Ole Madsen

Ole Madsen
Wageningen University & Research | WUR · Animal Breeding and Genomics Centre

About

276
Publications
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Publications

Publications (276)
Preprint
Full-text available
Wild boars exhibit genetic and phenotypic diversity shaped by migrations and local adaptations. Its expansion across Eurasia, especially in central Asia, remains underexplored. Here, we present newly sequenced whole-genome data of 47 wild boars from Eastern Asia, Central Asia, and Europe, combined with 49 existing genomes, creating a comprehensive...
Article
Full-text available
Background The objectives of this study were to estimate genetic parameters and studying the influence of early-life and parental factors on the semen traits of boars. The dataset included measurements on 449,966 ejaculates evaluated using a Computer-Assisted Sperm Analysis (CASA) system from 5692 artificial insemination (AI) boars. In total, we co...
Article
Full-text available
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...
Preprint
Full-text available
Systematic characterization of the molecular states of cells in livestock tissues is essential for understanding cellular and genetic mechanisms underlying economically and ecologically important physiological traits. This knowledge contributes to the advancement of sustainable and precision agriculture-food systems. Here, as part of the Farm anima...
Article
Full-text available
Background There is increasing interest in using intestinal organoids to study complex traits like feed efficiency (FE) and host-microbe interactions. The aim of this study was to investigate differences in the molecular phenotype of organoids derived from pigs divergent for FE as well as their responses to challenge with adherent and invasive Esch...
Preprint
Full-text available
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 focussing on purebred lines for traits with commercial relevance as growth and meat quality. However, l...
Article
Full-text available
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 genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show...
Preprint
Full-text available
The systematic characterization of cellular heterogeneity among tissues and cell-type-specific regulation underlying complex phenotypes remains elusive in pigs. Within the Pig Genotype-Tissue Expression (PigGTEx) project, we present a single-cell transcriptome atlas of adult pigs encompassing 229,268 high-quality nuclei from 19 tissues, annotated t...
Preprint
Full-text available
The systematic characterization of cellular heterogeneity among tissues and cell-type-specific regulation underlying complex phenotypes remains elusive in pigs. Within the Pig Genotype-Tissue Expression (PigGTEx) project, we present a single-cell transcriptome atlas of adult pigs encompassing 229,268 high-quality nuclei from 19 tissues, annotated t...
Preprint
Full-text available
Background DNA methylation is a process by which methyl groups are added to the DNA molecule. Methylation of promoters influence gene expression, as the addition of a methyl group can prevent the binding of certain transcription factors and repress the transcription of the associated gene. Bioinformatics pipelines are a series of computational step...
Article
Full-text available
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 be...
Preprint
Full-text available
Background Organoids are in vitro model systems generated from tissues. Organoids express specific physiological functions associated with their original tissue location and they express tissue-segment-specific genes. The aim of this study was to investigate the resemblance of duodenum, ileum (with or without Peyer’s Patches (PP) – PP could be reco...
Article
Full-text available
The pig IPEC-J2 and chicken SL-29 cell lines are of interest because of their untransformed nature and wide use in functional studies. Molecular characterization of these cell lines is important to gain insight into possible molecular aberrations. The aim of this paper is to provide a molecular and epigenetic characterization of the IPEC-J2 and SL-...
Chapter
Global warming is expected to result in larger temperature fluctuations by which heat stress may become an important stressor for animals, affecting health and productivity. Animals can cope with and adapt to heat stress by changing their physiology. To investigate general physiological reactions to heat stress in muscle and heart tissues of chicke...
Preprint
Full-text available
Organoids are in vitro model systems generated from tissues. Organoids express specific physiological functions associated with their original tissue location and they express tissue-segment-specific genes. The aim of this study was to culture pig organoids from different areas of intestinal segments: duodenum, ileum (with or without Peyers Patches...
Preprint
Full-text available
The Farm animal Genotype-Tissue Expression (FarmGTEx, https://www.farmgtex.org/) project has been established to develop a comprehensive public resource of genetic regulatory variants in domestic animal species, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biology discovery and exploitation in...
Preprint
Full-text available
The Farm animal Genotype-Tissue Expression (FarmGTEx, https://www.farmgtex.org/) project has been established to develop a comprehensive public resource of genetic regulatory variants in domestic animal species, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biology discovery and exploitation in...
Article
Full-text available
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 post-zygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized...
Article
Full-text available
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 pi...
Poster
Full-text available
Background Objective Our aim is to investigate the transcriptomic landscape of the intestinal organoids derived from pigs divergent for FE and their responses when challenged with Escherichia coli (E. coli). Conclusions Figure 1. Design of the experimental setup. Pigs were selected for a low or high feed efficient (FE) phenotype. Tissues were harve...
