scholarly journals A locus conferring tolerance to Theileria infection in African cattle

2021 ◽  
Author(s):  
David Wragg ◽  
Elizabeth Anne Jessie Cook ◽  
Perle Latre de Late ◽  
Tatjana Sitt ◽  
Johanneke Dinie Hemmink ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Genetic Locus ◽  
Genomic Region ◽  
Chromosome 15 ◽  
Reference Allele ◽  
Cattle Disease ◽  
African Cattle ◽  
Cattle Diseases ◽  
Exposure Testing ◽  
Independent Cohort

East Coast fever, a tick-borne cattle disease caused by the Theileria parva parasite, is among the biggest natural killers of cattle in East Africa, leading to over 1 million deaths annually. Here we report on the genetic analysis of a cohort of Boran cattle demonstrating heritable tolerance to infection by T. parva (h2 = 0.65, s.e. 0.57). Through a linkage analysis we identify a 6 Mb genomic region on Bos taurus chromosome 15 that is significantly associated with survival outcome following T. parva exposure. Testing this locus in an independent cohort of animals replicates this association with survival following T. parva infection. A stop gained polymorphism in this region was found to be highly associated with survival across both related and unrelated animals, with only one of the 20 homozygote carriers (T/T) of this change succumbing to the disease in contrast to 44 out of 97 animals homozygote for the reference allele (C/C). Consequently, we present a genetic locus linked to tolerance of one of Africa's most important cattle diseases, raising the promise of marker-assisted selection for cattle that are less susceptible to infection by T. parva.

scholarly journals The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
N. Z. Gebrehiwot ◽  
E. M. Strucken ◽  
H. Aliloo ◽  
K. Marshall ◽  
J. P. Gibson
Keyword(s):  
Genetic Diversity ◽  
Bos Taurus ◽  
Large Population ◽  
Bos Indicus ◽  
Principal Component ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
African Cattle ◽  
Snp Data

Abstract Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

scholarly journals Genetic mapping of a cellular DNA region involved in induction of thymic lymphomas (Mlvi-1) to mouse chromosome 15.

1985 ◽  
Vol 5 (4) ◽  
pp. 894-897 ◽  
Author(s):  
C A Kozak ◽  
P G Strauss ◽  
P N Tsichlis
Keyword(s):  
Mouse Chromosome ◽  
Genetic Locus ◽  
Leukemia Virus ◽  
Moloney Murine Leukemia Virus ◽  
Chromosome 15 ◽  
Dna Integration ◽  
Common Domain ◽  
Cellular Oncogenes ◽  
Cellular Dna ◽  
Mouse Somatic Cell

Mlvi-1 defines a genetic locus representing a common domain for proviral DNA integration in Moloney murine leukemia virus-induced rat thymic lymphomas. Cellular sequences homologous to Mlvi-1 are present in mouse DNA, and we have used hamster-mouse somatic cell hybrids to chromosomally map Mlvi-1 in the mouse genome. Results demonstrated that Mlvi-1 maps to mouse chromosome 15 and that it is distinct from the Mlvi-2 integration region and from the cellular oncogenes c-myc and c-sis, which also map to this chromosome. Therefore, Mlvi-1 may contain novel sequences involved in the establishment and maintenance of virus-induced murine tumors, many of which contain abnormalities of chromosome 15.

scholarly journals Novel functional sequences uncovered through a bovine multiassembly graph

2021 ◽  
Vol 118 (20) ◽  
pp. e2101056118
Author(s):  
Danang Crysnanto ◽  
Alexander S. Leonard ◽  
Zih-Hua Fang ◽  
Hubert Pausch
Keyword(s):  
Genetic Diversity ◽  
Reference Genome ◽  
Bos Taurus ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Reference Allele ◽  
Genomic Analyses ◽  
Reference Quality ◽  
Reference Genomes

Many genomic analyses start by aligning sequencing reads to a linear reference genome. However, linear reference genomes are imperfect, lacking millions of bases of unknown relevance and are unable to reflect the genetic diversity of populations. This makes reference-guided methods susceptible to reference-allele bias. To overcome such limitations, we build a pangenome from six reference-quality assemblies from taurine and indicine cattle as well as yak. The pangenome contains an additional 70,329,827 bases compared to the Bos taurus reference genome. Our multiassembly approach reveals 30 and 10.1 million bases private to yak and indicine cattle, respectively, and between 3.3 and 4.4 million bases unique to each taurine assembly. Utilizing transcriptomes from 56 cattle, we show that these nonreference sequences encode transcripts that hitherto remained undetected from the B. taurus reference genome. We uncover genes, primarily encoding proteins contributing to immune response and pathogen-mediated immunomodulation, differentially expressed between Mycobacterium bovis–infected and noninfected cattle that are also undetectable in the B. taurus reference genome. Using whole-genome sequencing data of cattle from five breeds, we show that reads which were previously misaligned against the Bos taurus reference genome now align accurately to the pangenome sequences. This enables us to discover 83,250 polymorphic sites that segregate within and between breeds of cattle and capture genetic differentiation across breeds. Our work makes a so-far unused source of variation amenable to genetic investigations and provides methods and a framework for establishing and exploiting a more diverse reference genome.

