Copy number variation detection using SNP genotyping arrays in three Chinese pig breeds.

We performed genome-wide CNV detection based on SNP genotyping data of 96 Chinese-native Tibetan, Dahe and Wuzhishan pigs. These pigs are particularly interesting because of their excellent adaptation to hypoxia or small body size, which facilitates the use of them as models of different human diseases in addition to valuable agricultural animals. A total of 105 CNV regions (CNVRs) were identified, encompassing 16.71 Mb of the pig genome. Seven of 10 (70%) CNVRs selected randomly were validated by quantitative real-time PCR. Comparison with previous studies revealed 25 (23.81%) novel CNVRs, indicating that CNV coverage of the pig genome is still incomplete and there exists large diversity between pig breeds. Functional analysis of genes located in these CNVRs confirmed the high representation of genes involved in sensory perception, neurological system processes and other basic metabolic processes. In addition, the majority of these CNVRs were detected to span reported pig QTL that affect various traits, which highlighted three biologically interesting genes with copy number changes (i.e., ANKRD34B, FAM110B and ABCG1). These genes may have economic importance in pig breeding and are worth being further investigated. We also obtained some CNVRs harboring genes that had human orthologs involved in human diseases such as cardiovascular disease and Alzheimer's disease. The findings of this study are a significant extension of the coverage of CNVRs in the pig genome and provide valuable resources for follow-up-associated studies of CNVs in pig complex traits as well as important implications of human diseases.

Dong K ，Pu Y ，Yao N ，Shu G ，Liu X ，He X ，Zhao Q ，Guan W ，Ma Y ... -  《-》

Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays.

Wang J ，Wang H ，Jiang J ，Kang H ，Feng X ，Zhang Q ，Liu JF ... -  《PLoS One》

A comprehensive survey of copy number variation in 18 diverse pig populations and identification of candidate copy number variable genes associated with complex traits.

Chen C ，Qiao R ，Wei R ，Guo Y ，Ai H ，Ma J ，Ren J ，Huang L ... -  《BMC GENOMICS》

Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs.

Qiu Y ，Ding R ，Zhuang Z ，Wu J ，Yang M ，Zhou S ，Ye Y ，Geng Q ，Xu Z ，Huang S ，Cai G ，Wu Z ，Yang J ... -  《BMC GENOMICS》

Copy number variants in Italian Large White pigs detected using high-density single nucleotide polymorphisms and their association with back fat thickness.

The aim of this study was to identify copy number variants (CNVs) in Italian Large White pigs and test them for association with back fat thickness (BFT). Within a population of 12 000 performance-tested pigs, two groups of animals with extreme and divergent BFT estimated breeding values (EBVs; 147 with negative and 150 with positive EBVs) were genotyped with the Illumina Porcine SNP60 BeadChip. CNVs were detected with PENNCNV software. We identified a total of 4146 CNV events in 170 copy number variation regions (CNVRs) located on 15 porcine autosomes. Validation of detected CNVRs was carried out (i) by comparing CNVRs already detected by other studies and (ii) by semiquantitative fluorescent multiplex (SQFM) PCR of a few CNVRs. Most of CNVRs detected in Italian Large White pigs (71.2%) were already reported in other pig breeds/populations, and 82.1% of the CNV events detected by PENNCNV were confirmed by SQFM PCR. For each CNVR, we compared the occurrence of CNV events between the pigs of the high and low BFT EBV tails. Sixteen regions showed significance at P < 0.10, and seven were significant at P < 0.05 but were not significant after Bonferroni correction (Fisher's exact test). These results indicated that CNVs could explain a limited fraction of the genetic variability of fat deposition in Italian Large White pigs. However, it was interesting to note that one of these CNVRs encompassed the ZPLD1 gene. In humans, a rare CNV event including this gene is associated with obesity. Studies identifying CNVs in pigs could assist in elucidating the genetic mechanisms underlying human obesity.

Schiavo G ，Dolezal MA ，Scotti E ，Bertolini F ，Calò DG ，Galimberti G ，Russo V ，Fontanesi L ... -  《-》