Michael Paul Mullen

Mycobacterium tuberculosis , the causative agent of human tuberculosis (hTB), is currently classed as the thirteenth leading cause of death worldwide. Mycobacterium bovis , a close evolutionary relative of M. tuberculosis , causes bovine tuberculosis (bTB) and is one of the most damaging infectious diseases to livestock agriculture. Previous studies have shown that the pathogenesis of bTB disease is comparable to hTB disease, and that the bovine and human alveolar macrophage (bAM and hAM, respectively) transcriptomes are extensively reprogrammed in response to infection with these intracellular mycobacterial pathogens. However, although M. bovis and M. tuberculosis share over 99% identity at the genome level, the innate immune responses to these pathogens have been shown to be different in human or cattle hosts. In this study, a multi-omics integrative approach was applied to encompass functional genomics and GWAS data sets across the two primary hosts ( Bos taurus and Homo sapiens ) and both pathogens ( M. bovis and M. tuberculosis ). Four different experimental infection groups were used, each with parallel non-infected control cells: 1) bAM infected with M. bovis , 2) bAM infected with M. tuberculosis , 3) hAM infected with M. tuberculosis , and 4) human monocyte-derived macrophages (hMDM) infected with M. tuberculosis . RNA-seq data from these experiments 24 hours post-infection (24 hpi) was analysed using three separate computational pipelines: 1) differentially expressed genes, 2) differential gene expression interaction networks, and 3) combined pathway analysis. The results of these analyses were then integrated with high-resolution bovine and human GWAS data sets to detect novel quantitative trait loci (QTLs) for resistance to mycobacterial infection and resilience to disease. Results from this study revealed common and unique response macrophage pathways for both pathogens and identified 32 genes (12 bovine and 20 human) significantly enriched for SNPs associated with disease resistance, the majority of which encode key components of the NF-κB signalling pathway and that also drive formation of the granuloma.

Bovine tuberculosis (bTB), caused by infection with Mycobacterium bovis , is a major disease affecting cattle globally as well as being a zoonotic risk to human health. The key innate immune cell that first encounters M. bovis is the alveolar macrophage, previously shown to be substantially reprogrammed during intracellular infection by the pathogen. Here we use multi-omics and network biology approaches to analyse the macrophage transcriptional response to M. bovis infection and identify core infection response pathways and gene modules. These outputs were integrated with results from genome-wide associations of M. bovis infection to enhance the detection of putative genomic variants for disease resistance. Our results show that network-based integration of relevant transcriptomics data can extract additional information from large genome-wide associations and that this approach could also be used to integrate relevant functional genomics outputs with results from genomic association studies for human tuberculosis caused by the related Mycobacterium tuberculosis .

SUMMARY: The Galway sheep population is the only native Irish sheep breed and represents an important livestock genetic resource, which is currently categorised as “at-risk”. In the present study, comparative population genomics analyses of Galway sheep and other sheep populations of European origin were used to investigate the microevolution and recent genetic history of the breed. These analyses support the hypothesis that British Leicester sheep were used in the formation of the Galway breed and suggest more recent gene flow from the Suffolk sheep breed. When compared to conventional and endangered breeds, the Galway breed was intermediate in effective population size, genomic inbreeding and runs of homozygosity. This indicates that, although the Galway breed is declining, it is still relatively genetically diverse and that conservation and management plans informed by genomic information may aid its recovery. The Galway breed also exhibited distinct genomic signatures of artificial or natural selection when compared to other breeds, which highlighted candidate genes that may be involved in meat and wool production.

Background: Bovine tuberculosis is caused by infection with Mycobacterium bovis , which can also cause disease in a range of other mammals, including humans. Alveolar macrophages are the key immune effector cells that first encounter M. bovis and how the macrophage epigenome responds to mycobacterial pathogens is currently not well understood. Results: Here, we have used chromatin immunoprecipitation sequencing (ChIP-seq), RNA-seq and miRNA-seq to examine the effect of M. bovis infection on the bovine alveolar macrophage (bAM) epigenome. We show that H3K4me3 is more prevalent, at a genome-wide level, in chromatin from M. bovis -infected bAM compared to control non-infected bAM; this was particularly evident at the transcriptional start sites of genes that determine programmed macrophage responses to mycobacterial infection (e.g. M1/M2 macrophage polarisation). This pattern was also supported by the distribution of RNA Polymerase II (PolII) ChIP-seq results, which highlighted significantly increased transcriptional activity at genes demarcated by permissive chromatin. Identification of these genes enabled integration of high-density GWAS data, which revealed genomic regions associated with resilience to infection with M. bovis in cattle. Conclusions: Through integration of these data, we show that bAM transcriptional reprogramming occurs through differential distribution of H3K4me3 and PolII at key immune genes. Furthermore, this subset of genes can be used to prioritise genomic variants from a relevant GWAS data set.

