We proposed a novel statistical approach for the analysis of cDNA experiments based on mixed-model methodology combined with mixtures of distributions. Our objective was to detect genes that may be involved in conferring heritable differences in susceptibility to common infections in intensive pig production. We employed a microarray expression profiling strategy and a mixed-model approach to the analysis of the expression data. A cDNA microarray of pig with 6,420 probes from immune tissues and cells was used to compare gene expression in peripheral blood leukocytes of two pigs showing extreme performance in their response to infection with Actinobacillus pleuropneumoniae. Principal components analyses were used to identify the two most extreme-performing pigs after infection (i.e., pigs whose measured responses to infection fell at the extremes). Blood samples and expression profiles from 0 to 24 h after infection were compared using a bivariate, mixed-model approach, in which the effect gene x immunological status interaction was treated as a random effect. Bayesian model-based clustering via mixtures of normal distributions of the resulting BLUP of the random interaction was approached and resulted in a list of 307 differentially expressed genes, of which 179 were down-regulated in the susceptible pig. The majority of the differentially expressed genes were derived from a cDNA library of leukocytes of A. pleuropneumoniae-challenged pigs that were subtracted against leukocytes before the challenge. These results provide evidence that the proposed statistical approach was useful in enhancing the knowledge of the mechanisms involved in the genetics of the immune response.

A genome linkage scan was carried out using a resource flock of 1029 sheep in six half-sib families. The families were offspring of sires derived by crossing divergent lines of sheep selected for response to challenge with the intestinal parasitic nematode Trichostrongylus colubriformis. All animals in the resource flock were phenotypically assessed for worm resistance soon after weaning using a vaccination/challenge regime. After correcting for fixed effects using a least squares linear model the faecal egg count data obtained following the first challenge and the faecal egg count data obtained after the second challenge were designated Trait 1 and Trait 2, respectively. A total of 472 lambs drawn from the phenotypic extremes of the Trait 2 faecal egg count distribution were genotyped with a panel of 133 microsatellite markers covering all 26 sheep autosomes. Detection of quantitative trait loci (QTL) for each of the faecal egg count traits was determined using interval analysis with the Animap program with recombination rates between markers derived from an existing marker map. No chromosomal regions attained genome-wide significance for QTL influencing either of the traits. However, one region attained chromosome-wide significance and five other regions attained point-wise significance for the presence of QTL affecting parasite resistance.

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.

A whole genome scan for quantitative trait loci (QTL) affecting 11 fleece and wool traits was carried out in a flock of medium wool Merino sheep. The flock consisted of 489, sheep in 5 sire groups with family sizes ranging from 59 to 139 offspring. On average 73% of the animals in each family were genotyped with a panel of 130 microsatellite markers, spread throughout the genome. Interval analysis of the data revealed 18 peaks with maximum logarithm of the odds scores (LOD) greater than or equal to 2. Critical P-values for QTL detection, accounting for the large number of hypotheses tested, were estimated by calculating the expected false discovery rate (FDR). For the distribution of LOD score peaks found the FDR always exceeded 0.65 indicating that little evidence was found against all null hypotheses of no QTL present. Evidence for a QTL affecting mean fibre diameter (LOD=2.01) was found on chromosome 1 in agreement with previously reported results of a candidate gene study. The results of the present study may be useful to indicate, chromosomal segments on which to concentrate future genotyping for QTL although the conservative conclusion that must be drawn is that no significant evidence for the segregation of fleece and wool QTL was found in this flock.

