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Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Aerts J, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt R, Jann O, Jones SJM, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas FW, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel RD, Silveri L, Skow LC, Smith TPL, Sonstegard TS, Taylor JF, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G, Zhao S. A physical map of the bovine genome. Genome Biol 2008; 8:R165. [PMID: 17697342 PMCID: PMC2374996 DOI: 10.1186/gb-2007-8-8-r165] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 07/20/2007] [Accepted: 08/14/2007] [Indexed: 11/10/2022] Open
Abstract
A new physical map of the bovine genome has been constructed by integrating data from genetic and radiation hybrid maps, and a new bovine BAC map, with the bovine genome draft assembly. Background Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project. Results A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly. Conclusion Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans.
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Sellick GS, Pitchford WS, Morris CA, Cullen NG, Crawford AM, Raadsma HW, Bottema CDK. Effect of myostatin F94L on carcass yield in cattle. Anim Genet 2007; 38:440-6. [PMID: 17617213 DOI: 10.1111/j.1365-2052.2007.01623.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, a highly significant quantitative trait locus (QTL) for meat percentage, eye muscle area (EMA) and silverside percentage was found on cattle chromosome 2 at 0-15 cM, a region containing the positional candidate gene growth differentiation factor 8 (GDF8), which has the common alias myostatin (MSTN). Loss-of-function mutations in the MSTN gene are known to cause an extreme 'double muscling' phenotype in cattle. In this study, highly significant associations of MSTN with cattle carcass traits were found using maternally inherited MSTN haplotypes from outbred Limousin and Jersey cattle in a linkage disequilibrium analysis. A previously reported transversion in MSTN (AF320998.1:g.433C>A), resulting in the amino acid substitution of phenylalanine by leucine at position 94 of the protein sequence (F94L), was the only polymorphism consistently related to increased muscling. Overall, the size of the g.433C>A additive effect on carcass traits was moderately large, with the g.433A allele found to be associated with a 5.5% increase in silverside percentage and EMA and a 2.3% increase in total meat percentage relative to the g.433C allele. The phenotypic effects of the g.433A allele were partially recessive. This study provides strong evidence that a MSTN genotype can produce an intermediate, non-double muscling phenotype, which should be of significant value for beef cattle producers.
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Keane OM, Dodds KG, Crawford AM, McEwan JC. Transcriptional profiling of Ovis aries identifies Ovar-DQA1 allele frequency differences between nematode-resistant and susceptible selection lines. Physiol Genomics 2007; 30:253-61. [PMID: 17488886 DOI: 10.1152/physiolgenomics.00273.2006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Gastrointestinal nematodes are a major cause of disease in grazing livestock; however, individual animals differ in their response to infection. To identify genes whose expression correlates with resistance status, transcriptional profiling of resistant and susceptible sheep was undertaken. Transcription profiles were taken at three time points during the growth of lambs. The number of genes differentially expressed increased as animals were exposed to longer nematode challenge. Almost 300 genes, with a variety of functions, were differentially expressed overall, although genes more highly expressed in resistant animals typically had major histocompatibility complex (MHC) II, free radical scavenging or smooth muscle-specific functions. The Ovar-DQA1 gene was 8.4-fold more highly expressed in resistant animals. This was due in part to a higher frequency of DQA1 null alleles in susceptible animals. The null allele of DQA1 was also associated with susceptibility in a separate selection flock, presenting the hypothesis that failure to present parasite antigens to immune cells led to nematode susceptibility. To test this hypothesis, commercial rams from three breeds were genotyped for the null allele of DQA1. The homozygous null allele was associated with susceptibility in only one of the three breeds tested indicating that the null allele does not cause susceptibility to intestinal parasites per se but is probably in linkage disequilibrium with additional polymorphisms in the MHC region. A combination of these polymorphisms may contribute to susceptibility in some populations. The extent of linkage disequilibrium between polymorphisms may vary from breed to breed or population to population.
