Haja N Kadarmideen

• DVM MVSc PhD
• Professor at Aarhus University

Dietary lipids provide energy, are cellular structural components, and are involved in physiological processes. Lipids are the dietary source in supplementary diet experiments in pigs. This study aims to investigate the dietary effects of PUFAs on the hepatic transcriptome and physiological pathways of two diets on two pig breeds. Polish Landrace (...

Transcriptomic data is often expensive and difficult to generate in large cohorts relative to genomic data; therefore, it is often important to integrate multiple transcriptomic datasets from both microarray‐ and next generation sequencing (NGS)‐based transcriptomic data across similar experiments or clinical trials to improve analytical power and...

In cattle, the in vitro production (IVP) of embryos is becoming more relevant than embryos produced in vivo, i.e. after ovarian stimulation and embryo transfer (MOET). However, the effects of IVP on the developmental programming of specific organs in the postnatal calves are yet unknown. Previously, we reported an epigenomic and transcriptomic prof...

Cattle production is one of the key contributors to global warming due to methane emission, which is a by-product of converting feed stuff into milk and meat for human consumption. Rumen hosts numerous microbial communities that are involved in the digestive process, leading to notable amounts of methane emission. The key factors underlying differe...

Transcriptomic data is often expensive and difficult to generate in large cohorts in comparison to genomic data and therefore is often important to integrate multiple transcriptomic datasets from both microarray and next generation sequencing (NGS) based transcriptomic data across similar experiments or clinical trials to improve analytical power a...

In cattle, several calves born after IVP (“in vitro” embryo production) present similar birthweight to those generated after MOET (multiple ovulation and embryo transfer). However, the underlying molecular patterns in organs involved in the developmental process are unknown and could indicate physiological programming. The objectives of this study...

Pregnancy rates for in vitro produced (IVP) embryos are usually lower than for embryos produced in vivo after ovarian superovulation (MOET). This is potentially due to alterations in their trophectoderm (TE), the outermost layer in physical contact with the maternal endometrium. The main objective was to apply a multi-omics data integration approac...

Epistasis is the interaction between genes or genetic variants (such as Single Nucleotide Polymorphisms or SNPs) that influences a phenotype or a disease outcome. Statistically and biologically, significant evidence of epistatic loci for several traits and diseases is well known in human, animals, and plants. However, there is no straightforward wa...

In cattle, ovarian superovulation followed by invivo embryo collection and transfer (MOET), and the invitro production (IVP) of embryos are used all over the world to improve animal genetics. Application of MOET has resulted in the production of billions of healthy animals during the past 40 years, and IVP has evolved and given rise to significant...

DNA methylation in gene or gene body could influence gene transcription. Moreover, methylation in gene regions along with CpG island regions could modulate the transcription to undetectable gene expression levels. Therefore, it is necessary to investigate the methylation levels within the gene, gene body, CpG island regions, and their overlapped re...

The main goal was to apply machine learning (ML) methods on integrated multi-transcriptomic data, to identify endometrial genes capable of predicting uterine receptivity according to their expression patterns in the cow. Public data from five studies were re-analyzed. In all of them, endometrial samples were obtained at day 6-7 of the estrous cycle...

Based on in-vitro produced (IVP) bovine embryos, embryo proper and embryonic/fetal membranes were studied in 12 pregnancies from day 26 to 47. The embryos/fetuses displayed external as well as internal development of organs and structures according to the expectations from comparable in-vivo studies. However, the embryonic/fetal membranes were shor...

Feed efficiency (FE) is a key trait in pig production, as improvement in FE has positive economic and environmental impact. FE is a complex phenotype and testing animals for FE is costly. Therefore, there has been a desire to find functionally relevant single nucleotide polymorphisms (SNPs) as biomarkers, to improve our biological understanding of...

