Eintrag weiter verarbeiten
Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays
Gespeichert in:
| Zeitschriftentitel: | Animal Genetics |
|---|---|
| Personen und Körperschaften: | , , , , , , , , , , |
| In: | Animal Genetics, 49, 2018, 3, S. 226-236 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Wiley
|
| Schlagwörter: |
| author_facet |
Bai, H. Sun, Y. Liu, N. Liu, Y. Xue, F. Li, Y. Xu, S. Ni, A. Ye, J. Chen, Y. Chen, J. Bai, H. Sun, Y. Liu, N. Liu, Y. Xue, F. Li, Y. Xu, S. Ni, A. Ye, J. Chen, Y. Chen, J. |
|---|---|
| author |
Bai, H. Sun, Y. Liu, N. Liu, Y. Xue, F. Li, Y. Xu, S. Ni, A. Ye, J. Chen, Y. Chen, J. |
| spellingShingle |
Bai, H. Sun, Y. Liu, N. Liu, Y. Xue, F. Li, Y. Xu, S. Ni, A. Ye, J. Chen, Y. Chen, J. Animal Genetics Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays Genetics Animal Science and Zoology General Medicine |
| author_sort |
bai, h. |
| spelling |
Bai, H. Sun, Y. Liu, N. Liu, Y. Xue, F. Li, Y. Xu, S. Ni, A. Ye, J. Chen, Y. Chen, J. 0268-9146 1365-2052 Wiley Genetics Animal Science and Zoology General Medicine http://dx.doi.org/10.1111/age.12652 <jats:title>Summary</jats:title><jats:p>Beak deformity (crossed beaks) is found in several indigenous chicken breeds including Beijing‐You studied here. Birds with deformed beaks have reduced feed intake and poor production performance. Recently, copy number variation (<jats:styled-content style="fixed-case">CNV</jats:styled-content>) has been examined in many species and is recognized as a source of genetic variation, especially for disease phenotypes. In this study, to unravel the genetic mechanisms underlying beak deformity, we performed genome‐wide <jats:styled-content style="fixed-case">CNV</jats:styled-content> detection using Affymetrix chicken high‐density 600K data on 48 deformed‐beak and 48 normal birds using <jats:sc>penncnv</jats:sc>. As a result, two and eight <jats:styled-content style="fixed-case">CNV</jats:styled-content> regions (<jats:styled-content style="fixed-case">CNVR</jats:styled-content>s) covering 0.32 and 2.45 Mb respectively on autosomes were identified in deformed‐beak and normal birds respectively. Further <jats:styled-content style="fixed-case">RT</jats:styled-content>‐<jats:styled-content style="fixed-case">qPCR</jats:styled-content> studies validated nine of the 10 <jats:styled-content style="fixed-case">CNVR</jats:styled-content>s. The ratios of six <jats:styled-content style="fixed-case">CNVR</jats:styled-content>s were significantly different between deformed‐beak and normal birds (<jats:italic>P </jats:italic><<jats:italic> </jats:italic>0.01). Within these six regions, three and 21 known genes were identified in deformed‐beak and normal birds respectively. Bioinformatics analysis showed that these genes were enriched in six <jats:styled-content style="fixed-case">GO</jats:styled-content> terms and one <jats:styled-content style="fixed-case">KEGG</jats:styled-content> pathway. Five candidate genes in the <jats:styled-content style="fixed-case">CNVR</jats:styled-content>s were further validated using <jats:styled-content style="fixed-case">RT</jats:styled-content>‐<jats:styled-content style="fixed-case">qPCR</jats:styled-content>. The expression of <jats:italic><jats:styled-content style="fixed-case">LRIG</jats:styled-content>2</jats:italic> (<jats:italic>leucine rich repeats and immunoglobulin like domains 2</jats:italic>) was lower in birds with deformed beaks (<jats:italic>P </jats:italic><<jats:italic> </jats:italic>0.01). Therefore, the <jats:italic><jats:styled-content style="fixed-case">LRIG</jats:styled-content>2</jats:italic> gene could be considered a key factor in view of its known functions and its potential roles in beak deformity. Overall, our results will be helpful for future investigations of the genomic structural variations underlying beak deformity in chickens.</jats:p> Genome‐wide detection of <scp>CNV</scp>s associated with beak deformity in chickens using high‐density 600K <scp>SNP</scp> arrays Animal Genetics |
