High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds
[EN] Background: With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for wo...
| Autores: | , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2017 |
| País: | España |
| Institución: | Universidad de León |
| Repositorio: | BULERIA. Repositorio Institucional de la Universidad de León |
| OAI Identifier: | oai:buleria.unileon.es:10612/24375 |
| Acceso en línea: | https://hdl.handle.net/10612/24375 |
| Access Level: | acceso abierto |
| Palabra clave: | Genética Producción animal Veterinaria Churra sheep Merino sheep Wool selection 3109 Ciencias Veterinarias 3104 Producción Animal |
| id |
ES_d53e90eae6f29c303ae99a737027ea13 |
|---|---|
| oai_identifier_str |
oai:buleria.unileon.es:10612/24375 |
| network_acronym_str |
ES |
| network_name_str |
España |
| repository_id_str |
|
| dc.title.none.fl_str_mv |
High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds |
| title |
High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds |
| spellingShingle |
High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds Gutiérrez Gil, Beatriz Genética Producción animal Veterinaria Churra sheep Merino sheep Wool selection 3109 Ciencias Veterinarias 3104 Producción Animal |
| title_short |
High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds |
| title_full |
High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds |
| title_fullStr |
High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds |
| title_full_unstemmed |
High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds |
| title_sort |
High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds |
| dc.creator.none.fl_str_mv |
Gutiérrez Gil, Beatriz Esteban Blanco, Cristina Wiener, Pamela Chitneedi, Praveen Krishna Suárez Vega, Aroa Arranz Santos, Juan José |
| author |
Gutiérrez Gil, Beatriz |
| author_facet |
Gutiérrez Gil, Beatriz Esteban Blanco, Cristina Wiener, Pamela Chitneedi, Praveen Krishna Suárez Vega, Aroa Arranz Santos, Juan José |
| author_role |
author |
| author2 |
Esteban Blanco, Cristina Wiener, Pamela Chitneedi, Praveen Krishna Suárez Vega, Aroa Arranz Santos, Juan José |
| author2_role |
author author author author author |
| dc.contributor.none.fl_str_mv |
Producción Animal Facultad de Veterinaria |
| dc.subject.none.fl_str_mv |
Genética Producción animal Veterinaria Churra sheep Merino sheep Wool selection 3109 Ciencias Veterinarias 3104 Producción Animal |
| topic |
Genética Producción animal Veterinaria Churra sheep Merino sheep Wool selection 3109 Ciencias Veterinarias 3104 Producción Animal |
| description |
[EN] Background: With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a coarse-wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals. Results: Based on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2-His847Arg, NCAPG-Ser585Phe, LCORL-Asp1214Glu and LCORL-Ile1441Leu) were included. Conclusions: Here, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition |
| publishDate |
2017 |
| dc.date.none.fl_str_mv |
2017 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
| format |
article |
| status_str |
publishedVersion |
| dc.identifier.none.fl_str_mv |
https://hdl.handle.net/10612/24375 |
| url |
https://hdl.handle.net/10612/24375 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.relation.none.fl_str_mv |
info:eu-repo/grantAgreement/MINECO/Programa Estatal de I+D+I Orientada a los Retos de la Sociedad/ AGL2015-66035-R info:eu-repo/grantAgreement/MINECO/Programa Nacional de Contratación e Incorporación/RYC-2012-10230 |
| dc.rights.none.fl_str_mv |
http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess |
| rights_invalid_str_mv |
http://creativecommons.org/licenses/by/4.0/ |
| eu_rights_str_mv |
openAccess |
| dc.publisher.none.fl_str_mv |
BioMed Central |
| publisher.none.fl_str_mv |
BioMed Central |
| dc.source.none.fl_str_mv |
reponame:BULERIA. Repositorio Institucional de la Universidad de León instname:Universidad de León |
| instname_str |
Universidad de León |
| reponame_str |
BULERIA. Repositorio Institucional de la Universidad de León |
| collection |
BULERIA. Repositorio Institucional de la Universidad de León |
| repository.name.fl_str_mv |
|
| repository.mail.fl_str_mv |
|
| _version_ |
1869420662623305728 |
| spelling |
High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breedsGutiérrez Gil, BeatrizEsteban Blanco, CristinaWiener, PamelaChitneedi, Praveen KrishnaSuárez Vega, AroaArranz Santos, Juan JoséGenéticaProducción animalVeterinariaChurra sheepMerino sheepWool selection3109 Ciencias Veterinarias3104 Producción Animal[EN] Background: With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a coarse-wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals. Results: Based on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2-His847Arg, NCAPG-Ser585Phe, LCORL-Asp1214Glu and LCORL-Ile1441Leu) were included. Conclusions: Here, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass compositionSIThis work was supported by the AGL2015-66035-R project funded by the Spanish Ministry of Economy and Competitiveness (MINECO) and co-funded by the European Regional Development Fund. We thank the National Association of Spanish Churra Breeders for the close collaboration with our research group and the support for generating sequencing data of Churra genomes. B Gutiérrez-Gil is funded through the Spanish “Ramón y Cajal” Program (RYC-2012-10230) from MINECO. The support and availability to the computing facilities of the Foundation of Supercomputing Center of Castile and León (FCSCL) (http://www.fcsc.es) are greatly acknowledged. The ovine SNP50 K-chip HapMap dataset used in this work was provided by the Inter‑ national Sheep Genomics Consortium (ISGC) and obtained from http://www. sheephapmap.org in agreement with the ISGC Terms of Access. We are also grateful to the ISGC for the whole-genome sequencing datasets belonging to the project PRJNA160933 available at the SRA (https://www.ncbi.nlm.nih.gov/ sra) that were analyzed in this study. In addition, we are grateful to the Austral‑ ian Cooperative Research Centre for Sheep Industry Innovation for generating the whole-genome sequencing datasets included in project PRJNA325682 of the SRA and also included in this studyBioMed CentralProducción AnimalFacultad de Veterinaria2017info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://hdl.handle.net/10612/24375reponame:BULERIA. Repositorio Institucional de la Universidad de Leóninstname:Universidad de LeónInglésinfo:eu-repo/grantAgreement/MINECO/Programa Estatal de I+D+I Orientada a los Retos de la Sociedad/ AGL2015-66035-R info:eu-repo/grantAgreement/MINECO/Programa Nacional de Contratación e Incorporación/RYC-2012-10230http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:buleria.unileon.es:10612/243752026-06-24T12:43:27Z |
| score |
15,811543 |