Insights Into Long Non-Coding RNA and mRNA Expression in the Jejunum of Lambs Challenged With Escherichia coli F17

Chen, Wei-Hao; Lv, Xiaoyang; Zhang, Weibo; Hu, Tingyan; Cao, Xiukai; Ren, Ziming; Getachew, Tesfaye; Mwacharo, Joram M.; Haile, Aynalem; Sun, Wei

doi:10.3389/fvets.2022.819917

Cited by 5 publications

(5 citation statements)

References 74 publications

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“…Amongst the 35 protein-coding genes located in the first preserved region identified in the present study, is the LYPD8 gene, which has been suggested to play a role in intestinal immunity in mice (Hsu et al, 2021) and more recently in sheep (Chen et al, 2022). The HSPA4 gene, identified within the second most conserved region in the JER, is a heat shock protein (HSP) 70 gene and is well known for its integral role in cellular stress response to heat (Deb et al, 2014).…”

Section: Runs Of Homozygosity Detectedmentioning

confidence: 62%

Pedigree and genome-based patterns of homozygosity in the South African Ayrshire, Holstein, and Jersey breeds

Visser

Lashmar²,

Reding³

et al. 2023

Front. Genet.

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The erosion of genetic diversity limits long-term genetic gain and impedes the sustainability of livestock production. In the South African (SA) dairy industry, the major commercial dairy breeds have been applying estimated breeding values (EBVs) and/or have been participating in Multiple Across Country Evaluations (MACE). The transition to genomic estimated breeding values (GEBVs) in selection strategies requires monitoring of the genetic diversity and inbreeding of current genotyped animals, especially considering the comparatively small population sizes of global dairy breeds in SA. This study aimed to perform a homozygosity-based evaluation of the SA Ayrshire (AYR), Holstein (HST), and Jersey (JER) dairy cattle breeds. Three sources of information, namely 1) single nucleotide polymorphism (SNP) genotypes (3,199 animals genotyped for 35,572 SNPs) 2) pedigree records (7,885 AYR; 28,391 HST; 18,755 JER), and 3) identified runs of homozygosity (ROH) segments were used to quantify inbreeding related parameters. The lowest pedigree completeness was for the HST population reducing from a value of 0.990 to 0.186 for generation depths of one to six. Across all breeds, 46.7% of the detected ROH were between 4 megabase pairs (Mb) and 8 Mb in length. Two conserved homozygous haplotypes were identified in more than 70% of the JER population on Bos taurus autosome (BTA) 7. The JER breed displayed the highest level of inbreeding across all inbreeding coefficients. The mean (± standard deviation) pedigree-based inbreeding coefficient (FPED) ranged from 0.051 (±0.020) for AYR to 0.062 (±0.027) for JER, whereas SNP-based inbreeding coefficients (FSNP) ranged from 0.020 (HST) to 0.190 (JER) and ROH-based inbreeding coefficients, considering all ROH segment coverage (FROH), ranged from 0.053 (AYR) to 0.085 (JER). Within-breed Spearman correlations between pedigree-based and genome-based estimates ranged from weak (AYR: 0.132 between FPED and FROH calculated for ROH <4Mb in size) to moderate (HST: 0.584 between FPED and FSNP). Correlations strengthened between FPED and FROH as the ROH length category was considered lengthened, suggesting a dependency on breed-specific pedigree depth. The genomic homozygosity-based parameters studied proved useful in investigating the current inbreeding status of reference populations genotyped to implement genomic selection in the three most prominent South African dairy cattle breeds.

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Section: Runs Of Homozygosity Detectedmentioning

confidence: 62%

Pedigree and genome-based patterns of homozygosity in the South African Ayrshire, Holstein, and Jersey breeds

Visser

Lashmar²,

Reding³

et al. 2023

Front. Genet.