Previous work using Southern analysis of genomic DNA detected a polymorphism at the 5' end of the sheep and cattle IgE gene. Identical length differences found between fragments following digestion with restriction enzymes indicated that the basis for the polymorphism was an insertion/deletion event. To characterise the polymorphism, the entire cattle and sheep CE genes were sequenced including 668 bp of 5' untranslated DNA. Sequence comparison revealed a high degree of similarity between the ovine and bovine genes at both the nucleotide and amino acid level. A feature of the 5' untranslated DNA was the presence of an :37 bp repeat starting at --365 upstream of the CE Start site. PCR primers were designed to span most of the 5' untranslated sequence, including the repeat unit, and used to amplify genomic DNA from a panel of 40 sheep. Three alleles were found with frequencies of 0.7, 0.29, 0.01 which were identical to the Southern analysis results. Sequencing of the two commonest alleles revealed the basis for the polymorphism was a 36 bp deletion from the 87 bp repeat.Association studies in a sheep selection flock phenotypically assessed for parasite resistance found a highly significant association between one of the IgE alleles and resistance to the intestinal nematode parasite Trichostrongylus colubriformis (P = 0.005), Attempts to confirm this finding in two other flocks using linkage analysis and genotype association failed to find any significant associations between the IgE polymorphism and resistance to either 7: colubriformis or Haemonchus contortus. (C) 2001 Elsevier Science B.V. All rights reserved.

Animal GeneticsVolume 31, Issue 2 p. 148-148 Dinucleotide repeat polymorphism at the ovine Mcma1, Mcma2, Mcma5, Mcma8, Mcma9, Mcma11, Mcma14, Mcma20, Mcma24, Mcma26 loci J F Maddox, J F Maddox Centre for Animal Biotechnology, University of Melbourne, Parkville 3052, Australia;Search for more papers by this authorC D Riffkin, C D Riffkin Centre for Animal Biotechnology, University of Melbourne, Parkville 3052, Australia;Search for more papers by this authorK J Beh, K J Beh McMaster Laboratory, CSIRO Division of Animal Production, Locked Bag 1, Delivery Centre, Blacktown 2148, AustraliaSearch for more papers by this author J F Maddox, J F Maddox Centre for Animal Biotechnology, University of Melbourne, Parkville 3052, Australia;Search for more papers by this authorC D Riffkin, C D Riffkin Centre for Animal Biotechnology, University of Melbourne, Parkville 3052, Australia;Search for more papers by this authorK J Beh, K J Beh McMaster Laboratory, CSIRO Division of Animal Production, Locked Bag 1, Delivery Centre, Blacktown 2148, AustraliaSearch for more papers by this author First published: 09 October 2008 https://doi.org/10.1046/j.1365-2052.2000.00593.xCitations: 4 J. Maddox ( [email protected]) Read the full textAbout ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat No abstract is available for this article.Citing Literature Volume31, Issue2March 2000Pages 148-148 RelatedInformation

Animal GeneticsVolume 31, Issue 3 p. 228-241 Brief Notes First published: 02 January 2002 https://doi.org/10.1046/j.1365-2052.2000.031003228.xCitations: 9About ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinked InRedditWechat No abstract is available for this article.Citing Literature Volume31, Issue3June 2000Pages 228-241 RelatedInformation

Animal GeneticsVolume 27, Issue 1 p. 57-57 Ovine dinucleotide repeat polymorphism at the McM218, McM150 and McMl38 loci D. J. Hulme, D. J. Hulme McMaster Laboratory, CSIRO Division of Animal Health, Locked Bag 1, Blacktown, NSW 2148, AustraliaSearch for more papers by this authorK. P. Davies, K. P. Davies Centre for Animal Biotechnology, Department of Veterinary Science, The University of Melbourne, Parkville, Vic. 3052, AustraliaSearch for more papers by this authorK. J. Beh, K. J. Beh McMaster Laboratory, CSIRO Division of Animal Health, Locked Bag 1, Blacktown, NSW 2148, AustraliaSearch for more papers by this authorJ. F. Maddox, J. F. Maddox Centre for Animal Biotechnology, Department of Veterinary Science, The University of Melbourne, Parkville, Vic. 3052, AustraliaSearch for more papers by this author D. J. Hulme, D. J. Hulme McMaster Laboratory, CSIRO Division of Animal Health, Locked Bag 1, Blacktown, NSW 2148, AustraliaSearch for more papers by this authorK. P. Davies, K. P. Davies Centre for Animal Biotechnology, Department of Veterinary Science, The University of Melbourne, Parkville, Vic. 3052, AustraliaSearch for more papers by this authorK. J. Beh, K. J. Beh McMaster Laboratory, CSIRO Division of Animal Health, Locked Bag 1, Blacktown, NSW 2148, AustraliaSearch for more papers by this authorJ. F. Maddox, J. F. Maddox Centre for Animal Biotechnology, Department of Veterinary Science, The University of Melbourne, Parkville, Vic. 3052, AustraliaSearch for more papers by this author First published: February 1996 https://doi.org/10.1111/j.1365-2052.1996.tb01179.xCitations: 3AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article.Citing Literature Volume27, Issue1February 1996Pages 57-57 RelatedInformation

