Copy number variation (CNV) as a promising genetic marker: distribution, validation methods and candidate genes in genomes of livestock species (review)
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...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | Russian |
| Published: |
Federal Agricultural Research Center of the North-East named N.V. Rudnitsky
2020-08-01
|
| Series: | Аграрная наука Евро-Северо-Востока |
| Subjects: | |
| Online Access: | https://www.agronauka-sv.ru/jour/article/view/574 |
| _version_ | 1797290276387028992 |
|---|---|
| author | O. A. Koshkina T. E. Deniskova N. A. Zinovieva |
| author_facet | O. A. Koshkina T. E. Deniskova N. A. Zinovieva |
| author_sort | O. A. Koshkina |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-07T19:20:07Z |
| format | Article |
| id | doaj.art-790b20fb337f42f5899c1e210dd7c13c |
| institution | Directory Open Access Journal |
| issn | 2072-9081 2500-1396 |
| language | Russian |
| last_indexed | 2024-03-07T19:20:07Z |
| publishDate | 2020-08-01 |
| publisher | Federal Agricultural Research Center of the North-East named N.V. Rudnitsky |
| record_format | Article |
| series | Аграрная наука Евро-Северо-Востока |
| spelling | doaj.art-790b20fb337f42f5899c1e210dd7c13c2024-02-29T11:31:12ZrusFederal Agricultural Research Center of the North-East named N.V. RudnitskyАграрная наука Евро-Северо-Востока2072-90812500-13962020-08-0121435536810.30766/2072-9081.2020.21.4.355-368400Copy number variation (CNV) as a promising genetic marker: distribution, validation methods and candidate genes in genomes of livestock species (review)O. A. Koshkina0T. E. Deniskova1N. A. Zinovieva2L. K. Ernst Federal Science Center for Animal HusbandryL. K. Ernst Federal Science Center for Animal HusbandryL. K. Ernst Federal Science Center for Animal HusbandryCopy 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.https://www.agronauka-sv.ru/jour/article/view/574genetic polymorphismgenome organizationquantitative trait loci (qtl)dna chipseconomically significant traits |
| spellingShingle | O. A. Koshkina T. E. Deniskova N. A. Zinovieva Copy number variation (CNV) as a promising genetic marker: distribution, validation methods and candidate genes in genomes of livestock species (review) Аграрная наука Евро-Северо-Востока genetic polymorphism genome organization quantitative trait loci (qtl) dna chips economically significant traits |
| title | Copy number variation (CNV) as a promising genetic marker: distribution, validation methods and candidate genes in genomes of livestock species (review) |
| title_full | Copy number variation (CNV) as a promising genetic marker: distribution, validation methods and candidate genes in genomes of livestock species (review) |
| title_fullStr | Copy number variation (CNV) as a promising genetic marker: distribution, validation methods and candidate genes in genomes of livestock species (review) |
| title_full_unstemmed | Copy number variation (CNV) as a promising genetic marker: distribution, validation methods and candidate genes in genomes of livestock species (review) |
| title_short | Copy number variation (CNV) as a promising genetic marker: distribution, validation methods and candidate genes in genomes of livestock species (review) |
| title_sort | copy number variation cnv as a promising genetic marker distribution validation methods and candidate genes in genomes of livestock species review |
| topic | genetic polymorphism genome organization quantitative trait loci (qtl) dna chips economically significant traits |
| url | https://www.agronauka-sv.ru/jour/article/view/574 |
| work_keys_str_mv | AT oakoshkina copynumbervariationcnvasapromisinggeneticmarkerdistributionvalidationmethodsandcandidategenesingenomesoflivestockspeciesreview AT tedeniskova copynumbervariationcnvasapromisinggeneticmarkerdistributionvalidationmethodsandcandidategenesingenomesoflivestockspeciesreview AT nazinovieva copynumbervariationcnvasapromisinggeneticmarkerdistributionvalidationmethodsandcandidategenesingenomesoflivestockspeciesreview |