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Wang Y, van Oers MM, Crawford AM, Vlak JM, Jehle JA. Genomic analysis of Oryctes rhinoceros virus reveals genetic relatedness to Heliothis zea virus 1. Arch Virol 2006; 152:519-31. [PMID: 17106621 DOI: 10.1007/s00705-006-0872-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 09/28/2006] [Indexed: 11/24/2022]
Abstract
Oryctes rhinoceros virus (OrV) is an unassigned invertebrate dsDNA virus with enveloped and rod-shaped virions. Two cloned PstI fragments, C and D, of OrV DNA have been sequenced, consisting of 19,805 and 17,146 bp, respectively, and comprising about 30% of the OrV genome. For each of the two fragments, 20 open reading frames (ORFs) of 150 nucleotides or greater with no or minimal overlap were predicted. Ten of the predicted 40 ORFs revealed significant similarities to Heliothis zea virus 1 (HzV-1) ORFs, of which five, lef-4, lef-5, pif-2, dnapol and ac81, are homologues of conserved core genes in the family Baculoviridae, and one is homologous to baculovirus rr1. A baculovirus odv-e66 homologue is also present in OrV. Five ORFs encode proteins homologous to cellular thymidylate synthase (TS), patatin-like phospholipase, mitochondrial carrier protein, Ser/Thr protein phosphatase, and serine protease, respectively. TS is phylogenetically related to those of eukarya and nucleo-cytoplasmic large dsDNA viruses. However, the remaining 25 ORFs have poor or no sequence matches with the current databases. Both the gene content of the sequenced fragments and the phylogenetic analyses of the viral DNA polymerase suggest that OrV is most closely related to HzV-1. These findings and the re-evaluation of the relationship of HzV-1 to baculoviruses suggest that a new virus genus, Nudivirus, should be established, containing OrV and HzV-1, which are genetically related to members of the family Baculoviridae.
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Crawford AM, Paterson KA, Dodds KG, Diez Tascon C, Williamson PA, Roberts Thomson M, Bisset SA, Beattie AE, Greer GJ, Green RS, Wheeler R, Shaw RJ, Knowler K, McEwan JC. Discovery of quantitative trait loci for resistance to parasitic nematode infection in sheep: I. Analysis of outcross pedigrees. BMC Genomics 2006; 7:178. [PMID: 16846521 PMCID: PMC1574317 DOI: 10.1186/1471-2164-7-178] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2006] [Accepted: 07/18/2006] [Indexed: 11/10/2022] Open
Abstract
Background Currently most pastoral farmers rely on anthelmintic drenches to control gastrointestinal parasitic nematodes in sheep. Resistance to anthelmintics is rapidly increasing in nematode populations such that on some farms none of the drench families are now completely effective. It is well established that host resistance to nematode infection is a moderately heritable trait. This study was undertaken to identify regions of the genome, quantitative trait loci (QTL) that contain genes affecting resistance to parasitic nematodes. Results Rams obtained from crossing nematode parasite resistant and susceptible selection lines were used to derive five large half-sib families comprising between 348 and 101 offspring per sire. Total offspring comprised 940 lambs. Extensive measurements for a range of parasite burden and immune function traits in all offspring allowed each lamb in each pedigree to be ranked for relative resistance to nematode parasites. Initially the 22 most resistant and 22 most susceptible progeny from each pedigree were used in a genome scan that used 203 microsatellite markers spread across all sheep autosomes. This study identified 9 chromosomes with regions showing sufficient linkage to warrant the genotyping of all offspring. After genotyping all offspring with markers covering Chromosomes 1, 3, 4, 5, 8, 12, 13, 22 and 23, the telomeric end of chromosome 8 was identified as having a significant QTL for parasite resistance as measured by the number of Trichostrongylus spp. adults in the abomasum and small intestine at the end of the second parasite challenge. Two further QTL for associated immune function traits of total serum IgE and T. colubiformis specific serum IgG, at the end of the second parasite challenge, were identified on chromosome 23. Conclusion Despite parasite resistance being a moderately heritable trait, this large study was able to identify only a single significant QTL associated with it. The QTL concerned adult parasite burdens at the end of the second parasite challenge when the lambs were approximately 6 months old. Our failure to discover more QTL suggests that most of the genes controlling this trait are of relatively small effect. The large number of suggestive QTL discovered (more than one per family per trait than would be expected by chance) also supports this conclusion.
