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Title: Estimates of genetic trend for single-step genomic evaluations
Contributor(s): Meyer, Karin  (author); Tier, Bruce  (author); Swan, Andrew  (author)
Publication Date: 2018
Early Online Version: 2018-08-03
Open Access: Yes
DOI: 10.1186/s12711-018-0410-1
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Abstract: Background: A common measure employed to evaluate the efficacy of livestock improvement schemes is the genetic trend, which is calculated as the means of predicted breeding values for animals born in successive time periods. This implies that different cohorts refer to the same base population. For genetic evaluation schemes integrating genomic information with records for all animals, genotyped or not, this is often not the case: expected means for pedigree founders are zero whereas values for genotyped animals are expected to sum to zero at the (mean) time corresponding to the frequencies that are used to center marker allele counts when calculating genomic relationships. Methods: The paper examines estimates of genetic trends from single-step genomic evaluations. After a review of methods which propose to align pedigree-based and genomic relationship matrices, simulation is used to illustrate the effects of alignments and choice of assumed gene frequencies on trajectories of genetic trends. Results: The results show that methods available to alleviate differences between the founder populations implied by the two types of relationship matrices perform well; in particular, the meta-founder approach is advantageous. An application to data from routine genetic evaluation of Australian sheep is shown, confirming their effectiveness for practical data. Conclusions: Aligning pedigree and genomic relationship matrices for single step genetic evaluation for populations under selection is essential. Fitting meta-founders is an effective and simple method to avoid distortion of estimates of genetic trends.
Publication Type: Journal Article
Source of Publication: Genetics Selection Evolution, v.50, p. 1-11
Publisher: BioMed Central Ltd
Place of Publication: United Kingdom
ISSN: 1297-9686
Field of Research (FOR): 070201 Animal Breeding
Socio-Economic Outcome Codes: 830311 Sheep - Wool
830301 Beef Cattle
830310 Sheep - Meat
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
Journal Article

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