Comparison of the genetic characteristics of directly measured and Fourier-transform mid-infrared-predicted bovine milk fatty acids and proteins
ABSTRACT: Fourier-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...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-11-01
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| Series: | Journal of Dairy Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0022030222006142 |
| _version_ | 1797988281672007680 |
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| author | Kathryn M. Tiplady Thomas J. Lopdell Richard G. Sherlock Thomas J.J. Johnson Richard J. Spelman Bevin L. Harris Stephen R. Davis Mathew D. Littlejohn Dorian J. Garrick |
| author_facet | Kathryn M. Tiplady Thomas J. Lopdell Richard G. Sherlock Thomas J.J. Johnson Richard J. Spelman Bevin L. Harris Stephen R. Davis Mathew D. Littlejohn Dorian J. Garrick |
| author_sort | Kathryn M. Tiplady |
| collection | DOAJ |
| description | ABSTRACT: Fourier-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. |
| first_indexed | 2024-04-11T08:01:32Z |
| format | Article |
| id | doaj.art-87ad00ec3d594691b9978de5dc621ff2 |
| institution | Directory Open Access Journal |
| issn | 0022-0302 |
| language | English |
| last_indexed | 2024-04-11T08:01:32Z |
| publishDate | 2022-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Dairy Science |
| spelling | doaj.art-87ad00ec3d594691b9978de5dc621ff22022-12-22T04:35:43ZengElsevierJournal of Dairy Science0022-03022022-11-011051297639791Comparison of the genetic characteristics of directly measured and Fourier-transform mid-infrared-predicted bovine milk fatty acids and proteinsKathryn M. Tiplady0Thomas J. Lopdell1Richard G. Sherlock2Thomas J.J. Johnson3Richard J. Spelman4Bevin L. Harris5Stephen R. Davis6Mathew D. Littlejohn7Dorian J. Garrick8Research and Development, Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New Zealand; School of Agriculture and Environment, Massey University, Ruakura, Hamilton 3240, New Zealand; Corresponding authorResearch and Development, Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New ZealandResearch and Development, Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New ZealandResearch and Development, Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New ZealandResearch and Development, Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New ZealandResearch and Development, Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New ZealandResearch and Development, Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New ZealandResearch and Development, Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New Zealand; School of Agriculture and Environment, Massey University, Ruakura, Hamilton 3240, New ZealandSchool of Agriculture and Environment, Massey University, Ruakura, Hamilton 3240, New ZealandABSTRACT: Fourier-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.http://www.sciencedirect.com/science/article/pii/S0022030222006142milk compositionFourier-transform mid-infrared spectroscopygenome-wide association studydairy cattle |
| spellingShingle | Kathryn M. Tiplady Thomas J. Lopdell Richard G. Sherlock Thomas J.J. Johnson Richard J. Spelman Bevin L. Harris Stephen R. Davis Mathew D. Littlejohn Dorian J. Garrick Comparison of the genetic characteristics of directly measured and Fourier-transform mid-infrared-predicted bovine milk fatty acids and proteins Journal of Dairy Science milk composition Fourier-transform mid-infrared spectroscopy genome-wide association study dairy cattle |
| title | Comparison of the genetic characteristics of directly measured and Fourier-transform mid-infrared-predicted bovine milk fatty acids and proteins |
| title_full | Comparison of the genetic characteristics of directly measured and Fourier-transform mid-infrared-predicted bovine milk fatty acids and proteins |
| title_fullStr | Comparison of the genetic characteristics of directly measured and Fourier-transform mid-infrared-predicted bovine milk fatty acids and proteins |
| title_full_unstemmed | Comparison of the genetic characteristics of directly measured and Fourier-transform mid-infrared-predicted bovine milk fatty acids and proteins |
| title_short | Comparison of the genetic characteristics of directly measured and Fourier-transform mid-infrared-predicted bovine milk fatty acids and proteins |
| title_sort | comparison of the genetic characteristics of directly measured and fourier transform mid infrared predicted bovine milk fatty acids and proteins |
| topic | milk composition Fourier-transform mid-infrared spectroscopy genome-wide association study dairy cattle |
| url | http://www.sciencedirect.com/science/article/pii/S0022030222006142 |
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