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Keane OM, Zadissa A, Wilson T, Hyndman DL, Greer GJ, Baird DB, McCulloch AF, Crawford AM, McEwan JC. Gene expression profiling of naïve sheep genetically resistant and susceptible to gastrointestinal nematodes. BMC Genomics 2006; 7:42. [PMID: 16515715 PMCID: PMC1450279 DOI: 10.1186/1471-2164-7-42] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Accepted: 03/06/2006] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Gastrointestinal nematodes constitute a major cause of morbidity and mortality in grazing ruminants. Individual animals or breeds, however, are known to differ in their resistance to infection. Gene expression profiling allows us to examine large numbers of transcripts simultaneously in order to identify those transcripts that contribute to an animal's susceptibility or resistance. RESULTS With the goal of identifying genes with a differential pattern of expression between sheep genetically resistant and susceptible to gastrointestinal nematodes, a 20,000 spot ovine cDNA microarray was constructed. This array was used to interrogate the expression of 9,238 known genes in duodenum tissue of four resistant and four susceptible female lambs. Naïve animals were used in order to look at genes that were differentially expressed in the absence of infection with gastrointestinal nematodes. Forty one unique known genes were identified that were differentially expressed between the resistant and susceptible animals. Northern blotting of a selection of the genes confirmed differential expression. The differentially expressed genes had a variety of functions, although many genes relating to the stress response and response to stimulus were more highly expressed in the susceptible animals. CONCLUSION We have constructed the first reported ovine microarray and used this array to examine gene expression in lambs genetically resistant and susceptible to gastrointestinal nematode infection. This study indicates that susceptible animals appear to be generating a hyper-sensitive immune response to non-nematode challenges. The gastrointestinal tract of susceptible animals is therefore under stress and compromised even in the absence of gastrointestinal nematodes. These factors may contribute to the genetic susceptibility of these animals.
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Jackson TA, Crawford AM, Glare TR. Oryctes virus—Time for a new look at a useful biocontrol agent. J Invertebr Pathol 2005; 89:91-4. [PMID: 16039310 DOI: 10.1016/j.jip.2005.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Accepted: 03/14/2005] [Indexed: 10/25/2022]
Abstract
The introduction of Oryctes virus into outbreak areas of the rhinoceros beetle, Oryctes rhinoceros (Coleoptera: Scarabaeidae), has been a major success for "classical" biocontrol with a virus and has led to a dramatic reduction in palm damage in many areas of the Asia/Pacific region. In recent years, however, there have been new reports of high levels of rhinoceros beetle damage to palms. Damage has been especially intense in SE Asia following the introduction of no-burn polices for land clearance and replanting, but outbreaks have also been reported from some Pacific Islands where control seems to have diminished over time. SE Asian studies show that there is considerable genetic variation among endemic Oryctes virus isolates and studies in new island release areas have shown rapid evolution of the virus. The consequences of such genetic variation are in need of further study. Furthermore, the taxonomic position of the virus is unclear, with its removal from the Baculoviridae to an "unassigned' virus, reflecting its novel characteristics. Genomic sequencing could help resolve the taxonomy of the virus and provide a basis for studying strain variation. Oryctes virus has achieved wide success in the past without the benefit of molecular analysis and identification techniques. In order to fully take advantage of this unique pathogen for protection of palms, a renewed, coordinated effort centered on genetic selection and distribution of effective strains is required.
