18 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
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
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
Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions
No full textBy its paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. We used whole-genome sequences (WGSs) of 386 domestic goats from 75 modern breeds and 7 wild goat species generated by the VarGoats goat genome project. Phylogenetic analyses indicated five domestic haplogroups Y1AA, Y1AB, Y1B, Y2A and Y2B. Haplogroup distributions for 180 domestic breeds indicate ancient paternal population bottlenecks during the migration into northern Europe, southern Asia and Africa. Sharing of haplogroups reveals male-mediated introgressions: from Asia into Madagascar and, more recently, into the South-African Boer goat; then from this breed into other southeastern African goats; and from Europe into native Korean and Ugandan goats. This study illustrates the power of the Y-chromosomal variation for the reconstructing the history of domestic species with a wide geographic range
Additional file 1 of Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection
No full textAdditional file 1: Table S1. Accession numbers of the sequenced goats in this study. Information on 226 goats from different breeds and ENA accessions for the sequence data. Table S2. 344 ROH islands observed in the 11 caprine populations investigated. Chromosomes and end positions of 1-Mb windows harbouring ROH-regions are provided. Breeds with a ROH-proportion exceeding 80% in this 1-Mb window are indicated with 1. The table on the right gives a summary over the 29 autosomes and the number of ROH islands. Table S3. List of the 1220 annotated genes in the regions of ROH islands. For each gene, the chromosome number, the start- and end position, the number of SNVs are given within a gene and that is part of the ROH (X), and also the average proportion of individuals of each population that has the X-SNPs in an ROH. The rows with the eight genes selected for Table 3 are marked in grey. Table S4. Information and the 226 individual genotypes for the two protein coding variants in the STC1 and TSHR genes. Table S5. Frequencies of the reference alleles at the two coding variants in STC1 and TSHR in samples from the 1372 individual sequences collected by the The VarGoats Consortium different origins
Inferring Domestic Goat Demographic History Through Ancient Genome Imputation
No full textGoats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a challenge in ancient genomic analysis is the relatively low genome coverage for most samples, limiting analysis to pseudohaploid genotypes. Genotype imputation offers potential to alleviate this limitation by improving information content and accuracy in low coverage genomes. To test this, we used published high coverage (>8✕) goat palaeogenomes, imputing downsampled genomes using the VarGoats dataset (1,372 individuals) as a reference panel. Measuring concordance between imputed and high coverage genotypes, we find high concordance after filtering for common (>5%), high confidence variants, with 0.5✕ genomes reaching >0.97 concordance. There is a trade-off between coverage, genotype probability (GP) thresholds, and genotype recovery, where higher coverage and more lenient GP thresholds result in higher recovery, and a reduction in heterozygous false-positive rates with stricter thresholds. We then imputed 36 goat palaeogenomes with ≥0.5✕ coverage to examine runs-of-homozygosity (ROH) and identity-by-descent (IBD) patterns. Using a novel approach combining ROH profiles across tools, we find that among Neolithic goats, ROH increases with distance from the Zagros Mountains, suggesting a large effect of the initial dispersal of managed herds. Inbreeding levels decrease across Southwest Asia in more recent periods. IBD mirrored this pattern, with less relatedness in the early herding site of Ganj Dareh compared to higher relatedness in goats from later in the dispersal process. These findings provide insights into the genetic consequences of early goat management on demography, and confirm the utility of imputation in leveraging low coverage palaeogenomes.</p
Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection
No full textBackground: The domestication of goat (Capra hircus) started 11,000 years ago in the fertile crescent. Breed formation in the nineteenth century, establishment of herd books, and selection for specific traits resulted in 10 modern goat breeds in Switzerland. We analyzed whole‑genome sequencing (WGS) data from 217 modern goats and nine wild Bezoar goats (Capra aegagrus). After quality control, 27,728,288 biallelic single nucleotide variants (SNVs) were used for the identification of runs of homozygosity (ROH) and the detection of ROH islands. Results: Across the 226 caprine genomes from 11 populations, we detected 344 ROH islands that harbor 1220 annotated genes. We compared the ROH islands between the modern breeds and the Bezoar goats. As a proof of principle, we confirmed a signature of selection, which contains the ASIP gene that controls several breed‑specific coat color patterns. In two other ROH islands, we identified two missense variants, STC1:p.Lys139Arg and TSHR:p.Ala239Thr, which might represent causative functional variants for domestication signatures. Conclusions: We have shown that the information from ROH islands using WGS data is suitable for the analysis of signatures of selection and allowed the detection of protein coding variants that may have conferred beneficial phenotypes during goat domestication. We hypothesize that the TSHR:p.Ala239Thr variant may have played a role in changing the seasonality of reproduction in modern domesticated goats. The exact functional significance of the STC1:p.Lys139Arg variant remains unclear and requires further investigation. Nonetheless, STC1 might represent a new domestication gene affecting relevant traits such as body size and/or milk yield in goats
