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United States Department of Agriculture

Agricultural Research Service

Research Project: Improving Genetic Predictions in Dairy Animals Using Phenotypic and Genomic Information

Location: Animal Genomics and Improvement Laboratory

Title: The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle

Authors
item Cole, John
item Hutchison, Jana
item Null, Daniel
item Vanraden, Paul
item Liu, Ge
item Schroeder, Steven
item Smith, Timothy
item Sonstegard, Tad
item Van Tassell, Curtis
item Bickhart, Derek

Submitted to: World Congress of Genetics Applied in Livestock Production
Publication Type: Proceedings
Publication Acceptance Date: April 21, 2014
Publication Date: August 17, 2014
Citation: Cole, J.B., Hutchison, J.L., Null, D.J., Van Raden, P.M., Liu, G., Schroeder, S.G., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P., Bickhart, D.M. 2014. The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.

Technical Abstract: Sequence data from 11 US Holstein bulls were analyzed to identify putative causal mutations associated with calving and conformation traits. The SNP ARS-BFGL-NGS-109285 at 57,589,121 bp (UMD 3.1 assembly) on BTA18 has large effects on 4 measures of body shape and size, 2 measures of dystocia, longevity, and lifetime economic merit. This region includes a human sialic acid Ig-like lectin 6 (Siglec-6) gene. We sequenced a homozygote for the minor allele, 4 carriers, and 3 non-carrier bulls from the same family. Three unrelated carrier bulls also were sequenced. Tandem duplications, insertions, and deletions were detected using custom analysis software that uses paired-end read alignments and split-read mapping. One duplication CNV and two tandem duplication events were detected within the gene. Predicted tandem duplications present in the carrier animals suggest that portions of two exons and a connecting intron within the Ig-like protein domains of Siglec-6 may have been duplicated.

Last Modified: 12/21/2014
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