R.P.M.A. Crooijmans

Wageningen University, Wageningen, Gelderland, Netherlands

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Publications (258)647.46 Total impact

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    ABSTRACT: Unraveling the genetic mechanisms associated with reduced gene flow between genetically differentiated populations is key to understand speciation. Different types of structural variations (SVs) have been found as a source of genetic diversity in a wide range of species. Previous studies provided detailed knowledge on the potential evolutionary role of SVs, especially copy number variations (CNVs), between well diverged species of e.g. primates. However, our understanding of their significance during ongoing speciation processes is limited due to the lack of CNV data from closely related species. The genus Sus (pig and its close relatives) which started to diverge ~4 Mya presents an excellent model for studying the role of CNVs during ongoing speciation. In this study, we identified 1408 CNV regions (CNVRs) across the genus Sus. These CNVRs encompass 624 genes and were found to evolve ~2.5 times faster than single nucleotide polymorphisms (SNPs). The majority of these copy number variable genes are olfactory receptors (ORs) known to play a prominent role in food foraging and mate recognition in Sus. Phylogenetic analyses, including novel Bayesian analysis, based on CNVRs that overlap ORs retain the well-accepted topology of the genus Sus whereas CNVRs overlapping genes other than ORs show evidence for random drift and/or admixture. We hypothesize that inter-specific variation in copy number of ORs provided the means for rapid adaptation to different environments during the diversification of the genus Sus in the Pliocene. Furthermore, these regions might have acted as barriers preventing massive gene flow between these species during the multiple hybridization events that took place later in the Pleistocene suggesting a possible prominent role of ORs in the ongoing Sus speciation.
    BMC Genomics 04/2015; 16(1):330. DOI:10.1186/s12864-015-1449-9 · 4.04 Impact Factor
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    ABSTRACT: Breeding of indigenous chicken in developing countries is mainly done by the resource-poor rural households that raise birds in a scavenging system characterized by low inputs, adverse climatic conditions and high disease pressure. As a result, indigenous chicken may have developed specific genetic adaptations for such challenging environments. In this study, genomic variation of indigenous chicken kept under low input production systems was assessed using autosomal microsatellite markers and whole genome re-sequence data. Indigenous chickens were further compared to high input commercial layers to identify selection signatures and candidate mutations that may explain the phenotypic divergence between these populations. Commercial layers had much lower nucleotide diversity (0.31 - 0.36) than indigenous chicken (0.58 - 0.62). We also identified up to 59 genomic regions with high Fst values (0.44 - 0.85) between indigenous and commercial chickens overlapping 16 genes. Five genes (SLC26A8, BRPF3, MAPK13, PDIA4 and MRPL32) out of the 16 are associated with the missense variants that could explain partially the phenotypic divergence between these populations. Selection signatures may reflect selection for different breeding goals together with very different production environments between indigenous and commercial populations. Differently to commercial chickens, indigenous chickens preserved a high genomic variability that may be important, for addressing present and future challenges associated with adaptability to the environment and to cope with farmers breeding goals.
    The 9th Egerton University International Conference, Egerton, Kenya; 03/2015
