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PROVIDER: PRJEB31574 | ENA |
REPOSITORIES: ENA
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Project description:SNP discovery in South African indigenous cattle breeds
| PRJNA393612 | ENA
Project description:Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. We successfully detected the genome-wide CNVs of 318 individuals from 24 Chinese indigenous cattle breeds and 37 yaks as outgroups. A total of 5,818 autosomal CNV regions (683 bp - 4,477,860 bp in size), covering ~14.34% of the bovine genome (UMD3.1), were identified, showing abundant CNV resources. Neighbor-joining clustering, principal component analysis (PCA), and population admixture analysis based on these CNVs support that most Chinese cattle breeds are hybrids of Bos taurus taurus (hereinafter to be referred as Bos taurus) and Bos taurus indicus (Bos indicus). The distribution patterns of the CNVs could to some extent be related to the geographical backgrounds of the habitat of the breeds, and admixture among cattle breeds from different districts. We analyzed the selective signatures of CNVs positively involved in high-altitude adaptation using pairwise Fst analysis within breeds with a strong Bos taurus background (taurine-type breeds) and within Bos taurus×Bos indicus hybrids, respectively. CNV-overlapping genes with strong selection signatures (at top 0.5% of Fst value), including LETM1 (Fst = 0.490), TXNRD2 (Fst=0.440) and STUB1 (Fst=0.420) within taurine-type breeds, and NOXA1 (Fst = 0.233), RUVBL1 (Fst=0.222) and SLC4A3 (Fst=0.154) within hybrids, were potentially involved in the adaptation to hypoxia. Thus, we provide a new profile of population structure from the CNV aspects of Chinese indigenous cattle and new insights into high-altitude adaptation in cattle.
2020-02-21 | GSE142218 | GEO
Project description:Animal African trypanosomosis, caused by blood protozoan parasites transmitted mainly by tsetse flies, represents a major constraint for millions of cattle in sub-Saharan Africa. Exposed cattle include West African taurine breeds called trypanotolerant according to their ability to control parasite development and to survive and grow in enzootic areas, and indicine breeds that are trypanosusceptible to the disease. Until now the genetic basis of trypanotolerance remains unclear. Here, we improved knowledge in the biological processes involved in trypanotolerance by identifying bovine genes differentially expressed during an experimental infection by Trypanosoma congolense and their biological functions. To this end, whole blood genome-wide transcriptome profiling by RNA sequencing was performed on five West African cattle breeds, three trypanotolerant taurine breeds (N'Dama, Lagune and Baoulé), one susceptible zebu (Zebu Fulani) and one African taurine x zebu admixed breed (Borgou), at four dates, one before and three during infection. As expected, infection had a major impact on cattle blood transcriptome whatever the breed. The functional analysis of differentially expressed genes over time in each breed confirmed an early activation of the innate immune response, followed by an activation of the humoral response and an inhibition of T cells functions at the chronic stage of infection. More importantly, we highlighted overlooked features, as a strong disturbance in host metabolism and cell production energy that differentiate trypantolerant and trypanosusceptible breeds. N'Dama breed showed the earliest regulation of immune response, associated with a strong activation of cellular energy production, this last feature being also shared with Lagune, and to a lesser extent with Baoulé. Susceptible Zebu Fulani breed was distinguished from other breeds by the strongest modification in lipid metabolism regulation. Lastly, basal differences in gene expression reflected the structuration of cattle genetic diversity, and could have consequences on the tolerant or susceptible phenotype. Overall, it would be of value to deeper investigate interactions between immune response and cell metabolism that likely impact disease outcome.
2023-02-28 | GSE197108 | GEO
Project description:The aim of this study was to perform genome-wide marker discovery in three South African indigenous cattle breeds through whole genome sequencing of pooled DNA samples, with specific objectives to search for new variants, validate newly identified variants using 1000 Bull Genomes Project data, perform functional annotation and enrichment analysis on identified SNPs, identify selective sweeps and a panel of breed-specific markers to discriminate between breeds
2021-03-06 | PRJEB31574 | EVA
Project description:We present the RNA-seq based transcriptome profile of ventral soft palate tissue from two Indian indigenous breeds (Malnad Gidda and Hallikar; Bos indicus) of cattle and Holstein Friesian (HF) crossbred calves. Differentially expressed gene pattern showed stronger innate immune response in the indigenous calves. We find that induction of innate and cell mediated immune response is associated with early viral clearance and mild form of foot-and-mouth disease.