A novel repetitive DNA sequence in the sheep parasitic nematode Ostertagia circumcincta was cloned and sequenced. This 1.2-kb sequence (Oc1B) was not found in the closely related cattle parasite Ostertagia ostertagi, nor in the more distantly related sheep parasites Haemonchus contortus or Trichostrongylus colubriformis. Sequences similar to Oc1B were found at various genomic locations and contained a pair of 33-bp direct repeats. Oc1B also contained a single copy of a 218-bp sequence (designated OcREP) which was present in 100 to 200 copies in the O. circumcincta genome and mostly organized in distinctive tandem arrays. The dual organizational pattern of OcREP as both a satellite-like sequence as well as interspersed as single copies amongst dissimilar sequences adds to the growing evidence for the fluidity of the parasitic nematode genome, and of eukaryotic genomes in general.

Animal GeneticsVolume 27, Issue 1 p. 57-58 Polymorphic Atlantic salmon, Salmo salar L., microsatellites at the SSOSL438, SSOSL439 and SSOSL444 loci A. Slettan, A. Slettan Department of Morphology, Genetics and Aquatic Biology, Norwegian College of Veterinary Medicine, PO Box 8146 Dep., N-0033 Oslo, NorwaySearch for more papers by this authorI. Olsaker, I. Olsaker Department of Morphology, Genetics and Aquatic Biology, Norwegian College of Veterinary Medicine, PO Box 8146 Dep., N-0033 Oslo, NorwaySearch for more papers by this author Ø Lie, Ø Lie Department of Morphology, Genetics and Aquatic Biology, Norwegian College of Veterinary Medicine, PO Box 8146 Dep., N-0033 Oslo, NorwaySearch for more papers by this author A. Slettan, A. Slettan Department of Morphology, Genetics and Aquatic Biology, Norwegian College of Veterinary Medicine, PO Box 8146 Dep., N-0033 Oslo, NorwaySearch for more papers by this authorI. Olsaker, I. Olsaker Department of Morphology, Genetics and Aquatic Biology, Norwegian College of Veterinary Medicine, PO Box 8146 Dep., N-0033 Oslo, NorwaySearch for more papers by this author Ø Lie, Ø Lie Department of Morphology, Genetics and Aquatic Biology, Norwegian College of Veterinary Medicine, PO Box 8146 Dep., N-0033 Oslo, NorwaySearch for more papers by this author First published: February 1996 https://doi.org/10.1111/j.1365-2052.1996.tb01180.xCitations: 78AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article.Citing Literature Volume27, Issue1February 1996Pages 57-58 RelatedInformation

The abundance of microsatellite sequences available for exploitation as genetic markers will lead eventually to dense genetic maps for a number of livestock species. Evenly spaced markers covering the entire genome selected from these maps can be used in linkage studies to detect markers associated with economically important traits and ultimately to track down the genes responsible. While such approaches are most readily applied to traits influenced by a single major gene, linkage analysis techniques have been applied to discover chromosome segments carrying genes with an effect on quantitative traits such as parasite resistance. However, given the relative sparsity of the sheep genetic map, discovery of the precise genes responsible will require supplementation of linkage methods with more direct approaches. These approaches will involve pinpointing gents by differential analysis of DNA or mRNA. This paper therefore provides a review of current strategies available for detection of genetic markers associated with important traits, with particular emphasis on approaches for detection of suitable candidate genes that can he tested for their effect on parasite resistance by linkage analysis. Genetic marker technology promises significant increases in accuracy when selecting livestock for breeding resulting in increased rates of generic progress.