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    ABSTRACT: The study investigated the genetic make-up of different ecotypes of indigenous chickens (ICs) in Kenya based on major histocompati-bility complex (MHC)-linked and non-MHC microsatellite markers. Blood samples were collected from eight regions (48 birds per region) of Kenya: Kakamega (KK), Siaya (BN), West Pokot (WP), Turkana (TK), Bomet (BM), Narok (NR), Lamu (LM) and Taita-Taveta (TT) and genotyped using two MHC-linked and ten non-MHC markers. All MHC-linked and non-MHC markers were polymorphic with a total of 140 alleles, of which 56 were identified in MHC-linked markers. Mean number of alleles (Na and Ne), private alleles, heterozygosity and genetic distances were higher for MHC-linked markers compared with non-MHC markers. The ad hoc statistic ΔK detected the true numbers of clusters to be three for MHC-linked markers and two in non-MHC markers. In conclusion , Kenyan ICs belong into two to three genetically distinct groups. Different markers systems have different clustering system. MHC-linked markers divided ICs into three mixed clusters, composing of individuals from the different ecotypes whereas non-MHC markers grouped ICs into two groups. These IC ecotypes host many and highly diverse MHC-linked alleles. Higher allelic diversity indicated a huge amount of genetic variation in the MHC region of ICs and supported their reputation of being hardy and resistant to diseases. Résumé Cette étude a cherché à connaître la configuration génétique de différents écotypes de poules autochtones du Kenya, sur la base de marqueurs microsatellites associés ou non au Complexe Majeur d'Histocompatibilité (CMH). Des échantillons sanguins ont été prélevés dans huit régions du Kenya (48 volailles par région): Kakamega (KK), Siaya (BN), Pokot Occidental (PO), Turkana (TK), Bomet (BM), Narok (NR), Lamu (LM) et Taita-Taveta (TT). Les échantillons ont été génotypés en utilisant deux marqueurs associés au CMH et 10 marqueurs non associés. Tous les marqueurs, aussi bien ceux associés au CMH que ceux non associés à celui-ci, ont été polymorphes avec un total de 140 allèles, dont 56 ont été identifiés avec des marqueurs associés au CMH. Le nombre moyen d'allèles (Na et Ne) et celui d'allèles privés, l'hétérozygotie et les distances génétiques ont été plus élevés pour les marqueurs associés au CMH que pour ceux non associés. La mesure statistique ad hoc ΔK a révélé que le vrai nombre de groupes est de trois pour les marqueurs associés au CMH et de deux pour les marqueurs non associés. En conclusion, les poules autochtones kényanes appa-rtiennent à 2–3 groupes génétiques différents. Des systèmes différents de marqueurs présentent des méthodes différentes de groupe-ment. Les marqueurs associés au CMH ont divisé les populations de poules autochtones en trois groupes mixtes, constitués d'individus provenant des différents écotypes, alors que les marqueurs non associés au CMH ont rassemblé les poules autochtones en deux groupes. Ces écotypes de poules autochtones abritent de nombreux et très divers allèles associés au CMH. Une plus grande diversité allélique est le reflet d'une grande quantité de variation génétique dans la région du CMH des poules autochtones, ce qui confirme leur renommée de volailles rustiques et résistantes aux maladies. Mots-clés: poule autochtone, écotype, CMH, structure populationnelle, diversité génétique Resumen Este estudio investigó la configuración genética de diferentes ecotipos de gallinas autóctonas de Kenia, basándose en marcadores microsatélites asociados y no asociados al Complejo Mayor de Histocompatibilidad (CMH). Se tomaron muestras de sangre en ocho regiones de Kenia (48 aves por región): Kakamega (KK), Siaya (BN), Pokot Occidental (PO), Turkana (TK), Bomet (BM), Narok (NR), Lamu (LM) y Taita-Taveta (TT). Las muestras sanguíneas fueron genotipadas usando dos marcadores asociados al CMH y 10 marcadores no asociados. Todos los marcadores, tanto asociados como no asociados al CMH, fueron polimórficos con un total de 140 alelos, de los cuales 56 fueron identificados en marcadores asociados al CMH. El número medio de alelos (Na y Ne) y de alelos privados, la heterocigosis y las distancias genéticas fueron mayores para los marcadores asociados al CMH que para los marcadores no asociados. El estadístico ad hoc ΔK detectó que el número real de conglomerados era de tres para los marca-dores asociados al CMH y de dos para los marcadores no asociados. En conclusión, las gallinas autóctonas keniatas pertenecen a 2–3 grupos genéticos distintos. Sistemas de marcadores distintos presentan diferentes modos de agrupación. Los marcadores asociados al CMH dividieron las poblaciones de gallinas autóctonas en tres conglomerados mixtos, formados por individuos de los diferentes eco-tipos, mientras que los marcadores no asociados al CMH agruparon las gallinas autóctonas en dos grupos. Estos ecotipos de gallinas autóctonas albergan muchos y muy diversos alelos asociados al CMH. Una mayor diversidad alélica fue reflejo de una gran cantidad de variación genética en la región del CMH de las gallinas autóctonas, lo cual confirma la fama de estas aves de ser rústicas y resistentes a enfermedades.
