Identification of genome-wide copy number variations among diverse pig breeds by array CGH

Abstract

Background: Recent studies have shown that copy number variation (CNV) in mammalian genomes contributes to phenotypic diversity, including health and disease status. In domestic pigs, CNV has been catalogued by several reports, but the extent of CNV and the phenotypic effects are far from clear. The goal of this study was to identify CNV regions (CNVRs) in pigs based on array comparative genome hybridization (aCGH).

Results: Here a custom-made tiling oligo-nucleotide array was used with a median probe spacing of 2506 bp for screening 12 pigs including 3 Chinese native pigs (one Chinese Erhualian, one Tongcheng and one Yangxin pig), 5 European pigs (one Large White, one Pietrain, one White Duroc and two Landrace pigs), 2 synthetic pigs (Chinese new line DIV pigs) and 2 crossbred pigs (Landrace × DIV pigs) with a Duroc pig as the reference. Two hundred and fifty-nine CNVRs across chromosomes 1-18 and X were identified, with an average size of 65.07 kb and a median size of 98.74 kb, covering 16.85 Mb or 0.74% of the whole genome. Concerning copy number status, 93 (35.91%) CNVRs were called as gains, 140 (54.05%) were called as losses and the remaining 26 (10.04%) were called as both gains and losses. Of all detected CNVRs, 171 (66.02%) and 34 (13.13%) CNVRs directly overlapped with Sus scrofa duplicated sequences and pig QTLs, respectively. The CNVRs encompassed 372 full length Ensembl transcripts. Two CNVRs identified by aCGH were validated using real-time quantitative PCR (qPCR).

Conclusions: Using 720 K array CGH (aCGH) we described a map of porcine CNVs which facilitated the identification of structural variations for important phenotypes and the assessment of the genetic diversity of pigs.

Figure 1

Graphical representation of the CNVRs. Blue lines represent gain predicted status, losses are indicated in green, and regions with both gains and losses status are represented in red. X axis values are chromosome position in Mb. Y axis values are chromosome names. Chromosome sizes are represented in proportion to the real size of the Sus scrofa karyotype obtained from the Ensembl database.

Figure 2

CNVR characteristics.A: Size range distribution of the CNVRs; B: Number of transcripts in CNVRs.

Figure 3

The dendrogram of 12 pigs generated by average linkage clustering algorithm of Cluster 3.0 software.

Figure 4

Validation of CNVR _100 (KIT gene) detected from the CGH array data using real-time quantitative PCR analysis. The x-axis represents the animals and the y-axis shows the relative quantification value (2^-ΔΔCt values for qPCR; 2*(2^Sample signal) values for array CGH).