Using mid-infrared spectroscopy to increase GWAS power to detect QTL associated with blood urea nitrogen
journal contributionposted on 10.05.2022, 00:58 authored by I van den Berg, PN Ho, TV Nguyen, M Haile-Mariam, TDW Luke, Jennie PryceJennie Pryce
Blood urea nitrogen (BUN) is an indicator trait for urinary nitrogen excretion. Measuring BUN level requires a blood sample, which limits the number of records that can be obtained. Alternatively, BUN can be predicted using mid-infrared (MIR) spectroscopy of a milk sample and thus records become available on many more cows through routine milk recording processes. The genetic correlation between MIR predicted BUN (MBUN) and BUN is 0.90. Hence, genetically, BUN and MBUN can be considered as the same trait. The objective of our study was to perform genome-wide association studies (GWAS) for BUN and MBUN, compare these two GWAS and detect quantitative trait loci (QTL) for both traits, and compare the detected QTL with previously reported QTL for milk urea nitrogen (MUN). The dataset used for our analyses included 2098 and 18,120 phenotypes for BUN and MBUN, respectively, and imputed whole-genome sequence data. The GWAS for MBUN was carried out using either the full dataset, the 2098 cows with records for BUN, or 2000 randomly selected cows, so that the dataset size is comparable to that for BUN. The GWAS results for BUN and MBUN were very different, in spite of the strong genetic correlation between the two traits. We detected 12 QTL for MBUN, on bovine chromosomes 2, 3, 9, 11, 12, 14 and X, and one QTL for BUN on chromosome 13. The QTL detected on chromosomes 11, 14 and X overlapped with QTL detected for MUN. The GWAS results were highly sensitive to the subset of records used. Hence, caution is warranted when interpreting GWAS based on small datasets, such as for BUN. MBUN may provide an attractive alternative to perform a more powerful GWAS to detect QTL for BUN.
This research was part of the DairyBio program, which is jointly funded by Dairy Australia (Melbourne, Australia), Agriculture Victoria (Melbourne, Australia) and The Gardiner Foundation (Melbourne, Australia).
JournalGenetics Selection Evolution
Article NumberARTN 27
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.
Read the peer-reviewed publication
Science & TechnologyLife Sciences & BiomedicineAgriculture, Dairy & Animal ScienceGenetics & HeredityAgricultureGENOME-WIDE ASSOCIATIONQUANTITATIVE TRAIT LOCIMILK UREASEQUENCE DATACATTLEPREDICTIONIMPUTATIONYIELDBREEDAnimalsBlood Urea NitrogenCattleFemaleGenome-Wide Association StudyMilkNitrogenPhenotypePolymorphism, Single NucleotideQuantitative Trait LociDairy & Animal Science