Copy number variation in livestock: A mini review

Abstract

Copy number variation (CNV) is a phenomenon in which sections of the genome, ranging from one kilo base pair (Kb) to several million base pairs (Mb), are repeated and the number of repeats vary between the individuals in a population. It is an important source of genetic variation in an individual which is now being utilized rather than single nucleotide polymorphisms (SNPs), as it covers the more genomic region. CNVs alter the gene expression and change the phenotype of an individual due to deletion and duplication of genes in the copy number variation regions (CNVRs). Earlier, researchers extensively utilized SNPs as the main source of genetic variation. But now, the focus is on identification of CNVs associated with complex traits. With the recent advances and reduction in the cost of sequencing, arrays are developed for genotyping which cover the maximum number of SNPs at a time that can be used for detection of CNVRs and underlying quantitative trait loci (QTL) for the complex traits to accelerate genetic improvement. CNV studies are also being carried out to understand the evolutionary mechanism in the domestication of livestock and their adaptation to the different environmental conditions. The main aim of the study is to review the available data on CNV and its role in genetic variation among the livestock.

Identification of Loci and Pathways Associated with Heifer Conception Rate in U.S. Holsteins

“…One of the most significant SNPs associated with HCR1 and TBRD on BTA1 was located approximately 1 kb from Neuroligin 1 ( NLGN1 ), which produces neuronal cell surface proteins and is involved in cellular signaling changes ( Table S2 ). The uterine epithelium contains a wide variety of adhesion molecules, which become particularly important during early pregnancy for conceptus implantation [ 54 , 55 , 56 ]. During the establishment of pregnancy and implantation, the uterine epithelium undergoes many changes.…”

Concordance rate between copy number variants detected using either high- or medium-density single nucleotide polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle

“…In cattle, typically between 18 and 51 CNVs are called per animal from high-density genotypes (c.a. 700,000 SNPs) [3][4][5], whereas other cattle studies using mediumdensity genotypes (c.a. 50,000 SNPs) have reported between 1 and 7 CNVs per animal [25,26], which is consistent with the results of the present study.…”

“…By convention, CNVs typically have a minimum length of 1 kb; deletions or duplications that are shorter are usually considered to be indels [2]. Copy number variants are a common feature of the bovine genome, with the average number of CNVs per individual, identified from highdensity genotype data, ranging from 18 to 51 [3][4][5]. In cattle, there are reported associations between CNVs and milk production [6], meat tenderness [7], and health traits [8].…”

A STUDY OF GENETIC MECHANISMS UNDERLYING THE FAT TAIL PHENOTYPE IN SHEEP: METHODOLOGICAL APPROACHES AND IDENTIFIED CANDIDATE GENES (review)

“…А н а л и з в а р и а ц и и ч и с л а к о п и й (copy number variation, CNV). Анализ вариации числа копий -это биоинформационный подход для детекции генов-кандидатов и идентификации QTL, а также для изучения эволюционных механизмов одомашнивания животных и их приспособленности к различным условиям окружающей среды (55). Феномен CNV заключается в том, что некоторые участки генома размером от одной тысячи до миллионов пар оснований присутствуют в нескольких копиях, число которых варьируется у особей внутри популяции (55).…”

“…Анализ вариации числа копий -это биоинформационный подход для детекции генов-кандидатов и идентификации QTL, а также для изучения эволюционных механизмов одомашнивания животных и их приспособленности к различным условиям окружающей среды (55). Феномен CNV заключается в том, что некоторые участки генома размером от одной тысячи до миллионов пар оснований присутствуют в нескольких копиях, число которых варьируется у особей внутри популяции (55). Вариация числа копий -важный источник генетической изменчивости у особи, поскольку CNV способны изменять экспрессию генов и, соответственно, фенотип из-за делеции или дупликации генов в регионах вариации (56)(57)(58).…”