Functional & Integrative Genomics

, Volume 18, Issue 5, pp 559–567 | Cite as

Integrating CNVs into meta-QTL identified GBP4 as positional candidate for adult cattle stature

  • Xiu-Kai Cao
  • Yong-Zhen Huang
  • Yi-Lei Ma
  • Jie Cheng
  • Zhen-Xian Qu
  • Yun Ma
  • Yue-Yu Bai
  • Feng Tian
  • Feng-Peng Lin
  • Yu-Lin Ma
  • Hong ChenEmail author
Original Article


Copy number variation (CNV) of DNA sequences, functionally significant but yet fully ascertained, is believed to confer considerable increments in unexplained heritability of quantitative traits. Identification of phenotype-associated CNVs (paCNVs) therefore is a pressing need in CNV studies to speed up their exploitation in cattle breeding programs. Here, we provided a new avenue to achieve this goal that is to project the published CNV data onto meta-quantitative trait loci (meta-QTL) map which connects causal genes with phenotypes. Any CNVs overlapping meta-QTL therefore will be potential paCNVs. This study reported potential paCNVs in Bos taurus autosome 3 (BTA3). Notably, overview indexes and CNVs both highlighted a narrower region (BTA3 54,500,000–55,000,000 bp, named BTA3_INQTL_6) within one constructed meta-QTL. Then, we ascertained guanylate-binding protein 4 (GBP4) among the nine positional candidate genes was significantly associated with adult cattle stature, including body weight (BW, P < 0.05) and withers height (WHT, P < 0.05), fitting GBP4 CNV either with three levels or with six levels in the model. Although higher copy number downregulated the mRNA levels of GBP2 (P < 0.05) and GBP4 (P < 0.05) in 1-Mb window (54.0–55.0 Mb) in muscle and adipose, additional analyses will be needed to clarify the causality behind the ascertained association.


Meta-analysis Overview analysis GBP CNV Cattle stature 


Funding information

This work was supported by the National 863 Program of China [2013AA102505], the Program of National Beef Cattle and Yak Industrial Technology System [CARS-37], the National Natural Science Foundation of China [31272408, 31601926], Bio-breeding capacity-building and industry specific projects from the National Development and Reform Commission [2014-2573], Specific Projects of Science and Technology in Henan Province [141100110200], Science and Technology Co-ordinator Innovative engineering projects of Shaanxi Province [2014KTZB02-02-02-02, 2015KTCL02-08], Project of breeding and application of Pinan Cattle, and Haixi Project of Qinghai Province: Identification of key genes of growth and high-quality meat in Yak Multi hybrids.

Compliance with ethical standards

This study was approved by the Northwest A&F University Ethics Committee.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10142_2018_613_MOESM1_ESM.xlsx (79 kb)
ESM 1 (XLSX 78 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
  2. 2.College of Life ScienceXinyang Normal UniversityXinyangChina
  3. 3.Henan Genetic Performance Determination Center for CattleZhengzhouChina
  4. 4.College of Food Science and EngineeringNorthwest A&F UniversityYanglingChina
  5. 5.Biyang Bureau of Animal HusbandryBiyangChina
  6. 6.Animal Disease Control Center of Haixi Mongolian and Tibetan Autonomous PrefectureDelinghaChina

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