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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Publications at this Location » Publication #347938

Research Project: Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency

Location: Cell Wall Biology and Utilization Research

Title: Copy number variation in dairy cattle using next-generation sequencing

item CHUD, TATIANE - Universidad De Sao Paulo
item Bickhart, Derek
item Cole, John
item DE SILVA, MARCOS - Universidade De Sao Paulo
item MUNARI, DANISIO - Universidade De Sao Paulo

Submitted to: International Plant and Animal Genome IX Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/15/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Gene copy number variants (CNV) have been shown to be associated with several production traits in dairy cattle; however, the detection and validation of CNVs in crossbred cattle is currently lacking. In order to provide a basis for future association studies, we sought to identify CNV regions (CNVRs) within the Girolando composite breed, resulting from a mating of the Holstein (taurine) and Gir (indicine) breeds. A read-depth method was performed using CNVnator software on NGS data from two Girolando, two Gir, and ten Holstein bulls. The individual CNVs were merged into CNVRs based on genomic regions overlapping by at least 1 bp. In total, a composite of 1,286 CNVRs (520 deletions, 255 duplications, 511 mixed) was identified on the genomes of all samples. We observed 34 CNVRs (nine deletions, 25 mixed) in common (overlapping > 50%) only between Girolando and Holstein and 181 CNVRs (20 deletions, 21 duplications,140 mixed) only in Girolando and Gir, suggesting parent-of-origin inheritance from Holstein and Gir cattle, respectively. One of these Holstein-specific CNVRs intersected with the interleukin 6 family cytokine (LIF) gene which is linked to fat production and fertility traits in Holstein. Genes related to disease resistance (e.g., the CD4 gene) also coincided with CNVRs present only in Gir and Girolando cattle, suggesting an indicine origin for the CNV. These results showed evidence of specific CNVRs shared by Girolando and purebred breeds which may be targeted for future selective breeding.