| doi_str_mv |
10.1111/age.12652 |
| facet_avail |
Online |
| finc_class_facet |
Biologie |
| format |
ElectronicArticle |
| fullrecord |
blob:ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTExMS9hZ2UuMTI2NTI |
| id |
ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTExMS9hZ2UuMTI2NTI |
| institution |
DE-D275 DE-Bn3 DE-Brt1 DE-D161 DE-Gla1 DE-Zi4 DE-15 DE-Pl11 DE-Rs1 DE-105 DE-14 DE-Ch1 DE-L229 |
| imprint |
Wiley, 2018 |
| imprint_str_mv |
Wiley, 2018 |
| issn |
0268-9146 1365-2052 |
| issn_str_mv |
0268-9146 1365-2052 |
| language |
English |
| mega_collection |
Wiley (CrossRef) |
| match_str |
bai2018genomewidedetectionofcnvsassociatedwithbeakdeformityinchickensusinghighdensity600ksnparrays |
| publishDateSort |
2018 |
| publisher |
Wiley |
| recordtype |
ai |
| record_format |
ai |
| series |
Animal Genetics |
| source_id |
49 |
| title |
Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays |
| title_unstemmed |
Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays |
| title_full |
Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays |
| title_fullStr |
Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays |
| title_full_unstemmed |
Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays |
| title_short |
Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays |
| title_sort |
genome‐wide detection of <scp>cnv</scp>s associated with beak deformity in chickens using high‐density 600k <scp>snp</scp> arrays |
| topic |
Genetics Animal Science and Zoology General Medicine |
| url |
http://dx.doi.org/10.1111/age.12652 |
| publishDate |
2018 |
| physical |
226-236 |
| description |
<jats:title>Summary</jats:title><jats:p>Beak deformity (crossed beaks) is found in several indigenous chicken breeds including Beijing‐You studied here. Birds with deformed beaks have reduced feed intake and poor production performance. Recently, copy number variation (<jats:styled-content style="fixed-case">CNV</jats:styled-content>) has been examined in many species and is recognized as a source of genetic variation, especially for disease phenotypes. In this study, to unravel the genetic mechanisms underlying beak deformity, we performed genome‐wide <jats:styled-content style="fixed-case">CNV</jats:styled-content> detection using Affymetrix chicken high‐density 600K data on 48 deformed‐beak and 48 normal birds using <jats:sc>penncnv</jats:sc>. As a result, two and eight <jats:styled-content style="fixed-case">CNV</jats:styled-content> regions (<jats:styled-content style="fixed-case">CNVR</jats:styled-content>s) covering 0.32 and 2.45 Mb respectively on autosomes were identified in deformed‐beak and normal birds respectively. Further <jats:styled-content style="fixed-case">RT</jats:styled-content>‐<jats:styled-content style="fixed-case">qPCR</jats:styled-content> studies validated nine of the 10 <jats:styled-content style="fixed-case">CNVR</jats:styled-content>s. The ratios of six <jats:styled-content style="fixed-case">CNVR</jats:styled-content>s were significantly different between deformed‐beak and normal birds (<jats:italic>P </jats:italic><<jats:italic> </jats:italic>0.01). Within these six regions, three and 21 known genes were identified in deformed‐beak and normal birds respectively. Bioinformatics analysis showed that these genes were enriched in six <jats:styled-content style="fixed-case">GO</jats:styled-content> terms and one <jats:styled-content