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Genomic copy number variation of the CHKB gene alters gene expression and affects growth traits of Chinese domestic yak (Bos grunniens) breeds

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Abstract

Copy number variation (CNV) influences the mRNA transcription levels and phenotypic traits through gene dosage, position effects, alteration of downstream pathways, and modulation of the structure and position of chromosomes. A previous study using the read depth approach to genome resequencing analysis revealed CNVs of the choline kinase beta (CHKB) gene in the copy number variable regions (CNVRs) of yak breeds may influence muscle development and therefore the phenotypic traits of yak breeds. Further work is required to attain a more complete understanding and validate the importance of the detected CNVR of the CHKB gene found in yak breeds, because there is no association studies of the CHKB gene with yak growth traits that have been reported. The goal of this study was to determine the distribution of CHKB copy numbers in five Chinese domestic yak breeds and evaluate their impact on gene expression and growth traits. The data were analyzed using real-time quantitative PCR. In this study, the normal CNV of the CHKB gene was found to be significantly (p < 0.05) associated with greater chest girth and body weight for three age groups of Datong yaks. Our results indicated that the copy number of the CHKB gene is negatively correlated with the mRNA expression level. From this result, we conclude that CNVs of the CHKB gene could be novel markers for growth traits of Chinese domestic yak breeds and might therefore provide a novel opportunity to utilize data on CNVs in designing molecular markers for the selection of animal breeding programs for larger populations of various yaks.

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Abbreviations

aCGH:

Array-based comparative genomic hybridization

BTF3:

Bovine basic transcription factor 3

CHKB:

Choline kinase beta

CHRM3:

Cholinergic receptor muscarinic 3

CNV:

Copy number variation

CNVRs:

Copy number variable regions

Ct:

Comparative threshold cycle

CYP4A11:

Cytochrome P450 family 4 subfamily A member 11

GAPDH:

Glyceraldehyde-3-phosphate dehydrogenase gene

GDNA:

Genomic DNA

GPC1:

Glypican 1

KCNJ12:

Potassium voltage-gated channel subfamily J member 12

KLF6:

Kruppel-like factor

LEPR:

Leptin receptor

MAPK10:

Mitogen-activated protein kinase 10

MYH3:

Myosin heavy chain 3

MyHC I:

Type I myosin heavy chain, cardiac muscle complex

NAHR:

Non-allelic homologous recombination

PCR:

Polymerase chain reaction

PGC-1α:

Peroxisome proliferator-activated receptor gamma coactivator 1-alpha

PLA2G2D:

Phospholipase A2 group IID

qPCR:

Quantitative real-time polymerase chain reaction

QTLs:

Quantitative trait locus

RHACD8:

Alpha chain (CD8A) gene

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Acknowledgements

We thank Mr. Yong Feng Zhang for guidance and technical assistance during the laboratory work and Dr. Hong Bo Wang, Ms. Li Xiaoxiao, and Mr. Peng Tang for blood sample collection.

Funding

This research was funded by the Innovation Project of Chinese Academy of Agricultural Sciences (Grant number CAAS-ASTIP-2014-LIHPS-01) and the Program of National Beef Cattle and Yak Industrial Technology System (Grant number CARS-37).

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Authors and Affiliations

  1. Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Chinese Academy of Agricultural Science, Lanzhou, 730050, Gansu, China

    Habtamu Abera Goshu, Min Chu, Wu Xiaoyun, Bao Pengjia, Ding Xue Zhi & Ping Yan

  2. Oromia Agricultural Research Institute, Bako Agricultural Research Center, Bako, Ethiopia

    Habtamu Abera Goshu

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  1. Habtamu Abera Goshu
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  2. Min Chu
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Contributions

HA performed the data analysis and literature review. PY, MC, BP, and DXZ contributed to guidance and supervision during this study. WX was involved in drafting the manuscript and performing the laboratory work. HA wrote the manuscript and prepared the graphics.

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Correspondence to Habtamu Abera Goshu or Ping Yan.

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Habtamu Abera Goshu declares that he has no conflict of interest. Min Chu declares that she has no conflict of interest. Wu Xiaoyun declares that he has no conflict of interest. Bao Pengjia declares that he has no conflict of interest. Ding Xue Zhi declares that he has no conflict of interest. Ping Yan declares that she has no conflict of interest.

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All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards.

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Communicated by S. Hohmann.

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Goshu, H.A., Chu, M., Xiaoyun, W. et al. Genomic copy number variation of the CHKB gene alters gene expression and affects growth traits of Chinese domestic yak (Bos grunniens) breeds. Mol Genet Genomics 294, 549–561 (2019). https://doi.org/10.1007/s00438-018-01530-y

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