GWAS and genomic prediction of milk urea nitrogen in Australian and New Zealand dairy cattle
journal contributionposted on 20.05.2022, 05:31 authored by I van den Berg, PN Ho, TV Nguyen, M Haile-Mariam, IM MacLeod, PR Beatson, E O’Connor, Jennie PryceJennie Pryce
Background: Urinary nitrogen leakage is an environmental concern in dairy cattle. Selection for reduced urinary nitrogen leakage may be done using indicator traits such as milk urea nitrogen (MUN). The result of a previous study indicated that the genetic correlation between MUN in Australia (AUS) and MUN in New Zealand (NZL) was only low to moderate (between 0.14 and 0.58). In this context, an alternative is to select sequence variants based on genome-wide association studies (GWAS) with a view to improve genomic prediction accuracies. A GWAS can also be used to detect quantitative trait loci (QTL) associated with MUN. Therefore, our objectives were to perform within-country GWAS and a meta-GWAS for MUN using records from up to 33,873 dairy cows and imputed whole-genome sequence data, to compare QTL detected in the GWAS for MUN in AUS and NZL, and to use sequence variants selected from the meta-GWAS to improve the prediction accuracy for MUN based on a joint AUS-NZL reference set. Results: Using the meta-GWAS, we detected 14 QTL for MUN, located on chromosomes 1, 6, 11, 14, 19, 22, 26 and the X chromosome. The three most significant QTL encompassed the casein genes on chromosome 6, PAEP on chromosome 11 and DGAT1 on chromosome 14. We selected 50,000 sequence variants that had the same direction of effect for MUN in AUS and MUN in NZL and that were most significant in the meta-analysis for the GWAS. The selected sequence variants yielded a genetic correlation between MUN in AUS and MUN in NZL of 0.95 and substantially increased prediction accuracy in both countries. Conclusions: Our results demonstrate how the sharing of data between two countries can increase the power of a GWAS and increase the accuracy of genomic prediction using a multi-country reference population and sequence variants selected based on a meta-GWAS.
This research was part of DairyBio, which is jointly funded by Dairy Australia (Melbourne, Australia) and Agriculture Victoria (Melbourne, Australia) and The Gardiner Foundation (Melbourne, Australia).
JournalGenetics Selection Evolution
Article NumberARTN 15
Rights Statement© The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
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Science & TechnologyLife Sciences & BiomedicineAgriculture, Dairy & Animal ScienceGenetics & HeredityAgricultureSEQUENCE VARIANTSPRODUCTION TRAITSWIDE ASSOCIATIONCSN1S1 PROMOTERHOLSTEINYIELDPOPULATIONIMPUTATIONMUTATIONSEXCRETIONAnimalsAustraliaCattleFemaleGenome-Wide Association StudyGenomicsLactationMilkNew ZealandNitrogenUreaDairy & Animal Science