Applying multi-omics data to study the genetic background of bovine respiratory disease infection in feedlot crossbred cattle

Li, Jiyuan; Mukiibi, Robert; Jiminez, Janelle A.; Wang, Zhiquan; Akanno, E. C.; Timsit, Edouard; Plastow, Graham

doi:10.3389/fgene.2022.1046192

Cited by 8 publications

(15 citation statements)

References 72 publications

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“…Further, some of the differentially methylated genes ( TGM3, NRG1, RETN, IL1R2, ADGRE1, ALPL, KREMEN1, TRPC5, MN1, ALOX5AP, DYSF, ITGA9, NUPR1, SLC28A3, IGLON5, PTPN5, GLT1D1, DPYS, WIPI1, CFB, LOC511106, IL3RA ) also overlapped with previously identified differentially expressed genes in studies of BRD susceptibility of pre-weaned calves and feedlot cattle [43, 65]. Of these, NUPR1, CFB and ADGRE1 were also associated with identified trans-eQTLs [43].…”

Section: Discussionmentioning

confidence: 68%

“…Nevertheless, epigenetic changes may also play a role since a significant number of genes have been identified in this study as differentially methylated between healthy calves and those diagnosed with BRD. Although we have not generated RNA-Sequencing data from these calves to compare their blood transcriptomic profiles, when we compared our results with the results of previous transcriptomics, eQTL and genome-wide association (GWAS) studies many of the differentially methylated genes have been also identified and prioritised as good candidate genes for BRD resistance in these studies [43, 65]. Specifically, eight genes ( KPNA6, NEIL3, ADCK1, ZNF507, REEP3, AHSA1, SEPTIN11 and IgLON5) identified as differentially methylated were also identified within significant GWAS windows in the study of BRD susceptibility in pre-weaned Holstein calves [65].…”

Section: Discussionmentioning

confidence: 99%

“…Specifically, eight genes ( KPNA6, NEIL3, ADCK1, ZNF507, REEP3, AHSA1, SEPTIN11 and IgLON5) identified as differentially methylated were also identified within significant GWAS windows in the study of BRD susceptibility in pre-weaned Holstein calves [65]. Further, some of the differentially methylated genes ( TGM3, NRG1, RETN, IL1R2, ADGRE1, ALPL, KREMEN1, TRPC5, MN1, ALOX5AP, DYSF, ITGA9, NUPR1, SLC28A3, IGLON5, PTPN5, GLT1D1, DPYS, WIPI1, CFB, LOC511106, IL3RA ) also overlapped with previously identified differentially expressed genes in studies of BRD susceptibility of pre-weaned calves and feedlot cattle [43, 65]. Of these, NUPR1, CFB and ADGRE1 were also associated with identified trans-eQTLs [43].…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, it has been suggested that an epigenetic component may be involved since disease episodes early in a calf’s life has been reported to negatively impact lifetime performance and age at first calving [40, 41]. Therefore, studying the methylation profile of these calves may provide further data for future breeding programs designed to improve herd resistance [37, 38, 42, 43] as well as increase our understanding of the underlying mechanisms of disease susceptibility. This endeavour would be greatly advantageous in improving genetic resistance, welfare of animals and subsequently reducing resultant economic losses.…”

Section: Introductionmentioning

confidence: 99%

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Identification of methylation markers for age and Bovine Respiratory Disease in dairy cattle

Attree,

Griffiths,

Panchal

et al. 2023

Preprint

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Methylation profiles of animals is known to differ by age and disease status. Bovine respiratory disease (BRD), a complex infectious disease, primarily affects calves and has significant impact on animal welfare and the cattle industry, predominantly from production losses. BRD susceptibility is multifactorial, influenced by both environmental and genetic factors. We investigated the epigenetic profile of BRD susceptibility in calves and age-related methylation differences between healthy calves and adult dairy cows using Reduced Representation Bisulfite Sequencing (RRBS).We identified 3,452 genes within differentially methylated regions between calves and adults. Functional analysis revealed enrichment of developmental pathways including cell fate commitment and tissue morphogenesis. Between healthy and BRD affected calves, 964 genes were identified within differentially methylated regions. Immune and vasculature regulatory pathways were enriched and key candidates in BRD susceptibility involved in complement cascade regulation, vasoconstriction and respiratory cilia structure and function were identified.