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    ABSTRACT: Background The domestic turkey (Meleagris gallopavo) is an important agricultural species that is largely used as a meat-type bird. Characterizing genetic variation in populations of domesticated species and associating these variation patterns with the evolution, domestication, and selective breeding is critical for understanding the dynamics of genomic change in these species. Intense selective breeding and population bottlenecks are expected to leave signatures in the genome of domesticated species, such as unusually low nucleotide diversity or the presence of exceptionally extended haplotype homozygosity. These patterns of variation in selected populations are highly useful to not only understand the consequences of selective breeding and population dynamics, but also to provide insights into biological mechanisms that may affect physiological processes important to bring changes in phenotype of interest.ResultsWe observed 54 genomic regions in heritage and commercial turkey populations on 14 different chromosomes that showed statistically significant (P¿<¿0.05) reduction in genomic variation indicating candidate selective sweeps. Areas with evidence of selective sweeps varied from 1.5 Mb to 13.8 Mb in length. Out of these 54 sweeps, 23 overlapped at least partially between two or more populations. Overlapping sweeps were found on 13 different chromosomes. The remaining 31 sweeps were population-specific and were observed on 12 different chromosomes, with 26 of these regions present only in commercial populations. Genes that are known to affect growth were enriched in the sweep regions.Conclusion The turkey genome showed large sweep regions. The relatively high number of sweep regions in commercial turkey populations compared to heritage varieties and the enrichment of genes important to growth in these regions, suggest that these sweeps are the result of intense selection in these commercial lines, moving specific haplotypes towards fixation.
    BMC Genetics 11/2014; 15(1):117. DOI:10.1186/s12863-014-0117-4 · 2.36 Impact Factor
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    ABSTRACT: Abstract Text: In 2010 an abnormally large number of German Longhaired Pointers (GLP) was offered for treatment of thyroid cancer. Pedigree analysis revealed a potential monogenic background. Histo-pathological examination revealed a variety of sub-types of thyroid cancer. In total 20 cases, ranging from 4.5 to 13 years old, and 28 controls were genotyped with the >170K CanineHD BeadChip. A GWAS resulted in a number of, and not in a single, genome-wide suggestive peaks. This lead to the hypothesis that there are two types of thyroid cancer in the GLP of which only one is highly heritable. When only affected dogs younger than 7 years were included in the GWAS, a single region with 5 SNP in complete LD between cases and controls was detected. This suggests the presence of a major gene that explains the onset of thyroid cancer in the German Longhaired Pointer. Keywords: Thyroid cancer Dogs Major gene
    10th World Congress on Genetics Applied to Livestock Production; 08/2014
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    ABSTRACT: The independent domestication of local wild boar populations in Asia and Europe about 10,000 years ago led to distinct European and Asian pig breeds, each with very different phenotypic characteristics. During the Industrial Revolution, Chinese breeds were imported to Europe to improve commercial traits in European breeds. Here we demonstrate the presence of introgressed Asian haplotypes in European domestic pigs and selection signatures on some loci in these regions, using whole genome sequence data. The introgression signatures are widespread and the Asian haplotypes are rarely fixed. The Asian introgressed haplotypes are associated with regions harbouring genes involved in meat quality, development and fertility. We identify Asian-derived non-synonymous mutations in the AHR gene that associate with increased litter size in multiple European commercial lines. These findings demonstrate that increased fertility was an important breeding goal for early nineteenth century pig farmers, and that Asian variants of genes related to this trait were preferentially selected during the development of modern European pig breeds.
    Nature Communications 07/2014; 5:4392. DOI:10.1038/ncomms5392 · 10.74 Impact Factor
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    ABSTRACT: The merging of populations after an extended period of isolation and divergence is a common phenomenon, in natural settings as well as due to human interference. Individuals with such hybrid origins contain genomes that essentially form a mosaic of different histories and demographies. Pigs are an excellent model species to study hybridization because European and Asian wild boars diverged ~1.2 Mya and pigs were domesticated independently in Europe and Asia. During the Industrial Revolution in England, pigs were imported from China to improve the local pigs. This study utilizes the latest genomics tools to identify the origin of haplotypes in European domesticated pigs that are descendant from Asian and European populations. Our results reveal fine-scale haplotype structure representing different ancient demographic events, as well as a mosaic composition of those distinct histories due to recently introgressed haplotypes in the pig genome. As a consequence, nucleotide diversity in the genome of European domesticated pigs is higher when at least one haplotype of Asian origin is present, and haplotype length correlates negatively with recombination frequency and nucleotide diversity. Another consequence is that the inference of past effective population size is influenced by the background of the haplotypes in an individual, but we demonstrate that by careful sorting based on the origin of haplotypes both distinct demographic histories can be reconstructed. Future detailed mapping of the genomic distribution of variation will enable a targeted approach to increase genetic diversity of captive and wild populations, thus facilitating conservation efforts in the near future.This article is protected by copyright. All rights reserved.