scholarly journals Feature Selection and K-nearest Neighbor for Diagnosis Cow Disease

2021 ◽  
Vol 5 (02) ◽  
pp. 249-253
Author(s):  
Yeni Kustiyahningsih
Keyword(s):  
Feature Selection ◽  
Nearest Neighbor ◽  
Disease Classification ◽  
Training Data ◽  
Test Results ◽  
K Nearest Neighbor ◽  
Data Set ◽  
Cattle Disease ◽  
Cattle Diseases ◽  
Cattle Breeders

The large number of cattle population that exists can increase the potential for developing cow disease. Lack of knowledge about various kinds of cattle diseases and their handling solutions is one of the causes of decreasing cow productivity. The aim of this research is to classify cattle disease quickly and accurately to assist cattle breeders in accelerating detection and handling of cattle disease. This study uses K-Nearest Neighbour (KNN) classification method with the F-Score feature selection. The KNN method is used for disease classification based on the distance between training data and test data, while F-Score feature selection is used to reduce the attribute dimensions in order to obtain the relevant attributes. The data set used was data on cattle disease in Madura with a total of 350 data consisting of 21 features and 7 classes. Data were broken down using K-fold Cross Validation using k = 5. Based on the test results, the best accuracy was obtained with the number of features = 18 and KNN (k = 3) which resulted in an accuracy of 94.28571, a recall of 0.942857 and a precision of 0.942857.

scholarly journals Genome-wide local ancestry and direct evidence for mitonuclear co-adaptation in African hybrid cattle populations (Bos taurus/indicus)

2021 ◽  
Author(s):  
James A. Ward ◽  
Gillian P. McHugo ◽  
Michael J. Dover ◽  
Thomas J. Hall ◽  
Said Ismael Ng’ang’a ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Phenotypic Diversity ◽  
Bos Indicus ◽  
Snp Array ◽  
Human Migration ◽  
Nuclear Genes ◽  
Local Ancestry ◽  
African Cattle ◽  
Mitochondrial Haplotypes ◽  
Wide Range

AbstractDomestic cattle have a key economic role in African societies, providing an important source of mobile wealth through supply of meat, milk, cowhide, fuel, transport, and traction. The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which share a common ancestor 150-500 thousand years ago. Human migration and trade from Asia have left a peak of zebu nuclear ancestry in East Africa and most cattle populations across the continent have a hybrid genetic composition. Notwithstanding this, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu nuclear ancestry. In this regard, the efficient functioning of the mitochondrion relies on a network of biochemical interactions between the products of 37 mitochondrial genes and more than one thousand nuclear genes; therefore, admixed African cattle represent ideal populations for evaluating mitonuclear interactions and mismatch between the nuclear and mitochondrial genomes. Using high-density SNP array data from 18 different cattle populations, including ten African admixed breeds, we find strong evidence for mitonuclear coevolution in hybrid African cattle with significant retention of Bos taurus alleles at mitochondrially-targeted nuclear genes, particularly those genes with products that directly interact with mtDNA-encoded protein subunits in OXPHOS and ribosomal complexes, or that have functions in mtDNA replication. We also show that subspecific local ancestry varies substantially across the genomes of admixed populations, with a marked signal of taurine ancestry at the major histocompatibility (MHC) gene cluster, which likely reflects adaptation to infectious disease challenges facing African livestock. Our results demonstrate that African admixed cattle represent an excellent comparative model for studying the phenotypic consequences of mitonuclear mismatch and genomic introgression in humans and other large mammals.

scholarly journals Possible Phenotypic Consequences of Structural Differences in Idic(15) in a Small Cohort of Patients

2019 ◽  
Vol 20 (19) ◽  
pp. 4935
Author(s):  
Márta Czakó ◽  
Ágnes Till ◽  
András Szabó ◽  
Réka Ripszám ◽  
Béla Melegh ◽  
...  
Keyword(s):  
Copy Number ◽  
Clinical Symptoms ◽  
Copy Number Gain ◽  
Genomic Region ◽  
Comparative Genomic ◽  
Chromosome 15 ◽  
Factors Influencing ◽  
15Q Duplication ◽  
Segmental Aneuploidy ◽  
Structural Differences