An interplay between gene expression, mineral concentration, and beef quality traits in Bos indicus muscle has been reported previously under a network approach. However, growing evidence suggested that miRNAs not only modulate gene expression but are also involved with mineral homeostasis. To our knowledge, understanding of the miRNA–gene expressi...

Simple Summary Reproductive performance has direct economic implications on the beef cattle industry. The majority of Zebu breeds (e.g., Nellore; Bos taurus indicus) have poor reproductive performance compared to other cattle breeds. In this context, genetic progress can be achieved for fertility and reproduction through the use of genomic selectio...

Feed efficiency (FE) is an economically important trait. Thus, reliable predictors would help to reduce the production cost and provide sustainability to the pig industry. We carried out metabolome-transcriptome integration analysis on 40 purebred Duroc and Landrace uncastrated male pigs to identify potential gene-metabolite interactions and explor...

Improvement of feed efficiency (FE) is key for Sustainability and cost reduction in pig production. Our aim was to characterize the muscle transcriptomic profiles in Danbred Duroc (Duroc; n = 13) and Danbred Landrace (Landrace; n = 28), in relation to FE for identifying potential biomarkers. RNA-seq data on the 41 pigs was analyzed employing differ...

Resorption of bones and cartilage coupled with structural changes in the inflamed joints are the major hallmark of rheumatoid arthritis (RA). Genetic polymorphisms in pro-inflammatory interleukins (ILs) appear to play an important role in the susceptibility towards progressive RA. We therefore aimed to investigate the association of single nucleoti...

DNA methylation of different gene components, including different exons and introns, or different lengths of exons and introns is associated with differences in gene expression. To investigate the methylation of porcine gene components associated with the boar taint (BT) trait, this study used reduced representation bisulfite sequencing (RRBS) data...

Modifications of the endometrial transcriptome at day 7 of the estrus cycle are crucial to maintain gestation after transfer of in-vitro produced (IVP) embryos, although these changes are still largely unknown. The aim of this study was to identify genes, and their related biological mechanisms, important for pregnancy establishment based on the en...

Skeletal muscles constitute a high proportion of the cellular mass that is essential for the growth traits in cattle. Resveratrol (RSV) is a natural polyphenol compound involved in pleiotropic biological activities of muscle. Therefore, the aim of our study was to investigate the transcriptome-level effects of RSV on bovine primary myoblast to reve...

Feed efficiency (FE) is an economically important trait. Thus, reliable predictors would help to reduce the production cost and provide sustainability to the pig industry. We carried out metabolome-transcriptome integration analysis on 40 purebred Duroc and Landrace male uncastrated pigs to identify potential gene-metabolite interactions and explor...

During the early stages of pregnancy, the uterine endometrium undergoes dramatic morphologic and functional changes accompanied with dynamic variation in gene expression. Pregnancy-stage specific differentially expressed gene (DEG)-transcript-probes were investigated and identified by comparing endometrium transcriptome at 9th day (9D), 12th day (1...

Metabolites represent the ultimate response of biological systems, so metabolomics is considered the link between genotypes and phenotypes. Feed efficiency is one of the most important phenotypes in sustainable pig production and is the main breeding goal trait. We utilized metabolic and genomic datasets from a total of 108 pigs from our own previo...

Feed efficiency (FE) is a key trait in pig production, as it has both high economic and environmental impact. FE is a challenging phenotype to study, as it is complex and affected by many factors, such as metabolism, growth and activity level. Furthermore, testing for FE is expensive, as it requires costly equipment to measure feed intake of indivi...

DNA methylation in gene or promoter or gene body could restrict/promote the gene transcription. Moreover, methylation in the gene regions along with CpG island regions could modulate the transcription to undetectable gene expression levels. Therefore, it is necessary to investigate the methylation levels within the gene, gene body, CpG island regio...

Metabolites represent the ultimate response of biological systems, so metabolomics is considered to link the genotypes and phenotypes. Feed efficiency is one of the most important phenotypes in sustainable pig production and is the main breeding goal trait. We utilized metabolic and genomic datasets from a total of 108 pigs from our own previously...