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Diez-Tascón C, Keane OM, Wilson T, Zadissa A, Hyndman DL, Baird DB, McEwan JC, Crawford AM. Microarray analysis of selection lines from outbred populations to identify genes involved with nematode parasite resistance in sheep. Physiol Genomics 2005; 21:59-69. [PMID: 15623564 DOI: 10.1152/physiolgenomics.00257.2004] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Gastrointestinal nematodes infect sheep grazing contaminated pastures. Traditionally, these have been controlled with anthelmintic drenching. The selection of animals resistant to nematodes is an alternative to complete reliance on drugs, but the genetic basis of host resistance is poorly understood. Using a 10,204 bovine cDNA microarray, we have examined differences in gene expression between genetically resistant and susceptible lambs previously field challenged with larval nematodes. Northern blot analysis for a selection of genes validated the data obtained from the microarrays. The results identified over one hundred genes that were differentially expressed based on conservative criteria. The microarray results were further analyzed to identify promoter motifs common to the differentially expressed genes. Motifs identified in upregulated gene promoters were primarily restricted to those promoters; however, motifs identified in downregulated gene promoters were also found in the promoters of upregulated genes but not in the promoters of genes whose expression was unaltered. Protein Annotators’ Assistant was used for lexical analysis of the differentially expressed genes, and Gene Ontology was used to look for metabolic and cell signaling pathways associated with parasite resistance. Two pathways represented by genes differentially expressed in resistant animals were those involved with the development of an acquired immune response and those related to the structure of the intestine smooth muscle. Genes involved in these processes appear from our analysis to be key genetic determinants of parasite resistance.
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Kuchel H, Siebert BD, Bottema CDK, Webb GC, Crawford AM, Duncan SJ, McDonald PA, McEwan JC, Pitchford WS. Physical mapping of the stearoyl-CoA desaturase (SCD) locus in sheep. Anim Genet 2004; 35:163. [PMID: 15025592 DOI: 10.1111/j.1365-2052.2004.01114.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Crawford AM. The use of genetic modification technologies in the discovery of genes affecting production traits and disease resistance in animals. N Z Vet J 2003; 51:52-7. [PMID: 16032300 DOI: 10.1080/00480169.2003.36340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Genetic modification technologies, developed initially in laboratory strains of selected bacteria and viruses, are essential tools for understanding the genomes of livestock. These tools allow researchers to: isolate, sequence and characterise any livestock gene; locate genes on chromosomes; follow the inheritance of any gene and/or chromosomal region in any pedigree; detect phenotypic variation due to, or associated with, variation in the DNA sequence of a gene and identify the genetic alteration causing this. Most of the many thousands of genes identified in livestock vary between individuals. Finding the best type of the key genes affecting animal productivity is an exciting and a daunting task. It is only possible with the use of laboratory-based genetic modification techniques. This review will briefly describe the technologies now in use and, using local examples, show how molecular geneticists are using these to help identify genetic alterations and breed healthier or more productive animals. As with any new technology, a new language evolves to describe new products and processes. The new language makes communication easier between participants in the field but more difficult for others to understand the technology. A glossary of terms has therefore been added to this review to help readers less familiar with molecular genetics.
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Page BT, Casas E, Heaton MP, Cullen NG, Hyndman DL, Morris CA, Crawford AM, Wheeler TL, Koohmaraie M, Keele JW, Smith TPL. Evaluation of single-nucleotide polymorphisms in CAPN1 for association with meat tenderness in cattle. J Anim Sci 2002; 80:3077-85. [PMID: 12542147 DOI: 10.2527/2002.80123077x] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Micromolar calcium activated neutral protease (CAPN1) was evaluated as a candidate gene for a quantitative trait locus (QTL) on BTA29 affecting meat tenderness by characterization of nucleotide sequence variation in the gene. Single-nucleotide polymorphisms (SNP) were identified by sequencing all 22 exons and 19 of the 21 introns in two sires (Piedmontese x Angus located at the U.S. Meat Animal Research Center in Clay Center, NE; Jersey x Limousin located at AgResearch in New Zealand) of independent resource populations previously shown to be segregating meat tenderness QTL on BTA29. The majority of the 38 SNP were found in introns or were synonymous substitutions in the coding regions, with two exceptions. Exons 14 and 9 contained SNP that were predicted to alter the protein sequence by the substitution of isoleucine for valine in Domain III of the protein, and alanine for glycine in Domain II of the protein. The resource populations were genotyped for these two SNP in addition to six intronic polymorphisms and two silent substitutions. Analysis of genotypes and shear force values in both populations revealed a difference between paternal CAPN1 alleles in which the allele encoding isoleucine at position 530 and glycine at position 316 associated with decreased meat tenderness (increased shear force values) relative to the allele encoding valine at position 530 and alanine at position 316 (P < 0.05). The association of maternal alleles with meat tenderness phenotypes is consistent with the hypothesis of CAPN1 as the gene underlying the QTL effect in two independent resource populations and presents the possibility of using these markers for selective breeding to reduce the numbers of animals with unfavorable meat tenderness traits.
