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  1. Article ; Online: Transcription profiling provides insights into gene pathways involved in horn and scurs development in cattle

    Lehnert Sigrid A / Barris Wes / Reverter Antonio / Mariasegaram Maxy / Dalrymple Brian / Prayaga Kishore

    BMC Genomics, Vol 11, Iss 1, p

    2010  Volume 370

    Abstract: Abstract Background Two types of horns are evident in cattle - fixed horns attached to the skull and a variation called scurs, which refers to small loosely attached horns. Cattle lacking horns are referred to as polled. Although both the Poll and Scurs ... ...

    Abstract Abstract Background Two types of horns are evident in cattle - fixed horns attached to the skull and a variation called scurs, which refers to small loosely attached horns. Cattle lacking horns are referred to as polled. Although both the Poll and Scurs loci have been mapped to BTA1 and 19 respectively, the underlying genetic basis of these phenotypes is unknown, and so far, no candidate genes regulating these developmental processes have been described. This study is the first reported attempt at transcript profiling to identify genes and pathways contributing to horn and scurs development in Brahman cattle, relative to polled counterparts. Results Expression patterns in polled, horned and scurs tissues were obtained using the Agilent 44 k bovine array. The most notable feature when comparing transcriptional profiles of developing horn tissues against polled was the down regulation of genes coding for elements of the cadherin junction as well as those involved in epidermal development. We hypothesize this as a key event involved in keratinocyte migration and subsequent horn development. In the polled-scurs comparison, the most prevalent differentially expressed transcripts code for genes involved in extracellular matrix remodelling, which were up regulated in scurs tissues relative to polled. Conclusion For this first time we describe networks of genes involved in horn and scurs development. Interestingly, we did not observe differential expression in any of the genes present on the fine mapped region of BTA1 known to contain the Poll locus.
    Keywords Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Biotechnology ; TP248.13-248.65
    Subject code 572
    Language English
    Publishing date 2010-06-01T00:00:00Z
    Publisher BioMed Central
    Document type Article ; Online
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  2. Article: Analysis of copy number variants in the cattle genome

    Kijas, James W / Barendse, William / Barris, Wes / Harrison, Blair / McCulloch, Russell / McWilliam, Sean / Whan, Vicki

    Gene. 2011 Aug. 15, v. 482, no. 1-2

    2011  

    Abstract: Copy number variation (CNV) is likely to be an important component of heritable variation in livestock. To characterise CNVs in cattle, we performed a genome wide survey to determine the number, location and gene content of these genomic features. A ... ...

    Abstract Copy number variation (CNV) is likely to be an important component of heritable variation in livestock. To characterise CNVs in cattle, we performed a genome wide survey to determine the number, location and gene content of these genomic features. A tiling oligonucleotide array with ~385,000 probes was used for comparative genomic hybridisation of both taurine and zebu cattle. Using a conservative set of calling criteria, a total of 51 CNV were detected that collectively spanned approximately half of one percent of the bovine genome. The size of the average CNV within each animal ranged from 213kb up to 335kb. Half of the CNV were detected in a single animal only, whilst the remainder was independently identified in multiple individuals. Analysis was performed to determine the gene content for each CNV region. This revealed that the majority of CNV (82%) spanned at least one gene, with a number of CNV containing genes which are known to control aspects of phenotypic variation in cattle. Whilst additional studies are required to determine the impact of individual CNV, this study confirmed them as an important class of genomic variation in cattle.
    Keywords cattle ; comparative genomic hybridization ; genes ; genetic variation ; phenotypic variation ; surveys ; zebu
    Language English
    Dates of publication 2011-0815
    Size p. 73-77.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2011.04.011
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  3. Article ; Online: Transcription profiling provides insights into gene pathways involved in horn and scurs development in cattle.

    Mariasegaram, Maxy / Reverter, Antonio / Barris, Wes / Lehnert, Sigrid A / Dalrymple, Brian / Prayaga, Kishore

    BMC genomics

    2010  Volume 11, Page(s) 370

    Abstract: Background: Two types of horns are evident in cattle - fixed horns attached to the skull and a variation called scurs, which refers to small loosely attached horns. Cattle lacking horns are referred to as polled. Although both the Poll and Scurs loci ... ...

