Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays.
Copy number variations (CNVs) are important forms of genetic variation complementary to SNPs, and can be considered as promising markers for some phenotypic and economically important traits or diseases susceptibility in domestic animals. In the present study, we performed a genome-wide CNV identification in 14 individuals selected from diverse populations, including six types of Chinese indigenous breeds, one Asian wild boar population, as well as three modern commercial foreign breeds. We identified 63 CNVRs in total, which covered 9.98 Mb of polymorphic sequence and corresponded to 0.36% of the genome sequence. The length of these CNVRs ranged from 3.20 to 827.21 kb, with an average of 158.37 kb and a median of 97.85 kb. Functional annotation revealed these identified CNVR have important molecular function, and may play an important role in exploring the genetic basis of phenotypic variability and disease susceptibility among pigs. Additionally, to confirm these potential CNVRs, we performed qPCR for 12 randomly selected CNVRs and 8 of them (66.67%) were confirmed successfully. CNVs detected in diverse populations herein are essential complementary to the CNV map in the pig genome, which provide an important resource for studies of genomic variation and the association between various economically important traits and CNVs.
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National College of Animal Science and Technology, China Agricultural University, Beijing, China.
Jiying
J
Wang
Haifei
H
Wang
Jicai
J
Jiang
Huimin
H
Kang
Xiaotian
X
Feng
Qin
Q
Zhang
Jian-Feng
JF
Liu
D000818:Animals; D001947:Breeding; D056915:DNA Copy Number Variations / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D060005:Genotyping Techniques / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D034421:Sus scrofa / Q000235:genetics*