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Funct Integr Genomics. 2018 Sep;18(5):559-567. doi: 10.1007/s10142-018-0613-0. Epub 2018 May 8.

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

Author information

1
College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling, 712100, Shaanxi, China.
2
College of Life Science, Xinyang Normal University, Xinyang, 464000, Henan, China.
3
Henan Genetic Performance Determination Center for Cattle, Zhengzhou, 450046, Henan, China.
4
College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi, China.
5
Biyang Bureau of Animal Husbandry, Biyang, 463700, Henan, China.
6
Animal Disease Control Center of Haixi Mongolian and Tibetan Autonomous Prefecture, Delingha, 817000, China.
7
College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling, 712100, Shaanxi, China. hongchen1212@163.com.

Abstract

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.

KEYWORDS:

CNV; Cattle stature; GBP; Meta-analysis; Overview analysis

PMID:
29737453
DOI:
10.1007/s10142-018-0613-0
[Indexed for MEDLINE]

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