    Abstract Background: Two types of horns are evident in cattle - fixed horns attached to the skull and a variation called scurs, which refers to small loosely attached horns. Cattle lacking horns are referred to as polled. Although both the Poll and Scurs loci have been mapped to BTA1 and 19 respectively, the underlying genetic basis of these phenotypes is unknown, and so far, no candidate genes regulating these developmental processes have been described. This study is the first reported attempt at transcript profiling to identify genes and pathways contributing to horn and scurs development in Brahman cattle, relative to polled counterparts.
    Results: Expression patterns in polled, horned and scurs tissues were obtained using the Agilent 44 k bovine array. The most notable feature when comparing transcriptional profiles of developing horn tissues against polled was the down regulation of genes coding for elements of the cadherin junction as well as those involved in epidermal development. We hypothesize this as a key event involved in keratinocyte migration and subsequent horn development. In the polled-scurs comparison, the most prevalent differentially expressed transcripts code for genes involved in extracellular matrix remodelling, which were up regulated in scurs tissues relative to polled.
    Conclusion: For this first time we describe networks of genes involved in horn and scurs development. Interestingly, we did not observe differential expression in any of the genes present on the fine mapped region of BTA1 known to contain the Poll locus.
    MeSH term(s) Animals ; Cattle/anatomy & histology ; Cattle/genetics ; Cattle/growth & development ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks ; Horns/growth & development ; Male ; Oligonucleotide Array Sequence Analysis ; Polymerase Chain Reaction ; Reproducibility of Results
    Language English
    Publishing date 2010-06-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/1471-2164-11-370
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  4. Article ; Online ; Research data: (with research data) SNP discovery in nonmodel organisms: strand bias and base-substitution errors reduce conversion rates.

    Gonçalves da Silva, Anders / Barendse, William / Kijas, James W / Barris, Wes C / McWilliam, Sean / Bunch, Rowan J / McCullough, Russell / Harrison, Blair / Hoelzel, A Rus / England, Phillip R

    Molecular ecology resources

    2015  Volume 15, Issue 4, Page(s) 723–736

    Abstract: Single nucleotide polymorphisms (SNPs) have become the marker of choice for genetic studies in organisms of conservation, commercial or biological interest. Most SNP discovery projects in nonmodel organisms apply a strategy for identifying putative SNPs ... ...

    Abstract Single nucleotide polymorphisms (SNPs) have become the marker of choice for genetic studies in organisms of conservation, commercial or biological interest. Most SNP discovery projects in nonmodel organisms apply a strategy for identifying putative SNPs based on filtering rules that account for random sequencing errors. Here, we analyse data used to develop 4723 novel SNPs for the commercially important deep-sea fish, orange roughy (Hoplostethus atlanticus), to assess the impact of not accounting for systematic sequencing errors when filtering identified polymorphisms when discovering SNPs. We used SAMtools to identify polymorphisms in a velvet assembly of genomic DNA sequence data from seven individuals. The resulting set of polymorphisms were filtered to minimize 'bycatch'-polymorphisms caused by sequencing or assembly error. An Illumina Infinium SNP chip was used to genotype a final set of 7714 polymorphisms across 1734 individuals. Five predictors were examined for their effect on the probability of obtaining an assayable SNP: depth of coverage, number of reads that support a variant, polymorphism type (e.g. A/C), strand-bias and Illumina SNP probe design score. Our results indicate that filtering out systematic sequencing errors could substantially improve the efficiency of SNP discovery. We show that BLASTX can be used as an efficient tool to identify single-copy genomic regions in the absence of a reference genome. The results have implications for research aiming to identify assayable SNPs and build SNP genotyping assays for nonmodel organisms.
    MeSH term(s) Animals ; Computational Biology/methods ; Genotyping Techniques/methods ; High-Throughput Nucleotide Sequencing/methods ; Polymorphism, Single Nucleotide ; Vertebrates/classification ; Vertebrates/genetics
    Language English
    Publishing date 2015-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2406833-0
    ISSN 1755-0998 ; 1755-098X ; 1755-098X
    ISSN (online) 1755-0998
    ISSN 1755-098X
    DOI 10.1111/1755-0998.12343
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  5. Article ; Online: Analysis of copy number variants in the cattle genome.

    Kijas, James W / Barendse, William / Barris, Wes / Harrison, Blair / McCulloch, Russell / McWilliam, Sean / Whan, Vicki

    Gene

    2011  Volume 482, Issue 1-2, Page(s) 73–77

    Abstract: Copy number variation (CNV) is likely to be an important component of heritable variation in livestock. To characterise CNVs in cattle, we performed a genome wide survey to determine the number, location and gene content of these genomic features. A ... ...