    Molecular Ecology 05/2014; 23(16). DOI:10.1111/mec.12807 · 5.84 Impact Factor
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    ABSTRACT: Copy number variation refers to regions along chromosomes that harbor a type of structural variation, such as duplications or deletions. Copy number variants (CNVs) play a role in many important traits as well as in genetic diversity. Previous analyses of chickens using array comparative genomic hybridizations or single-nucleotide polymorphism chip assays have been performed on various breeds and genetic lines to discover CNVs. In this study, we assessed individuals from two highly inbred (inbreeding coefficiency > 99.99%) lines, Leghorn G-B2 and Fayoumi M15.2, to discover novel CNVs in chickens. These lines have been previously studied for disease resistance, and to our knowledge, this represents the first global assessment of CNVs in the Fayoumi breed. Genomic DNA from individuals was examined using the Agilent chicken 244 K comparative genomic hybridization array and quantitative PCR. We identified a total of 273 CNVs overall, with 112 CNVs being novel and not previously reported. Quantitative PCR using the standard curve method validated a subset of our array data. Through enrichment analysis of genes within CNV regions, we observed multiple chromosomes, terms and pathways that were significantly enriched, largely dealing with the major histocompatibility complex and immune responsiveness. Using an additional round of computational and statistical analysis with a different bioinformatic pipeline, we identified 43 CNVs among these as high-confidence regions, 14 of which were found to be novel. We further compared and contrasted individuals of the two inbred lines to discover regions that have a significant difference in copy number between lines. A total of 40 regions had significant deletions or duplications between the lines. Gene Ontology analysis of genomic regions containing CNVs between lines also was performed. This between-line candidate CNV list will be useful in studies with these two unique genetic lines, which may harbor variations that underlie quantitative trait loci for disease resistance and other important traits. Through the global discovery of novel CNVs in chicken, these data also provide resources for further genetic and functional genomics studies.
    Animal Genetics 03/2014; 45(3). DOI:10.1111/age.12141 · 2.21 Impact Factor
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    ABSTRACT: Although all farm animals have an original source of domestication, a large variety of modern breeds exist that are phenotypically highly distinct from the ancestral wild population. This phenomenon can be the result of artificial selection or gene flow from other sources into the domesticated population. The Eurasian wild boar (Sus scrofa) has been domesticated at least twice in two geographically distinct regions during the Neolithic revolution when hunting shifted to farming. Prior to the establishment of the commercial European pig breeds we know today, some 200 years ago Chinese pigs were imported into Europe to improve local European pigs. Commercial European domesticated pigs are genetically more diverse than European wild boars, although historically the latter represents the source population for domestication. In this study we examine the cause of the higher diversity within the genomes of European commercial pigs compared to their wild ancestors by testing two different hypotheses. In the first hypothesis we consider that European commercial pigs are a mix of different European wild populations as a result of movement throughout Europe, hereby acquiring haplotypes from all over the European continent. As an alternative hypothesis, we examine whether the introgression of Asian haplotypes into European breeds during the Industrial Revolution caused the observed increase in diversity. By using re-sequence data for chromosome 1 of 136 pigs and wild boars, we show that an Asian introgression of about 20% into the genome of European commercial pigs explains the majority of the increase in genetic diversity. These findings confirm that the Asian hybridization, that was used to improve production traits of local breeds, left its signature in the genome of the commercial pigs we know today.
    Frontiers in Genetics 01/2014; 5:442. DOI:10.3389/fgene.2014.00442
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    ABSTRACT: The pig, Sus scrofa, is a foreign species to the American continent. Although pigs originally introduced in the Americas should be related to those from the Iberian Peninsula and Canary islands, the phylogeny of current creole pigs that now populate the continent is likely to be very complex. Because of the extreme climates that America harbors, these populations also provide a unique example of a fast evolutionary phenomenon of adaptation. Here, we provide a genome wide study of these issues by genotyping, with a 60k SNP chip, 206 village pigs sampled across 14 countries and 183 pigs from outgroup breeds that are potential founders of the American populations, including wild boar, Iberian, international and Chinese breeds. Results show that American village pigs are primarily of European ancestry, although the observed genetic landscape is that of a complex conglomerate. There was no correlation between genetic and geographical distances, neither continent wide nor when analyzing specific areas. Most populations showed a clear admixed structure where the Iberian pig was not necessarily the main component, illustrating how international breeds, but also Chinese pigs, have contributed to extant genetic composition of American village pigs. We also observe that many genes related to the cardiovascular system show an increased differentiation between altiplano and genetically related pigs living near sea level.Heredity advance online publication, 19 December 2012; doi:10.1038/hdy.2012.109.
