Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids
CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV.Here, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eur...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2021
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/119851 |
| _version_ | 1855517690180927488 |
|---|---|
| author | Jang, J. Terefe, Endashaw Kim, K. Lee, Y.H. Belay, G. Tijjani, A. Han Jianlin Hanotte, Olivier H. Kim, H. |
| author_browse | Belay, G. Han Jianlin Hanotte, Olivier H. Jang, J. Kim, H. Kim, K. Lee, Y.H. Terefe, Endashaw Tijjani, A. |
| author_facet | Jang, J. Terefe, Endashaw Kim, K. Lee, Y.H. Belay, G. Tijjani, A. Han Jianlin Hanotte, Olivier H. Kim, H. |
| author_sort | Jang, J. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV.Here, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics VST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs.For some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments. |
| format | Journal Article |
| id | CGSpace119851 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1198512024-05-01T08:15:34Z Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids Jang, J. Terefe, Endashaw Kim, K. Lee, Y.H. Belay, G. Tijjani, A. Han Jianlin Hanotte, Olivier H. Kim, H. animal breeding genetics bos taurus bos indicus livestock biotechnology CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV.Here, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics VST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs.For some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments. 2021-12 2022-06-15T14:09:48Z 2022-06-15T14:09:48Z Journal Article https://hdl.handle.net/10568/119851 en Open Access Springer Jang, J., Terefe, E., Kim, K., Lee, Y.H., Belay, G., Tijjani, A., Han, J. L., Hanotte, O. and Kim, H. 2021. Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids. BMC Genomics 22:531. |
| spellingShingle | animal breeding genetics bos taurus bos indicus livestock biotechnology Jang, J. Terefe, Endashaw Kim, K. Lee, Y.H. Belay, G. Tijjani, A. Han Jianlin Hanotte, Olivier H. Kim, H. Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids |
| title | Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids |
| title_full | Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids |
| title_fullStr | Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids |
| title_full_unstemmed | Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids |
| title_short | Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids |
| title_sort | population differentiated copy number variation of bos taurus bos indicus and their african hybrids |
| topic | animal breeding genetics bos taurus bos indicus livestock biotechnology |
| url | https://hdl.handle.net/10568/119851 |
| work_keys_str_mv | AT jangj populationdifferentiatedcopynumbervariationofbostaurusbosindicusandtheirafricanhybrids AT terefeendashaw populationdifferentiatedcopynumbervariationofbostaurusbosindicusandtheirafricanhybrids AT kimk populationdifferentiatedcopynumbervariationofbostaurusbosindicusandtheirafricanhybrids AT leeyh populationdifferentiatedcopynumbervariationofbostaurusbosindicusandtheirafricanhybrids AT belayg populationdifferentiatedcopynumbervariationofbostaurusbosindicusandtheirafricanhybrids AT tijjania populationdifferentiatedcopynumbervariationofbostaurusbosindicusandtheirafricanhybrids AT hanjianlin populationdifferentiatedcopynumbervariationofbostaurusbosindicusandtheirafricanhybrids AT hanotteolivierh populationdifferentiatedcopynumbervariationofbostaurusbosindicusandtheirafricanhybrids AT kimh populationdifferentiatedcopynumbervariationofbostaurusbosindicusandtheirafricanhybrids |