Dataset Information

Effects of Land Transport Stress on Variations in Ruminal Microbe Diversity and Immune Functions in Different Breeds of Cattle.

ABSTRACT: The intensity and specialization of beef cattle production make off-site fattening, and introduce new breeds need transportation to achieve the goals. The present study was aimed to investigate effects of land transport stress on hormones levels, microbial fermentation, microbial composition, immunity and correlation among them among Simmental Crossbred Cattle (SC), Native Yellow Cattle (NY), and Cattle Yak (CY). High-throughput sequencing was used to investigate the rumen microbial diversity. After transport stress cortisol (COR), adrenocorticotropic hormone (ACTH) and pro-inflammatory cytokines IL-6, TNF-?, and IL-1? were increased (p < 0.05) in all groups. Rumen lipopolysaccharide (LPS) was increased (p < 0.05) in SC and CY groups. Total volatile fatty acids were increased (p < 0.05) in all groups. The ruminal microbiota about OTUs, Chao1, and Shannon in SC and CY groups were higher than before transport. Prevotella1 in NY group was higher (p < 0.05) than other groups before transport; after transport Firmicutes and Lactobacillus were increased (p < 0.05) than other groups in CY. Lactobacillus was positively correlated with IL-6 and IL-4. Under transport stress, cattle may suffer from inflammatory response through modulating HPA axis and microbiota metabolite affects the secretion of hormone levels and immune function and breeds factor affect the performance of stress resistance.

SUBMITTER: Li F

PROVIDER: S-EPMC6770003 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Effects of Land Transport Stress on Variations in Ruminal Microbe Diversity and Immune Functions in Different Breeds of Cattle.

Li Fengpeng F Shah Ali Mujtaba AM Wang Zhisheng Z Peng Quanhui Q Hu Rui R Zou Huawei H Tan Cui C Zhang Xiangfei X Liao Yupeng Y Wang Yongjie Y Wang Xueying X Zeng Lei L Xue Bai B Wang Lizhi L

Animals : an open access journal from MDPI 20190823 9

The intensity and specialization of beef cattle production make off-site fattening, and introduce new breeds need transportation to achieve the goals. The present study was aimed to investigate effects of land transport stress on hormones levels, microbial fermentation, microbial composition, immunity and correlation among them among Simmental Crossbred Cattle (SC), Native Yellow Cattle (NY), and Cattle Yak (CY). High-throughput sequencing was used to investigate the rumen microbial diversity. A ...[more]

PMID: 31450840

Similar Datasets

Project description:Copy number variations (CNVs) comprise deletions, duplications, and insertions found within the genome larger than 50 bp in size. CNVs are thought to be primary role-players in breed formation and adaptation. South Africa boasts a diverse ecology with harsh environmental conditions and a broad spectrum of parasites and diseases that pose challenges to livestock production. This has led to the development of composite cattle breeds which combine the hardiness of Sanga breeds and the production potential of the Taurine breeds. The prevalence of CNVs within these respective breeds of cattle and the prevalence of CNV regions (CNVRs) in their diversity, adaptation and production is however not understood. This study therefore aimed to ascertain the prevalence, diversity, and correlations of CNVRs within cattle breeds used in South Africa. Illumina Bovine SNP50 data and PennCNV were utilized to identify CNVRs within the genome of 287 animals from seven cattle breeds representing Sanga, Taurine, Composite, and cross breeds. Three hundred and fifty six CNVRs of between 36 kb to 4.1 Mb in size were identified. The null hypothesis that one CNVR loci is independent of another was tested using the GENEPOP software. One hunded and two and seven of the CNVRs in the Taurine and Sanga/Composite cattle breeds demonstrated a significant (p ? 0.05) association. PANTHER overrepresentation analyses of correlated CNVRs demonstrated significant enrichment of a number of biological processes, molecular functions, cellular components, and protein classes. CNVR genetic variation between and within breed group was measured using phiPT which allows intra-individual variation to be suppressed and hence proved suitable for measuring binary CNVR presence/absence data. Estimate PhiPT within and between breed variance was 2.722 and 0.518 respectively. Pairwise population PhiPT values corresponded with breed type, with Taurine Holstein and Angus breeds demonstrating no between breed CNVR variation. Phylogenetic trees were drawn. CNVRs primarily clustered animals of the same breed type together. This study successfully identified, characterized, and analyzed 356 CNVRs within seven cattle breeds. CNVR correlations were evident, with many more correlations being present among the exotic Taurine breeds. CNVR genetic diversity of Sanga, Taurine and Composite breeds was ascertained with breed types exposed to similar selection pressures demonstrating analogous incidences of CNVRs.