    Heredity 12/2013; DOI:10.1038/hdy.2012.109 · 3.80 Impact Factor
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    ABSTRACT: Cultural transmission of migratory traditions enables species to deal with their environment based on experiences from earlier generations. Also, it allows a more adequate and rapid response to rapidly changing environments. When individuals break with their migratory traditions new population structures can emerge that may affect gene flow. Recently, the migratory traditions of the Barnacle Goose Branta leucopsis changed, and new populations differing in migratory distance emerged. Here, we investigate the population genetic structure of the Barnacle Goose to evaluate the consequences of altered migratory traditions. We used a set of 358 Single Nucleotide Polymorphisms (SNP) markers to genotype 418 individuals from breeding populations in Greenland, Spitsbergen, Russia, Sweden and the Netherlands, the latter two being newly emerged populations. We used Discriminant Analysis of Principal Components, FST , linkage disequilibrium and a comparison of gene flow models using migrate-n to show that there is significant population structure, but that relatively many pairs of SNPs are in linkage disequilibrium, suggesting recent admixture between these populations. Despite the assumed traditions of migration within populations we also show that genetic exchange occurs between all populations. The newly established non-migratory population in the Netherlands is characterized by high emigration into other populations which suggests more exploratory behaviour, possibly as a result of shortened parental care. These results suggest that migratory traditions in populations are subject to change in geese and that such changes have population genetic consequences. We argue that the emergence of non-migration likely resulted from developmental plasticity. This article is protected by copyright. All rights reserved.
    Molecular Ecology 10/2013; 22(23). DOI:10.1111/mec.12548 · 5.84 Impact Factor
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    ABSTRACT: Immunoglobulins play an important role in maintenance of mucosal homeostasis in the gut. The antigen binding specificity of these immunoglobulins depends for a large part on the hypervariable CDR3 region. To gain knowledge about isotype-specific development of the CDR3 repertoire we examined CDR3 spectratypes at multiple time points between 4 and 70 days post hatch. In order to identify clonal expansions deviation from the normal distribution (SS) and the average CDR3 length was calculated. IgA-CDR3 regions were studied in more detail by DNA sequence analysis at day 7 and 70 and preferential VH pseudogene usage was estimated. The SS of CDR3 repertoires of the IgM, IgG and IgA isotypes successively increased, but for each isotype this increase was transiently. The length of the CDR3 regions decreased with age for IgM becoming similar to the CDR3 length of IgA at day 70. The IgA- and IgG-CDR3 lengths did not change with age. On average, the CDR3 length of IgA was the shortest. IgA CDR3 sequences were similar between animals aged 7 and 70 days. A limited number of pseudogenes was used, and no differences in pseudogene usage were observed between animals aged 7 and 70 days. Of the identified VH pseudogenes, half of the sequences used VH15, whilst a number of the pseudogenes were not used at all. We conclude that CDR3 spectratype profiles change during aging, whilst at the CDR3-sequence level, variation in VH pseudogene usage for ileal IgA is limited suggesting conservation during ontogeny.
    Molecular Immunology 09/2013; 56(4):811-818. DOI:10.1016/j.molimm.2013.08.005 · 3.00 Impact Factor
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    ABSTRACT: Background The process of speciation is fundamental to evolutionary biology but remains poorly understood. Confusion can arise because the conclusions of studies that rely upon a limited number of genetic loci may not reflect the true evolutionary history of the species. Whole-genome data, however, can overcome this issue by providing an unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analysed the genomes of 10 wild pigs, representing five morphologically and/or geographically well-defined species of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene flow thus reconciling previous conflicting results obtained from a limited number of loci. We show that these multiple events of reticulation involved both natural and human mediated dispersal. Conclusions Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and reversing the speciation process in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.
    Genome Biology 08/2013; · 10.47 Impact Factor
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    Dataset: ng.2657-S1
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    ABSTRACT: The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A viruses. We present the duck genome sequence and perform deep transcriptome analyses to investigate immune-related genes. Our data indicate that the duck possesses a contractive immune gene repertoire, as in chicken and zebra finch, and this repertoire has been shaped through lineage-specific duplications. We identify genes that are responsive to influenza A viruses using the lung transcriptomes of control ducks and ones that were infected with either a highly pathogenic (A/duck/Hubei/49/05) or a weakly pathogenic (A/goose/Hubei/65/05) H5N1 virus. Further, we show how the duck's defense mechanisms against influenza infection have been optimized through the diversification of its β-defensin and butyrophilin-like repertoires. These analyses, in combination with the genomic and transcriptomic data, provide a resource for characterizing the interaction between host and influenza viruses.
