Insights and applications from sequencing the bovine genome

2008 ◽  
Vol 20 (1) ◽  
pp. 54 ◽  
Author(s):  
David L. Adelson
Keyword(s):  
Genome Sequence ◽  
Association Studies ◽  
Bovine Genome ◽  
Genetic Selection ◽  
Genetic Association Studies ◽  
Physiological Data ◽  
Economic Traits ◽  
Bovine Genome Sequence ◽  
Breeding Schemes ◽  
And Function

Humans have sought to improve/tailor cattle since their domestication a few thousand years ago. Up until the last 40–50 years, consistent genetic improvement of cattle was a hit or miss proposition. Recent progress has been more rapid, thanks to applications of quantitative genetics to breeding schemes. With the availability of the bovine genome sequence, genetic selection and on-farm management are likely to be revolutionised yet again. Genetic association studies that were previously impossible to carry out due to a lack of markers are now possible. In addition to improved genetic mapping of economic traits, the bovine genome sequence allows us to create a common context for genetic and physiological data, which will provide novel insights into gene regulation and function.

Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence

2008 ◽  
Vol 39 (2) ◽  
pp. 97-104 ◽  
Author(s):  
H. Nilsen ◽  
B. Hayes ◽  
P. R. Berg ◽  
A. Roseth ◽  
K. K. Sundsaasen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Bovine Genome ◽  
Bovine Chromosome ◽  
Chromosome 6 ◽  
Bovine Genome Sequence ◽  
Snp Map

scholarly journals Evaluation of the accuracy of imputed sequence variants and their utility for causal variant detection in cattle

2016 ◽  
Author(s):  
Hubert Pausch ◽  
Iona M MacLeod ◽  
Ruedi Fries ◽  
Reiner Emmerling ◽  
Phil J Bowman ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Milk Fat ◽  
Association Studies ◽  
Bovine Genome ◽  
Reference Population ◽  
Whole Genome Sequence ◽  
Sequence Variants ◽  
Whole Genome ◽  
Segmental Duplications ◽  
Fat Percentage

AbstractBackgroundThe availability of dense genotypes and whole-genome sequence variants from various sources offers the opportunity to compile large data sets consisting of tens of thousands of individuals with genotypes at millions of polymorphic sites that may enhance the power of genomic analyses. The imputation of missing genotypes ensures that all individuals have genotypes for a shared set of variants.ResultsWe evaluated the accuracy of imputation from dense genotypes to whole-genome sequence variants in 249 Fleckvieh and 450 Holstein cattle using Minimac and FImpute. The sequence variants of a subset of the animals were reduced to the variants that were included in the Illumina BovineHD genotyping array and subsequently inferred in silico using either within-or multi-breed reference populations. The accuracy of imputation varied considerably across chromosomes and dropped at regions where the bovine genome contains segmental duplications. Depending on the imputation strategy, the correlation between imputed and true genotypes ranged from 0.898 to 0.952. The accuracy of imputation was higher with Minimac than FImpute particularly for variants with low MAF. Considering a multi-breed reference population increased the accuracy of imputation, particularly when FImpute was used to infer genotypes. When the sequence variants were imputed using Minimac, the true genotypes were more correlated to predicted allele dosages than best-guess genotypes. The computing costs to impute 23,256,743 sequence variants in 6958 animals were ten-fold higher with Minimac than FImpute. Association studies with imputed sequence variants revealed seven quantitative trait loci (QTL) for milk fat percentage. Two causal mutations in the DGAT1 and GHR genes were the most significantly associated variants at two QTL on chromosomes 14 and 20 when Minimac was used to infer genotypes.ConclusionsThe population-based imputation of millions of sequence variants in large cohorts is computationally feasible and provides accurate genotypes. However, the accuracy of imputation is low at regions where the genome contains large segmental duplications or the coverage with array-derived SNPs is poor. Using a reference population that includes individuals from many breeds increases the accuracy of imputation particularly at low-frequency variants. Considering allele dosages rather than best-guess genotypes as explanatory variables is advantageous to detect causal mutations in association studies with imputed sequence variants.