Association studies have indicated profound effects of copy number variations (CNVs) on various phenotypes in different species. In this study, we identified the CNV distributions and expression levels of guanylate-binding protein 6 (GBP6) associated with the growth traits of Chinese cattle. The results showed that the phenotypic values of body siz...

Improvement of feed efficiency (FE) is key for sustainability and cost reduction in pig production. Our aim was to characterize the muscle transcriptomic profiles in Danbred Duroc (Duroc) and Danbred Landrace (Landrace), in relation to FE for identifying potential biomarkers. RNA-seq data was analyzed employing differential gene expression methods,...

Modifications of the endometrial transcriptome at day 7 of the estrus cycle are crucial to maintain gestation after transfer of in-vitro produced (IVP) embryos. The aim of this study was to identify genes, and their related biological mechanisms, in the endometria of recipient lactating dairy cows that become pregnant in the subsequent estrus cycle...

Interactions among genomic loci have often been overlooked in genome-wide association studies, revealing the combinatorial effects of variants on phenotype or disease manifestation. Unexplained genetic variance, interactions among causal genes of small effects, and biological pathways could be identified using a network biology approach. The main o...

We hypothesized that late gestation malnutrition differentially affects expandability of adipose tissues to predispose for early postnatal visceral adiposity. Twin‐lambs born to dams fed HIGH (150%/110% of required energy/protein, respectively), NORM (100% of requirements) or LOW (50% of NORM) diets during the last trimester were used. Postnatally,...

Improving feed efficiency (FE) is a major goal of pig breeding, reducing production costs and providing sustainability to the pig industry. Reliable predictors for FE could assist pig producers. We carried out untargeted blood metabolite profiling in uncastrated males from Danbred Duroc (n = 59) and Danbred Landrace (n = 50) pigs at the beginning a...

Background: Genotyping by sequencing (GBS) still has problems with missing genotypes. Imputation is important for using GBS for genomic predictions, especially for low depths, due to the large number of missing genotypes. Minor allele frequency (MAF) is widely used as a marker data editing criteria for genomic predictions. In this study, three imp...

Genetic polymorphisms in the interleukin 6 gene (IL-6) and its promoter regions have extensively been studied because of their potential role in the pathogenesis of rheumatoid arthritis (RA). Due to the confounding results, reported in several studies, we performed the systematic literature search on IL-6 -572 G/C polymorphism (rs1800796 SNP) and a...

Background Genotyping by sequencing (GBS) is a robust method to genotype markers. Many factors can influence the genotyping quality. One is that heterozygous genotypes could be wrongly genotyped as homozygotes, dependent on the genotyping depths. In this study, a method correcting this type of genotyping error was demonstrated. The efficiency of th...

Boar taint (BT) is an offensive flavor observed in non‐castrated male pigs that reduces the carcass price. Surgical castration effectively avoids the taint but is associated with animal welfare concerns. The functional annotation of farm animal genomes for understanding the biology of complex traits can be used in the selection of breeding animals...

Residual feed intake (RFI) is designed to estimate net efficiency of feed use, so low RFI animals are considered for selection to reduce feeding costs. However, metabolic profiling of cows and availability of predictive metabolic biomarkers for RFI are scarce. Therefore, this study aims to generate a better understanding of metabolic mechanisms beh...

Birth weight variation is influenced by fetal and maternal genetic and non-genetic factors, and has been reproducibly associated with future cardio-metabolic health outcomes. In expanded genome-wide association analyses of own birth weight (n = 321,223) and offspring birth weight (n = 230,069 mothers), we identified 190 independent association sign...

Epigenetic changes are important for understanding complex trait variation and inheritance in pigs that are also a valuable biomedical model for human health research. Testis is the main organ for reproduction and boar taint in pigs; however, there have been no studies to-date on adult pig testis epigenome. The main objective of this study was to e...