Among human supernumerary marker chromosomes, the occurrence of isodicentric form of 15 origin is relatively well known due to its high frequency, both in terms of gene content and associated clinical symptoms. The associated epilepsy and autism are typically more severe than in cases with interstitial 15q duplication, despite copy number gain of approximately the same genomic region. Other mechanisms besides segmental aneuploidy and epigenetic changes may also cause this difference. Among the factors influencing the expression of members of the GABAA gene cluster, the imprinting effect and copy number differences has been debated. Limited numbers of studies investigate factors influencing the interaction of GABAA cluster homologues. Five isodicentric (15) patients are reported with heterogeneous symptoms, and structural differences of their isodicentric chromosomes based on array comparative genomic hybridization results. Relations between the structure and the heterogeneous clinical picture are discussed, raising the possibility that the structure of the isodicentric (15), which has an asymmetric breakpoint and consequently a lower copy number segment, would be the basis of the imbalance of the GABAA homologues. Studies of trans interaction and regulation of GABAA cluster homologues are needed to resolve this issue, considering copy number differences within the isodicentric chromosome 15.

scholarly journals Genetic Variation at the O-Antigen Biosynthetic Locus in Pseudomonas aeruginosa

2002 ◽  
Vol 184 (13) ◽  
pp. 3614-3622 ◽  
Author(s):  
Christopher K. Raymond ◽  
Elizabeth H. Sims ◽  
Arnold Kas ◽  
David H. Spencer ◽  
Tanya V. Kutyavin ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genetic Variation ◽  
Dna Sequencing ◽  
Genetic Locus ◽  
Gene Clusters ◽  
Genomic Region ◽  
Functional Gene ◽  
Specific Site ◽  
O Antigen ◽  
Divergent Gene

ABSTRACT The outer carbohydrate layer, or O antigen, of Pseudomonas aeruginosa varies markedly in different isolates of these bacteria, and at least 20 distinct O-antigen serotypes have been described. Previous studies have indicated that the major enzymes responsible for O-antigen synthesis are encoded in a cluster of genes that occupy a common genetic locus. We used targeted yeast recombinational cloning to isolate this locus from the 20 internationally recognized serotype strains. DNA sequencing of these isolated segments revealed that at least 11 highly divergent gene clusters occupy this region. Homology searches of the encoded protein products indicated that these gene clusters are likely to direct O-antigen biosynthesis. The O15 serotype strains lack functional gene clusters in the region analyzed, suggesting that O-antigen biosynthesis genes for this serotype are harbored in a different portion of the genome. The overall pattern underscores the plasticity of the P. aeruginosa genome, in which a specific site in a well-conserved genomic region can be occupied by any of numerous islands of functionally related DNA with diverse sequences.

scholarly journals Microsatellite DNA Variation and the Evolution, Domestication and Phylogeography of Taurine and Zebu Cattle (Bos taurus and Bos indicus)

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 1071-1086 ◽  
Author(s):  
David E MacHugh ◽  
Mark D Shriver ◽  
Ronan T Loftus ◽  
Patrick Cunningham ◽  
Daniel G Bradley
Keyword(s):  
Bos Taurus ◽  
Bos Indicus ◽  
Phylogenetic Reconstruction ◽  
Divergence Time ◽  
Strong Support ◽  
Zebu Cattle ◽  
Genetic Introgression ◽  
African Cattle ◽  
African Populations ◽  
Taurine Cattle

Genetic variation at 20 microsatellite loci was surveyed to determine the evolutionary relationships and molecular biogeography of 20 different cattle populations from Africa, Europe and Asia. Phylogenetic reconstruction and multivariate analysis highlighted a marked distinction between humpless (taurine) and humped (zebu) cattle, providing strong support for a separate origin for domesticated zebu cattle. A molecular clock calculation using bison (Bison sp.) as an outgroup gave an estimated divergence time between the two subspecies of 610,000-850,000 years. Substantial differences in the distribution of alleles at 10 of these loci were observed between zebu and taurine cattle. These markers subsequently proved very useful for investigations of gene flow and admixture in African populations. When these data were considered in conjunction with previous mitochondrial and Y chromosomal studies, a distinctive male-mediated pattern of zebu genetic introgression was revealed. The introgression of zebu-specific alleles in African cattle afforded a high resolution perspective on the hybrid nature of African cattle populations and also suggested that certain West African populations of valuable disease-tolerant taurine cattle are under threat of genetic absorption by migrating zebu herds.

Sign in / Sign up

Export Citation Format

Share Document