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Diez-Tascón C, Maddox JF, Dodds KG, Crawford AM. Ovine T-cell receptor gamma genes contain polymorphic microsatellites. Anim Genet 2002; 33:468-70. [PMID: 12464026 DOI: 10.1046/j.1365-2052.2002.00938_2.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Diez-Tascón C, Dodds KG, Crawford AM. Linkage mapping of the ovine single-stranded DNA-binding protein 1 (SSBP1) using microsatellite marker OARCDT7. Anim Genet 2002; 33:468. [PMID: 12464025 DOI: 10.1046/j.1365-2052.2002.00938_1.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Diez-Tascón C, Dodds KG, Zadissa A, Crawford AM. Linkage mapping of the ovine ANLN gene using an insertion/deletion polymorphism. Anim Genet 2002; 33:243-4. [PMID: 12030940 DOI: 10.1046/j.1365-2052.2002.t01-10-00876.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Diez-Tascón C, Dodds KG, Crawford AM. An insertion/deletion polymorphism in the fourth intron of POP5 is used for linkage mapping in sheep. Anim Genet 2002; 33:229-30. [PMID: 12030930 DOI: 10.1046/j.1365-2052.2002.00876.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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McRae AF, McEwan JC, Dodds KG, Wilson T, Crawford AM, Slate J. Linkage disequilibrium in domestic sheep. Genetics 2002; 160:1113-22. [PMID: 11901127 PMCID: PMC1462013 DOI: 10.1093/genetics/160.3.1113] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The last decade has seen a dramatic increase in the number of livestock QTL mapping studies. The next challenge awaiting livestock geneticists is to determine the actual genes responsible for variation of economically important traits. With the advent of high density single nucleotide polymorphism (SNP) maps, it may be possible to fine map genes by exploiting linkage disequilibrium between genes of interest and adjacent markers. However, the extent of linkage disequilibrium (LD) is generally unknown for livestock populations. In this article microsatellite genotype data are used to assess the extent of LD in two populations of domestic sheep. High levels of LD were found to extend for tens of centimorgans and declined as a function of marker distance. However, LD was also frequently observed between unlinked markers. The prospects for LD mapping in livestock appear encouraging provided that type I error can be minimized. Properties of the multiallelic LD coefficient D' were also explored. D' was found to be significantly related to marker heterozygosity, although the relationship did not appear to unduly influence the overall conclusions. Of potentially greater concern was the observation that D' may be skewed when rare alleles are present. It is recommended that the statistical significance of LD is used in conjunction with coefficients such as D' to determine the true extent of LD.
