Dense genetic maps of human, mouse, and rat genomes that are based on coding genes and on microsatellite and single-nucleotide polymorphism markers have been complemented by precise gene homolog alignment with moderate-resolution maps of livestock, companion animals, and additional mammal species. Comparative genetic assessment expands the utility of these maps in gene discovery, in functional genomics, and in tracking the evolutionary forces that sculpted the genome organization of modern mammalian species.

/pdf/the-promise-of-comparative-genomics-in-mammals-16sbdcyddp.pdf

The Promise of Comparative Genomics in Mammals

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.

/pdf/an-enhanced-linkage-map-of-the-sheep-genome-comprising-more-2w3idinz54.pdf

An Enhanced Linkage Map of the Sheep Genome Comprising More Than 1000 Loci

A small genetic region near the telomere of ovine chromosome 18 was previously shown to carry the mutation causing the callipyge muscle hypertrophy phenotype in sheep. Expression of this phenotype is the only known case in mammals of paternal polar overdominance gene action. A region surrounding two positional candidate genes was sequenced in animals of known genotype. Mutation detection focused on an inbred ram of callipyge phenotype postulated to have inherited chromosome segments identical-by-descent with exception of the mutated position. In support of this hypothesis, this inbred ram was homozygous over 210 Kb of sequence, except for a single heterozygous base position. This single polymorphism was genotyped in multiple families segregating the callipyge locus (CLPG), providing 100% concordance with animals of known CLPG genotype, and was unique to descendants of the founder animal. The mutation lies in a region of high homology among mouse, sheep, cattle, and humans, but not in any previously identified expressed transcript. A substantial open reading frame exists in the sheep sequence surrounding the mutation, although this frame is not conserved among species. Initial functional analysis indicates sequence encompassing the mutation is part of a novel transcript expressed in sheep fetal muscle we have named CLPG1.

/pdf/identification-of-the-single-base-change-causing-the-412sohu0ea.pdf

Identification of the Single Base Change Causing the Callipyge Muscle Hypertrophy Phenotype, the Only Known Example of Polar Overdominance in Mammals

In dairy cattle, the widespread use of artificial insemination has resulted in increased selection intensity, which has led to spectacular increase in productivity. However, cow fertility has concomitantly severely declined. It is generally assumed that this reduction is primarily due to the negative energy balance of high-producing cows at the peak of lactation. We herein describe the fine-mapping of a major fertility QTL in Nordic Red cattle, and identify a 660-kb deletion encompassing four genes as the causative variant. We show that the deletion is a recessive embryonically lethal mutation. This probably results from the loss of RNASEH2B, which is known to cause embryonic death in mice. Despite its dramatic effect on fertility, 13%, 23% and 32% of the animals carry the deletion in Danish, Swedish and Finnish Red Cattle, respectively. To explain this, we searched for favorable effects on other traits and found that the deletion has strong positive effects on milk yield. This study demonstrates that embryonic lethal mutations account for a non-negligible fraction of the decline in fertility of domestic cattle, and that associated positive effects on milk yield may account for part of the negative genetic correlation. Our study adds to the evidence that structural variants contribute to animal phenotypic variation, and that balancing selection might be more common in livestock species than previously appreciated.

/pdf/a-660-kb-deletion-with-antagonistic-effects-on-fertility-and-2a0j49pwzb.pdf

A 660-Kb deletion with antagonistic effects on fertility and milk production segregates at high frequency in Nordic Red cattle: additional evidence for the common occurrence of balancing selection in livestock.