Statistics of coverage and methylation rates in CpG context.

Significant pathways (P < 0.01).

GO terms and enriched genes associated with DMCs.

Histograms of log10 of read coverage per CpG site.

Regression of densities of genes, CpG islands and CpG island shores on methylation levels from one sample, all counted by 1 Mb windows.

Regression and correlation analysis of densities of genes, CpG islands and CpG island shores on methylation levels, all counted by 1 Mb windows.

Correlation analysis of the global CpG methylation patterns among nine samples. Note: Colors in the scatter plot indicate the number of CpG sites with identical methylation pattern (methylated or non-methylated): yellow denotes many correlations, blue denotes lack of correlation and green denotes different methylation patterns. Numbers in the upper...

Total number of aligned cytosine methylation in different contexts.

Details of 12,738 DMCs with chromosomes, positions, P-values, Q-values, associated genes, genetic features and methylation levels.

Background: Inflammatory bowel disease (IBD) is a group of chronic diseases related to inflammatory processes in the digestive tract generally associated with an immune response to an altered gut microbiome in genetically predisposed subjects. For years, both researchers and clinicians have been reporting increased rates of anxiety and depression d...

Meat quality is a complex trait that is influenced by genetic and environmental factors, which includes mineral concentration. However, the association between mineral concentration and meat quality, and the specific molecular pathways underlying this association, are not well explored. We therefore analyzed gene expression as measured with RNA-seq...

Summary of pathway analysis from ClueGo for genes clustered into the selected modules. Spreadsheet tabs are divided by module.

Genes targeted by eQTLs for each selected module. Genes with MM ≥ 0.8 are highlighted in bold. Spreadsheet tabs are divided by module.

Summary statistics of meat quality traits and mineral concentration in Nelore cattle.

Correlation matrix of mineral concentration and meat quality traits in Nelore cattle. Each cell displays the correlation value when significant (p ≤ 0.05). The matrix is color-coded by correlation according to the color legend.

Gene list and module membership for each selected module. Spreadsheet tabs are divided by module.

Summary of pathway analysis from ClueGo for hub genes.

The proportion of variance explained by the module eigengene (MEs).

Native domestic breeds represent important cultural heritage and genetic diversity relevant for production traits, environmental adaptation and food security. However, risks associated with low effective population size, such as inbreeding and genetic drift, have elevated concerns over whether unique within‐breed lineages should be kept separate or...

Purpose Oocyte maturation is a complex process involving nuclear and cytoplasmic modulations, during which oocytes acquire their ability to become fertilized and support embryonic development. The oocyte is apparently “primed” for maturation during its development in the dominant follicle. As bovine oocytes immediately resume meiosis when cultured,...

In this paper we first provide a brief review of main results from our previously published studies on genome-wide gene expression (transcriptomics) in donor and recipient cattle used in in vitro production (IVP) of embryos and embryo transfer (ET). Then, we present novel results from applying integrative systems genomics and biological analyses wh...

Background The first choice drug for treatment of Attention Deficit Hyperactivity Disorder (ADHD) in Denmark and several other countries is Methylphenidate (MPH). More than 30% of the children treated with MPH have been reported to switch to another drug due to lack of efficacy or adverse reactions. Most likely, a significant fraction of this indiv...

Background Selection for feed efficiency is crucial for overall profitability and sustainability in dairy cattle production. Key regulator genes and genetic markers derived from co-expression networks underlying feed efficiency could be included in the genomic selection of the best cows. The present study identified co-expression networks associate...

Birth weight (BW) variation is influenced by fetal and maternal genetic and non-genetic factors, and has been reproducibly associated with future cardio-metabolic health outcomes. These associations have been proposed to reflect the lifelong consequences of an adverse intrauterine environment. In earlier work, we demonstrated that much of the negat...

