ARS | Publication request: Segmental duplication and copy number variation of the patched domain containing 3 (PTCHD3) locus on pig chromosome 10

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: October 3, 2007
Publication Date: January 2, 2008
Citation: Nonneman, D.J., Kuehn, L.A. 2008. Segmental duplication and copy number variation of the patched domain containing 3 (PTCHD3) locus on pig chromosome 10 (abstract). Plant and Animal Genome XVI Conference Proceedings. Poster No. P578.

Technical Abstract: Mammalian genomes contain numerous blocks of highly homologous duplicated regions that can vary in copy number. We identified a segmental duplication encompassing the PTCHD3 gene, which has predicted hedgehog receptor activity, in a QTL region for nipple number on SSC10. A 3-fold coverage BAC screen of the CHORI-242 library using exon 4 of PTCHD3 as probe identified 15 positive clones that aligned to four different loci on SSC10p (57.1, 59.1, 59.3 and 63.5 Mb) on the BAC fingerprint map. Radiation hybrid mapping of BAC ends confirmed their location in the genome. This region is also duplicated in the human and the integration sites correspond to the same regions on the comparative map. The duplicated regions are located at breakpoints of rearrangements between human, pig, and other species. PCR sequencing and subcloning of representative BACs revealed these loci were unique and the entire gene was duplicated. Three of the duplicated genes are expressed at low levels and translation of open reading frames implies that only one of the forms would produce a protein product. Copy number for each duplication was estimated separately by quantitative PCR and ranged from 0-6 copies. Estimated copy number of eight sires of a Meishan/White composite resource population was fitted in a model predicting backcross progeny nipple number. Copy number was significantly associated with nipple number for all forms of the PTCHD3 gene in White composite sires. PTCHD3 copy number may affect nipple number or be in linkage disequilibrium with the causative variation.