Diseases of the musculoskeletal system

Transmissible Spongiform Encephalopathies (TSE's) are neurodegenerative disorders characterized by a long generation time, spongy degeneration in the cerebral gray matter, neuronal loss and proliferation and hypertrophy of glial cells. An abnormal form of the prion protein (PrP) plays a major part in TSE pathogenesis and has been hypothesized to be the only component of the infectious agent. Some animals exposed to scrapie, the TSE affecting sheep and goats, seem to be resistant to development of the disease. Alleles encoding amino acid substitutions at codons 136 (A/V) and 171 (Q/R/H) have been associated with scrapie resistance. Other amino acid substitutions at codons 112 (Mff), 137 (Mff), 141 (L/F), 154 (R/H), and 211 (R/Q) have been reported but not associated with scrapie resistance. It may be possible to reduce the incidence of ovine scrapie by increasing the frequency of resistant genotypes (AA-136, RR171, or QR-171 ). Thus, an important consideration is the frequency of these genotypes in different breeds of sheep. In this study, the genetic sequence for codons 104-175 was determined for at least ten animals of ten sheep breeds (n=207). Genotypes at codons 112, 136, 154, and 171 were determined. For codon 136, the frequency of the susceptible allele (V) was less than 0.20 in all breeds. In contrast, the frequency of the susceptible allele (Q) at codon 171 ranged from 0.27 (St. Croix) to 0.96 (Hampshire). In addition, a previously unreported substitution was found at codon 143 (H/R), with frequencies as high as 0.40. Introduction Scrapie, a neurodegenerative disorder affecting sheep and goats, is one of a group of diseases known as transmissible spongiform encephalopathies (TSEs). Up until the 1960's, it was believed that scrapie and other TSEs were caused by a slow acting virus. Alper et al. (1967) demonstrated that the scrapie agent was resistant to levels of UV radiation that would destroy most known pathogens, including viruses. Prusiner et al. (1981) found a protein that was in scrapie infected tissues but not in normal tissues. It was then shown (Prusiner, 1982) that the protein was present in two isoforms. Based on these findings, Prusiner (1982) formulated the "protein-only" hypothesis for TSE transmission. The prion protein (PrP) is expressed in nervous tissue and in the lymphoreticular system. PrPc is the normal form and PrPsc is the abnormal, disease causing form (Figure 1 ). It is thought that the abnormal form serves as a template for a posttranslational misfolding of the normal cellular protein. Accumulation of the abnormal, protease resistant PrPsc is associated with disease. Another protein, protein X, is thought to take part in this refolding process and may be one of the reasons for species specificity of prion diseases (Prusiner 1996). The ovine PrP gene sequence contains three exons and covers over 20 kb of DNA (Westaway et al. 1994). The PrP open reading frame (ORF) is contained in exon three. There have been seven polymorphisms reported in the ovine ORF (Bossers et al. 1996); two of these ( codons 136 and 171) have been associated with scrapie susceptibility. Perhaps amino acid substitutions at these sites increase the chances of PrPsc propagation when an animal is exposed to scrapie. Animals differ in PrP amino acid sequences and therefore differ in susceptibility to the scrapie agent. Furthermore, alleles encoding these amino acid changes vary between breeds as do the polymorphisms that are most important in scrapie susceptibility. Therefore, it would be interesting to know allele frequencies at the various polymorphic sites in breeds of sheep. The purpose of this project was to determine allele frequencies at PrP polymorphisms in ten different

Characterization of the Prion Protein (PRP) Gene in Ten Breeds of Sheep

Spider Lamb Syndrome (SLS) is a semi-lethal congenital disorder, causing severe skeletal abnormalities in sheep. The syndrome has now been disseminated into several sheep breeds in the United States, Canada, and Australia. The mode of inheritance for SLS is autosomal recessive, making the identification and culling of carrier animals difficult due to their normal phenotype. Two large pedigrees segregating for the SLS mutation were established, and a genome scan with genetic markers from previously published genome maps of cattle and sheep was used to map the locus causing SLS. Genetic linkage between SLS and several microsatellite markers, OarJMP8, McM214, OarJMP12, and BL1038, was detected, thereby mapping the SLS locus to the telomeric end of ovine Chromosome (Chr) 6. Alignment of ovine Chr 6 with its evolutionary ortholog, human Chr 4, revealed a positional candidate gene, fibroblast growth factor receptor 3 (FGFR3).

Localization of the locus causing Spider Lamb Syndrome to the distal end of ovine Chromosome 6.

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Characterization of the Prion Protein (PRP) Gene in Ten Breeds of Sheep

Localization of the locus causing Spider Lamb Syndrome to the distal end of ovine Chromosome 6.