Selection of sheep for resistance to internal parasites represents a viable option for future parasite control. Many phenotypic measures are available for determining the level of infection in individual sheep, although no phenotypic markers are available which allow prediction of an individual's resistance status. Genetic markers are therefore the best way to incorporate parasite resistance into selection programmes. With the recent development of genetic maps, several experiments are underway to search for markers linked to parasite-resistance genes in sheep. It can be predicted confidently that markers associated with resistance will be discovered within 12 months. Markers useful as selection criteria will be available within 5 years, although considerable quantitative genetic analysis needs to be done to find the best way to utilise marker information in selection programmes. In future, methods for differential DNA analysis or mRNA expression will lead to isolation of the genes involved.

We report the first extensive ovine genetic linkage map covering 2070 cM of the sheep genome. The map was generated from the linkage analysis of 246 polymorphic markers, in nine three-generation full-sib pedigrees, which make up the AgResearch International Mapping Flock. We have exploited many markers from cattle so that valuable comparisons between these two ruminant linkage maps can be made. The markers, used in the segregation analyses, comprised 86 anonymous microsatellite markers derived from the sheep genome, 126 anonymous microsatellites from cattle, one from deer, and 33 polymorphic markers of various types associated with known genes. The maximum number of informative meioses within the mapping flock was 222. The average number of informative meioses per marker was 140 (range 18-209). Linkage groups have been assigned to all 26 sheep autosomes.

Animal GeneticsVolume 26, Issue 5 p. 369a-370 Polymorphic sheep microsatellites at the McM2, McM131, McM135, McM136, McM140, McM200, McM214, McM373, McM505, McM507 and McM512 loci D J Hulme, Corresponding Author D J Hulme McMaster Laboratory, CSIRO Division of Animal Health, Locked Bag 1, Blacktown, NSW 2148, AustraliaCorrespondenceSearch for more papers by this authorA J Smith, A J Smith McMaster Laboratory, CSIRO Division of Animal Health, Locked Bag 1, Blacktown, NSW 2148, AustraliaSearch for more papers by this authorJ P Silk, J P Silk McMaster Laboratory, CSIRO Division of Animal Health, Locked Bag 1, Blacktown, NSW 2148, Australia CSIRO Division of Plant Industry, Canberra, ACT, AustraliaSearch for more papers by this authorJ M Redwin, J M Redwin McMaster Laboratory, CSIRO Division of Animal Health, Locked Bag 1, Blacktown, NSW 2148, Australia Dept. Veterinary Pathology, University of Sydney, NSW, AustraliaSearch for more papers by this authorK J Beh, K J Beh CSIRO Division of Plant Industry, Canberra, ACT, AustraliaSearch for more papers by this author D J Hulme, Corresponding Author D J Hulme McMaster Laboratory, CSIRO Division of Animal Health, Locked Bag 1, Blacktown, NSW 2148, AustraliaCorrespondenceSearch for more papers by this authorA J Smith, A J Smith McMaster Laboratory, CSIRO Division of Animal Health, Locked Bag 1, Blacktown, NSW 2148, AustraliaSearch for more papers by this authorJ P Silk, J P Silk McMaster Laboratory, CSIRO Division of Animal Health, Locked Bag 1, Blacktown, NSW 2148, Australia CSIRO Division of Plant Industry, Canberra, ACT, AustraliaSearch for more papers by this authorJ M Redwin, J M Redwin McMaster Laboratory, CSIRO Division of Animal Health, Locked Bag 1, Blacktown, NSW 2148, Australia Dept. Veterinary Pathology, University of Sydney, NSW, AustraliaSearch for more papers by this authorK J Beh, K J Beh CSIRO Division of Plant Industry, Canberra, ACT, AustraliaSearch for more papers by this author First published: October 1995 https://doi.org/10.1111/j.1365-2052.1995.tb02681.xCitations: 9 AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article.Citing Literature Volume26, Issue5October 1995Pages 369a-370 RelatedInformation

