Population Structure, and Selection Signatures underlying High-Altitude Adaptation Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Cattle
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PROVIDER: PRJNA596234 | ENA |
REPOSITORIES: ENA
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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: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.
| S-EPMC7033542 | biostudies-literature
Project description:Single nucleotide polymorphism was widely used to perform genetic and evolution research in pigs. However, little is known about the effect of copy number variation (CNV) on characteristics in pigs. This study performed a genome-wide comparison of CNVs between Wannan black pigs (WBP) and Asian wild boars (AWB), using whole genome resequencing data. By using Manta, we detected in total 28,720 CNVs that covered approximately 1.98% of the pig genome length. We identified 288 selected CNVs (top 1%) by performing Fst statistics. Functional enrichment analyses for genes located in selected CNVs were found to be muscle related (NDN, TMOD4, SFRP1, and SMYD3), reproduction related (GJA1, CYP26B1, WNT5A, SRD5A2, PTPN11, SPEF2, and CCNB1), residual feed intake (RFI) related (MAP3K5), and ear size related (WIF1). This study provides essential information on selected CNVs in Wannan black pigs for further research on the genetic basis of the complex phenotypic and provides essential information for direction in the protection and utilization of Wannan black pig.
| S-EPMC9690591 | biostudies-literature
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.
| S-EPMC5962699 | biostudies-literature
Project description:The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data
2019-03-16 | GSE128372 | GEO
Project description:Investigation of how gene expression and epigenetics contribute to conservation of birth weight at high altitudes by examining mRNA and DNA methylation differences between placentas of indigenous Andeans and placentas of European descent residing at high and low altitude
2023-03-15 | GSE100988 | GEO
Project description:It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ?35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%), which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in further evolutionary and medical studies.
| S-EPMC3210162 | biostudies-literature
Project description:CNV plays an important role in the chicken genomic studies,it is imperative need to investigate the extent and pattern of CNVs using array comparative genomic hybridization (aCGH) in chinese chicken breeds for future studies associating phenotype to genome architecture. we describe systematic and genome-wide analysis of CNVs loci in five Chinese indigenous chicken breeds were evaluated by aCGH.
2014-10-10 | GSE49889 | GEO
Project description:Ethiopia indigenous chicken breeds are typically divided into low and high altitude chicken breeds. Firstly, representative city of low altitude such as Awash is an altitude of around 950 meters above sea level and have a climate which is humidity and high temperature with 37℃ between May and June. Secondly, representative city of high altitude such as Addis Ababa is the capital of Ethiopia in eastern Africa and this city is an altitude of over 2,400 meters above sea level and has a climate which is generally comparable with the average annual temperature of around 16℃. These chicken breeds are adapted to the environmental (climate, temperature and altitude) on the city. Moreover, in Awash, chicken breed is more adapted to heat resistance. So we generated RNA sequencing (RNA-seq) data of Ethiopia indigenous chicken breeds such as low altitude chicken breed (adapted heat) and high altitude chicken breed (Non-adapted heat) to compare the gene expression profiling induced by heat stress (HS). Therefore, we identified 13 hub differentially expressed genes (DEGs) using cuffdiff within cufflinks, which validated by real-time quantitative-PCR (qRT-PCR) in Kenya chicken breed for biological and technical validation. These hub DEGs were subjected to pathway enrichment, protein/protein interaction, and the partial correlation coefficient with information theory (PCIT) to determine their involvement in heat stress and immune response. Our findings suggest that not only hub DEGs but also many others DEGs may play a role in heat stress and immune response.
2018-09-13 | GSE119387 | GEO
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.
2014-12-30 | GSE47086 | GEO