2021-12-06 | GSE167574 | GEO
Project description:Bovine tropical theileriosis is a major haemoprotozoan disease associated with high rates of morbidity and mortality particularly in exotic and crossbred cattle. It is one of the major constraints for of the livestock development programmes in India and southern Asia. Indigenous cattle (Bos indicus) are less affected by this disease than exotic and crossbred cattle. Genetic basis of resistance to tropical theileriosis in indigenous cattle is not well studied. Recent studies gives an idea that differentially genes expressed in exotic and indigenous breeds play an important role in breed specific resistance to tropical theileriosis. The present study was designed to visualize the global gene expression profiling in PBMCs derived from indigenous (Tharparkar) and crossbred cattle with in vitro infection of T. annulata. T. annulata Parbhani strain, originally isolated from Maharashtra (India) and maintained as cryopreserved stabilates of ground-up tick tissue sporozoite (GUTS) of infected H. anatolicum anatolicum was used as infective material. Two separate microarray experiments were carried out using separately each for crossbred and Tharparkar cattle. The crossbred cattle showed 1082 differentially expressed genes (DEGs). Out of total DEGs, 597 genes were downregulated and 485 were upregulated. Their fold change varies from 2283.93 to -4816.02. Tharparkar cattle showed 875 differentially expressed genes. Out of total DEGs in Tharparkar cattle, 451 genes were downregulated and 424 genes were upregulated. Their fold change varies from 94.93 to -19.20. A subset of genes was validated by quantitative RT-PCR and results correlated well with data obtained from the microarrays indicating that the microarray results gave an accurate report of transcript level. Functional annotation study of differentially expressed genes has confirmed their involvement in various pathways including response to oxidative stress, immune system regulation, cell proliferation, cytoskeletal changes, kinases activity and apoptosis. Gene network analysis of these differentially expressed genes provided an effective way to understand the interaction among them. It is therefore, hypothesised that the dissimilar susceptibility to tropical theileriosis exhibited by indigenous and crossbred cattle is due to breed-specific differences in the interaction of infected cells with other immune cells, which ultimately influences the immune response generated against T. annulata infection. Global gene expression profiling in PBMCs derived from indigenous (Tharparkar) and crossbred cattle were studied after in vitro infection of T. annulata Parbhani strain at 2h time period. Two separate microarray experiments were carried out using Bovine (V2) Gene Expression Microarray, 4x44K (Agilent). Two biological replicate samples were profiled per condition (i.e. replicates samples each in crossbred and Tharparkar cattle).
2016-07-01 | E-GEOD-81419 | biostudies-arrayexpress
Project description:Transcriptional profiling of lymph nodes of three cattle breeds (Bonsmara, Brahman, Holstein-Friesian) in response to the cattle tick (Rhipicephalus microplus) larvae and adult infestation. Emphasis is placed on firstly, comparing transcriptional responses within a cattle breed, before and after infestation, and secondly, comparing differentially expressed genes common between the breeds.
2021-03-31 | GSE147918 | GEO
Project description:Genome-wide variants discovery from 1082 indigenous African cattle samples using Bovine High-Density SNP Genotyping Array.
2024-05-03 | PRJEB74477 | EVA
Project description:Background: African animal trypanosomiasis (AAT) caused by tsetse fly-transmitted protozoa of the genus Trypanosoma is a major constraint on livestock and agricultural production in Africa and is among the top ten global cattle diseases impacting on the poor. Here we show that a functional genomics approach can be used to identify temporal changes in host peripheral blood mononuclear cell (PBMC) gene expression due to disease progression. We also show that major gene expression differences exist between cattle from trypanotolerant and trypanosusceptible breeds. Using bovine long oligonucleotide microarrays and real time quantitative reverse transcription PCR (qRT-PCR) validation we analysed PBMC gene expression in naïve trypanotolerant and trypanosusceptible cattle experimentally challenged with Trypanosoma congolense across a 34-day infection time course. Results: Trypanotolerant N’Dama cattle displayed a rapid and distinct transcriptional response to infection, with a ten-fold higher number of genes differentially expressed at day 14 post infection compared to trypanosusceptible Boran cattle. These analyses identified coordinated temporal gene expression changes for both breeds in responses to trypanosome infection. In addition, a panel of genes were identified that showed pronounced differences in gene expression between the two breeds, which may underlie the phenomena of trypanotolerance and trypanosusceptibility. Gene ontology (GO) analysis demonstrate that the products of these genes may contribute to increased mitochondrial mRNA translational efficiency, a more pronounced B cell response, an elevated activation status and a heightened response to stress in trypanotolerant cattle. Conclusions: This study has revealed an extensive and diverse range of cellular processes that are altered temporally in response to trypanosome infection in African cattle. Results indicate that the trypanotolerant N’Dama cattle respond more rapidly and with a greater magnitude to infection compared to the trypanosusceptible Boran cattle. Specifically, a subset of the genes analyzed by qRT-PCR, which display significant breed differences, could collectively contribute to the trypanotolerance trait in N’Dama.
2009-01-22 | GSE14451 | GEO