The frequencies of mutations with lethal effects are of significant economic importance in cattle production. The elimination or at least management of such mutations in the national breeding herd is a desirable objective; however, estimation of the potential pleiotropic effects on other traits of economic importance would ascertain if strategic matings of carrier animals would be advantageous. Therefore, the objective of the current study was to estimate the effects of 2 such lethal recessives, complex vertebral malformation (CVM) and brachyspina (BY), on milk and fertility traits in Holstein-Friesian dairy cattle. Complex vertebral malformation and BY SNP genotypes and phenotypes (expressed as predicted transmitting abilities [PTA]) on 10,707 dairy cows were obtained through the Irish Cattle Breeding Federation. The association between each SNP and deregressed PTA was analyzed in ASREML using a weighted mixed animal model. Only cows with an adjusted reliability of >10% were included in the analysis and included n = 6,876 for milk yield and composition traits and n = 1,193, n = 264, n = 4,566, n = 8,564, n = 152, and n = 2,380 cows for calving interval, survival, calving difficulty, gestation length, calf mortality, and maternal calving difficulty, respectively. Complex vertebral malformation (minor allele frequency of 1.7%) was associated with both increased milk protein (0.019 [SE 0.006]; P < 0.01) and increased milk fat concentration (0.039 [SE 0.0132]; P < 0.01) whereas no associations (P > 0.05) were observed between CVM and any of the other milk traits (milk yield, milk fat yield, and milk protein yield) or fertility traits (calving interval, survival, calving difficulty, gestation length, calf mortality, and maternal calving difficulty). Significant associations were observed between BY (P < 0.01) and increased milk yield (73.21 kg [SE 30.12]; P < 0.05). No associations (P > 0.05) were observed between BY and any of the fertility traits considered. These results provide additional evidence that carriers of these recessive mutations exhibit effects on milk production and/or composition in Holstein Friesian cattle, however, with no evidence of effects on the fertility traits examined. Cognizance and monitoring of the potential pleiotrophic effects of lethal recessives such as examined in this study will aid livestock breeders when considering elimination of carriers to minimize reduction of the genetic merit of farm enterprises and inform the benefits of strategic matings in controlling these mutations in the population while also sustaining productivity. Copyright © 2017. American Society of Animal Science .

Signal transducer and activator of transcription (STAT) genes encode for a family of proteins that are involved in pre- and post-natal growth and development. In cattle, variants in these genes have been associated with economically important traits including milk production and embryonic survival. The objective of this study was to estimate the effects of polymorphisms in the STAT1, STAT3, and STAT5 genes on milk production, composition, and fertility traits in Holstein Friesian dairy cattle. STAT genotypes (n = 8) on 10,707 dairy cattle were obtained through the Irish Cattle Breeding Federation (ICBF). The phenotypes (n = 16) for milk production, milk composition, and fertility traits also were obtained from the ICBF and expressed as predicted transmitting abilities (PTAs). The association between each SNP and deregressed PTA was analyzed in ASREML using a weighted mixed animal model. The association analysis included n = 6,876 for milk yield and composition traits. The analysis for fertility traits included n = 1,193, 264, 4,566, 8,564, 152, and 2,380 cows for calving interval, survival, calving difficulty, gestation length, calf mortality, and maternal calving difficulty, respectively. In the analysis of the STAT variants with milk traits (milk protein concentration, milk fat concentration, milk yield, milk fat yield, milk protein yield), a significant association (P < 0.05) was observed between STAT3 (25042) and STAT5 variants (12195, 13244, 13319, 13516) and milk protein percentage. STAT3 variants (19069, 25042) were associated (P < 0.001) with milk fat percentage; additionally STAT5 variants (13244, 13516) were also found to be associated (P < 0.05) with this trait. The G allele of STAT3 (25042) was also associated with increased milk yield (17.01 kg, s.e. 6.708, P < 0.05). No associations were observed between STAT1 and the remaining polymorphisms analyzed in either STAT3 or STAT5 with the milk production and milk composition traits examined. Associations were observed between STAT3 (19069) and gestation length (0.11 days, s.e. 0.056, P < 0.05) and STAT5 (12195) with calf mortality (2.04, s.e. 1.017, P < 0.05). None of the six remaining polymorphisms considered in this study within the STAT genes were associated with any of the aforementioned fertility traits. These results support a multifaceted role of the STAT family in milk production, composition, and fertility which warrants further functional analysis and consideration for incorporation into genetic evaluation programs for maximizing the rate of genetic gain. Copyright © 2017. American Society of Animal Science .