Article
Full-text available
Background: The liver is the central metabolic organ of animals. In chicken, knowledge on the relationship between gene expression in the liver and fat deposition during development is still limited. A time-course transcriptomic study from the embryonic (day 12) to the egg-producing period (day 180 after hatch) was performed to profile slow-growing...
Article
Full-text available
Organoids are self-organizing, self-renewing three-dimensional cellular structures that resemble organs in structure and function. They can be derived from adult stem cells, embryonic stem cells, or induced pluripotent stem cells. They contain most of the relevant cell types with a topology and cell-to-cell interactions resembling that of the in vi...
Conference Paper
Feed efficiency (FE) is an important trait in livestock production. It is common to measure and improve FE via the feed conversion ratio (FCR), but the underlying biological mechanisms are still largely unknown and complex. Adult stem-cell derived organoids are powerful experimental models to study mammalian biology, and offer possibilities to adva...
Article
Full-text available
Increasing human disturbance and climate change have a major impact on habitat integrity and size, with far‐reaching consequences for wild fauna and flora. Specifically, population decline and habitat fragmentation result in small, isolated populations. To what extend different endangered species can cope with small population size is still largely...
Article
Full-text available
Temperature and CO2 concentration during incubation have profound effects on broiler chick development, and numerous studies have identified significant effects on hatch heart weight (HW) as a result of differences in these parameters. Early life environment has also been shown to affect broiler performance later in life; it has thus been suggested...
Article
Full-text available
Fat traits are important in the chicken industry where there is a desire for high intramuscular fat (IMF) and low abdominal fat. However, there is limited knowledge on the relationship between the dynamic status of gene expression and the body fat deposition in chicken. Transcriptome data were obtained from breast muscle and abdominal fat of female...
Article
Full-text available
Growth is dependent on genotype and diet, even at early developmental stages. In this study, we investigated the effects of genotype, sex, and body weight on the fetal muscle transcriptome of purebred Iberian and crossbred Iberian x Large White pigs sharing the same uterine environment. RNA sequencing was performed on 16 purebred and crossbred fetu...
Article
Full-text available
Wild boar (Sus scrofa) drastically colonized mainland Eurasia and North Africa, most likelyfrom East Asia during the Plio-Pleistocene (2–1Mya). In recent studies, based on genome-wide information, it was hypothesized that wild boar did not replace the species it encoun-tered, but instead exchanged genetic materials with them through admixture. The...
Article
Functional annotation of genomes is a prerequisite for contemporary basic and applied genomic research, yet farmed animal genomics is deficient in such annotation. To address this, the FAANG (Functional Annotation of Animal Genomes) Consortium is producing genome-wide data sets on RNA expression, DNA methylation, and chromatin modification, as well...
Article
Full-text available
Livestock populations can be used to study recessive defects caused by deleterious alleles. The frequency of deleterious alleles including recessive lethal alleles can stay at high or moderate frequency within a population, especially if recessive lethal alleles exhibit an advantage for favourable traits in heterozygotes. In this study, we report s...
Data
Screen capture of the deletion boundary in the JBrowse genome browser. (PDF)
Data
Genetic drift simulation for SSC18 lethal recessive with allele frequency 5.4% (10.8% carrier frequency). (PDF)
Data
WGS sequenced individuals in the Large White breed. (PDF)
Data
LRR signal intensities within the haplotype region for two "fresh born" homozygotes of the 212kb deletion. (PDF)
Data
JBrowse screen capture showing aligned liver ChipSeq data (H3K27Ac, H3K4Me3) on Sscrofa11.1. (PDF)
Data
Markers and genomic positions. (XLSX)
Data
Haplotypes from the four tracked carrier-by-carrier matings, including parent animals. (XLSX)
Data
Deletion carrier frequency and the number of genotyped animals per time point from 2006–2018. (PDF)
Data
Primer information for the genes used for RT-qPCR. (PDF)
Data
Expression fold change of the BBS9 gene (RT-qPCR) in 8 carriers, and 10 non-carriers. (PDF)
Data
Logistic regression to distinguish carrier from non-carrier animals (farm 2 litters). (PDF)
Data
Results from two CxC (CC1: 11-may-2017, CC3: 19-may-2017) matings on farm 1. (PDF)
Data
Results from two CxC (CC2: 18-may-2017, CC4: 01-jul-2017) matings on farm 2. (PDF)
Data
Gene expression measured in fragments per kilobase per million (FPKM) for BBS9 and BMPER gene in one SSC18 deletion carrier animal (LW) and two non-carrier pigs (DU/PI). (PDF)
Data
Dumeco-W carriers for SSC18 deletion including birth dates. (PDF)
Data
Estimated breeding values (EBV) for seven traits including the overall selection index (TSI). (PDF)
Data