    Abstract Copy number variation (CNV) is likely to be an important component of heritable variation in livestock. To characterise CNVs in cattle, we performed a genome wide survey to determine the number, location and gene content of these genomic features. A tiling oligonucleotide array with ~385,000 probes was used for comparative genomic hybridisation of both taurine and zebu cattle. Using a conservative set of calling criteria, a total of 51 CNV were detected that collectively spanned approximately half of one percent of the bovine genome. The size of the average CNV within each animal ranged from 213 kb up to 335 kb. Half of the CNV were detected in a single animal only, whilst the remainder was independently identified in multiple individuals. Analysis was performed to determine the gene content for each CNV region. This revealed that the majority of CNV (82%) spanned at least one gene, with a number of CNV containing genes which are known to control aspects of phenotypic variation in cattle. Whilst additional studies are required to determine the impact of individual CNV, this study confirmed them as an important class of genomic variation in cattle.
    MeSH term(s) Animals ; Cattle/genetics ; Comparative Genomic Hybridization ; DNA Copy Number Variations/genetics ; Female ; Genome/genetics ; Male ; Pedigree ; Reproducibility of Results
    Language English
    Publishing date 2011-08-15
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2011.04.011
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1357: Show issues Location:
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  6. Article: Association weight matrix for the genetic dissection of puberty in beef cattle

    Fortes, Marina R.S / Reverter, Antonio / Zhang, Yuandan / Collis, Eliza / Nagaraj, Shivashankar H / Jonsson, Nick N / Prayaga, Kishore C / Barris, Wes / Hawken, Rachel J

    Proceedings of the National Academy of Sciences of the United States of America. 2010 Aug. 3, v. 107, no. 31

    2010  

    Abstract: We describe a systems biology approach for the genetic dissection of complex traits based on applying gene network theory to the results from genome-wide associations. The associations of single-nucleotide polymorphisms (SNP) that were individually ... ...

    Abstract We describe a systems biology approach for the genetic dissection of complex traits based on applying gene network theory to the results from genome-wide associations. The associations of single-nucleotide polymorphisms (SNP) that were individually associated with a primary phenotype of interest, age at puberty in our study, were explored across 22 related traits. Genomic regions were surveyed for genes harboring the selected SNP. As a result, an association weight matrix (AWM) was constructed with as many rows as genes and as many columns as traits. Each {i, j} cell value in the AWM corresponds to the z-score normalized additive effect of the ith gene (via its neighboring SNP) on the jth trait. Columnwise, the AWM recovered the genetic correlations estimated via pedigree-based restricted maximum-likelihood methods. Rowwise, a combination of hierarchical clustering, gene network, and pathway analyses identified genetic drivers that would have been missed by standard genome-wide association studies. Finally, the promoter regions of the AWM-predicted targets of three key transcription factors (TFs), estrogen-related receptor γ (ESRRG), Pal3 motif, bound by a PPAR-γ homodimer, IR3 sites (PPARG), and Prophet of Pit 1, PROP paired-like homeobox 1 (PROP1), were surveyed to identify binding sites corresponding to those TFs. Applied to our case, the AWM results recapitulate the known biology of puberty, captured experimentally validated binding sites, and identified candidate genes and gene-gene interactions for further investigation.
    Keywords additive effect ; beef cattle ; binding sites ; genes ; genetic correlation ; genome-wide association study ; phenotype ; promoter regions ; puberty ; single nucleotide polymorphism ; transcription factors
    Language English
    Dates of publication 2010-0803
    Size p. 13642-13647.
    Publishing place National Academy of Sciences
    Document type Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1002044107
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  7. Article ; Online: Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel

    Cavanagh Julie AL / Zenger Kyall R / Collins Andrew R / Nicholas Frank W / Khatkar Mehar S / Barris Wes / Schnabel Robert D / Taylor Jeremy F / Raadsma Herman W

    BMC Genomics, Vol 9, Iss 1, p

    2008  Volume 187

    Abstract: Abstract Background The extent of linkage disequilibrium (LD) within a population determines the number of markers that will be required for successful association mapping and marker-assisted selection. Most studies on LD in cattle reported to date are ... ...

