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Animal genetics2016; 47(5); 560-569; doi: 10.1111/age.12451

Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array.

Abstract: Copy number variation (CNV), an essential form of genetic variation, has been increasingly recognized as one promising genetic marker in the analysis of animal genomes. Here, we used the Equine 70K single nucleotide polymorphism genotyping array for the genome-wide detection of CNVs in 96 horses from three diverse Chinese breeds: Debao pony (DB), Mongolian horse (MG) and Yili horse (YL). A total of 287 CNVs were determined and merged into 122 CNV regions (CNVRs) ranging from 199 bp to 2344 kb in size and distributed in a heterogeneous manner on chromosomes. These CNVRs were integrated with seven existing reports to generate a composite genome-wide dataset of 1558 equine CNVRs, revealing 69 (56.6%) novel CNVRs. The majority (69.7%) of the 122 CNVRs overlapped with 438 genes, whereas 30.3% were located in intergenic regions. Most of these genes were associated with common CNVRs, which were shared by divergent horse breeds. As many as 60, 42 and 91 genes overlapping with the breed-specific ss were identified in DB, MG and YL respectively. Among these genes, FGF11, SPEM1, PPARG, CIDEB, HIVEP1 and GALR may have potential relevance to breed-specific traits. These findings provide valuable information for understanding the equine genome and facilitating association studies of economically important traits with equine CNVRs in the future.
© 2016 Stichting International Foundation for Animal Genetics.
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Publication Date: 2016-07-21 PubMed ID: 27440410DOI: 10.1111/age.12451Google Scholar: Lookup
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Summary

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The research article presents an analysis detailing the identification of variations in the number of gene copies, known as copy number variation (CNV), within three breeds of horses in China using a 70K single nucleotide polymorphism genotyping array.

Methodology

  • The researchers utilized the Equine 70K single nucleotide polymorphism genotyping array, genomic tool that allows for detection of thousands of genetic variations.
  • The sample population consisted of 96 horses stemming from three Chinese breeds: the Debao pony, Mongolian horse, and Yili horse.

Findings

  • This genome-wide survey detected about 287 CNVs, which were later merged into 122 CNV regions (CNVRs), differing in size and dispersed unevenly across the chromosomes.
  • The researchers compared these CNVRs with data from seven previous studies, resulting in a composite database of 1558 equine CNVRs. This comparison revealed 69 CNVRs that had not been previously identified.
  • They found that the majority of these CNVRs (about 69.7%) were associated with 438 genes while the rest (around 30.3%) were located in a non-gene-coding (intergenic) region.
  • The shared presence of these CNVRs was notable across the different horse breeds tested.

Implications

  • Within each breed-specific set, a different collection of overlapping genes was identified. For example, the Debao pony, Mongolian horse, and Yili horse had 60, 42, and 91 breed-specific overlapping genes, respectively.
  • Among these breed-specific genes, FGF11, SPEM1, PPARG, CIDEB, HIVEP1, and GALR were identified as potentially relevant to traits specific to each breed.
  • These findings provide important groundwork for further studies aiming to associate economically significant traits with equine CNVRs.

This study highlights the importance of CNVs in understanding genetic diversity in different horse breeds. It also contributes to the wider field of genomics, providing additional information on equine genomes.

Cite This Article

APA
Kader A, Liu X, Dong K, Song S, Pan J, Yang M, Chen X, He X, Jiang L, Ma Y. (2016). Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array. Anim Genet, 47(5), 560-569. https://doi.org/10.1111/age.12451

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 47
Issue: 5
Pages: 560-569

Researcher Affiliations

Kader, Adiljan
  • The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
  • Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 83000, China.
Liu, Xuexue
  • The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
Dong, Kunzhe
  • The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
  • United States Department of Agriculture, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA.
Song, Shen
  • The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
  • Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100094, China.
Pan, Jianfei
  • The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
Yang, Min
  • The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
Chen, Xiaofei
  • The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
He, Xiaohong
  • The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
Jiang, Lin
  • The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China. jianglin@caas.cn.
Ma, Yuehui
  • The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China. mayuehui@caas.cn.

MeSH Terms

  • Animals
  • Breeding
  • China
  • DNA Copy Number Variations
  • Genotype
  • Horses / genetics
  • Oligonucleotide Array Sequence Analysis / veterinary
  • Polymorphism, Single Nucleotide

Citations

This article has been cited 15 times.
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