Comparison of genomic prediction accuracies in dairy cattle lactation traits using five classes of functional variants versus generic SNP
Abstract Background Genomic selection, typically employing genetic markers from SNP chips, is routine in modern dairy cattle breeding. This study assessed the impact of functional sequence variants on genomic prediction accuracy relative to 50 k SNP chip markers for fat percent, protein percent, mil...
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| Format: | Article |
| Language: | deu |
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BMC
2025-04-01
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| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-025-00966-2 |
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| author | Setegn Worku Alemu Thomas J. Lopdell Alexander J. Trevarton Russell G. Snell Mathew D. Littlejohn Dorian J. Garrick |
| author_facet | Setegn Worku Alemu Thomas J. Lopdell Alexander J. Trevarton Russell G. Snell Mathew D. Littlejohn Dorian J. Garrick |
| author_sort | Setegn Worku Alemu |
| collection | DOAJ |
| description | Abstract Background Genomic selection, typically employing genetic markers from SNP chips, is routine in modern dairy cattle breeding. This study assessed the impact of functional sequence variants on genomic prediction accuracy relative to 50 k SNP chip markers for fat percent, protein percent, milk volume, fat yield, and protein yield in lactating dairy cattle. The functional variants were identified through GWAS, RNA-seq, Histone modification ChIP-seq, ATAC-seq, or were coding variants. The genomic prediction accuracy obtained using each class of functional variants was compared with matched numbers of SNPs randomly selected from the Illumina 50 k SNP chip. Results The investigation revealed that variants identified by GWAS or RNA-seq, significantly improved the prediction accuracy across all five traits. Contributions from ChIP-seq, ATAC-seq, and coding variants varied. Some variants identified using ChIP-seq showed marked improvements, while others reduced accuracy in protein yield predictions. Relative to a matched number of 32,595 SNPs from the SNP chip, pooling all the functional variants demonstrated prediction accuracy increases of 1.76% for fat percent, 2.97% for protein percent, 0.51% for milk volume, and 0.26% for fat yield, but with a slight decrease of 0.43% in protein yield. Conclusion The study demonstrates that functional variants can improve prediction accuracy relative to equivalent numbers of variants from a generic SNP panel, with percent traits showing more significant gains than yield traits. The main advantage of using functional variants for genomic prediction was achievement of comparable accuracy using a smaller, more selective set of loci. This is particularly evident in trait-specific scenarios. Our findings indicate that specific combinations of functional variants comprising 16 k variants can achieve genomic prediction accuracy comparable to employing a standard panel of twice the size (32.6 k), especially for percent traits. This highlights the potential for the development of more efficient, trait-focused SNP panels utilizing functional variants. |
| format | Article |
| id | doaj-art-ebd97547e63146cd8e4b1a20bb032747 |
| institution | DOAJ |
| issn | 1297-9686 |
| language | deu |
| publishDate | 2025-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj-art-ebd97547e63146cd8e4b1a20bb0327472025-08-20T03:06:55ZdeuBMCGenetics Selection Evolution1297-96862025-04-0157111510.1186/s12711-025-00966-2Comparison of genomic prediction accuracies in dairy cattle lactation traits using five classes of functional variants versus generic SNPSetegn Worku Alemu0Thomas J. Lopdell1Alexander J. Trevarton2Russell G. Snell3Mathew D. Littlejohn4Dorian J. Garrick5AL Rae Centre for Genetics and Breeding, Massey UniversityLICSchool of Biological Sciences, University of AucklandSchool of Biological Sciences, University of AucklandAL Rae Centre for Genetics and Breeding, Massey UniversityAL Rae Centre for Genetics and Breeding, Massey UniversityAbstract Background Genomic selection, typically employing genetic markers from SNP chips, is routine in modern dairy cattle breeding. This study assessed the impact of functional sequence variants on genomic prediction accuracy relative to 50 k SNP chip markers for fat percent, protein percent, milk volume, fat yield, and protein yield in lactating dairy cattle. The functional variants were identified through GWAS, RNA-seq, Histone modification ChIP-seq, ATAC-seq, or were coding variants. The genomic prediction accuracy obtained using each class of functional variants was compared with matched numbers of SNPs randomly selected from the Illumina 50 k SNP chip. Results The investigation revealed that variants identified by GWAS or RNA-seq, significantly improved the prediction accuracy across all five traits. Contributions from ChIP-seq, ATAC-seq, and coding variants varied. Some variants identified using ChIP-seq showed marked improvements, while others reduced accuracy in protein yield predictions. Relative to a matched number of 32,595 SNPs from the SNP chip, pooling all the functional variants demonstrated prediction accuracy increases of 1.76% for fat percent, 2.97% for protein percent, 0.51% for milk volume, and 0.26% for fat yield, but with a slight decrease of 0.43% in protein yield. Conclusion The study demonstrates that functional variants can improve prediction accuracy relative to equivalent numbers of variants from a generic SNP panel, with percent traits showing more significant gains than yield traits. The main advantage of using functional variants for genomic prediction was achievement of comparable accuracy using a smaller, more selective set of loci. This is particularly evident in trait-specific scenarios. Our findings indicate that specific combinations of functional variants comprising 16 k variants can achieve genomic prediction accuracy comparable to employing a standard panel of twice the size (32.6 k), especially for percent traits. This highlights the potential for the development of more efficient, trait-focused SNP panels utilizing functional variants.https://doi.org/10.1186/s12711-025-00966-2 |
| spellingShingle | Setegn Worku Alemu Thomas J. Lopdell Alexander J. Trevarton Russell G. Snell Mathew D. Littlejohn Dorian J. Garrick Comparison of genomic prediction accuracies in dairy cattle lactation traits using five classes of functional variants versus generic SNP Genetics Selection Evolution |
| title | Comparison of genomic prediction accuracies in dairy cattle lactation traits using five classes of functional variants versus generic SNP |
| title_full | Comparison of genomic prediction accuracies in dairy cattle lactation traits using five classes of functional variants versus generic SNP |
| title_fullStr | Comparison of genomic prediction accuracies in dairy cattle lactation traits using five classes of functional variants versus generic SNP |
| title_full_unstemmed | Comparison of genomic prediction accuracies in dairy cattle lactation traits using five classes of functional variants versus generic SNP |
| title_short | Comparison of genomic prediction accuracies in dairy cattle lactation traits using five classes of functional variants versus generic SNP |
| title_sort | comparison of genomic prediction accuracies in dairy cattle lactation traits using five classes of functional variants versus generic snp |
| url | https://doi.org/10.1186/s12711-025-00966-2 |
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