Publications by authors named "Martien A M Groenen"

Article Synopsis
  • Italian local turkey populations are crucial for maintaining genetic diversity, and efforts should focus on in vivo preservation methods.
  • Advanced genomic techniques, including whole genome sequencing and genotyping, revealed significant genetic variability and isolation among different turkey populations in Italy.
  • Findings highlight the role of selective sweeps in shaping genetic traits related to heat stress and growth, suggesting potential benefits in adapting to climate change, which can inform conservation and selection strategies for these turkeys.
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Background: Integration of high throughput DNA genotyping and RNA-sequencing data enables the discovery of genomic regions that regulate gene expression, known as expression quantitative trait loci (eQTL). In pigs, efforts to date have been mainly focused on purebred lines for traits with commercial relevance as such growth and meat quality. However, little is known on genetic variants and mechanisms associated with the robustness of an animal, thus its overall health status.

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Article Synopsis
  • The text discusses a study on genomic diversity in the great tit (Parus major), focusing on how environmental factors and demographic history impact genetic variation across different populations in Europe.
  • The research, which is one of the most extensive genomic surveys for a wild vertebrate, involved analyzing about 500,000 SNP markers from 647 individuals across 29 populations to understand patterns of genomic divergence.
  • Findings revealed that genetic differentiation varied significantly among populations, influenced by factors like local recombination rates and natural selection, with reduced diversity noted in island populations and evidence of recent adaptive changes at the edges of the species' range.
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The recognition that climate change is occurring at an unprecedented rate means that there is increased urgency in understanding how organisms can adapt to a changing environment. Wild great tit () populations represent an attractive ecological model system to understand the genomics of climate adaptation. They are widely distributed across Eurasia and they have been documented to respond to climate change.

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  • The FarmGTEx project aims to create a public database of genetic variants in livestock to connect genetic differences with physical traits, benefiting both animal breeding and human health research.
  • The pilot phase, PigGTEx, involved analyzing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples from pigs, leading to the development of a genotype imputation panel and associations between millions of genetic variants and transcriptomic traits across 34 different tissues.
  • The study highlights the tissue-specific regulatory effects of these variants, revealing molecular mechanisms affecting 207 complex pig traits while also demonstrating the relevance of pigs as models for understanding human gene expression and genetic regulation.
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Suids, both domesticated and wild, are found on all continents except for Antarctica and provide valuable food resources for humans in addition to serving as important models for biomedical research. Continuing advances in genome sequencing have allowed researchers to compare the genomes from diverse populations of suids helping to clarify their evolution and dispersal. Further analysis of these samples may provide clues to improve disease resistance/resilience and productivity in domestic suids as well as better ways of classifying and conserving genetic diversity within wild and captive suids.

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Assisted reproductive technologies (ARTs), including in vitro maturation and fertilization (IVF), are increasingly used in human and animal reproduction. Whether these technologies directly affect the rate of de novo mutation (DNM), and to what extent, has been a matter of debate. Here we take advantage of domestic cattle, characterized by complex pedigrees that are ideally suited to detect DNMs and by the systematic use of ART, to study the rate of de novo structural variation (dnSV) in this species and how it is impacted by IVF.

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Background: China has one third of the worldwide indigenous pig breeds. The Henan province is one of the earliest pig domestication centers of China (about 8000 years ago). However, the precise genetic characteristics of the Henan local pig breeds are still obscure.

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Background: The domesticated turkey (Meleagris gallopavo) is a species of significant agricultural importance and is the second largest contributor, behind broiler chickens, to world poultry meat production. The previous genome is of draft quality and partly based on the chicken (Gallus gallus) genome. A high-quality reference genome of M.

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Article Synopsis
  • Structural variants (SVs) are genomic changes like deletions and duplications that significantly affect gene expression, highlighting their importance in genetic research.
  • This study created a high-quality catalog of SVs in cattle, identifying 13,731 variants, including deletions and duplications, with a validation confirming over 60% are true population variants.
  • Two notable duplications were found to likely impact genes relevant to cattle health traits, suggesting a need for further investigation into these genetic factors.
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Luchuan pig, an obese indigenous Chinese porcine breed, has a desirable meat quality and reproductive capacity. Duroc, a traditional western breed, shows a faster growth rate, high feed efficiency and high lean meat rate. Given the unique features these two porcine breeds have, it is of interest to investigate the underlying molecular mechanisms behind their distinctive nature.