Animal GeneticsVolume 25, Issue 6 p. 434-435 Ten polymorphic ovine microsatellites D J Hulme, D J Hulme McMaster Laboratory, CSIRO Division of Animal Health, Private Bag 1, Glebe, 2037, NSW, AustraliaSearch for more papers by this authorJ P Silk, J P Silk McMaster Laboratory, CSIRO Division of Animal Health, Private Bag 1, Glebe, 2037, NSW, Australia *CSIRO Division of Plant Industry. Canberra. ACT, AustraliaSearch for more papers by this authorJ M Redwin, J M Redwin McMaster Laboratory, CSIRO Division of Animal Health, Private Bag 1, Glebe, 2037, NSW, Australia Molecular Animal Genetics Centre, CSIRO Division of Tropical Animal Production, Ritchie Research Complex. University of Queensland. St Lucia. Qld, Australia.Search for more papers by this authorW. Barendse, W. Barendse McMaster Laboratory, CSIRO Division of Animal Health, Private Bag 1, Glebe, 2037, NSW, Australia ‡current address Department of Veterinary Pathology, University of Sydney. Sydney, NSW, AustraliaSearch for more papers by this authorK J Beh, K J Beh McMaster Laboratory, CSIRO Division of Animal Health, Private Bag 1, Glebe, 2037, NSW, AustraliaSearch for more papers by this author D J Hulme, D J Hulme McMaster Laboratory, CSIRO Division of Animal Health, Private Bag 1, Glebe, 2037, NSW, AustraliaSearch for more papers by this authorJ P Silk, J P Silk McMaster Laboratory, CSIRO Division of Animal Health, Private Bag 1, Glebe, 2037, NSW, Australia *CSIRO Division of Plant Industry. Canberra. ACT, AustraliaSearch for more papers by this authorJ M Redwin, J M Redwin McMaster Laboratory, CSIRO Division of Animal Health, Private Bag 1, Glebe, 2037, NSW, Australia Molecular Animal Genetics Centre, CSIRO Division of Tropical Animal Production, Ritchie Research Complex. University of Queensland. St Lucia. Qld, Australia.Search for more papers by this authorW. Barendse, W. Barendse McMaster Laboratory, CSIRO Division of Animal Health, Private Bag 1, Glebe, 2037, NSW, Australia ‡current address Department of Veterinary Pathology, University of Sydney. Sydney, NSW, AustraliaSearch for more papers by this authorK J Beh, K J Beh McMaster Laboratory, CSIRO Division of Animal Health, Private Bag 1, Glebe, 2037, NSW, AustraliaSearch for more papers by this author First published: December 1994 https://doi.org/10.1111/j.1365-2052.1994.tb00543.xCitations: 38 AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article.Citing Literature Volume25, Issue6December 1994Pages 434-435 RelatedInformation

Animal GeneticsVolume 26, Issue 2 p. 124-125 Five polymorphic ovine microsatellites A J Smith, Corresponding Author A J Smith CSIRO Division of Animal Health, McMaster Laboratory, Private Bag 1, PO Glebe, New South Wales 2037, AustraliaCorrespondenceSearch for more papers by this authorD J Hulme, D J Hulme CSIRO Division of Animal Health, McMaster Laboratory, Private Bag 1, PO Glebe, New South Wales 2037, AustraliaSearch for more papers by this authorK J Beh, K J Beh CSIRO Division of Animal Health, McMaster Laboratory, Private Bag 1, PO Glebe, New South Wales 2037, AustraliaSearch for more papers by this author A J Smith, Corresponding Author A J Smith CSIRO Division of Animal Health, McMaster Laboratory, Private Bag 1, PO Glebe, New South Wales 2037, AustraliaCorrespondenceSearch for more papers by this authorD J Hulme, D J Hulme CSIRO Division of Animal Health, McMaster Laboratory, Private Bag 1, PO Glebe, New South Wales 2037, AustraliaSearch for more papers by this authorK J Beh, K J Beh CSIRO Division of Animal Health, McMaster Laboratory, Private Bag 1, PO Glebe, New South Wales 2037, AustraliaSearch for more papers by this author First published: April 1995 https://doi.org/10.1111/j.1365-2052.1995.tb02649.xCitations: 5AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat No abstract is available for this article.Citing Literature Volume26, Issue2April 1995Pages 124-125 RelatedInformation