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Abstract
OBJECTIVE To determine whether family factors are predictive of outcome in children with anxiety disorders who are receiving cognitive-behavioral treatment. METHOD Participants were 61 children aged 8 to 12 years (mean = 10.0, SD = 1.4) with Axis I anxiety disorders who had been referred to a large Toronto children's hospital. Parents and children completed measures assessing family functioning, parenting stress, parental frustration, and parental psychopathology before and after treatment. Outcome measures included clinician-rated functioning (Children's Global Assessment Scale) and self- and parent-rated anxiety (Revised Children's Manifest Anxiety Scale). RESULTS Child ratings of family dysfunction and frustration predicted clinician-rated improvement (total R2 = 0.28, p < .001). Mother and father reports of family dysfunction, and maternal parenting stress, predicted mother-rated child improvement (total R2 = 0.18, p < .01). Father-rated somatization and child reports of family dysfunction and frustration predicted child-rated improvement (total R2 = 0.25, p < .001). Several family factors improved with treatment. CONCLUSION Family dysfunction appears to be related to less favorable treatment outcome in children with anxiety disorders.
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Maddox JF, Davies KP, Crawford AM, Hulme DJ, Vaiman D, Cribiu EP, Freking BA, Beh KJ, Cockett NE, Kang N, Riffkin CD, Drinkwater R, Moore SS, Dodds KG, Lumsden JM, van Stijn TC, Phua SH, Adelson DL, Burkin HR, Broom JE, Buitkamp J, Cambridge L, Cushwa WT, Gerard E, Galloway SM, Harrison B, Hawken RJ, Hiendleder S, Henry HM, Medrano JF, Paterson KA, Schibler L, Stone RT, van Hest B. An Enhanced Linkage Map of the Sheep Genome Comprising More Than 1000 Loci. Genome Res 2001. [DOI: 10.1101/gr.135001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A medium-density linkage map of the ovine genome has been developed. Marker data for 550 new loci were generated and merged with the previous sheep linkage map. The new map comprises 1093 markers representing 1062 unique loci (941 anonymous loci, 121 genes) and spans 3500 cM (sex-averaged) for the autosomes and 132 cM (female) on the X chromosome. There is an average spacing of 3.4 cM between autosomal loci and 8.3 cM between highly polymorphic [polymorphic information content (PIC) ≥ 0.7] autosomal loci. The largest gap between markers is 32.5 cM, and the number of gaps of >20 cM between loci, or regions where loci are missing from chromosome ends, has been reduced from 40 in the previous map to 6. Five hundred and seventy-three of the loci can be ordered on a framework map with odds of >1000 : 1. The sheep linkage map contains strong links to both the cattle and goat maps. Five hundred and seventy-two of the loci positioned on the sheep linkage map have also been mapped by linkage analysis in cattle, and 209 of the loci mapped on the sheep linkage map have also been placed on the goat linkage map. Inspection of ruminant linkage maps indicates that the genomic coverage by the current sheep linkage map is comparable to that of the available cattle maps. The sheep map provides a valuable resource to the international sheep, cattle, and goat gene mapping community.
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Maddox JF, Davies KP, Crawford AM, Hulme DJ, Vaiman D, Cribiu EP, Freking BA, Beh KJ, Cockett NE, Kang N, Riffkin CD, Drinkwater R, Moore SS, Dodds KG, Lumsden JM, van Stijn TC, Phua SH, Adelson DL, Burkin HR, Broom JE, Buitkamp J, Cambridge L, Cushwa WT, Gerard E, Galloway SM, Harrison B, Hawken RJ, Hiendleder S, Henry HM, Medrano JF, Paterson KA, Schibler L, Stone RT, van Hest B. An enhanced linkage map of the sheep genome comprising more than 1000 loci. Genome Res 2001; 11:1275-89. [PMID: 11435411 PMCID: PMC311104 DOI: 10.1101/gr.gr-1350r] [Citation(s) in RCA: 192] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A medium-density linkage map of the ovine genome has been developed. Marker data for 550 new loci were generated and merged with the previous sheep linkage map. The new map comprises 1093 markers representing 1062 unique loci (941 anonymous loci, 121 genes) and spans 3500 cM (sex-averaged) for the autosomes and 132 cM (female) on the X chromosome. There is an average spacing of 3.4 cM between autosomal loci and 8.3 cM between highly polymorphic [polymorphic information content (PIC) > or = 0.7] autosomal loci. The largest gap between markers is 32.5 cM, and the number of gaps of > 20 cM between loci, or regions where loci are missing from chromosome ends, has been reduced from 40 in the previous map to 6. Five hundred and seventy-three of the loci can be ordered on a framework map with odds of > 1000 : 1. The sheep linkage map contains strong links to both the cattle and goat maps. Five hundred and seventy-two of the loci positioned on the sheep linkage map have also been mapped by linkage analysis in cattle, and 209 of the loci mapped on the sheep linkage map have also been placed on the goat linkage map. Inspection of ruminant linkage maps indicates that the genomic coverage by the current sheep linkage map is comparable to that of the available cattle maps. The sheep map provides a valuable resource to the international sheep, cattle, and goat gene mapping community.