style="fixed-case">KEGG</jats:styled-content> pathway. Five candidate genes in the <jats:styled-content style="fixed-case">CNVR</jats:styled-content>s were further validated using <jats:styled-content style="fixed-case">RT</jats:styled-content>‐<jats:styled-content style="fixed-case">qPCR</jats:styled-content>. The expression of <jats:italic><jats:styled-content style="fixed-case">LRIG</jats:styled-content>2</jats:italic> (<jats:italic>leucine rich repeats and immunoglobulin like domains 2</jats:italic>) was lower in birds with deformed beaks (<jats:italic>P </jats:italic><<jats:italic> </jats:italic>0.01). Therefore, the <jats:italic><jats:styled-content style="fixed-case">LRIG</jats:styled-content>2</jats:italic> gene could be considered a key factor in view of its known functions and its potential roles in beak deformity. Overall, our results will be helpful for future investigations of the genomic structural variations underlying beak deformity in chickens.</jats:p> |
| container_issue |
3 |
| container_start_page |
226 |
| container_title |
Animal Genetics |
| container_volume |
49 |
| format_de105 |
Article, E-Article |
| format_de14 |
Article, E-Article |
| format_de15 |
Article, E-Article |
| format_de520 |
Article, E-Article |
| format_de540 |
Article, E-Article |
| format_dech1 |
Article, E-Article |
| format_ded117 |
Article, E-Article |
| format_degla1 |
E-Article |
| format_del152 |
Buch |
| format_del189 |
Article, E-Article |
| format_dezi4 |
Article |
| format_dezwi2 |
Article, E-Article |
| format_finc |
Article, E-Article |
| format_nrw |
Article, E-Article |
| _version_ |
1792340920313577472 |
| geogr_code |
not assigned |
| last_indexed |
2024-03-01T16:10:52.16Z |
| geogr_code_person |
not assigned |
| openURL |
url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fvufind.svn.sourceforge.net%3Agenerator&rft.title=Genome%E2%80%90wide+detection+of+CNVs+associated+with+beak+deformity+in+chickens+using+high%E2%80%90density+600K+SNP+arrays&rft.date=2018-06-01&genre=article&issn=1365-2052&volume=49&issue=3&spage=226&epage=236&pages=226-236&jtitle=Animal+Genetics&atitle=Genome%E2%80%90wide+detection+of+%3Cscp%3ECNV%3C%2Fscp%3Es+associated+with+beak+deformity+in+chickens+using+high%E2%80%90density+600K+%3Cscp%3ESNP%3C%2Fscp%3E+arrays&aulast=Chen&aufirst=J.&rft_id=info%3Adoi%2F10.1111%2Fage.12652&rft.language%5B0%5D=eng |
| SOLR | |
| _version_ | 1792340920313577472 |
| author | Bai, H., Sun, Y., Liu, N., Liu, Y., Xue, F., Li, Y., Xu, S., Ni, A., Ye, J., Chen, Y., Chen, J. |
| author_facet | Bai, H., Sun, Y., Liu, N., Liu, Y., Xue, F., Li, Y., Xu, S., Ni, A., Ye, J., Chen, Y., Chen, J., Bai, H., Sun, Y., Liu, N., Liu, Y., Xue, F., Li, Y., Xu, S., Ni, A., Ye, J., Chen, Y., Chen, J. |
| author_sort | bai, h. |
| container_issue | 3 |
| container_start_page | 226 |
| container_title | Animal Genetics |
| container_volume | 49 |
| description | <jats:title>Summary</jats:title><jats:p>Beak deformity (crossed beaks) is found in several indigenous chicken breeds including Beijing‐You studied here. Birds with deformed beaks have reduced feed intake and poor production performance. Recently, copy number variation (<jats:styled-content style="fixed-case">CNV</jats:styled-content>) has been examined in many species and is recognized as a source of genetic variation, especially for disease phenotypes. In this study, to unravel the genetic mechanisms underlying beak deformity, we performed genome‐wide <jats:styled-content style="fixed-case">CNV</jats:styled-content> detection using Affymetrix chicken high‐density 600K data on 48 deformed‐beak and 48 normal birds using <jats:sc>penncnv</jats:sc>. As a result, two and eight <jats:styled-content style="fixed-case">CNV</jats:styled-content> regions (<jats:styled-content style="fixed-case">CNVR</jats:styled-content>s) covering 0.32 and 2.45 Mb respectively on autosomes were identified in deformed‐beak and normal birds respectively. Further <jats:styled-content style="fixed-case">RT</jats:styled-content>‐<jats:styled-content style="fixed-case">qPCR</jats:styled-content> studies validated nine of the 10 <jats:styled-content style="fixed-case">CNVR</jats:styled-content>s. The ratios of six <jats:styled-content style="fixed-case">CNVR</jats:styled-content>s were significantly different between deformed‐beak and normal birds (<jats:italic>P </jats:italic><<jats:italic> </jats:italic>0.01). Within these six regions, three and 21 known genes were identified in deformed‐beak and normal birds respectively. Bioinformatics analysis showed that these genes were enriched in six <jats:styled-content style="fixed-case">GO</jats:styled-content> terms and one <jats:styled-content style="fixed-case">KEGG</jats:styled-content> pathway. Five candidate genes in the <jats:styled-content style="fixed-case">CNVR</jats:styled-content>s were further validated using <jats:styled-content style="fixed-case">RT</jats:styled-content>‐<jats:styled-content style="fixed-case">qPCR</jats:styled-content>. The expression of <jats:italic><jats:styled-content style="fixed-case">LRIG</jats:styled-content>2</jats:italic> (<jats:italic>leucine rich repeats and immunoglobulin like domains 2</jats:italic>) was lower in birds with deformed beaks (<jats:italic>P </jats:italic><<jats:italic> </jats:italic>0.01). Therefore, the <jats:italic><jats:styled-content style="fixed-case">LRIG</jats:styled-content>2</jats:italic> gene could be considered a key factor in view of its known functions and its potential roles in beak deformity. Overall, our results will be helpful for future investigations of the genomic structural variations underlying beak deformity in chickens.</jats:p> |
| doi_str_mv | 10.1111/age.12652 |
| facet_avail | Online |
| finc_class_facet | Biologie |
| format | ElectronicArticle |
| format_de105 | Article, E-Article |
| format_de14 | Article, E-Article |
| format_de15 | Article, E-Article |
| format_de520 | Article, E-Article |
| format_de540 | Article, E-Article |
| format_dech1 | Article, E-Article |
| format_ded117 | Article, E-Article |
| format_degla1 | E-Article |
| format_del152 | Buch |
| format_del189 | Article, E-Article |
| format_dezi4 | Article |
| format_dezwi2 | Article, E-Article |
| format_finc | Article, E-Article |
| format_nrw | Article, E-Article |
| geogr_code | not assigned |
| geogr_code_person | not assigned |
| id | ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTExMS9hZ2UuMTI2NTI |
| imprint | Wiley, 2018 |
| imprint_str_mv | Wiley, 2018 |
| institution | DE-D275, DE-Bn3, DE-Brt1, DE-D161, DE-Gla1, DE-Zi4, DE-15, DE-Pl11, DE-Rs1, DE-105, DE-14, DE-Ch1, DE-L229 |
| issn | 0268-9146, 1365-2052 |
| issn_str_mv | 0268-9146, 1365-2052 |
| language | English |
| last_indexed | 2024-03-01T16:10:52.16Z |
| match_str | bai2018genomewidedetectionofcnvsassociatedwithbeakdeformityinchickensusinghighdensity600ksnparrays |
| mega_collection | Wiley (CrossRef) |
| physical | 226-236 |
| publishDate | 2018 |
| publishDateSort | 2018 |
| publisher | Wiley |
| record_format | ai |
| recordtype | ai |
| series | Animal Genetics |
| source_id | 49 |
