ena-PROJECT-Animal Breeding and Genomics Centre-23-11-2012-10:52:08:835-7
Copy number variation in porcine genomes
Copy number variable regions (CNVRs) can result in drastic phenotypic differences. Studying copy number variation (CNV) in pigs is of interest because of their very rich natural and domestication history that led to many different phenotypes. To investigate the evolutionary dynamic of CNVRs in pigs, we applied read depth (RD) method on whole genome sequence data from 16 individuals, comprising wild and domestic pigs from Asia and Europe. We identified 3,118 CNVRs with an average size of 13 Kb comprising a total of 39.2 Mb and 545 overlapping genes. Functional analyses revealed that CNVRs are enriched with genes related to sensory perception, neurological process, and response to stimulus, suggesting that they contributed to adaptation in the wild and behavioral changes during domestication. CNVRs overlapping fertility related genes (BTN1A1 and F5) were found in Asian and some European domestic pig breeds that were selected for high fertility. A small portion of CNVRs was unique to domestic pigs and may have been selected during domestication. The majority of CNVRs, however, is shared between wild and domesticated individuals, indicating that domestication had minor effect on the overall diversity of CNVRs in pigs. Also, the excess of CNVRs in non-genic regions implies that a major part of these variations is likely to be neutral or nearly neutral. Comparison between different populations showed that larger populations have more CNVRs. This result highlights that CNVRs are, like other genetic variation such as SNPs and microsatellites, mostly reflecting demographic history rather than phenotypic diversity.
Copy number variable regions (CNVRs) can result in drastic phenotypic differences. Studying copy number variation (CNV) in pigs is of interest because of their very rich natural and domestication history that led to many different phenotypes. To investigate the evolutionary dynamic of CNVRs in pigs, we applied read depth (RD) method on whole genome sequence data from 16 individuals, comprising wild and domestic pigs from Asia and Europe. We identified 3,118 CNVRs with an average size of 13 Kb comprising a total of 39.2 Mb and 545 overlapping genes. Functional analyses revealed that CNVRs are enriched with genes related to sensory perception, neurological process, and response to stimulus, suggesting that they contributed to adaptation in the wild and behavioral changes during domestication. CNVRs overlapping fertility related genes (BTN1A1 and F5) were found in Asian and some European domestic pig breeds that were selected for high fertility. A small portion of CNVRs was unique to domestic pigs and may have been selected during domestication. The majority of CNVRs, however, is shared between wild and domesticated individuals, indicating that domestication had minor effect on the overall diversity of CNVRs in pigs. Also, the excess of CNVRs in non-genic regions implies that a major part of these variations is likely to be neutral or nearly neutral. Comparison between different populations showed that larger populations have more CNVRs. This result highlights that CNVRs are, like other genetic variation such as SNPs and microsatellites, mostly reflecting demographic history rather than phenotypic diversity.