Comparison of the genetic characteristics of directly measured and Fourier-transform mid-infrared-predicted bovine milk fatty acids and proteins.

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dc.citation.issue12
dc.citation.volume105
dc.contributor.authorTiplady KM
dc.contributor.authorLopdell TJ
dc.contributor.authorSherlock RG
dc.contributor.authorJohnson TJJ
dc.contributor.authorSpelman RJ
dc.contributor.authorHarris BL
dc.contributor.authorDavis SR
dc.contributor.authorLittlejohn MD
dc.contributor.authorGarrick DJ
dc.coverage.spatialUnited States
dc.date.accessioned2024-04-11T23:25:55Z
dc.date.accessioned2024-07-25T06:51:02Z
dc.date.available2022-10-26
dc.date.available2024-04-11T23:25:55Z
dc.date.available2024-07-25T06:51:02Z
dc.date.issued2022-12
dc.description.abstractFourier-transform mid-infrared (FT-MIR) spectroscopy is a high-throughput and inexpensive methodology used to evaluate concentrations of fat and protein in dairy cattle milk samples. The objective of this study was to compare the genetic characteristics of FT-MIR predicted fatty acids and individual milk proteins with those that had been measured directly using gas and liquid chromatography methods. The data used in this study was based on 2,005 milk samples collected from 706 Holstein-Friesian × Jersey animals that were managed in a seasonal, pasture-based dairy system, with milk samples collected across 2 consecutive seasons. Concentrations of fatty acids and protein fractions in milk samples were directly determined by gas chromatography and high-performance liquid chromatography, respectively. Models to predict each directly measured trait based on FT-MIR spectra were developed using partial least squares regression, with spectra from a random selection of half the cows used to train the models, and predictions for the remaining cows used as validation. Variance parameters for each trait and genetic correlations for each pair of measured/predicted traits were estimated from pedigree-based bivariate models using REML procedures. A genome-wide association study was undertaken using imputed whole-genome sequence, and quantitative trait loci (QTL) from directly measured traits were compared with QTL from the corresponding FT-MIR predicted traits. Cross-validation prediction accuracies based on partial least squares for individual and grouped fatty acids ranged from 0.18 to 0.65. Trait prediction accuracies in cross-validation for protein fractions were 0.53, 0.19, and 0.48 for α-casein, β-casein, and κ-casein, 0.31 for α-lactalbumin, 0.68 for β-lactoglobulin, and 0.36 for lactoferrin. Heritability estimates for directly measured traits ranged from 0.07 to 0.55 for fatty acids; and from 0.14 to 0.63 for individual milk proteins. For FT-MIR predicted traits, heritability estimates were mostly higher than for the corresponding measured traits, ranging from 0.14 to 0.46 for fatty acids, and from 0.30 to 0.70 for individual proteins. Genetic correlations between directly measured and FT-MIR predicted protein fractions were consistently above 0.75, with the exceptions of C18:0 and C18:3 cis-3, which had genetic correlations of 0.72 and 0.74, respectively. The GWAS identified trait QTL for fatty acids with likely candidates in the DGAT1, CCDC57, SCD, and GPAT4 genes. Notably, QTL for SCD were largely absent in the FT-MIR predicted traits, and QTL for GPAT4 were absent in directly measured traits. Similarly, for directly measured individual proteins, we identified QTL with likely candidates in the CSN1S1, CSN3, PAEP, and LTF genes, but the QTL for CSN3 and LTF were absent in the FT-MIR predicted traits. Our study indicates that genetic correlations between directly measured and FT-MIR predicted fatty acid and protein fractions are typically high, but that phenotypic variation in these traits may be underpinned by differing genetic architecture.
dc.description.confidentialfalse
dc.edition.editionDecember 2022
dc.format.pagination9763-9791
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/36307235
dc.identifier.citationTiplady KM, Lopdell TJ, Sherlock RG, Johnson TJJ, Spelman RJ, Harris BL, Davis SR, Littlejohn MD, Garrick DJ. (2022). Comparison of the genetic characteristics of directly measured and Fourier-transform mid-infrared-predicted bovine milk fatty acids and proteins.. J Dairy Sci. 105. 12. (pp. 9763-9791).
dc.identifier.doi10.3168/jds.2022-22089
dc.identifier.eissn1525-3198
dc.identifier.elements-typejournal-article
dc.identifier.issn0022-0302
dc.identifier.piiS0022-0302(22)00614-2
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/71007
dc.languageeng
dc.publisherElsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association
dc.publisher.urihttps://www.sciencedirect.com/science/article/pii/S0022030222006142?via%3Dihub
dc.relation.isPartOfJ Dairy Sci
dc.rights(c) 2022 The Author/s
dc.rightsCC BY 4.0
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectFourier-transform mid-infrared spectroscopy
dc.subjectdairy cattle
dc.subjectgenome-wide association study
dc.subjectmilk composition
dc.subjectFemale
dc.subjectCattle
dc.subjectAnimals
dc.subjectFatty Acids
dc.subjectGenome-Wide Association Study
dc.subjectMilk
dc.subjectMilk Proteins
dc.subjectCaseins
dc.titleComparison of the genetic characteristics of directly measured and Fourier-transform mid-infrared-predicted bovine milk fatty acids and proteins.
dc.typeJournal article
pubs.elements-id457722
pubs.organisational-groupOther
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