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Gomez JC, Crawford AM. Superior efficacy of olanzapine over haloperidol: analysis of patients with schizophrenia from a multicenter international trial. J Clin Psychiatry 2001; 62 Suppl 2:6-11. [PMID: 11232753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
BACKGROUND Previously, a double-blind, 6-week, parallel-group trial compared the therapeutic profiles of olanzapine (5-20 mg/day; N = 1,336) and haloperidol (5-20 mg/day; N = 660) in 1996 patients with DSM-III-R schizophrenia (83.1%) or schizophreniform (1.9%) or schizoaffective disorders (15.0%) and showed olanzapine to have a superior, broader spectrum of efficacy as well as a more favorable adverse event profile. The present post hoc analysis examined the efficacy of olanzapine compared with haloperidol in the schizophrenic cohort of that study and in subgroups of schizophrenic patients defined by baseline symptom profile and course of illness. METHOD A total of 1,658 patients were included. Patients were included in analyses of change if they had both a baseline and at least 1 postbaseline measurement (N = 1,622; 1,096 olanzapine-treated patients, 526 haloperidol-treated patients). An analysis of variance was used to compare treatment effects on efficacy measurements including the Brief Psychiatric Rating Scale (BPRS; scored 0-6) and the Positive and Negative Syndrome Scale (total, positive subscale, and negative subscale scores). RESULTS Olanzapine-treated patients exhibited statistically significantly greater improvements from baseline (last observation carried forward) on all efficacy measurements. Olanzapine-treated patients with predominantly positive, predominantly negative, or mixed symptoms had statistically significantly greater improvements in BPRS total scores compared with similar haloperidol-treated patients. Patients with primarily chronic negative symptoms and patients with chronic or subchronic courses of illness had statistically significantly greater mean improvements from baseline on the BPRS total with olanzapine compared with haloperidol. Furthermore, within the olanzapine treatment group, patients with a subchronic course of illness had greater mean improvements than patients with a chronic course of illness. CONCLUSION Olanzapine was more effective than haloperidol in treating a varied spectrum of patients with schizophrenia, including patients with positive, negative, or mixed symptom profiles and either a chronic or subchronic course of illness.
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Jones B, Basson BR, Walker DJ, Crawford AM, Kinon BJ. Weight change and atypical antipsychotic treatment in patients with schizophrenia. J Clin Psychiatry 2001; 62 Suppl 2:41-4. [PMID: 11232752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Schizophrenic patients who have been prescribed atypical antipsychotics have a potential risk of gaining weight. The implications of weight gain for clinical care may differ depending on whether a patient is underweight or overweight at baseline. The exact mechanism for weight gain is not known, but several factors have been identified that can help predict which patients are at risk for gaining weight. These factors include better clinical outcome, increased appetite, and low baseline body mass index. In patients treated with olanzapine for up to 3 years, weight gain trended toward a plateau at approximately 36 weeks. Weight gain interventions, including behavioral modifications, show promise in controlling or reducing weight in patients treated with antipsychotics.
