Copy number variation (CNV) as a promising genetic marker: distribution, validation methods and candidate genes in genomes of livestock species (review)

Abstract

Copy number variations (CNVs) are repetitive genome segments, ranging from one thousand to several million base pairs and varying between individuals in a population. Due to a larger genome coverage compared to SNP markers, CNVs are important sources of genetic variation and are currently considered as an alternative type of DNA markers. The identification of CNV regions (CNVRs) which overlap with genes and quantitative trait loci (QTLs) in livestock genomes are of the greatest interest. In the review, the results of studies on CNV in various livestock species, are summarized and analyzed including the identification of candidate genes whose loci overlap with CNV regions. In addition, the methodological approaches for detection of copy number variations are briefly described. The number of identified CNVRs and a genome coverage ratio were 51-1265 and 0.5-20 % in cattle, 565 CNVRs and 5.84 % in pigs, 978 CNVR and 8.96 % in goats, 3488 CNVR and 2.7 % in sheep. Loci of functional candidate genes associated with economically significant traits overlap with CNVR in all livestock species. There were identified genes associated with growth and development indicators (MYH3 and GBP4 in cattle; ANP32B, GYS1 and CAV1 in pigs; MYLK4 in goats; SHE, BAG4, PIGY and ORMDL1 in sheep); affecting the reproductive traits and fertility (PRP1 and PRP6 in goats; PTGS1 in sheep); associated with meat productivity (KDM5B, ADAM8 and SHH in goats); responsible for various coat and skin colour phenotypes (KIT in pigs; ASIP, AHCY and ITCH in sheep and goats) and involved in the regulation of metabolic processes (PPARA, RXRA, ADD1, FASN and PPP1CA in sheep). The analysis of international experience showed that identified CNVs could be proposed as potential candidates for selection according to economically significant traits in livestock.