Cargando…
Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences
BACKGROUND: In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability. RESULTS: In this study, we describe the first French cattle genome variation dataset obtained by sequen...
Autores principales: | , , , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111192/ https://www.ncbi.nlm.nih.gov/pubmed/27846802 http://dx.doi.org/10.1186/s12711-016-0268-z |
_version_ | 1782467820418760704 |
---|---|
author | Boussaha, Mekki Michot, Pauline Letaief, Rabia Hozé, Chris Fritz, Sébastien Grohs, Cécile Esquerré, Diane Duchesne, Amandine Philippe, Romain Blanquet, Véronique Phocas, Florence Floriot, Sandrine Rocha, Dominique Klopp, Christophe Capitan, Aurélien Boichard, Didier |
author_facet | Boussaha, Mekki Michot, Pauline Letaief, Rabia Hozé, Chris Fritz, Sébastien Grohs, Cécile Esquerré, Diane Duchesne, Amandine Philippe, Romain Blanquet, Véronique Phocas, Florence Floriot, Sandrine Rocha, Dominique Klopp, Christophe Capitan, Aurélien Boichard, Didier |
author_sort | Boussaha, Mekki |
collection | PubMed |
description | BACKGROUND: In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability. RESULTS: In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data. CONCLUSIONS: To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12711-016-0268-z) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5111192 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-51111922016-11-25 Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences Boussaha, Mekki Michot, Pauline Letaief, Rabia Hozé, Chris Fritz, Sébastien Grohs, Cécile Esquerré, Diane Duchesne, Amandine Philippe, Romain Blanquet, Véronique Phocas, Florence Floriot, Sandrine Rocha, Dominique Klopp, Christophe Capitan, Aurélien Boichard, Didier Genet Sel Evol Rsearch Article BACKGROUND: In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability. RESULTS: In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data. CONCLUSIONS: To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12711-016-0268-z) contains supplementary material, which is available to authorized users. BioMed Central 2016-11-15 /pmc/articles/PMC5111192/ /pubmed/27846802 http://dx.doi.org/10.1186/s12711-016-0268-z Text en © The Author(s) 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Rsearch Article Boussaha, Mekki Michot, Pauline Letaief, Rabia Hozé, Chris Fritz, Sébastien Grohs, Cécile Esquerré, Diane Duchesne, Amandine Philippe, Romain Blanquet, Véronique Phocas, Florence Floriot, Sandrine Rocha, Dominique Klopp, Christophe Capitan, Aurélien Boichard, Didier Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences |
title | Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences |
title_full | Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences |
title_fullStr | Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences |
title_full_unstemmed | Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences |
title_short | Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences |
title_sort | construction of a large collection of small genome variations in french dairy and beef breeds using whole-genome sequences |
topic | Rsearch Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111192/ https://www.ncbi.nlm.nih.gov/pubmed/27846802 http://dx.doi.org/10.1186/s12711-016-0268-z |
work_keys_str_mv | AT boussahamekki constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT michotpauline constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT letaiefrabia constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT hozechris constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT fritzsebastien constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT grohscecile constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT esquerrediane constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT duchesneamandine constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT philipperomain constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT blanquetveronique constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT phocasflorence constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT floriotsandrine constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT rochadominique constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT kloppchristophe constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT capitanaurelien constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences AT boicharddidier constructionofalargecollectionofsmallgenomevariationsinfrenchdairyandbeefbreedsusingwholegenomesequences |