Genome-wide association study between copy number variants and hoof health traits in Holstein dairy cattle.

Butty, Adrien M; Chud, Tatiane C S; Cardoso, Diercles F; Lopes, Lucas S F; Miglior, Filippo; Schenkel, Flavio S; Cánovas, Angela; Häfliger, Irene M.; Drögemüller, Cord; Stothard, Paul; Malchiodi, Francesca; Baes, Christine F. (2021). Genome-wide association study between copy number variants and hoof health traits in Holstein dairy cattle. (In Press). Journal of dairy science American Dairy Science Association 10.3168/jds.2020-19879

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Genome-wide association studies based on SNP have been completed for multiple traits in dairy cattle; however, copy number variants (CNV) could add genomic information that has yet to be harnessed. The objectives of this study were to identify CNV in genotyped Holstein animals and assess their association with hoof health traits using deregressed estimated breeding values as pseudophenotypes. A total of 23,256 CNV comprising 1,645 genomic regions were identified in 5,845 animals. Fourteen genomic regions harboring structural variations, including 9 deletions and 5 duplications, were associated with at least 1 of the studied hoof health traits. This group of traits included digital dermatitis, interdigital dermatitis, heel horn erosion, sole ulcer, white line lesion, sole hemorrhage, and interdigital hyperplasia; no regions were associated with toe ulcer. Twenty candidate genes overlapped with the regions associated with these traits including SCART1, NRXN2, KIF26A, GPHN, and OR7A17. In this study, an effect on infectious hoof lesions could be attributed to the PRAME (Preferentially Expressed Antigen in Melanoma) gene. Almost all genes detected in association with noninfectious hoof lesions could be linked to known metabolic disorders. The knowledge obtained considering information of associated CNV to the traits of interest in this study could improve the accuracy of estimated breeding values. This may further increase the genetic gain for these traits in the Canadian Holstein population, thus reducing the involuntary animal losses due to lameness.

Item Type:

Journal Article (Original Article)

Division/Institute:

05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH)

UniBE Contributor:

Häfliger, Irene Monika; Drögemüller, Cord and Baes, Christine Francoise

Subjects:

500 Science > 590 Animals (Zoology)
600 Technology > 630 Agriculture
500 Science > 570 Life sciences; biology

ISSN:

0022-0302

Publisher:

American Dairy Science Association

Language:

English

Submitter:

Cord Drögemüller

Date Deposited:

06 May 2021 08:28

Last Modified:

06 May 2021 08:28

Publisher DOI:

10.3168/jds.2020-19879

PubMed ID:

33896633

Uncontrolled Keywords:

dairy cattle functional analysis genotype structural variant

BORIS DOI:

10.48350/156144

URI:

https://boris.unibe.ch/id/eprint/156144

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