Martien A. M. Groenen
A5025255020- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Animal Genetics and Reproduction
- Genetic diversity and population structure
- Animal Nutrition and Physiology
- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Livestock and Poultry Management
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- Molecular Biology Techniques and Applications
- Genomic variations and chromosomal abnormalities
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genomics and Chromatin Dynamics
- Nutrition, Genetics, and Disease
- Physiological and biochemical adaptations
- Wheat and Barley Genetics and Pathology
- Gene expression and cancer classification
- Genetics and Plant Breeding
- RNA modifications and cancer
- Aquaculture disease management and microbiota
- Avian ecology and behavior
- Genetics, Bioinformatics, and Biomedical Research
- Animal Behavior and Reproduction
- Meat and Animal Product Quality
Wageningen University & Research
2016-2025
Topigs Norsvin (Netherlands)
2022
Centre for BioSystems Genomics
2009-2019
Aristotle University of Thessaloniki
2015
Hendrix Genetics (Netherlands)
2010
Graduate School Experimental Plant Sciences
1989-2008
University of Bologna
2006
Leiden University
1985-1987
Radboud University Nijmegen
1984-1985
For 10,000 years pigs and humans have shared a close complex relationship. From domestication to modern breeding practices, shaped the genomes of domestic pigs. Here we present assembly analysis genome sequence female Duroc pig (Sus scrofa) comparison with wild from Europe Asia. Wild emerged in South East Asia subsequently spread across Eurasia. Our results reveal deep phylogenetic split between European Asian boars ∼1 million ago, selective sweep indicates selection on genes involved RNA...
The dissection of complex traits economic importance to the pig industry requires availability a significant number genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted discover several hundreds thousands porcine SNPs using next generation sequencing technologies and use these SNPs, well others from different public sources, design high-density SNP genotyping assay.A total 19 reduced representation libraries derived four swine breeds (Duroc, Landrace,...
Domestication of wild boar ( Sus scrofa ) and subsequent selection have resulted in dramatic phenotypic changes domestic pigs for a number traits, including behavior, body composition, reproduction, coat color. Here we used whole-genome resequencing to reveal some the loci that underlie evolution European pigs. Selective sweep analyses revealed strong signatures at three harboring quantitative trait explain considerable part one most characteristic morphological pig—the elongation back an...
A consensus linkage map has been developed in the chicken that combines all of genotyping data from three available mapping populations. Genotyping were contributed by laboratories have using East Lansing and Compton reference populations Animal Breeding Genetics Group Wageningen University Wageningen/Euribrid population. The resulting genome contains 1889 loci. framework is presented 480 loci ordered on 50 groups. Framework are defined as whose order relative to one another supported odds...
A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided cost-effective assembly the genome sequence domestic turkey (Meleagris gallopavo). Heterozygosity sequenced source allowed discovery more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, current (∼1.1 Gb) includes 917 Mb assigned to specific chromosomes. Annotation identified nearly 16,000 genes, 15,093 recognized as protein...
Ning Li and colleagues report the whole-genome sequence of duck, Anas platyrhynchos, a natural host avian influenza viruses. They examine response to infection by comparing lung transcriptomes ducks that were infected with A The duck (Anas platyrhynchos) is one principal hosts We present genome perform deep transcriptome analyses investigate immune-related genes. Our data indicate possesses contractive immune gene repertoire, as in chicken zebra finch, this repertoire has been shaped through...
Abstract We describe the organization of a nascent international effort, Functional Annotation Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps functional elements in genomes domesticated animal species.
The resolution of the chicken consensus linkage map has been dramatically improved in this study by genotyping 12,945 single nucleotide polymorphisms (SNPs) on three existing mapping populations chicken: Wageningen (WU), East Lansing (EL), and Uppsala (UPP) populations. As many as 8599 SNPs could be included, bringing total number markers current to 9268. length sex average is 3228 cM, considerably smaller than previous estimates using WU EL populations, reflecting higher quality new map....
