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Genomic evaluation of Brown Swiss dairy cattle with limited national genotype data and integrated external information
ID Luštrek, Barbara (Author), ID Vandenplas, Jeremie (Author), ID Gorjanc, Gregor (Author), ID Potočnik, Klemen (Author)

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Abstract
This study demonstrated the feasibility of a genomic evaluation for the dairy cattle population for which the small national training population can be complemented with foreign information from international evaluations. National test-day milk yield data records for the Slovenian Brown Swiss cattle population were analyzed. Genomic evaluation was carried out using the single-step genomic best linear unbiased prediction method (ssGBLUP), resulting in genomic estimated breeding values (GEBV). The predominantly female group of genotyped animals, representing the national training population in the single-step genomic evaluation, was further augmented with 7,024 genotypes of foreign progeny-tested sires from an international Brown Swiss InterGenomics genomic evaluation (https://interbull.org/ib/whole_cop). Additionally, the estimated breeding values for the altogether 7,246 genotyped domestic and foreign sires from the 2019 sire multiple across-country evaluation (MACE), were added to the ssGBLUP as external pseudophenotypic information. The ssGBLUP method, with integration of MACE information by avoiding double counting, was then performed, resulting in MACE-enhanced GEBV (GEBVM). The methods were empirically validated with forward prediction. The validation group consisted of 315 domestic males and 1,041 domestic females born after 2012. Increase, inflation, and bias of the GEBV(M) reliability (REL) were assessed for the validation group with a focus on females. All individuals in the validation benefited from genomic evaluations using both methods, but the GEBV(M) REL increased most for the youngest selection candidates. Up to 35 points of GEBV REL could be assigned to national genomic information, and up to 17 points of GEBVM REL could additionally be attributed to the integration of foreign sire genomic and MACE information. Results indicated that the combined foreign progeny-tested sire genomic and external MACE information can be used in the single-step genomic evaluation as an equivalent replacement for domestic phenotypic information. Thus, an equal or slightly higher genomic breeding value REL was obtained sooner than the pedigree-based breeding value REL for the female selection candidates. When the abundant foreign progeny-tested sire genomic and MACE information was used to complement available national genomic and phenotypic information in single-step genomic evaluation, the genomic breeding value REL for young-female selection candidates increased approximately 10 points. Use of international information provides the possibility to upgrade small national training populations and obtain satisfying reliability of genomic breeding values even for the youngest female selection candidates, which will help to increase selection efficiency in the future.

Language:English
Keywords:genomic selection, single-step evaluation, forward prediction, genotyped cows, external information
Work type:Article
Typology:1.01 - Original Scientific Article
Organization:BF - Biotechnical Faculty
Publication status:Published
Publication version:Version of Record
Year:2021
Number of pages:Str. 5738-5754
Numbering:Vol. 104, no. 5
PID:20.500.12556/RUL-144723 This link opens in a new window
UDC:636.2
ISSN on article:1525-3198
DOI:10.3168/jds.2020-19493 This link opens in a new window
COBISS.SI-ID:54260739 This link opens in a new window
Publication date in RUL:09.03.2023
Views:809
Downloads:21
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Record is a part of a journal

Title:Journal of dairy science
Shortened title:J. dairy sci.
Publisher:Elsevier, Fass, American Dairy Science Association
ISSN:1525-3198
COBISS.SI-ID:520752665 This link opens in a new window

Licences

License:CC BY-NC-ND 4.0, Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Link:http://creativecommons.org/licenses/by-nc-nd/4.0/
Description:The most restrictive Creative Commons license. This only allows people to download and share the work for no commercial gain and for no other purposes.

Secondary language

Language:Slovenian
Keywords:govedo, pasme, rjava pasma, genetika, genomika, mlečnost, Slovenija

Projects

Funder:Other - Other funder or multiple funders
Funding programme:Slovenia, Ministry of Agriculture, Forestry and Food

Funder:ARRS - Slovenian Research Agency
Project number:P4-0092
Name:Zdravje živali, okolje in varna hrana

Funder:UKRI - UK Research and Innovation
Funding programme:BBSRC
Project number:BBS/E/D/30002275

Funder:Other - Other funder or multiple funders
Funding programme:The University of Edinburgh, Data-Driven Innovation Chancellor’s fellowship

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