27 research outputs found
VarGoats international initiative, a 1000 goat genomes project
No full textInternational audienceGoats were domesticated ~10,000 years ago from their bezoar wild ancestor Capra aegagrus. These founder animals spread out from domestication centres in Europe, Asia, and Africa during the next few thousand years, which resulted in many populations becoming locally adapted to diverse environmental constraints such as heat, altitude, disease resistance, etc. After a very long period of soft selection for production traits, the situation changed dramatically with the emergence of the breed concept about 200 years ago. Selection pressure was strongly increased, and gene flow between populations (or newly formed breeds) was seriously reduced, leading to the fragmentation of the initial gene pool. Currently, there are more than 1000 goat breeds worldwide, 18% of which are either threatened or already extinct. Through the generation of domestic breeds sequence data and their analysis together with existing data of domestic and wild animals, VarGoats collaborative project aims at becoming the first step of a 1000 goat genomes project. VarGoats Consortium is coordinated by the Institut National de la Recherche Agronomique INRA (France), and includes an international team of partner
Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions
No full textBy their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographical range
VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity
No full textAbstract
Background: Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra.
Findings: A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identifed 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin.
Conclusions: We report on an unprecedented international efort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal efects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies
Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions
No full textBy their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographical range
Quelques résultats du programme VarGoats : « 1000 génomes caprins »
No full textInternational audienceLe projet VarGoats (http://www.goatgenome.org/vargoats.html) est un projet de reséquençage de génomes caprins. Nos objectifs sont multiples : caractériser la diversité génétique internationale, mais aussi caractériser finement les races françaises et africaines, détecter des traces de sélection pour identifier les voies métaboliques impliquées dans l’expression des traits zootechniques sélectionnés et les mécanismes d’adaptation, identifier des mutations « perte de fonction » ayant un fort impact sur l’expression des phénotypes à l’aide de l’étude de variants de type SNP, CNV ou variants de structure.Nous présenterons :-la méthode de constitution des jeux de données, comprenant majoritairement des chèvres domestiques mais aussi quelques espèces sauvages du genre Capra.-les jeux de données à notre disposition (données brutes, séquences alignées permettant d’étudier les variants de structure, fichiers de variants -petites insertions/délétion et SNP-, fichiers de variants filtrés)-l’organisation du consortium mise en place pour leur étude.Après une phase préliminaire qui s’est concentrée sur les chèvres françaises (n=200), nous présenterons des premiers résultats des groupes de travail obtenus sur les jeux de 1159 et 1372 animaux représentant la diversité génétique mondiale. Il s’agit en particulier de résultats sur la différenciation génétique entre races, sur les variants de structure, la caractérisation des mutations « perte de fonction », et la reconstruction de l’histoire de la domestication des chèvres à l’aide de l’étude des séquences du chromosome Y
The VarGoats 1000 genome project dataset: an alternative approach for WGS data filtering for large-scale analysis of livestock diversity
No full textInternational audienceGoat domestication started ca. 11,000 years ago from the bezoar, Capra aegagrus, in SW Asia. Afterward, domestic goats followed the expansion of human populations out of the Fertile Crescent and spread to Europe, Asia, and Africa in a process which lasted a few thousand years. As a result, many populations became locally adapted to highly contrasting environmental conditions. Hybridization with wild goat species also occurred, playing a role in goats’ evolution through adaptive introgression. These phenomena, combined with the more recent human-mediated selection, shaped the global diversity we observe today. VarGoats is a large-scale collaborative effort to assess goat global genomic variation. Currently, the project has assembled a database of 1327 genomes from 133 local and transboundary domestic goat populations from 4 continents (Europe, Africa, Asia, and Oceania), and 45 genomes from 8 wild goat species. Variant calling followed by quality filtering procedures retained a data set of > 28M biallelic SNPs. Preliminary evaluations showed that commonly adopted variant filtering approaches relying on Minor Allele Frequency (MAF) and Linkage Disequilibrium (LD) may not be suitable to process a data set representative of global diversity across multiple species, due to notable differences in LD structure and in the presence/frequency of variants at the local vs. global scale. Thus, we devised a novel approach based on Minor Allele Count (MAC) and marker spacing (bp-space) specifically designed to avoid biases introduced by standard filtering procedures and adequately represent continental and species-specific variation. The comparison of the effects of MAF+LD pruning versus the newly proposed MAC+bp-space method showed that the latter permits to thin down the starting ca. 28M variants to ca. 13M with only a negligible reduction (1.52%) in bezoar and wild goat diversity. In contrast, the LD-based filtering would have caused a loss of 7.55% of bezoar-specific markers and of 20.59% of wild goat specific variants, potentially hampering downstream analyses