Pictures and X-rays from mummified piglets. A: Picture of a homozygous del/del mummified piglet (7360). B: X-ray of homozygous del/del mummified piglet (7360). C: X-ray of mummified piglet 7659 (status unknown). D: X-ray of homozygous del/del mummified piglet (8609). (PDF)
Data
Genetic progress for growth (daily gain) in the Large White breed. (PDF)
Data
Simulation of the SSC18 carrier frequency with current selective advantage over 200 generations starting with lower carrier frequency (2%). (PDF)
Data
Simulation of the SSC18 carrier frequency if selection would be exclusively applied on growth. (PDF)
Data
Allele specific expression test of the BMPER gene for three non-carriers pigs. Heterozygous coding variants of the BMPER canonical transcript (XM_013990842.2) are used to test for allelic imbalance. (PDF)
Data
Association analysis using deregressed breeding values (DEBV) for 16 traits in the Large White breed. (PDF)
Data
RT-qPCR results for BBS9 expression in 8 carriers and 10 non-carriers. (PDF)
Conference Paper
Improving feed efficiency is an important trait in livestock production. So far, feed conversion ratio (FCR) has been used to improve feed efficiency. However, the underlying biological mechanisms of feed efficiency are still not clear and very complex. Adult stem-cell derived organoids have already proven to be powerful experimental models of mamm...
Article
Full-text available
For reproductive traits such as total number born (TNB), variance due to different environments is highly relevant in animal breeding. In this study, we aimed to perform a gene-network analysis for TNB in pigs across different environments using genomic reaction norm models. Thus, based on relevant single-nucleotide polymorphisms and linkage disequ...
Poster
Difficult questions confront clinicians attempting to improve patient outcomes for a wide range of cancer types. A large animal model with genetic, anatomic, and physiologic similarities to humans is required for transitioning between preclinical mouse models and human clinical trials in order to address unmet clinical needs. We previously reported...
Article
Human soft-tissue sarcomas (STS) are rare, aggressive mesenchymal tumors with a late stage 5-year survival rate (50-60%) that has for decades remained unchanged. Research into STS treatment is hampered by the limited human STS cell line availability and the large number of STS subtypes. Therefore, there is a need to develop STS cell lines and anima...
Article
Full-text available
Human soft-tissue sarcomas (STS) are rare mesenchymal tumors with a 5-year survival rate of 50%, highlighting the need for further STS research. Research has been hampered by limited human sarcoma cell line availability and the large number of STS subtypes, making development of STS cell lines and animal models representative of the diverse human S...
Poster
Human soft-tissue sarcomas (STS) are rare, aggressive mesenchymal tumors with a late stage 5-year survival rate (50-60%) that has for decades remained unchanged. Research into STS treatment is hampered by the limited human STS cell line availability and the large number of STS subtypes. Therefore, there is a need to develop STS cell lines and anima...
Article
Full-text available
Background Iron deficiency is a common childhood micronutrient deficiency that results in altered hippocampal function and cognitive disorders. However, little is known about the mechanisms through which neonatal iron deficiency results in long lasting alterations in hippocampal gene expression and function. DNA methylation is an epigenetic mark in...
Poster
DNA methylation is an epigenetic regulator of gene expression that plays a role in many cellular processes affecting a variety of traits. In this study DNA methylation was assessed in neuronal tissue from three pigs (frontal lobe) and one great tit (whole brain) using reduced representation and whole genome bisulfite sequencing, respectively. In ad...
Poster
The world is changing rapidly and organisms need to adapt to those changes. Animal personality describes how individuals differ in how well they cope with such challenges and is an important factor for explaining fitness of individuals and viability of populations. The search for hereditary mechanisms underlying these animal personality traits has...
Article
Full-text available
Background Studies on vertebrate DNA methylomes have revealed a regulatory role of tissue specific DNA methylation in relation to gene expression. However, it is not well known how tissue-specific methylation varies between different functional and structural components of genes and genomes. Using whole-genome bisulfite sequencing data we here desc...
Article
Number of teats (NT) is an important trait affecting both piglet’s welfare and the production level of pig farms. Biologically, embryonic mammary gland development requires the coordination of many signaling pathways necessary for the proper development of teats. Several QTL for NT have been identified; however, further analysis is still lacking. T...
Article
Number of teats (NT) is an important trait affecting both piglet's welfare and the production level of pig farms. Biologically, embryonic mammary gland development requires the coordination of many signaling pathways necessary for the proper development of teats. Several QTL for NT have been identified; however, further analysis is still lacking. T...