Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy Cattle
Structural variations (SVs) are large DNA segments of deletions, duplications, copy number variations, inversions and translocations in a re-sequenced genome compared to a reference genome. They have been found to be associated with several complex traits in dairy cattle and could potentially help t...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-02-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/11/2/541 |
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| author | Long Chen Jennie E. Pryce Ben J. Hayes Hans D. Daetwyler |
| author_facet | Long Chen Jennie E. Pryce Ben J. Hayes Hans D. Daetwyler |
| author_sort | Long Chen |
| collection | DOAJ |
| description | Structural variations (SVs) are large DNA segments of deletions, duplications, copy number variations, inversions and translocations in a re-sequenced genome compared to a reference genome. They have been found to be associated with several complex traits in dairy cattle and could potentially help to improve genomic prediction accuracy of dairy traits. Imputation of SVs was performed in individuals genotyped with single-nucleotide polymorphism (SNP) panels without the expense of sequencing them. In this study, we generated 24,908 high-quality SVs in a total of 478 whole-genome sequenced Holstein and Jersey cattle. We imputed 4489 SVs with R2 > 0.5 into 35,568 Holstein and Jersey dairy cattle with 578,999 SNPs with two pipelines, FImpute and Eagle2.3-Minimac3. Genome-wide association studies for production, fertility and overall type with these 4489 SVs revealed four significant SVs, of which two were highly linked to significant SNP. We also estimated the variance components for SNP and SV models for these traits using genomic best linear unbiased prediction (GBLUP). Furthermore, we assessed the effect on genomic prediction accuracy of adding SVs to GBLUP models. The estimated percentage of genetic variance captured by SVs for production traits was up to 4.57% for milk yield in bulls and 3.53% for protein yield in cows. Finally, no consistent increase in genomic prediction accuracy was observed when including SVs in GBLUP. |
| first_indexed | 2024-03-09T00:45:16Z |
| format | Article |
| id | doaj.art-fd8c3d21fabf4ce7a576cc7b3a69bfde |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-09T00:45:16Z |
| publishDate | 2021-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-fd8c3d21fabf4ce7a576cc7b3a69bfde2023-12-11T17:37:22ZengMDPI AGAnimals2076-26152021-02-0111254110.3390/ani11020541Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy CattleLong Chen0Jennie E. Pryce1Ben J. Hayes2Hans D. Daetwyler3Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, AustraliaAgriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, AustraliaAgriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, AustraliaAgriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, AustraliaStructural variations (SVs) are large DNA segments of deletions, duplications, copy number variations, inversions and translocations in a re-sequenced genome compared to a reference genome. They have been found to be associated with several complex traits in dairy cattle and could potentially help to improve genomic prediction accuracy of dairy traits. Imputation of SVs was performed in individuals genotyped with single-nucleotide polymorphism (SNP) panels without the expense of sequencing them. In this study, we generated 24,908 high-quality SVs in a total of 478 whole-genome sequenced Holstein and Jersey cattle. We imputed 4489 SVs with R2 > 0.5 into 35,568 Holstein and Jersey dairy cattle with 578,999 SNPs with two pipelines, FImpute and Eagle2.3-Minimac3. Genome-wide association studies for production, fertility and overall type with these 4489 SVs revealed four significant SVs, of which two were highly linked to significant SNP. We also estimated the variance components for SNP and SV models for these traits using genomic best linear unbiased prediction (GBLUP). Furthermore, we assessed the effect on genomic prediction accuracy of adding SVs to GBLUP models. The estimated percentage of genetic variance captured by SVs for production traits was up to 4.57% for milk yield in bulls and 3.53% for protein yield in cows. Finally, no consistent increase in genomic prediction accuracy was observed when including SVs in GBLUP.https://www.mdpi.com/2076-2615/11/2/541genome sequencestructural variantsaccuracygenome-wide association studiesgenomic predictiongenomic selection |
| spellingShingle | Long Chen Jennie E. Pryce Ben J. Hayes Hans D. Daetwyler Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy Cattle Animals genome sequence structural variants accuracy genome-wide association studies genomic prediction genomic selection |
| title | Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy Cattle |
| title_full | Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy Cattle |
| title_fullStr | Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy Cattle |
| title_full_unstemmed | Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy Cattle |
| title_short | Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy Cattle |
| title_sort | investigating the effect of imputed structural variants from whole genome sequence on genome wide association and genomic prediction in dairy cattle |
| topic | genome sequence structural variants accuracy genome-wide association studies genomic prediction genomic selection |
| url | https://www.mdpi.com/2076-2615/11/2/541 |
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