The VarGoats 1000 genome project dataset: an alternative approach for WGS data filtering for large-scale analysis of livestock diversity
No full textInternational audienceGoat domestication started ca. 11,000 years ago from the bezoar, Capra aegagrus, in SW Asia. Afterward, domestic goats followed the expansion of human populations out of the Fertile Crescent and spread to Europe, Asia, and Africa in a process which lasted a few thousand years. As a result, many populations became locally adapted to highly contrasting environmental conditions. Hybridization with wild goat species also occurred, playing a role in goats’ evolution through adaptive introgression. These phenomena, combined with the more recent human-mediated selection, shaped the global diversity we observe today. VarGoats is a large-scale collaborative effort to assess goat global genomic variation. Currently, the project has assembled a database of 1327 genomes from 133 local and transboundary domestic goat populations from 4 continents (Europe, Africa, Asia, and Oceania), and 45 genomes from 8 wild goat species. Variant calling followed by quality filtering procedures retained a data set of > 28M biallelic SNPs. Preliminary evaluations showed that commonly adopted variant filtering approaches relying on Minor Allele Frequency (MAF) and Linkage Disequilibrium (LD) may not be suitable to process a data set representative of global diversity across multiple species, due to notable differences in LD structure and in the presence/frequency of variants at the local vs. global scale. Thus, we devised a novel approach based on Minor Allele Count (MAC) and marker spacing (bp-space) specifically designed to avoid biases introduced by standard filtering procedures and adequately represent continental and species-specific variation. The comparison of the effects of MAF+LD pruning versus the newly proposed MAC+bp-space method showed that the latter permits to thin down the starting ca. 28M variants to ca. 13M with only a negligible reduction (1.52%) in bezoar and wild goat diversity. In contrast, the LD-based filtering would have caused a loss of 7.55% of bezoar-specific markers and of 20.59% of wild goat specific variants, potentially hampering downstream analyses
Quelques résultats du programme VarGoats : « 1000 génomes caprins »
No full textInternational audienceLe projet VarGoats (http://www.goatgenome.org/vargoats.html) est un projet de reséquençage de génomes caprins. Nos objectifs sont multiples : caractériser la diversité génétique internationale, mais aussi caractériser finement les races françaises et africaines, détecter des traces de sélection pour identifier les voies métaboliques impliquées dans l’expression des traits zootechniques sélectionnés et les mécanismes d’adaptation, identifier des mutations « perte de fonction » ayant un fort impact sur l’expression des phénotypes à l’aide de l’étude de variants de type SNP, CNV ou variants de structure.Nous présenterons :-la méthode de constitution des jeux de données, comprenant majoritairement des chèvres domestiques mais aussi quelques espèces sauvages du genre Capra.-les jeux de données à notre disposition (données brutes, séquences alignées permettant d’étudier les variants de structure, fichiers de variants -petites insertions/délétion et SNP-, fichiers de variants filtrés)-l’organisation du consortium mise en place pour leur étude.Après une phase préliminaire qui s’est concentrée sur les chèvres françaises (n=200), nous présenterons des premiers résultats des groupes de travail obtenus sur les jeux de 1159 et 1372 animaux représentant la diversité génétique mondiale. Il s’agit en particulier de résultats sur la différenciation génétique entre races, sur les variants de structure, la caractérisation des mutations « perte de fonction », et la reconstruction de l’histoire de la domestication des chèvres à l’aide de l’étude des séquences du chromosome Y
Quelques résultats du programme VarGoats : « 1000 génomes caprins »
No full textInternational audienceLe projet VarGoats (http://www.goatgenome.org/vargoats.html) est un projet de reséquençage de génomes caprins. Nos objectifs sont multiples : caractériser la diversité génétique internationale, mais aussi caractériser finement les races françaises et africaines, détecter des traces de sélection pour identifier les voies métaboliques impliquées dans l’expression des traits zootechniques sélectionnés et les mécanismes d’adaptation, identifier des mutations « perte de fonction » ayant un fort impact sur l’expression des phénotypes à l’aide de l’étude de variants de type SNP, CNV ou variants de structure.Nous présenterons :-la méthode de constitution des jeux de données, comprenant majoritairement des chèvres domestiques mais aussi quelques espèces sauvages du genre Capra.-les jeux de données à notre disposition (données brutes, séquences alignées permettant d’étudier les variants de structure, fichiers de variants -petites insertions/délétion et SNP-, fichiers de variants filtrés)-l’organisation du consortium mise en place pour leur étude.Après une phase préliminaire qui s’est concentrée sur les chèvres françaises (n=200), nous présenterons des premiers résultats des groupes de travail obtenus sur les jeux de 1159 et 1372 animaux représentant la diversité génétique mondiale. Il s’agit en particulier de résultats sur la différenciation génétique entre races, sur les variants de structure, la caractérisation des mutations « perte de fonction », et la reconstruction de l’histoire de la domestication des chèvres à l’aide de l’étude des séquences du chromosome Y