    Abstract Abstract Background The extent of linkage disequilibrium (LD) within a population determines the number of markers that will be required for successful association mapping and marker-assisted selection. Most studies on LD in cattle reported to date are based on microsatellite markers or small numbers of single nucleotide polymorphisms (SNPs) covering one or only a few chromosomes. This is the first comprehensive study on the extent of LD in cattle by analyzing data on 1,546 Holstein-Friesian bulls genotyped for 15,036 SNP markers covering all regions of all autosomes. Furthermore, most studies in cattle have used relatively small sample sizes and, consequently, may have had biased estimates of measures commonly used to describe LD. We examine minimum sample sizes required to estimate LD without bias and loss in accuracy. Finally, relatively little information is available on comparative LD structures including other mammalian species such as human and mouse, and we compare LD structure in cattle with public-domain data from both human and mouse. Results We computed three LD estimates, D ', Dvol and r 2 , for 1,566,890 syntenic SNP pairs and a sample of 365,400 non-syntenic pairs. Mean D ' is 0.189 among syntenic SNPs, and 0.105 among non-syntenic SNPs; mean r 2 is 0.024 among syntenic SNPs and 0.0032 among non-syntenic SNPs. All three measures of LD for syntenic pairs decline with distance; the decline is much steeper for r 2 than for D ' and Dvol . The value of D ' and Dvol are quite similar. Significant LD in cattle extends to 40 kb (when estimated as r 2 ) and 8.2 Mb (when estimated as D '). The mean values for LD at large physical distances are close to those for non-syntenic SNPs. Minor allelic frequency threshold affects the distribution and extent of LD. For unbiased and accurate estimates of LD across marker intervals spanning < 1 kb to > 50 Mb, minimum sample sizes of 400 (for D ') and 75 (for r 2 ) are required. The bias due to small samples sizes increases with inter-marker interval. LD in cattle is much less extensive than in a mouse population created from crossing inbred lines, and more extensive than in humans. Conclusion For association mapping in Holstein-Friesian cattle, for a given design, at least one SNP is required for each 40 kb, giving a total requirement of at least 75,000 SNPs for a low power whole-genome scan (median r 2 > 0.19) and up to 300,000 markers at 10 kb intervals for a high power genome scan (median r 2 > 0.62). For estimation of LD by D' and Dvol with sufficient precision, a sample size of at least 400 is required, whereas for r 2 a minimum sample of 75 is adequate.
    Keywords Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Biotechnology ; TP248.13-248.65
    Subject code 333
    Language English
    Publishing date 2008-04-01T00:00:00Z
    Publisher BioMed Central
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Association weight matrix for the genetic dissection of puberty in beef cattle.

    Fortes, Marina R S / Reverter, Antonio / Zhang, Yuandan / Collis, Eliza / Nagaraj, Shivashankar H / Jonsson, Nick N / Prayaga, Kishore C / Barris, Wes / Hawken, Rachel J

    Proceedings of the National Academy of Sciences of the United States of America

    2010  Volume 107, Issue 31, Page(s) 13642–13647

    Abstract: We describe a systems biology approach for the genetic dissection of complex traits based on applying gene network theory to the results from genome-wide associations. The associations of single-nucleotide polymorphisms (SNP) that were individually ... ...

    Abstract We describe a systems biology approach for the genetic dissection of complex traits based on applying gene network theory to the results from genome-wide associations. The associations of single-nucleotide polymorphisms (SNP) that were individually associated with a primary phenotype of interest, age at puberty in our study, were explored across 22 related traits. Genomic regions were surveyed for genes harboring the selected SNP. As a result, an association weight matrix (AWM) was constructed with as many rows as genes and as many columns as traits. Each {i, j} cell value in the AWM corresponds to the z-score normalized additive effect of the ith gene (via its neighboring SNP) on the jth trait. Columnwise, the AWM recovered the genetic correlations estimated via pedigree-based restricted maximum-likelihood methods. Rowwise, a combination of hierarchical clustering, gene network, and pathway analyses identified genetic drivers that would have been missed by standard genome-wide association studies. Finally, the promoter regions of the AWM-predicted targets of three key transcription factors (TFs), estrogen-related receptor gamma (ESRRG), Pal3 motif, bound by a PPAR-gamma homodimer, IR3 sites (PPARG), and Prophet of Pit 1, PROP paired-like homeobox 1 (PROP1), were surveyed to identify binding sites corresponding to those TFs. Applied to our case, the AWM results recapitulate the known biology of puberty, captured experimentally validated binding sites, and identified candidate genes and gene-gene interactions for further investigation.
    MeSH term(s) Aging ; Animals ; Cattle/genetics ; Gene Regulatory Networks ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; Systems Biology
    Language English
    Publishing date 2010-07-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1002044107
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
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  9. Article: Validation of alternative methods of data normalization in gene co-expression studies.