    Nature Genetics 06/2013; 45(7). DOI:10.1038/ng.2657 · 29.65 Impact Factor
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    ABSTRACT: The aims of this study were to assess the genetic diversity of 17 populations of Vietnamese local chickens (VNN) and one Red Jungle Fowl population, together with six chicken populations of Chinese origin (CNO), and to provide priorities supporting the conservation of genetic resources using 20 microsatellites. Consequently, the VNN populations exhibited a higher diversity than did CNO populations in terms of number of alleles but showed a slightly lower observed heterozygosity. The VNN populations showed in total seven private alleles, whereas no CNO private alleles were found. The expected heterozygosity of 0.576 in the VNN populations was higher than the observed heterozygosity of 0.490, leading to heterozygote deficiency within populations. This issue could be partly explained by the Wahlund effect due to fragmentation of several populations between chicken flocks. Molecular analysis of variance showed that most of genetic variation was found within VNN populations. The Bayesian clustering analysis showed that VNN and CNO chickens were separated into two distinct groups with little evidence for gene flow between them. Among the 24 populations, 13 were successfully assigned to their own cluster, whereas the structuring was not clear for the remaining 11 chicken populations. The contributions of 24 populations to the total genetic diversity were mostly consistent across two approaches, taking into account the within- and between-populations genetic diversity and allelic richness. The black H'mong, Lien Minh, Luong Phuong and Red Jungle Fowl were ranked with the highest priorities for conservation according to Caballero and Toro's and Petit's approaches. In conclusion, a national strategy needs to be set up for Vietnamese chicken populations, with three main components: conservation of high-priority breeds, within-breed management with animal exchanges between flocks to avoid Wahlund effect and monitoring of inbreeding rate.
    Animal Genetics 05/2013; 44(5). DOI:10.1111/age.12045 · 2.21 Impact Factor
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    ABSTRACT: This study aimed to identify chromosomal regions associated with genetic variation in pre-weaning growth traits in Angora goats. A genome-wide scan was performed by genotyping 1042 offspring from 12 half-sib families using 88 microsatellite caprine markers covering 1368cM. Phenotypes were recorded at birth (BW) and weaning (WW) and analysed using GridQTL software. A total of six putative QTL were detected on six different chromosomes, all at chromosome-wide significance level. Four QTL were identified for BW on CHI 4, 8, 17 and 27 and two QTL for WW on CHI 16 and 19. QTL effects ranged from −0.32 to 0.25 in units of residual standard deviation in different families. Some of these QTL correspond to chromosomes where QTL associated with growth have been identified in other species. These chromosomal segments hold potential to influence weight gain in young goats.
    Small Ruminant Research 05/2013; 112(s 1–3):15–20. DOI:10.1016/j.smallrumres.2012.11.035 · 1.10 Impact Factor
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    ABSTRACT: Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ∼8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or appeared so as a result of admixture between introduced pigs and European wild boar. These pigs not only replaced those with Near Eastern signatures in Europe, they subsequently also replaced indigenous domestic pigs in the Near East. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria and Turkey. Our results firstly reveal the genetic signature of early domestic pigs in Eastern Turkey. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, nearly 1,000 years earlier than previously detected. By the 5(th) century AD, European signatures completely replaced the endemic lineages possibly coinciding with the demographic and societal changes during the Anatolian Bronze and Iron Ages.
    Molecular Biology and Evolution 04/2013; 30(4):824-32. DOI:10.1093/molbev/mss261 · 14.31 Impact Factor
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    ABSTRACT: Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition.
    PLoS Genetics 04/2013; 9(4):e1003453. DOI:10.1371/journal.pgen.1003453 · 8.17 Impact Factor

Publication Stats

6k Citations
647.46 Total Impact Points

Institutions

  • 1993–2015
    • Wageningen University
      • • Division of Fokkerij & Genetica
      • • Animal Breeding and Genomics Centre
      Wageningen, Gelderland, Netherlands
  • 2007
    • Lawrence Livermore National Laboratory
      Livermore, California, United States
  • 2006
    • University of Asmara
      Asmera, Maʼākel, Eritrea
  • 2000–2005
    • University of Wuerzburg
      Würzburg, Bavaria, Germany
  • 2002–2003
    • Institut de Cancérologie Gustave Roussy
      Île-de-France, France
  • 2001
    • Case Western Reserve University School of Medicine
      Cleveland, Ohio, United States