Project description:BACKGROUND:Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked reduction in population size of several native cattle breeds worldwide. Therefore, conservation management of native cattle breeds requires urgent attention to avoid their extinction. To this end, we genotyped nine Swedish native cattle breeds with genome-wide 150 K single nucleotide polymorphisms (SNPs) to investigate the level of genetic diversity and relatedness between these breeds. RESULTS:We used various SNP-based approaches on this dataset to connect the demographic history with the genetic diversity and population structure of these Swedish cattle breeds. Our results suggest that the Väne and Ringamåla breeds originating from southern Sweden have experienced population isolation and have a low genetic diversity, whereas the Fjäll breed has a large founder population and a relatively high genetic diversity. Based on the shared ancestry and the constructed phylogenetic trees, we identified two major clusters in Swedish native cattle. In the first cluster, which includes Swedish mountain cattle breeds, there was little differentiation among the Fjäll, Fjällnära, Swedish Polled, and Bohus Polled breeds. The second cluster consists of breeds from southern Sweden: Väne, Ringamåla and Swedish Red. Interestingly, we also identified sub-structuring in the Fjällnära breed, which indicates different breeding practices on the farms that maintain this breed. CONCLUSIONS:This study represents the first comprehensive genome-wide analysis of the genetic relatedness and diversity in Swedish native cattle breeds. Our results show that different demographic patterns such as genetic isolation and cross-breeding have shaped the genomic diversity of Swedish native cattle breeds and that the Swedish mountain breeds have retained their authentic distinct gene pool without significant contribution from any of the other European cattle breeds that were included in this study.

Project description:Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 mega bases or ~1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions such as immunity, lactation, reproduction and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research. The custom aCGH chips that interrogated the whole genome CNVs were build for 90 cattles from diverse breeds, with Hereford L1 Dominette 01449 as refference sample.

Project description:BackgroundThe genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds.ResultsAdmixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% Bos taurus admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% Bos indicus ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, F statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of Bos taurus breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the Bos indicus breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between Bos taurus dairy breeds. Effective population sizes (Ne) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high FROH coefficients and low FIS values point towards small population sizes. Nonetheless, the Ne of the Indian indigenous breeds is currently still larger than that of Bos taurus dairy breeds.ConclusionsThe changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large Ne since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle.

Project description:Our previous research revealed the advantages of separate feeding (SF) systems compared to total mixed ration (TMR) in terms of ruminal methane (CH4) production. The purpose of this experiment was to confirm the advantage of SF as a nutritional strategy for CH4 mitigation, and to determine the effects of different feeding systems (TMR and SF) on the rumen microbiome and associated metagenome of two different breeds and on CH4 emissions. We randomly allocated four Holstein (305 ± 29 kg) and four Hanwoo steers (292 ± 24 kg) to two groups; the steers were fed a commercial concentrate with tall fescue (75:25) as TMR or SF, in a crossover design (two successive 22-day periods). Neither feeding systems nor cattle breeds had an effect on the total tract digestibility of nutrients. The TMR feeding system and Hanwoo steers generated significantly more CH4 (P < 0.05) and had a higher yield [g/d and g/kg dry matter intake (DMI)] compared to the SF system and Holstein steers. A larger rumen acetate:propionate ratio was observed for the TMR than the SF diet (P < 0.05), and for Hanwoo than Holstein steers (P < 0.001), clearly reflecting a shift in the ruminal H2 sink toward CH4 production. The linear discriminant analysis (LDA) effect size (LEfSe) revealed a greater abundance (α < 0.05 and LDA > 2.0) of operational taxonomic units (OTUs) related to methanogenesis for Hanwoo steers compared to Holstein steers. Kendall's correlation analysis revealed wide variation of microbial co-occurrence patterns between feeding systems, indicating differential H2 thermodynamics in the rumen. A metagenome analysis of rumen microbes revealed the presence of 430 differentially expressed genes, among which 17 and 27 genes exhibited positive and negative associations with CH4 production, respectively (P < 0.001). A strong interaction between feeding system and breed was observed for microbial and metagenomic abundance. Overall, these results suggest that the TMR feeding system produces more CH4, and that Hanwoo cattle are higher CH4 emitters than SF diet and Holstein cattle, respectively. Interestingly, host-associated microbial interactions differed within each breed depending on the feeding system, which indicated that breed-specific feeding systems should be taken into account for farm management.

Dataset Information

Effects of Land Transport Stress on Variations in Ruminal Microbe Diversity and Immune Functions in Different Breeds of Cattle.

Publications

Effects of Land Transport Stress on Variations in Ruminal Microbe Diversity and Immune Functions in Different Breeds of Cattle.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure