A genome-screen experiment to detect quantitative trait loci affecting resistance to facial eczema disease in sheep

Facial eczema (FE) is a secondary photosensitization disease arising from liver cirrhosis caused by the mycotoxin sporidesmin. The disease affects sheep, cattle, deer and goats, and costs the New Zealand sheep industry alone an estimated NZ$63M annually. A long-term sustainable solution to this century-old FE problem is to breed for disease-resistant animals by marker-assisted selection. As a step towards finding a diagnostic DNA test for FE sensitivity, we have conducted a genome-scan experiment to screen for quantitative trait loci (QTL) affecting this trait in Romney sheep. Four F(1) sires, obtained from reciprocal matings of FE resistant and susceptible selection-line animals, were used to generate four outcross families. The resulting half-sib progeny were artificially challenged with sporidesmin to phenotype their FE traits measured in terms of their serum levels of liver-specific enzymes, namely gamma-glutamyl transferase and glutamate dehydrogenase. In a primary screen using selective genotyping on extreme progeny of each family, a total of 244 DNA markers uniformly distributed over all 26 ovine autosomes (with an autosomal genome coverage of 79-91%) were tested for linkage to the FE traits. Data were analysed using Haley-Knott regression. The primary screen detected one significant and one suggestive QTL on chromosomes 3 and 8 respectively. Both the significant and suggestive QTL were followed up in a secondary screen where all progeny were genotyped and analysed; the QTL on chromosome 3 was significant in this analysis.

The constituents of Microctonus sp. parasitoid venoms

Purified RNA transcripts from venom glands dissected from the parasitoid wasp Microctonus hyperodae were copied, cloned and sequenced using traditional dideoxy sequencing methods. Using mass spectrometry analysis of the trypsinised PAGE gel protein bands we identified the RNA transcripts for the 3 most abundant proteins found in the venom and hence obtained their full protein sequence. Other abundant transcripts were also further sequenced. To reduce the effort required to obtain transcript information we dissected venom glands from a second parasitoid, Microctonus aethiopoides (Morocco biotype). The RNA transcripts were purified and reverse transcribed but instead of cloning the cDNA it was directly sequenced using Roche GS20 pyrosequencing. Results from a single GS20 sequencing run provided data similar to that obtained by the traditional methods used in analysing transcripts from M. hyperodae in a fraction of the time and cost. Comparing the transcripts between the two species showed that a similar range of genes are expressed with the putative orthologs of seven of the eight full length genes characterised from M. hyperodae being found in M. aethiopoides. Pyrosequencing should provide a valuable new method for rapidly sampling transcripts from a wide range of specialised insect tissues.

Effect of myostatin F94L on carcass yield in cattle

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.

Genomic analysis of Oryctes rhinoceros virus reveals genetic relatedness to Heliothis zea virus 1

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.

The use of genetic modification technologies in the discovery of genes affecting production traits and disease resistance in animals

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.

Evaluation of single-nucleotide polymorphisms in CAPN1 for association with meat tenderness in cattle

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.

Linkage disequilibrium in domestic sheep

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.

Familial predictors of treatment outcome in childhood anxiety disorders

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.

Superior efficacy of olanzapine over haloperidol: analysis of patients with schizophrenia from a multicenter international trial

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.

Weight change and atypical antipsychotic treatment in patients with schizophrenia

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.

Fluid particle accelerations in fully developed turbulence

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.

Genetic variation within the Merino sheep breed: analysis of closely related populations using microsatellites

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.

Genetic characterisation of protective vaccine responses in sheep using multi-valent Dichelobacter nodosus vaccines

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.

Catalase gene is associated with facial eczema disease resistance in sheep

Facial eczema (FE) is a hepatogenous photosensitization disease of ruminant animals, particularly in sheep which vary widely in their susceptibility to the disease. The liver damage is caused by the mycotoxin, sporidesmin. There is evidence that the toxicity of sporidesmin is due to its ability to generate 'active oxygen' species. We evaluated the catalase gene, which encodes an enzyme with antioxidant functions, as a candidate for determining the susceptibility of sheep to the disease. Two microsatellite markers, OarSHP3 and OarSHP4, which flank the sheep catalase gene, were isolated from a Yeast Artificial Chromosome (YAC) clone. These markers mapped the catalase locus by linkage to ovine chromosome 15. Eleven informative markers spaced throughout chromosome 15, inclusive of the catalase marker OarSHP4, gave no significant linkage with the disease traits when analysed in four outcross resource pedigrees. However, OarSHP3 and OarSHP4 allele frequencies showed significant differences between FE resistant and susceptible selection-lines. Comparison of sequences of catalase cDNAs from sheep of resistant and susceptible lines showed only two silent mutations. A single nucleotide polymorphisms (KP1) in exon 6 of the catalase gene also showed significant differences in allele frequencies between the selection lines. The lack of evidence for linkage in outcross pedigrees, but the significant association in the genetic lines, implies that catalase is involved in determining the susceptibility of sheep to facial eczema, and that the candidate gene's effect is probably recessive or minor.

Isolation and mapping of the first ruminant multidrug resistance genes

The first ruminant multiple drug resistance gene (MDR1) has been cloned and sequenced from sheep. Sequence data revealed the sheep MDR1 gene to have high sequence and structural similarity to other characterized MDR proteins from humans and rodents. A restriction fragment length polymorphism was discovered using the EcoRI enzyme and used to map the MDR1 gene to sheep chromosome 4. Physical mapping using fluorescent in situ hybridisation confirmed this map placement and assigned the MDR1 locus in the region 4q15-q21. The ovine MDR2 gene was also cloned and found to map to the same region as MDR1.

A second-generation linkage map of the sheep genome

A genetic map of Ovis aries (haploid n = 27) was developed with 519 markers (504 microsatellites) spanning approximately 3063 cM in 26 autosomal linkage groups and 127 cM (female specific) of the X Chromosome (Chr). Genotypic data were merged from the IMF flock (Crawford et al., Genetics 140, 703, 1995) and the USDA mapping flock. Seventy-three percent (370/504) of the microsatellite markers on the map are common to the USDA-ARS MARC cattle linkage map, with 27 of the common markers derived from sheep. The number of common markers per homologous linkage group ranges from 5 to 22 and spans a total of 2866 cM (sex average) in sheep and 2817 cM in cattle. Marker order within a linkage group was consistent between the two species with limited exceptions. The reported translocation between the telomeric end of bovine Chr 9 (BTA 9) and BTA 14 to form ovine Chr 9 is represented by a 15-cM region containing 5 common markers. The significant genomic conservation of marker order will allow use of linkage maps in both species to facilitate the search for quantitative trait loci (QTLs) in cattle and sheep.

Cloning, sequencing and linkage mapping of the NRAMP1 gene of sheep and deer

The ovine NRAMP1 and cervine NRAMP1 cDNAs were cloned by RT PCR of RNA derived from macrophage enriched leukocyte preparations. The complete coding and 3' regions were sequenced. Both sheep and deer NRAMP1 proteins are 548 amino acids long. There are 77 and 73 amino acid differences, respectively, compared to the mouse Nramp1 sequence. Dinucleotide repeats were found in both the ovine and cervine 3' non-coding sequence. Amplification of these regions in individual sheep and deer showed them to be polymorphic microsatellites. They have polymorphism information content values of 0.76 and 0.84 in sheep and deer, respectively. Using these microsatellites, the ovine NRAMP1 gene was mapped in a linkage group on ovine chromosome 2q and cervine NRAMP1 was mapped in a linkage group syntenic with human chromosome 2, mouse chromosome 1 and sheep chromosome 2.

Microsatellite evolution: testing the ascertainment bias hypothesis

Previous studies suggest the median allele length of microsatellites is longest in the species from which the markers were derived, suggesting that an ascertainment bias was operating. We have examined whether the size distribution of microsatellite alleles between sheep and cattle is source dependent using a set of 472 microsatellites that can be amplified in both species. For those markers that were polymorphic in both species we report a significantly greater number of markers (P < 0.001) with longer median allele sizes in sheep, regardless of microsatellite origin. This finding suggests that any ascertainment bias operating during microsatellite selection is only a minor contributor to the variation observed.

Extensive genomic conservation of cattle microsatellite heterozygosity in sheep

We report the evaluation of 1036 bovine microsatellite primer pairs for their suitability as linkage markers in sheep. Approximately 58% (605/1036) of bovine primer pairs amplified a locus in sheep. Sixty-seven per cent (409/605) of amplified loci were detected as polymorphic. Marker heterozygosity, allele number and range of allele sizes were significantly lower in sheep than cattle sampled in this study. However, median fragment size was similar. These data suggest that high-resolution comparative linkage maps between closely related species can be constructed relatively efficiently.

The acute and long-term effect of olanzapine compared with placebo and haloperidol on serum prolactin concentrations

Prolactin elevation is both a common and a persistent event with the currently marketed antipsychotics, excluding clozapine. Elevations have been associated with both acute (galactorrhea, amenorrhea) and chronic (predisposition to osteoporosis) treatment-emergent adverse events. One of the defining criteria for an atypical antipsychotic is the relative lack of persistent prolactinemia. A double-blind, placebo- (N = 68) and haloperidol- (Hal: 15 +/- 5 mg/day, N = 69) controlled trial of three dose ranges of olanzapine (Olz-L: 5 +/- 2.5 mg/day, N = 65; Olz-M: 10 +/- 2.5 mg/day, N = 64; Olz-H: 15 +/- 2.5 mg/day, N = 69) in the treatment of schizophrenia afforded the opportunity to assess the temporal course of the influence of olanzapine and haloperidol on serum prolactin concentration. Consistent with its potent D2 antagonism, haloperidol was associated with a statistically significantly higher incidence of treatment-emergent prolactin elevation (72%) than seen with placebo (8%; p < 0.001) at week 2 of therapy. Expectedly, this elevation was also persistent at weeks 4 and 6. In contrast, olanzapine-associated treatment-emergent prolactin elevations were both lower in magnitude and transient. At week 2, 38% of the Olz-H, 24% of the Olz-M, and 13% of the Olz-L treatment groups exhibited a treatment-emergent prolactin elevation, with a mean increase of 0.35, 0.52, and 0.61 nmol/l, respectively; for haloperidol the mean increase was 1.23 nmol/l. For only the Olz-M and the Olz-H treatment groups did the week 2 incidence of treatment-emergent prolactin elevations differ statistically significantly from placebo. Both the incidence of elevations and the mean increase, in prolactin concentration were less than that seen with haloperidol. Furthermore, by treatment week 6, all three olanzapine groups exhibited incidences of treatment-emergent prolactin elevation that were comparable to placebo and were statistically significantly less than observed with haloperidol. Rapid adaptation was observed in the temporal course of prolactin elevations associated with olanzapine based on both the categorical analysis of treatment-emergent high values and the analyses of temporal change in mean concentrations. In contrast to haloperidol, the magnitudes of the treatment-emergent elevations associated with olanzapine were minimal. The rates of elevation were approximately one-half to one-third those observed with haloperidol and were significantly more transient. Olanzapine, even at the highest doses (15 +/- 2.5 mg/day) used, was not associated with persistent elevations of prolactin, consistent with an 'atypical' pharmacologic profile.

Olanzapine versus haloperidol: acute phase results of the international double-blind olanzapine trial

A 6-week acute phase of an international 1-year double-blind study was conducted comparing three dose ranges of olanzapine (5 +/- 2.5 mg/day, 10 +/- 2.5 mg/day, and 15 +/- 2.5 mg/day) with a fixed dose of olanzapine (1.0 mg/day) and with a dose range of haloperidol (15 +/- 5 mg/day) in the treatment of 431 patients with schizophrenia. The purpose was to determine whether olanzapine demonstrated a dose-related ability to decrease overall psychopathology with minimal associated extrapyramidal symptoms in patients with schizophrenia. The high-dose olanzapine group showed statistically significantly greater improvement in overall psychopathology based on mean change in the CGI Severity score and statistically significantly greater improvement in positive psychotic symptoms based on mean change in both the BPRS positive score and the PANSS positive score compared with the 1.0-mg/day olanzapine group. Analyses indicated that an increasing dose-response curve was observed across the range of all olanzapine dose groups. Acute extrapyramidal syndromes were reported less frequently among all olanzapine groups compared with the haloperidol group. Endpoint mean change on both the Simpson-Angus Scale and the Barnes Akathisia Scale reflected improvement for all olanzapine treatment groups compared with worsening for the haloperidol group. Olanzapine was associated with weight gain but did not appear to have any clinically meaningful effect on vital signs. Although olanzapine was associated with some increase in prolactin concentrations, increases were transient, occurred less often, and were of lesser magnitude than those observed with haloperidol.

The red deer (Cervus elaphus) contains two expressed major histocompatibility complex class II DQB genes

The highly variable second exons of the red deer (Cervus elaphus) major histocompatibility complex (MHC) DQB genes were cloned and sequenced. Eight different expressed DQB sequences were isolated from four unrelated red deer. Either two or three different DQB sequences were isolated from each individual, demonstrating that more than one DQB gene is expressed in red deer. This is consistent with other ruminant, which also have multiple expressed copies of the DQB gene. The sequences ranged in similarity from 81.3% to 97.6% with an average similarity of 90.2%; this indicates that at least one of the DQB genes is highly polymorphic.

Mapping the Horns (Ho) locus in sheep: a further locus controlling horn development in domestic animals

The presence or absence of horns in Merino sheep is under the genetic control of the autosomal Horns (Ho) locus. Sheep chromosome OOV1 is a candidate region for the Ho locus because it shows conserved synteny with cattle chromosome BBO1 where the cattle polled locus has been located. We demonstrate that the Ho locus in sheep is excluded from sheep chromosome OOV1 and we identified linkage between the Ho locus and markers from sheep chromosome OOV10. These data suggest that there are at least two loci affecting the presence or absence of horns in sheep and cattle. The orthologous regions to OOV10 are likely to be on cattle, human, and mouse chromosomes BBO12, HSA13, and MMU14.

Mutations in sheep microsatellites

During the construction of a primary linkage map of the sheep genome, a total of 46,225 parent-offspring transfer of microsatellite alleles were examined through the genotyping of the AgResearch International Mapping Flock. Any observations of mutations were thoroughly rechecked, including examination of new DNA samples, to yield five bona fide mutations from the study. This gave us an observed spontaneous mutation rate for microsatellites in sheep of 1.1 +/- 0.5 x 10(-4) mutations/gamete per locus. Untransformed lymphocytes were used as the source of DNA. Two of the mutations could have happened at either meiosis or during mitotic growth of the male germ cells. The other three mutations probably occurred early in the mitotic generation of the female germ cells. All of the mutations consisted of a 2-bp insertion and occurred in individuals heterozygous at the mutant locus.

Identification and genetic mapping of random amplified polymorphic DNA (RAPD) markers to the sheep genome

The random amplified polymorphic DNA (RAPD) assay utilizes the polymerase chain reaction (PCR) and short primers of arbitrary nucleotide sequence to amplify DNA. In this study, the RAPD assay was used to identify and map polymorphic markers in the AgResearch International Mapping Flock (IMF) sheep pedigrees. Sires and dams of eight of the full-sib IMF pedigrees were screened with 131 different 10-mer oligonucleotide primers. An average of 85 RAPD polymorphisms was identified between each parental pair, and 53 markers were contributed to the AgResearch IMF collaboration. Forty-five of the RAPD markers were mapped in the AgResearch IMF genetic linkage map, and at least one marker was located on 17 of the 26 autosomes and both sex chromosomes. Three lines of evidence were used to check for the homology of scored polymorphisms in different pedigrees, pedigree evaluation, segregation analysis, and Southern blot analysis. These results demonstrate that the RAPD assay is a powerful approach for identifying polymorphisms that can be used as markers for constructing a sheep genetic linkage map.

A linkage map of the ovine X chromosome

A genetic linkage map of the ovine X chromosome containing type I and type II markers has been constructed. The map contains 7 known gene markers and 14 microsatellite markers with a recombination length of 141.9 cM. Segregation of polymorphic markers was observed in a three-generation pedigree containing 480 animals. The maximum number of informative meioses was 912. Additional information was obtained for some markers by following segregation in the AgResearch International Mapping Flock, consisting of nine three-generation full-sib pedigrees. A pseudoautosomal region containing two markers has been identified at one end of the linkage map. Comparisons with mouse and human X chromosomes confirms the observation of Ohno (1973) that the gene content of the mammalian X chromosome is retained. In particular, the conserved grouping of the genes PHKA1, ATP7A, and XIST observed in both the human and the mouse X chromosome appears to be conserved in the sheep X chromosome, and XIST has been mapped to near the center of the chromosome. This study provides the first reported genetic linkage map combining both type I and type II markers for any ruminant X chromosome.

Exclusion probabilities for pedigree testing farm animals

Pedigree testing, using genetic markers, may be undertaken for a variety of situations, of which the classical paternity testing is only one. This has not always been made clear in the literature. Exclusion probabilities associated with various testing situations, including the use of autosomal or X-linked codominant marker systems with any number of alleles, are presented. These formulae can be used to determine the appropriate exclusion probability for the situation being investigated. One such situation is where sire groups of progeny are to be verified without knowledge of the dams' genotypes, in which case the classical paternity exclusion probability is too high, and if used may result in an optimistic declaration about the progeny that have not been excluded. On the other hand, if mating pairs are known then incorrect progeny can be excluded at a higher rate than suggested by paternity exclusion calculations. The formulae also assist in determining the usefulness of X-linked markers, particularly if the pedigree checks involve progeny of only one sex. A system of notation that is useful for the algebraic manipulation of genetic probabilities, including exclusion probabilities as presented here, is also given.

The linkage map of sheep Chromosome 6 compared with orthologous regions in other species

The genetic linkage map of sheep Chromosome (Chr) 6 has been extended to include 35 loci with the addition of 11 RFLP and 12 microsatellite loci. The sex-averaged linkage map now spans 154 cM from phosphodiesterase cyclic GMP beta polypeptide (PDE6B) to OarCP125, an anonymous sheep microsatellite. The male and female map lengths, at 180 cM and 132 cM respectively, did not differ significantly. The physical assignment of PDE6B to Chr 6q33-qter orientates the linkage map on sheep Chr 6 with PDE6B near the telomere and OarCP125 towards the centromere. The order and genetic distances between loci are similar for the sheep Chr 6 and cattle Chr 6 maps, except for the position of the casein genes. The sheep Chr 6 linkage map is also comparable to portions of human Chr 4, mouse Chrs 5 and 3, and pig Chr 8. The synteny between sheep Chr 6 and human Chr 4 has been extended from PDE6B (4p16.3) to epidermal growth factor (EGF, 4q25-q27). However, a region from platelet-derived growth factor receptor alpha polypeptide (PDGFRA) to bone morphogenetic protein 3 (BMP3), which spans 19 cM on sheep Chr 6, appears to be inverted with respect to the human and mouse loci. Other differences in the gene order between sheep, pig, and mouse suggest more complex rearrangements.

The impact of "media contact" on attitudes toward gay men

In order to understand better the relation between "media contact" and attitudes, college students were asked to view a documentary film depicting events surrounding the life and death of a prominent gay politician. The participants completed the Attitudes Toward Homosexuals Scale during screening sessions and either prior to or after viewing the documentary. The film had a significant and positive effect on attitudes. In addition, data on the mood of the subjects were collected and analyzed in light of Devine's (1989) model of prejudice. The findings suggest possible extensions for Devine's model.

Microsatellite evolution in congeneric mammals: domestic and bighorn sheep

We compared genotypes at eight (AC)n microsatellite loci in domestic sheep (Ovis aries) and wild Rocky Mountain bighorn sheep (O. canadensis). The domestic sheep had greater genetic variation, higher allele-size variances, and larger allele sizes than the wild sheep. Accumulating evidence from higher taxonomic comparisons shows that these parameters are biased if microsatellite loci are selected in one taxon and used in another. Our results demonstrate similar biases between congeneric species. We compared standard measures of genetic variation, differentiation, and distance within and between species (H, D, FST) to newer measures based on allele-size variance (SW, SB, RST). The size-based distances better detected species-level divergence, but standard measures better distinguished allopatric populations. Empirical calibration of these measures at the subspecies level is needed to establish their useful ranges.

An autosomal genetic linkage map of the sheep genome

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.

Cloning and sequencing of expressed DRB genes of the red deer (Cervus elaphus) Mhc

The expressed major histocompatibility complex (Mhc) class II DRB genes of 50 unrelated deer were examined by reverse transcription polymerase chain reaction, cloning, and sequencing of DRB exon 2. Deer, like other mammals, have at least one highly polymorphic Mhc class II DRB gene. Thirty-four different sequences were identified. Most of the variation in amino acid composition occurred at positions that have been shown to form the peptide binding site (PBS). Eighteen deer-specific substitutions were found, 11 of these occurred in the PBS. Significantly higher rates of replacement substitutions than silent substitutions were found in the deer sequences, indicating strong positive selection pressure for diversity in DRB sequences. Between one and four DRB sequences were found per deer. Inheritance of these sequences in pedigrees showed Mendelian segregation with up to two expressed DRB genes per haplotype. Sheep are the only other ruminant in which the presence of more than one expressed DRB gene has been demonstrated. Phylogenetic trees were constructed in an attempt to assign the deer DRB sequences to specific loci, but no clear segregation of the DRB sequences for different loci was found. It would seem likely that sequence exchange between the loci has occurred. As has been shown in other species, the alpha-helix and beta-sheet regions of exon 2 appeared to have different evolutionary histories.

Mutations in the sequence flanking the microsatellite at the KAP8 locus prevent the amplification of some alleles

The microsatellite described for the glycine- and tyrosine-rich keratin locus (KAP8) in sheep was used to type nine large three-generation families comprising the AgResearch International Mapping Flock. The apparent non-Mendelian inheritance in these families suggested that some of the microsatellite alleles were not being amplified. Sequence analysis showed that a deletion within one of the published primer sites was the likely cause of the 'null' alleles. By redesigning the primer all alleles could be amplified.