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Functional & Integrative Genomics

, Volume 14, Issue 2, pp 333–339 | Cite as

A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle

  • Lingyang Xu
  • Yali Hou
  • Derek M. Bickhart
  • Jiuzhou Song
  • Curtis P. Van Tassell
  • Tad S. Sonstegard
  • George E. Liu
Original Paper

Abstract

Gastrointestinal (GI) nematode infections are a worldwide threat to human health and animal production. In this study, we performed a genome-wide association study between copy number variations (CNVs) and resistance to GI nematodes in an Angus cattle population. Using a linear regression analysis, we identified one deletion CNV which reaches genome-wide significance after Bonferroni correction. With multiple mapped human olfactory receptor genes but no annotated bovine genes in the region, this significantly associated CNV displays high population frequencies (58.26 %) with a length of 104.8 kb on chr7. We further investigated the linkage disequilibrium (LD) relationships between this CNV and its nearby single nucleotide polymorphisms (SNPs) and genes. The underlining haplotype blocks contain immune-related genes such as ZNF496 and NLRP3. As this CNV co-segregates with linked SNPs and associated genes, we suspect that it could contribute to the detected variations in gene expression and thus differences in host parasite resistance.

Keywords

Copy number variation (CNV) Gastrointestinal nematodes Association 

Abbreviations

CNV

Copy number variation

CNVR

CNV region

GI

Gastrointestinal

SNP

Single nucleotide polymorphism

Notes

Acknowledgments

We thank Reuben Anderson and Alexandre Dimitriv for their technical assistance. This work was supported in part by AFRI grant no. 2011-67015-30183 from USDA NIFA. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. The USDA is an equal opportunity provider and employer.

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

10142_2014_371_MOESM1_ESM.docx (100 kb)
ESM 1 (DOCX 99 kb)
10142_2014_371_MOESM2_ESM.pdf (1.3 mb)
Table S1 (PDF 1378 kb)
10142_2014_371_MOESM3_ESM.pdf (50 kb)
Table S2 (PDF 50 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg (outside the USA) 2014

Authors and Affiliations

  • Lingyang Xu
    • 1
    • 2
  • Yali Hou
    • 3
  • Derek M. Bickhart
    • 4
  • Jiuzhou Song
    • 2
  • Curtis P. Van Tassell
    • 1
  • Tad S. Sonstegard
    • 1
  • George E. Liu
    • 1
  1. 1.GEL: Bovine Functional Genomics Laboratory, BARCUSDA-ARSBeltsvilleUSA
  2. 2.Department of Animal and Avian SciencesUniversity of MarylandCollege ParkUSA
  3. 3.Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
  4. 4.Animal Improvement Programs Laboratory, BARCUSDA-ARSBeltsvilleUSA

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