La Trobe
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Investigating the effect of imputed structural variants from whole‐genome sequence on genome‐wide association and genomic prediction in dairy cattle

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journal contribution
posted on 28.04.2021, 06:27 by Long Chen, Jennie Pryce, BJ Hayes, Hans Daetwyler
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‐Min-imac3. 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.

Funding

The authors acknowledge financial support from Agriculture Victoria, Dairy Australia, and the Gardiner Foundation through the DairyBio initiative and La Trobe University.

History

Publication Date

01/02/2021

Journal

Animals

Volume

11

Issue

2

Article Number

ARTN 541

Pagination

(p. 1-16)

Publisher

MDPI

ISSN

2076-2615

Rights Statement

The Author reserves all moral rights over the deposited text and must be credited if any re-use occurs. Documents deposited in OPAL are the Open Access versions of outputs published elsewhere. Changes resulting from the publishing process may therefore not be reflected in this document. The final published version may be obtained via the publisher’s DOI. Please note that additional copyright and access restrictions may apply to the published version.

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