| spelling | Bai, H. Sun, Y. Liu, N. Liu, Y. Xue, F. Li, Y. Xu, S. Ni, A. Ye, J. Chen, Y. Chen, J. 0268-9146 1365-2052 Wiley Genetics Animal Science and Zoology General Medicine http://dx.doi.org/10.1111/age.12652 <jats:title>Summary</jats:title><jats:p>Beak deformity (crossed beaks) is found in several indigenous chicken breeds including Beijing‐You studied here. Birds with deformed beaks have reduced feed intake and poor production performance. Recently, copy number variation (<jats:styled-content style="fixed-case">CNV</jats:styled-content>) has been examined in many species and is recognized as a source of genetic variation, especially for disease phenotypes. In this study, to unravel the genetic mechanisms underlying beak deformity, we performed genome‐wide <jats:styled-content style="fixed-case">CNV</jats:styled-content> detection using Affymetrix chicken high‐density 600K data on 48 deformed‐beak and 48 normal birds using <jats:sc>penncnv</jats:sc>. As a result, two and eight <jats:styled-content style="fixed-case">CNV</jats:styled-content> regions (<jats:styled-content style="fixed-case">CNVR</jats:styled-content>s) covering 0.32 and 2.45 Mb respectively on autosomes were identified in deformed‐beak and normal birds respectively. Further <jats:styled-content style="fixed-case">RT</jats:styled-content>‐<jats:styled-content style="fixed-case">qPCR</jats:styled-content> studies validated nine of the 10 <jats:styled-content style="fixed-case">CNVR</jats:styled-content>s. The ratios of six <jats:styled-content style="fixed-case">CNVR</jats:styled-content>s were significantly different between deformed‐beak and normal birds (<jats:italic>P </jats:italic><<jats:italic> </jats:italic>0.01). Within these six regions, three and 21 known genes were identified in deformed‐beak and normal birds respectively. Bioinformatics analysis showed that these genes were enriched in six <jats:styled-content style="fixed-case">GO</jats:styled-content> terms and one <jats:styled-content style="fixed-case">KEGG</jats:styled-content> pathway. Five candidate genes in the <jats:styled-content style="fixed-case">CNVR</jats:styled-content>s were further validated using <jats:styled-content style="fixed-case">RT</jats:styled-content>‐<jats:styled-content style="fixed-case">qPCR</jats:styled-content>. The expression of <jats:italic><jats:styled-content style="fixed-case">LRIG</jats:styled-content>2</jats:italic> (<jats:italic>leucine rich repeats and immunoglobulin like domains 2</jats:italic>) was lower in birds with deformed beaks (<jats:italic>P </jats:italic><<jats:italic> </jats:italic>0.01). Therefore, the <jats:italic><jats:styled-content style="fixed-case">LRIG</jats:styled-content>2</jats:italic> gene could be considered a key factor in view of its known functions and its potential roles in beak deformity. Overall, our results will be helpful for future investigations of the genomic structural variations underlying beak deformity in chickens.</jats:p> Genome‐wide detection of <scp>CNV</scp>s associated with beak deformity in chickens using high‐density 600K <scp>SNP</scp> arrays Animal Genetics |
| spellingShingle | Bai, H., Sun, Y., Liu, N., Liu, Y., Xue, F., Li, Y., Xu, S., Ni, A., Ye, J., Chen, Y., Chen, J., Animal Genetics, Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays, Genetics, Animal Science and Zoology, General Medicine |
| title | Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays |
| title_full | Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays |
| title_fullStr | Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays |
| title_full_unstemmed | Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays |
| title_short | Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays |
| title_sort | genome‐wide detection of <scp>cnv</scp>s associated with beak deformity in chickens using high‐density 600k <scp>snp</scp> arrays |
| title_unstemmed | Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays |
| topic | Genetics, Animal Science and Zoology, General Medicine |
| url | http://dx.doi.org/10.1111/age.12652 |