Project description:Here we describe a genome-wide analysis of copy number variations (CNVs) in Chinese domestic cattle by using array comparative genomic hybridization (array CGH) and quantitative PCR (qPCR). We conducted array CGH analysis on 30 male cattle individuals, animals from consisting of 12 breeds of Bos taurus/Bos indicus, 1 Bos grunniens and and two ones of Bubalus bubalis breeds for with beef, and/or dairy or dual purpose. We identified over 470 candidate CNV regions (CNVRs) in Bos B. taurus/B. indicus; 118 candidate CNV regions (CNVRs) in B. grunniens, 139 CNVRs in B. bubalis. Furthermore, based on the Y haplotypes of B. taurus/ B. indicus, Wwe also identified 69, 337, and 251 candidate CNV regions (CNVRs) in the sub-groups of Y1, Y2 and Y3 haplotypes.
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.
Project description:This SuperSeries is composed of the following subset Series: GSE13852: Expression profiling of Bos taurus lymph nodes upon infection with Ovine Herpesvirus 2 GSE13853: Expression profiling of Ovine Herpesvirus 2-infected lymph nodes from Bos taurus Refer to individual Series
Project description:This experiment was undertaken to document changes in gene expression in the skin of tick-resistant Brahman (Bos indicus) and tick-susceptible Holstein-Friesian (Bos taurus) cattle prior to, and following, infestation with the cattle tick Rhipicephalus (Boophilus) microplus Keywords: Disease state analysis
Project description:The Gayal (Bos frontalis) is a rare semi-domesticated cattle in China. Gayal has typical beef body shape and good meat production performance. Compared with other cattle species, it has the characteristics of tender meat and extremely low fat content. To explore the underlying mechanism responsible for the differences of meat quality between different breeds, the longissimus dorsi muscle (LM) from Gayal and Banna cattle (Bos taurus) were investigated using transcriptome analysis. The gene expression profiling identified 638 differentially expressed genes (DEGs) between LM muscles from Gayal and Banna cattle. Gene Ontology (GO) enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the gene products were mainly involved in the PPAR signaling pathway, lipid metabolism and amino acid metabolism pathway. Protein-protein interaction（PPI） network analysis showed APOB, CYP7A1, THBS2, ITGAV, IGFBP1 and IGF2R may have great impact on meat quality characteristics of Gayal. Moreover, three transcription factors, FOXA2, NEUROG2, and RUNX1, which may affect meat quality by regulating the expression of genes related to muscle growth and development have also been found. In summary, our research reveals the molecular mechanisms that cause Gayal meat quality characteristics. It will contribute to improving meat quality of cattle through molecular breeding.
Project description:Transciprional profiling of horn forming region of Bos taurus comparing horned, polled and scurred cattle. 3 condition experiment, Polled vs Horned, Polled vs Scurred, Scurred vs Horned, male and female samples, including dye swaps. 5 chips. No confounding between sex and chip. No confounding between indivdual and chip.
Project description:Cattle-yak, as the hybrid offspring of cattle (Bos taurus) and yak (Bos grunniens), demonstrates obvious heterosis in production performance. In this stuTMT technology and bioinformatics methods were used to screen differential protein of three cattle-yaks and yaks each in longissimus dorsi，