Historically, an animal’s genetic disease carrier status was only determined after the observation of affected offspring. Once identified, the livestock producer typically had two choices 1) cull any ancestor of the affected progeny, or 2) risk producing another affected calf. As molecular tests for causative mutations became available carrier animals could be identified, but often only AI bulls or elite pedigree animals were tested due to the high cost of testing. Commercial producers tried to minimize their genetic disease risk by purchasing bulls assumed to be free of genetic diseases. Very few commercial producers, especially smaller enterprises, tested their own breeding stock. For national breeding programs the disease risk of using a known carrier sire was determined from the estimated allele frequency in the national herd and pedigree relatedness. Both of these variables contain a level of error due to low sampling rates and unvalidated parentage. To aid cattle genomics a low cost, custom bovine Illumina single nucleotide polymorphism (SNP) genotype panel (International Dairy & Beef panel; IDB) was developed which contains 50 validated probes for Mendelian diseases and undesirable traits. Currently, ∼500,000 Irish beef and dairy animals have been genotyped using the IDB, representing 25% of the total bovine breeding stock. An additional 30,000 Irish cattle have been genotyped on other commercial SNP chips. While traditionally more dairy than beef animals are genotyped nationwide, Ireland has ∼400,000 beef animals genotyped, representing ∼40% of the national beef herd. SNP imputation using FImpute is used to decrease genotyping errors and remove missing genotypes to provide a comprehensive genetic disease profile on all genotyped animals. This level of genotyping allows a more accurate estimation of the disease frequency in the national herd as allele frequencies between AI, pedigree, and commercial herds can and does vary. Informed breeding decisions, via farm reports, can be made available to maximize genetic gain while avoiding carrier by carrier matings of lethal or undesirable traits/diseases based on the animals true carrier status instead of its hypothetical risk. Additionally, all animals are processed for SNP based parentage validation and parentage prediction (for non-validated parents) using an 800 parentage SNP set, which contains the ISAG parentage SNP, developed to effectively remove the risk of A) validating a false parent, B) predicting > 1 parent, and C) predicting a false parent which would occur if using the ISAG parentage SNP panel alone. Copyright © 2016. American Society of Animal Science.

Bevacizumab improves progression free survival (PFS) and overall survival (OS) in metastatic colorectal cancer patients however currently there are no biomarkers that predict response to this treatment. The aim of this study was to assess if differential protein expression can differentiate patients who respond to chemotherapy and bevacizumab, and to assess if select proteins correlate with patient survival.

The Finnish Landrace (Finnsheep) is a well known high-prolificacy sheep breed and has been used in many countries as a source of genetic material to increase fecundity of local breeds. Analyses to date have indicated that mutations with a large effect on ovulation rate are not responsible for the exceptional prolificacy of Finnsheep. The objectives of this study were to ascertain if: 1) any of 12 known mutations with large effects on ovulation rate in sheep, or 2) any other DNA sequence variants within the candidate genes GDF9 and BMP15 are implicated in the high prolificacy of the Finnish Landrace breed; using material from lines developed by divergent selection on ovulation rate. Genotyping results showed that none of 12 known mutations (FecB^B, FecX^B, FecX^G, FecX^GR, FecX^H, FecX^I, FecX^L, FecX^O, FecX^R, FecG^E, FecG^H, or FecG^T) were present in a sample of 108 Finnsheep and, thus, do not contribute to the exceptional prolificacy of the breed. However, DNA sequence analysis of GDF9 identified a previously known mutation, V371M, whose frequency differed significantly (PFecB^B, FecG^E, FecX^O and FecX^GR, the number of mutations within the TGFβ superfamily with a positive effect on prolificacy in the homozygous state.