pedigree-based BLUP with all animals (PBLUP), genomic BLUP (GBLUP), and single-step genomic BLUP in Hanwoo beef cattle
Our findings indicate that single-step genomic best linear unbiased prediction (ssGBLUP) generally generated higher prediction accuracy than the other three methods for body measurement traits in Hanwoo cattle, which could be implemented in practical breeding programs
Summary
There has been a growing interest in the genetic improvement of body measurement traits in farm animals. Body measurements have become routinely collected traits over the last three decades in this breed, which provide valuable resources to study the complete growing period [8] These traits have been proposed as indirect selection criteria for the genetic improvement of meat production in beef cattle [9, 10], and can be harnessed to accelerate the breeding progress. A decade ago, a method based on the GBLUP framework was proposed by Misztal et al [22], termed the single-step genomic best linear unbiased prediction (ssGBLUP), which uses simultaneously all pedigree, genotypic and phenotypic information from both genotyped and nongenotyped individuals. The literature on prediction of the breeding values of linear body measurement traits using genomic evaluations in field data of dairy cattle [25, 33, 34], beef cattle [35,36,37], goats [38,39,40], sheep [41], and pig [42] have been previously reported
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