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CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

Overview of attention for article published in BMC Genomics, March 2017
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Title
CNV discovery for milk composition traits in dairy cattle using whole genome resequencing
Published in
BMC Genomics, March 2017
DOI 10.1186/s12864-017-3636-3
Pubmed ID
Authors

Yahui Gao, Jianping Jiang, Shaohua Yang, Yali Hou, George E Liu, Shengli Zhang, Qin Zhang, Dongxiao Sun

Abstract

Copy number variations (CNVs) are important and widely distributed in the genome. CNV detection opens a new avenue for exploring genes associated with complex traits in humans, animals and plants. Herein, we present a genome-wide assessment of CNVs that are potentially associated with milk composition traits in dairy cattle. In this study, CNVs were detected based on whole genome re-sequencing data of eight Holstein bulls from four half- and/or full-sib families, with extremely high and low estimated breeding values (EBVs) of milk protein percentage and fat percentage. The range of coverage depth per individual was 8.2-11.9×. Using CNVnator, we identified a total of 14,821 CNVs, including 5025 duplications and 9796 deletions. Among them, 487 differential CNV regions (CNVRs) comprising ~8.23 Mb of the cattle genome were observed between the high and low groups. Annotation of these differential CNVRs were performed based on the cattle genome reference assembly (UMD3.1) and totally 235 functional genes were found within the CNVRs. By Gene Ontology and KEGG pathway analyses, we found that genes were significantly enriched for specific biological functions related to protein and lipid metabolism, insulin/IGF pathway-protein kinase B signaling cascade, prolactin signaling pathway and AMPK signaling pathways. These genes included INS, IGF2, FOXO3, TH, SCD5, GALNT18, GALNT16, ART3, SNCA and WNT7A, implying their potential association with milk protein and fat traits. In addition, 95 CNVRs were overlapped with 75 known QTLs that are associated with milk protein and fat traits of dairy cattle (Cattle QTLdb). In conclusion, based on NGS of 8 Holstein bulls with extremely high and low EBVs for milk PP and FP, we identified a total of 14,821 CNVs, 487 differential CNVRs between groups, and 10 genes, which were suggested as promising candidate genes for milk protein and fat traits.

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Mendeley readers

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The data shown below were compiled from readership statistics for 67 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 67 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 16 24%
Student > Master 12 18%
Researcher 10 15%
Professor > Associate Professor 5 7%
Student > Bachelor 4 6%
Other 8 12%
Unknown 12 18%
Readers by discipline Count As %
Agricultural and Biological Sciences 32 48%
Biochemistry, Genetics and Molecular Biology 10 15%
Veterinary Science and Veterinary Medicine 5 7%
Environmental Science 1 1%
Nursing and Health Professions 1 1%
Other 3 4%
Unknown 15 22%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 31 March 2017.
All research outputs
#20,412,387
of 22,962,258 outputs
Outputs from BMC Genomics
#9,311
of 10,686 outputs
Outputs of similar age
#269,165
of 308,778 outputs
Outputs of similar age from BMC Genomics
#169
of 201 outputs
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