Inbreeding has long been recognized as a primary cause of fitness reduction in both wild and domesticated populations. Consanguineous matings inheritance haplotypes that are identical by descent (IBD) result homozygous stretches along the genome offspring. Size position regions homozygosity (ROHs) expected to correlate with genomic features such GC content recombination rate, but also direction selection. Thus, ROHs should be non-randomly distributed across genome. Therefore, demographic...
Breed utilization, genetic improvement, and industry consolidation are predicted to have major impacts on the composition of commercial chickens. Consequently, question arises as whether sufficient diversity remains within stocks address future needs. With chicken genome sequence more than 2.8 million single-nucleotide polymorphisms (SNPs), it is now possible biodiversity using a previously unattainable metric: missing alleles. To achieve this assessment, 2551 informative SNPs were genotyped...
Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ∼8,500 BC. They then spread across the Middle and Near East westward into Europe alongside early agriculturalists. European either independently or more likely appeared so as a result of admixture between introduced wild boar. As result, boar mtDNA lineages replaced Eastern/Anatolian signatures subsequently indigenous domestic pig Anatolia. The specific details these processes, however, remain unknown. To...
Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity that display variation many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand relationship between genomic composition arising from breed development, genomes 13 traditional commercial European pig were scanned signatures...
Abstract For over 50 years, the great tit ( Parus major ) has been a model species for research in evolutionary, ecological and behavioural research; particular, learning cognition have intensively studied. Here, to provide further insight into molecular mechanisms behind these important traits, we de novo assemble reference genome whole-genome re-sequence another 29 individuals from across Europe. We show an overrepresentation of genes related neuronal functions, regions under positive...
Recent natural selection in a wild bird Many studies have found evidence of rapid evolution response to environmental change. In most cases, there has been some suggestion which traits might be responsive ahead time. Bosse et al. turn this approach on its head by using genomic regions with signature identify that are changing. great tits ( Parus major ) the United Kingdom, showing invariably contained genes associated bill growth. Indeed, U.K. birds not only longer bills, but these bills...
Abstract The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking polymorphisms variation phenotypes, helping fundamental biological discovery and exploitation animal breeding human biomedicine. Here we show results from the pilot phase PigGTEx by processing 5,457 RNA-sequencing 1,602 whole-genome sequencing samples passing quality control pigs. We build pig...
Abstract We tested the utility of genetic cluster analysis in ascertaining population structure a large data set for which was previously known. Each 600 individuals representing 20 distinct chicken breeds genotyped 27 microsatellite loci, and individual multilocus genotypes were used to infer clusters. Individuals from each breed inferred belong mostly same cluster. The clustering success rate, measuring fraction that properly their correct breeds, consistently ~98%. When markers highest...
Abstract In an experimental cross between Meishan and Dutch Large White Landrace lines, 619 F2 animals their parents were typed for molecular markers covering the entire porcine genome. Associations studied these two fatness traits: intramuscular fat content backfat thickness. Association analyses performed using interval mapping by regression under genetic models: (1) outbred line-cross model where founder lines assumed to be fixed different QTL alleles; (2) a half-sib unique allele...
The role of imprinting in body composition was investigated an experimental cross between Chinese Meishan pigs and commercial Dutch pigs. A whole-genome scan revealed significant evidence for five quantitative trait loci (QTL) affecting composition, which four were imprinted. Imprinting tested with a statistical model that separated the expression paternally maternally inherited alleles. For back fat thickness, expressed QTL found on Sus scrofa chromosome 2 (SSC2), Mendelian-expressed SSC7....
In a project on the biodiversity of chickens funded by European Commission (EC), eight laboratories collaborated to assess genetic variation within and between 52 populations from wide range chicken types. Twenty-two di-nucleotide microsatellite markers were used genotype DNA pools 50 birds each population. The polymorphism measures for average, least polymorphic population (inbred C line) most (Gallus gallus spadiceus) were, respectively, as follows: number alleles per locus, population:...