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Section: Discussionmentioning

confidence: 68%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Identification of methylation markers for age and Bovine Respiratory Disease in dairy cattle

Attree,

Griffiths,

Panchal

et al. 2023

Preprint

View full text Add to dashboard Cite

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“…Our objective in this study was to identify differences in gene expression and associated host-driven biological systems that may be impacted by marketing decisions and how these influence eventual BRD morbidity after backgrounding arrival, in order to explore potential mechanisms of BRD development or resistance that may be leveraged in future studies. While both our research group and others have used the blood RNA-Seq methodology to identify potential predictive markers and mechanisms related to BRD [ 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 ], this study, to our knowledge, is one of the first to utilize said technologies to evaluate how marketing decisions, with relationship to BRD, influence inflammatory- and immune-mediated mechanisms in cattle. Importantly, exposure to an auction market setting and an order-buyer facility for only three days was associated with the differential expression of 2961 genes representing 113 biological processes.…”

Section: Discussionmentioning

confidence: 99%

Influence of the At-Arrival Host Transcriptome on Bovine Respiratory Disease Incidence during Backgrounding

Green

Woolums

Karisch

et al. 2023

Veterinary Sciences

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Bovine respiratory disease (BRD) remains the leading disease within the U.S. beef cattle industry. Marketing decisions made prior to backgrounding may shift BRD incidence into a different phase of production, and the importance of host gene expression on BRD incidence as it relates to marketing strategy is poorly understood. Our objective was to compare the influence of marketing on host transcriptomes measured on arrival at a backgrounding facility on the subsequent probability of being treated for BRD during a 45-day backgrounding phase. This study, through RNA-Seq analysis of blood samples collected on arrival, evaluated gene expression differences between cattle which experienced a commercial auction setting (AUCTION) versus cattle directly shipped to backgrounding from the cow–calf phase (DIRECT); further analyses were conducted to determine differentially expressed genes (DEGs) between cattle which remained clinically healthy during backgrounding (HEALTHY) versus those that required treatment for clinical BRD within 45 days of arrival (BRD). A profound difference in DEGs (n = 2961) was identified between AUCTION cattle compared to DIRECT cattle, regardless of BRD development; these DEGs encoded for proteins involved in antiviral defense (increased in AUCTION), cell growth regulation (decreased in AUCTION), and inflammatory mediation (decreased in AUCTION). Nine and four DEGs were identified between BRD and HEALTHY cohorts in the AUCTION and DIRECT groups, respectively; DEGs between disease cohorts in the AUCTION group encoded for proteins involved in collagen synthesis and platelet aggregation (increased in HEALTHY). Our work demonstrates the clear influence marketing has on host expression and identified genes and mechanisms which may predict BRD risk.

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Transcriptional response to an alternative diet on liver, muscle, and rumen of beef cattle

Fernandes,

Reverter,

Keogh

et al. 2024

Sci Rep

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Feed cost represents a major economic determinant within cattle production, amounting to an estimated 75% of the total variable costs. Consequently, comprehensive approaches such as optimizing feed utilization through alternative feed sources, alongside the selection of feed-efficient animals, are of great significance. Here, we investigate the effect of two diets, traditional corn-grain fed and alternative by-product based, on 14 phenotypes related to feed, methane emission and production efficiency and on multi-tissue transcriptomics data from liver, muscle, and rumen wall, derived from 52 Nellore bulls, 26 on each diet. To this end, diets were contrasted at the level of phenotype, gene expression, and gene-phenotype network connectivity. As regards the phenotypic level, at a P value < 0.05, significant differences were found in favour of the alternative diet for average daily weight gain at finishing, dry matter intake at finishing, methane emission, carcass yield and subcutaneous fat thickness at the rib-eye muscle area. In terms of the transcriptional level of the 14,776 genes expressed across the examined tissues, we found 487, 484, and 499 genes differentially expressed due to diet in liver, muscle, and rumen, respectively (P value < 0.01). To explore differentially connected phenotypes across both diet-based networks, we focused on the phenotypes with the largest change in average number of connections within diets and tissues, namely methane emission and carcass yield, highlighting, in particular, gene expression changes involving SREBF2, and revealing the largest differential connectivity in rumen and muscle, respectively. Similarly, from examination of differentially connected genes across diets, the top-ranked most differentially connected regulators within each tissue were MEOX1, PTTG1, and BASP1 in liver, muscle, and rumen, respectively. Changes in gene co-expression patterns suggest activation or suppression of specific biological processes and pathways in response to dietary interventions, consequently impacting the phenotype. The identification of genes that respond differently to diets and their associated phenotypic effects serves as a crucial stepping stone for further investigations, aiming to build upon our discoveries. Ultimately, such advancements hold the promise of improving animal welfare, productivity, and sustainability in livestock farming.

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Applying multi-omics data to study the genetic background of bovine respiratory disease infection in feedlot crossbred cattle

Cited by 8 publications

References 72 publications

Identification of methylation markers for age and Bovine Respiratory Disease in dairy cattle

Identification of methylation markers for age and Bovine Respiratory Disease in dairy cattle

Influence of the At-Arrival Host Transcriptome on Bovine Respiratory Disease Incidence during Backgrounding

Transcriptional response to an alternative diet on liver, muscle, and rumen of beef cattle

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