Capturing benefits from the bovine genome sequence

2007 ◽  
Vol 47 (9) ◽  
pp. 1039 ◽  
Author(s):  
Ross L. Tellam
Keyword(s):  
Genome Sequence ◽  
Production Systems ◽  
Bovine Genome ◽  
Value Added ◽  
Nucleotide Polymorphisms ◽  
Pedigree Data ◽  
Breeding Programs ◽  
Efficient Management ◽  
Bovine Genome Sequence ◽  
Large Numbers

The bovine genome sequence in ‘draft’ form will be complete in 2007. The availability of the sequence and very large numbers of single nucleotide polymorphisms will have profound effects on livestock production. The dairy industry is well positioned to capture the benefits of this enormous and enabling resource because of its comprehensive databases containing phenotypic and pedigree data for large numbers of animals, intense utilisation of genetics in breeding programs and efficient management of reproductive performance. The bovine genome sequence will assist in the development of novel products, especially value-added products, and markedly enhance the rate of genetic gain in the Australian dairy population. The immediate challenge facing the industry is the integration of new technological capabilities into existing breeding programs and production systems.

scholarly journals Genetic Diversity of Toll-Like Receptors and Immunity toM. lepraeInfection

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Bryan E. Hart ◽  
Richard I. Tapping
Keyword(s):  
Association Studies ◽  
Genetic Association Studies ◽  
Adaptive Immune System ◽  
Mycobacterial Infection ◽  
Innate Immune ◽  
Genetic Associations ◽  
Toll Like Receptors ◽  
Adaptive Immune ◽  
Polymorphic Variants ◽  
And Function

Genetic association studies of leprosy cohorts across the world have identified numerous polymorphisms which alter susceptibility and outcome to infection withMycobacterium leprae. As expected, many of the polymorphisms reside within genes that encode components of the innate and adaptive immune system. Despite the preponderance of these studies, our understanding of the mechanisms that underlie these genetic associations remains sparse. Toll-like receptors (TLRs) have emerged as an essential family of innate immune pattern recognition receptors which play a pivotal role in host defense against microbes, including pathogenic strains of mycobacteria. This paper will highlight studies which have uncovered the association of specific TLR gene polymorphisms with leprosy or tuberculosis: two important diseases resulting from mycobacterial infection. This analysis will focus on the potential influence these polymorphic variants have on TLR expression and function and how altered TLR recognition or signaling may contribute to successful antimycobacterial immunity.

scholarly journals Monogenic forms of DSD: An update

2021 ◽  
Author(s):  
Kenneth McElreavey ◽  
Anu Bashamboo
Keyword(s):  
Genetic Factors ◽  
Association Studies ◽  
Genetic Diagnosis ◽  
Genetic Association Studies ◽  
Genetic Modifiers ◽  
Genomic Variants ◽  
Sequencing Technologies ◽  
Wide Range ◽  
And Function ◽  
Reproductive Phenotype

DSD encompasses a wide range of pathologies that impact gonad formation, development and function in both 46,XX and 46,XY individuals. The majority of these conditions are considered to be monogenic, although the expression of the phenotype may be influenced by genetic modifiers. Although considered monogenic, establishing the genetic etiology in DSD has been difficult compared to other congenital disorders for a number of reasons including the absence of family cases for classical genetic association studies and the lack of evolutionary conservation of key genetic factors involved in gonad formation. In recent years, the widespread use of genomic sequencing technologies has resulted in multiple genes being identified and proposed as novel monogenic causes of 46,XX and/or 46,XY DSD. In this review, we will focus on the main genomic findings of recent years, which consists of new candidate genes or loci for DSD as well as new reproductive phenotypes associated with genes that are well established to cause DSD. For each gene or loci, we summarise the data that is currently available in favor of or against a role for these genes in DSD or the contribution of genomic variants within well-established genes to a new reproductive phenotype. Based on this analysis we propose a series of recommendations that should aid the interpretation of genomic data and ultimately help to improve the accuracy and yield genetic diagnosis of DSD.