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  • The study focuses on characterizing the IPEC-J2 pig and SL-29 chicken cell lines due to their untransformed nature and significance in functional research.
  • It employs techniques like whole genome sequencing, gene expression analysis, and various epigenetic evaluations to explore molecular features and identify aberrations.
  • Findings indicate aneuploidy (heteroploidy) in both cell lines, with genes on these aneuploid chromosomes exhibiting higher expression compared to diploid ones, revealing complexities in gene regulation and chromatin accessibility.
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In general, the relationship between the predicted functional consequences of missense mutations mapping to genes known to be involved in human diseases and the severity of disease manifestations is weak. In this study, we tested in pigs whether missense single nucleotide polymorphisms (SNPs), predicted to have consequences on the function of genes related to lipid metabolism are associated with lipid phenotypes. Association analysis demonstrated that nine out of 72 nominally associated SNPs were classified as "highly" or "very highly consistent" in silico-predicted functional mutations and did not show association with lipid traits expected to be affected by inactivation of the corresponding gene.

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Background: In poultry, the population structure of local breeds is usually complex mainly due to unrecorded breeding. Local chicken breeds offer an interesting proxy to understand the complexity of population structure in the context of human-mediated development of diverse morphologies and varieties. We studied 37 traditional Dutch chicken breeds to investigate population structure and the corresponding genomic impact using whole-genome sequence data.

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Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches.

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Background: We previously reported a familial thyroid follicular cell carcinoma (FCC) in a large number of Dutch German longhaired pointers and identified two deleterious germline mutations in the TPO gene associated with disease predisposition. However, the somatic mutation profile of the FCC in dogs has not been investigated at a genome-wide scale.

Results: Herein, we comprehensively investigated the somatic mutations that potentially contribute to the inherited tumor formation and progression using high depth whole-genome sequencing.

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The German Longhaired Pointer (GLP) breed is a versatile pointer dog breed. In the current study, we investigated the genetic diversity of these dogs based on SNP array data and compared it to 11 other pointer setter breeds. The results show that GLPs have a relatively low level of inbreeding among these pointer breeds.

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Backfat is an important trait in pork production, and it has been included in the breeding objectives of genetic companies for decades. Although adipose tissue is a good energy storage, excessive fat results in reduced efficiency and economical losses. A large QTL for backfat thickness on chromosome 5 is still segregating in different commercial pig breeds.

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It is largely unknown how mammalian genomes evolve under rapid speciation and environmental adaptation. An excellent model for understanding fast evolution is provided by the genus Sus, which diverged relatively recently and lacks postzygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized to a tropical island environment.

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In the past 50 years, there has been a steep increase in the demand for poultry products, met by increasing production along with genetic selection for improved growth, efficiency, health and reproduction. The selection tends to reduce the number and type of genetic resources contributing to the majority of production. The University of Alberta maintains 10 heritage chicken lines (Brown Leghorn (BL), Light Sussex (LS), New Hampshire (NH), Saskatchewan Barred Rock (SaskBR), Shaver Barred Rock (ShaverBR), Shaver Rhode Island Red (RIR), White Leghorn (WL) and three commercial crosses called Alberta Meat Control strains 1957 (AMC-1957), 1978 sire line (AMC-1978-20S) and 1978 dam line (AMC-1978-30D), that played a large role in the evolution of the poultry industry in Canada.

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Article Synopsis
  • The liver plays a crucial role in metabolism, but research on its gene expression related to fat deposition in chickens is limited.
  • A study tracked gene expression from day 12 (embryo) to day 180 (post-hatch) to see how it correlates with fat accumulation.
  • The findings revealed 13,096 genes were active at all stages, highlighting key genes linked to fat metabolism that could help in breeding chickens with lower abdominal fat weight.
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Thyroid carcinomas (TCs) originating from follicular cells of the thyroid gland occur in both humans and dogs, and they have highly similar histomorphologic patterns. In dogs, TCs have not been extensively investigated, especially concerning the familial origin of TCs. Here, we report familial thyroid follicular cell carcinomas (FCCs) confirmed by histology in 54 Dutch origin German longhaired pointers.

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Article Synopsis
  • Clinical mastitis (CM) in lactating cows is influenced by genetics, with a key resistance QTL found on chromosome 6 in various dairy breeds.
  • Researchers identified a specific ~12 kb copy number variant (CNV) linked to this resistance, suggesting it affects the expression of the group-specific component gene (GC), which is related to vitamin D binding.
  • The study indicates that the CNV not only contributes to CM resistance but is also linked to improved milk yield and lower fertility, hinting that vitamin D pathways play a significant role in these traits.
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Structural variations (SVs) are an important source of phenotypic diversity in cattle. Here, 72 whole genome sequences representing taurine and zebu cattle were used to identify SVs. Applying multiple approaches, 16,738 SVs were identified.

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