Aims/hypothesis: A genetic risk score (GRS) consisting of 53 insulin resistance variants (GRS53) was recently demonstrated to associate with insulin resistance in adults. We speculated that the GRS53 might already associate with insulin resistance during childhood, and we therefore aimed to investigate this in populations of Danish children and ad...

Background Genetic epistasis is an often-overlooked area in the study of the genomics of complex traits. Genome-wide association studies are a useful tool for revealing potential causal genetic variants, but in this context, epistasis is generally ignored. Data complexity and interpretation issues make it difficult to process and interpret epistasi...

Background: Inflammatory bowel disease (IBD) is a group of chronic diseases related to inflammatory processes in the digestive tract generally associated with an immune response to an altered gut microbiome in genetically predisposed subjects. For years, both researchers and clinicians have been reporting increased rates of anxiety and depression d...

Supplementary material is available on the publisher’s website along with the published article.

Background: Essential oil (EO) dietary supplementation is a new strategy to improve animal health. EO compounds have antiparasitic, antimicrobial, antiviral, antimycotic, antioxidant and anti-inflammatory proprieties. Nutrigenomics investigations represent innovative approaches in understanding the relation between diet effect and gene expression...

A combination of better management and genetic selection for good health and fertility would provide a more effective long term solution for economic loss due to diseases and poor fertility. This would also help to address public concerns about the use of medical treatment in milk production. A balance in the genetic improvement of health and ferti...

Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed to identify expression quantitative trait loci (eQTLs) wit...

List of GO terms and KEGG pathways enriched in filtered eQTLs from liver and testis. Result table obtained from functional characterisation of liver and testis eQTLs with significant (FDR < 0.05) association with the summarised estimated breeding values of skatole and human nose scores. Gene symbols are included for each GO term and KEGG pathway. (...

Spreadsheet of the filtered multi-tissue eQTLs. Result table obtained from analysis of multi-tissue eQTLs with significant (FDR < 0.05) association with the summarised estimated breeding values of skatole and human nose scores. (XLS)

Spreadsheet of the candidate eQTLs. The candidate eQTLs were defined as filtered cis-acting eQTLs which enriched known boar taint QTL traits from the PigQTLdb. The candidate eQTLs could be useful in future development of biomarkers for gene-based selection schemes of pigs with lowered boar taint. The spreadsheet includes rs codes for SNPs, gene nam...

Spreadsheet of single-tissue the filtered eQTLs of liver and testis. Result table obtained from analysis of eQTLs with significant (FDR < 0.05) association with the summarised estimated breeding values of skatole and human nose scores. (XLS)

QTL traits enriched by the filtered multi-tissue eQTLs. Result table obtained from enrichment test with using filtered cis-acting eQTLs on known QTL traits from Animal Genome PigQTLdb. The test revealed QTL traits which were significantly (FDR < 0.05) overlapped by the eQTLs and the genes associated with the eQTLs that overlapped the QTL traits. (X...

Illustration of the study design. Liver, testis and ham muscle was obtained from non-castrated Danish Landrace male pigs. The liver and testis was subjected to RNA extraction and RNA-sequencing (RNA-Seq) to obtain gene expression profiles. DNA was extracted from ham muscle and subjected to genotyping by Illumina Porcine 60K SNP-chip. The software M...

Osteochondrosis (OC) in pigs is an abnormal condition in the bone development which has high economic and welfare implications. Select for OC resistance would be difficult to achieve due to low polygenic heritability (∼0.06 – 0.15; Kadarmideen et al. , 2004), unless a major gene exists. Segregation analysis provides evidence for major gene using on...

Adulthood of a dairy cow is reached when she is about 60 months old, but cows first calve at a much younger age. Therefore, most heifers are still growing during their first lactation and part of the energy and protein intake will be assigned to this purpose. As the cow grows closer to mature body weight and is able to use more energy and protein f...