scholarly journals High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly

BMC Genomics ◽  
2007 ◽  
Vol 8 (1) ◽  
pp. 310 ◽  
Author(s):  
Aparna Prasad ◽  
Thomas Schiex ◽  
Stephanie McKay ◽  
Brenda Murdoch ◽  
Zhiquan Wang ◽  
...  
Keyword(s):  
High Resolution ◽  
Genome Sequence ◽  
Radiation Hybrid ◽  
Bovine Genome ◽  
Sequence Assembly ◽  
Genome Sequence Assembly ◽  
Bovine Genome Sequence

Harnessing the bovine genome sequence for the Australian cattle and sheep industries

2005 ◽  
Vol 45 (8) ◽  
pp. 1011 ◽  
Author(s):  
B. P. Dalrymple
Keyword(s):  
Genome Sequence ◽  
Bovine Genome ◽  
Expression Data ◽  
Protein Coding ◽  
Bovine Genome Sequence ◽  
Number Of Genes ◽  
Mammalian Genomes ◽  
Non Coding Rnas ◽  
Human And Mouse ◽  
Cattle And Sheep

Genomics is an emerging science and the release of the human and mouse genomes has significantly altered our picture of the information content of mammalian genomes. A smaller number of protein coding genes, and a larger number of genes that do not appear to encode protein products, the so-called non-coding RNAs (ncRNAs), have been identified. The first 2 drafts of the bovine genome sequence have been released, and work to utilise the framework of the bovine genome to facilitate ovine genomics is underway. In anticipation of the requirement for a detailed analysis of the ruminant genomes, their transcriptomes, interactomes, regulomes and similar, we have been developing the informatics platform for the analysis and integration of genome sequences and expression data for cattle and sheep. This resource will enable us to utilise the ruminant datasets and integrate them with equivalent data from other mammals for the advancement of animal scientific research for applications in the cattle and sheep industries in Australia.

Abnormal Behavior and Cortical Connectivity Deficits in Mice Lacking Usp9x

2020 ◽  
Author(s):  
Maria A Kasherman ◽  
Laura Currey ◽  
Nyoman D Kurniawan ◽  
Oressia Zalucki ◽  
Michelle Sanchez Vega ◽  
...  
Keyword(s):  
Neurodevelopmental Disorders ◽  
Diffusion Tensor ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Brain Regions ◽  
Autism Spectrum ◽  
Abnormal Behavior ◽  
Loss Of Function ◽  
The Stability ◽  
And Function

Abstract Genetic association studies have identified many factors associated with neurodevelopmental disorders such as autism spectrum disorder (ASD). However, the way these genes shape neuroanatomical structure and connectivity is poorly understood. Recent research has focused on proteins that act as points of convergence for multiple factors, as these may provide greater insight into understanding the biology of neurodevelopmental disorders. USP9X, a deubiquitylating enzyme that regulates the stability of many ASD-related proteins, is one such point of convergence. Loss of function variants in human USP9X lead to brain malformations, which manifest as a neurodevelopmental syndrome that frequently includes ASD, but the underlying structural and connectomic abnormalities giving rise to patient symptoms is unknown. Here, we analyzed forebrain-specific Usp9x knockout mice (Usp9x−/y) to address this knowledge gap. Usp9x−/y mice displayed abnormal communication and social interaction behaviors. Moreover, the absence of Usp9x culminated in reductions to the size of multiple brain regions. Diffusion tensor magnetic resonance imaging revealed deficits in all three major forebrain commissures, as well as long-range hypoconnectivity between cortical and subcortical regions. These data identify USP9X as a key regulator of brain formation and function, and provide insights into the neurodevelopmental syndrome arising as a consequence of USP9X mutations in patients.

scholarly journals A second generation radiation hybrid map to aid the assembly of the bovine genome sequence

BMC Genomics ◽  
2006 ◽  
Vol 7 (1) ◽  
Author(s):  
Oliver C Jann ◽  
Jan Aerts ◽  
Michelle Jones ◽  
Nicola Hastings ◽  
Andy Law ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Radiation Hybrid ◽  
Second Generation ◽  
Bovine Genome ◽  
Bovine Genome Sequence ◽  
Radiation Hybrid Map
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