    Reverter, Antonio / Barris, Wes / McWilliam, Sean / Byrne, Keren A / Wang, Yong H / Tan, Siok H / Hudson, Nick / Dalrymple, Brian P

    Bioinformatics (Oxford, England)

    2005  Volume 21, Issue 7, Page(s) 1112–1120

    Abstract: Motivation: Clusters of genes encoding proteins with related functions, or in the same regulatory network, often exhibit expression patterns that are correlated over a large number of conditions. Protein associations and gene regulatory networks can be ... ...

    Abstract Motivation: Clusters of genes encoding proteins with related functions, or in the same regulatory network, often exhibit expression patterns that are correlated over a large number of conditions. Protein associations and gene regulatory networks can be modelled from expression data. We address the question of which of several normalization methods is optimal prior to computing the correlation of the expression profiles between every pair of genes.
    Results: We use gene expression data from five experiments with a total of 78 hybridizations and 23 diverse conditions. Nine methods of data normalization are explored based on all possible combinations of normalization techniques according to between and within gene and experiment variation. We compare the resulting empirical distribution of gene x gene correlations with the expectations and apply cross-validation to test the performance of each method in predicting accurate functional annotation. We conclude that normalization methods based on mixed-model equations are optimal.
    MeSH term(s) Algorithms ; Benchmarking/methods ; Computer Simulation ; Data Interpretation, Statistical ; Gene Expression Profiling/methods ; Gene Expression Profiling/standards ; Gene Expression Regulation/physiology ; Models, Genetic ; Models, Statistical ; Numerical Analysis, Computer-Assisted ; Oligonucleotide Array Sequence Analysis/methods ; Oligonucleotide Array Sequence Analysis/standards ; Software
    Language English
    Publishing date 2005-04-01
    Publishing country England
    Document type Comparative Study ; Evaluation Studies ; Journal Article ; Validation Studies
    ZDB-ID 1422668-6
    ISSN 1367-4803
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/bti124
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  10. Article: Gene expression profiling of the bovine gastrointestinal tract.

    Hansen, Christiane / Fu, Anna / Meng, Yan / Okine, Erasmus / Hawken, Rachel / Barris, Wes / Li, Changxi / Moore, Stephen S

    Genome

    2004  Volume 47, Issue 4, Page(s) 639–649

    Abstract: Basal gene expression levels across the bovine gastrointestinal tract (GI) were examined in an attempt to formulate genetic explanations for the differences in function that are known or thought to exist between the various regions. Gene expression along ...

    Abstract Basal gene expression levels across the bovine gastrointestinal tract (GI) were examined in an attempt to formulate genetic explanations for the differences in function that are known or thought to exist between the various regions. Gene expression along the tract was studied through the random sequencing of a total of 16 412 clones from seven tissue-specific cDNA libraries spanning its length. The expressed sequence tags (ESTs) within each library were clustered to reduce clone redundancy and obtain longer consensus sequences. BLASTN and BLASTX searches against the NCBI human RefSeq databases were used to find putative matches for the bovine sequences and gene ontology assignments were made. Notable similarities and differences in gene expression were observed among the various compartments of the GI tract of the bovine. Many of the prominent transcripts have yet to be reliably identified and the prominence of others may be worthy of further examination. This collection of ESTs represents an important resource for the future construction of a GI tract specific microarray for further gene expression studies.
    MeSH term(s) Animals ; Base Sequence ; Cattle ; DNA, Complementary/genetics ; Expressed Sequence Tags ; Gastrointestinal Tract/anatomy & histology ; Gastrointestinal Tract/metabolism ; Gene Expression ; Gene Expression Profiling ; Gene Library ; Humans ; Male
    Chemical Substances DNA, Complementary
    Language English
    Publishing date 2004-08
    Publishing country Canada
    Document type Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 639031-6
    ISSN 1480-3321 ; 0831-2796
    ISSN (online) 1480-3321
    ISSN 0831-2796
    DOI 10.1139/g04-030
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