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“…The mRNA expression dataset used in this study was obtained from our previous research [ 18 ]; the raw data are available on: , PRJNA759095, accessed on 10 October 2022.…”

Section: Methodsmentioning

confidence: 99%

“…In our previous study, lambs with different E. coli F17 susceptibility ( E. coli F17-antagonism and -sensitive, AN and SE) were identified in a challenge experiment, and we analyzed the jejunal microbiota diversity [ 17 ] and transcriptomic profiles [ 18 ] using RNA-seq and 16s rRNA-seq approaches, respectively. The present study consists of two parts, first, the jejunal metabolite composition E. coli F17 AN and SE lambs were profiled using UHPLC-MS/MS approach.…”

Section: Introductionmentioning

confidence: 99%

Integration of the Microbiome, Metabolome and Transcriptome Reveals Escherichia coli F17 Susceptibility of Sheep

Chen

Cao

et al. 2023

Animals

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Escherichia coli (E. coli) F17 is one of the most common pathogens causing diarrhea in farm livestock. In the previous study, we accessed the transcriptomic and microbiomic profile of E. coli F17-antagonism (AN) and -sensitive (SE) lambs; however, the biological mechanism underlying E. coli F17 infection has not been fully elucidated. Therefore, the present study first analyzed the metabolite data obtained with UHPLC-MS/MS. A total of 1957 metabolites were profiled in the present study, and 11 differential metabolites were identified between E. coli F17 AN and SE lambs (i.e., FAHFAs and propionylcarnitine). Functional enrichment analyses showed that most of the identified metabolites were related to the lipid metabolism. Then, we presented a machine-learning approach (Random Forest) to integrate the microbiome, metabolome and transcriptome data, which identified subsets of potential biomarkers for E. coli F17 infection (i.e., GlcADG 18:0-18:2, ethylmalonic acid and FBLIM1); furthermore, the PCCs were calculated and the interaction network was constructed to gain insight into the crosstalk between the genes, metabolites and bacteria in E. coli F17 AN/SE lambs. By combing classic statistical approaches and a machine-learning approach, our results revealed subsets of metabolites, genes and bacteria that could be potentially developed as candidate biomarkers for E. coli F17 infection in lambs.

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“…Ten healthy lambs in the high-dose challenge group (antagonistic type) and ten low-dose-challenged lambs with diarrhoea (sensitive type) were selected, according to intestinal pathological sections and the amount of bacterial adherence in the intestinal contents. Six lambs were selected as case and control groups in the antagonistic and sensitive groups [18]. Two mL of venous blood was taken in EDTA-K2 anticoagulant tubes and stored at −80 • C. Samples were named as containing A for the antagonistic type and not containing A for the susceptible type.…”

Section: Sample Collectionmentioning

confidence: 99%

A Study of the Resistance of Hu Sheep Lambs to Escherichia coli F17 Based on Whole Genome Sequencing

Duan,

Su,

et al. 2024

Animals

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This study aims to analyze the whole genome sequencing of E. coli F17 in antagonistic and susceptible Hu sheep lambs. The objective is to investigate the critical mutation loci in sheep and understand the genetic mechanism of sheep resistance to E. coli F17 at the genome level. Antagonist and susceptible venous blood samples were collected from Hu sheep lambs for whole genome sequencing and whole genome association analysis. A total of 466 genes with significant SNPs (p < 1.0 × 10−3) were found. GO and KEGG enrichment analysis and protein interaction network analysis were performed on these genes, and preliminary investigations showed that SNPs on CTNNB1, CDH8, APOD, HCLS1, Tet2, MTSS1 and YAP1 genes may be associated with the antagonism and susceptibility of Hu sheep lambs to E. coli F17. There are still some shortcomings that have not been explored via in vivo and in vitro functional experiments of the candidate genes, which will be our next research work. This study provides genetic loci and candidate genes for resistance of Hu sheep lambs to E. coli F17 infection, and provides a genetic basis for breeding disease-resistant sheep.

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Insights Into Long Non-Coding RNA and mRNA Expression in the Jejunum of Lambs Challenged With Escherichia coli F17

Cited by 5 publications

References 74 publications

Pedigree and genome-based patterns of homozygosity in the South African Ayrshire, Holstein, and Jersey breeds

Pedigree and genome-based patterns of homozygosity in the South African Ayrshire, Holstein, and Jersey breeds

Integration of the Microbiome, Metabolome and Transcriptome Reveals Escherichia coli F17 Susceptibility of Sheep

A Study of the Resistance of Hu Sheep Lambs to Escherichia coli F17 Based on Whole Genome Sequencing

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