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La Porta A, Voth GA, Crawford AM, Alexander J, Bodenschatz E. Fluid particle accelerations in fully developed turbulence. Nature 2001; 409:1017-9. [PMID: 11234005 DOI: 10.1038/35059027] [Citation(s) in RCA: 457] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The motion of fluid particles as they are pushed along erratic trajectories by fluctuating pressure gradients is fundamental to transport and mixing in turbulence. It is essential in cloud formation and atmospheric transport, processes in stirred chemical reactors and combustion systems, and in the industrial production of nanoparticles. The concept of particle trajectories has been used successfully to describe mixing and transport in turbulence, but issues of fundamental importance remain unresolved. One such issue is the Heisenberg-Yaglom prediction of fluid particle accelerations, based on the 1941 scaling theory of Kolmogorov. Here we report acceleration measurements using a detector adapted from high-energy physics to track particles in a laboratory water flow at Reynolds numbers up to 63,000. We find that, within experimental errors, Kolmogorov scaling of the acceleration variance is attained at high Reynolds numbers. Our data indicate that the acceleration is an extremely intermittent variable--particles are observed with accelerations of up to 1,500 times the acceleration of gravity (equivalent to 40 times the root mean square acceleration). We find that the acceleration data reflect the anisotropy of the large-scale flow at all Reynolds numbers studied.
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Paterson KA, Crawford AM. Ovine microsatellite OarKP6 isolated from a BAC containing the ovine interferon gamma gene. Anim Genet 2000; 31:343. [PMID: 11105225 DOI: 10.1046/j.1365-2052.2000.00667.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Diez-Tascón C, Littlejohn RP, Almeida PA, Crawford AM. Genetic variation within the Merino sheep breed: analysis of closely related populations using microsatellites. Anim Genet 2000; 31:243-51. [PMID: 11086533 DOI: 10.1046/j.1365-2052.2000.00636.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Genetic relationships among six populations of Merino sheep were investigated using microsatellites. The history of the six populations is relatively well documented, with all being derived from the Spanish Merino breed within the last 400 years. Genetic variation was highest amongst the Spanish and Portuguese populations, although the preservation of genetic diversity within the other populations was high. By a variety of different statistical tests the French Mutton, German Mutton and New Zealand Merino populations could be differentiated from each other and the Iberian Merinos, indicating that microsatellites are able to track relatively recent changes in the population structure of sheep breeds. The dendrograms constructed on the basis of microsatellite allelic frequencies showed that populations that have shared selection criteria (meat vs. wool) tend to cluster together.
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Raadsma HW, McEwan JC, Stear MJ, Crawford AM. Genetic characterisation of protective vaccine responses in sheep using multi-valent Dichelobacter nodosus vaccines. Vet Immunol Immunopathol 1999; 72:219-29. [PMID: 10614512 DOI: 10.1016/s0165-2427(99)00135-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protective vaccine responses to nine distinct serogroups of Dichelobacter nodosus (serogroups A-I) can be readily measured by serogroup-specific K-agglutinating antibody titres. On the basis of a large quantitative genetic experiment (1200 progeny from 129 sire groups), it was shown that variation in antibody responses following vaccination with a multi-valent pilus antigen D. nodosus vaccine (serogroups A-I) is, in part, under genetic control and thus heritable. Based on the genetic relationships between antibody responses to all nine antigens, results suggested that both genes for a broad-based and genes for serogroup-specific response contributed to genetic variation in vaccine response. Furthermore, preliminary data in 389 progeny showed that polymorphism within the ovine major histocompatibility (MHC) based on serological classification accounted for a significant proportion of the variation in vaccine responses. In subsequent experimentation, we examined the importance of genetic polymorphism within the ovine MHC, and the possibility of genes outside the MHC for their involvement in antigen-specific and broad-based vaccine response. Within two large half sib families(131, and 143 progeny), four MHC haplotypes were investigated and found to be associated with differential antibody responses to six out of eight distinct vaccine-antigens presented to the host in a multi-valent vaccine. The model used here shows how well characterised immunogens, quantitative genetic experimentation, and molecular gene mapping tools can be used to unravel genetic differences in host responses to commercial vaccines.
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