Regression was performed on the results of each simulation run and on the average heterozygosity over all runs. Heterozygosity, adjusted heterozygosity and number of alleles were examined as functions of distance from GDF The R parameter defines the rate of exponential increase a higher R reflects a faster response of the variable to small changes in distance near GDF The fit of the data to the relevant curve was measured by the significance of the fit and the percentage variation accounted for by the fitted curve V.
The fit to an exponential curve was not significant for Belgian Blue.
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Allele number Table 1 also increased with distance from GDF -8 in all breeds, but was not significant in the non-DM breeds. The other breeds had three or more alleles. Asturiana had 10 such pairs, Belgian Blue and Piedmontese each had six. The beef breeds had more marker pairs with significant LD than did the dairy breeds; Aberdeen Angus had a particularly large number of significant pairs 9.
Toro de Lidia also had nine significant pairs. We also compared levels of LD between the four markers at the telomeric end of chromosome 2 opposite end of the chromosome from GDF- 8. Out of 6 possible significant pairs, Belgian Blue had one and Toro de Lidia had two. The proportion of the variance in allele size because of breed is shown in Figure 4. The ratio of the mean-squared error between breeds to the residual within-breed mean-squared error ie the F -ratio is plotted as a function of distance from GDF Our expectation was that the ratio of these variances should be greater for markers near the gene because of selection on GDF -8 in some breeds but not others and because the DM breeds carry different alleles at this locus.
Ratio of variance in allele size because of breed to residual variance for each marker all breeds included as a function of distance from GDF Figure 5a shows the average final heterozygosity per locus over 24 runs as a function of chromosomal distance from the selected locus after 33 generations of evolution under the basic model initial heterozygosity at all loci was 0. Final heterozygosity increased with distance from the selected locus.
There was no dramatic difference in this ratio between the basic model and models assuming either smaller or larger population size, artificial insemination, overlapping generations, multiple 10 alleles, stronger selection or smaller allelic effect. Mutation both circular and alternative models and weaker selection did significantly increase the heterozygosity ratio; locus-specific mutation rates further increased the impact of mutation on heterozygosity.
With the higher mutation rate, heterozygosity was almost unchanged by selection. Standard error bars are shown. Additional simulations were performed to try to identify realistic conditions under which the hitchhiking effect would be lost. A low mutation rate was applied. The average heterozygosity at the end of these 33 further generations at 1cM from the selected gene was 0. Figure 5b shows the final heterozygosity as a function of chromosomal position for the basic mutation model as in Figure 5a but with 10 alleles rather than two and mutation allowed and the model described above mixed model where 50 generations of low selection preceded the 33 generations of basic selection.
When the period of low selection was included in the model, the heterozygosity profile became flat closer to the selected locus than for the basic model, as reflected in the lower value of R. A detailed analysis of bovine chromosome 2 demonstrates detectable effects of selection on GDF -8, the locus associated with double-muscling in several cattle breeds. We compared several population genetic measures between three DM and six non-DM breeds and found that they differed in their patterns of heterozygosity and numbers of alleles along chromosome 2, although some non-DM breeds showed similarity to the DM breeds in their heterozygosity patterns.
When heterozygosity was adjusted to account for intermarker diversity, the double-muscled breeds showed a significant correlation between heterozygosity and distance from GDF LD between pairs of loci was greater within DM breeds than dairy breeds. However, there was also a large amount of LD within the beef breeds and a breed used for bull-fighting. LD results were also consistent with Dunner et al , in that there was greater LD within Asturiana than Belgian Blue, suggesting a more recent introduction of the allele into Asturiana.
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Finally, the ratio of between- to within-breed variance in allele size increased with proximity to GDF -8, consistent with differences in selection history and allele frequencies between the breeds. The results from our analyses of chromosome 2 were not as dramatic as seen in the basic model we simulated.
Modifications of the basic model indicate several factors that could account for this difference. A very high mutation rate of the microsatellites near GDF -8 could explain why the reduction in heterozygosities near GDF -8 was not as large as might have been expected and why LD was not as strong.
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It seems unlikely that by chance, all or most of the microsatellites we chose had higher than average mutation rates, although between-locus variability in mutation rates could contribute to reducing the hitchhiking effect. A combination of weak selection and moderate mutation could possibly explain the pattern of results.
Alternatively, it may be that the history of double-muscling in some breeds is similar to the model we examined with a period of weak selection followed by stronger selection. If so, this could explain why the chromosome 2 results differed from the predictions of the basic model. Then, at some point in recent history, breeders began to select more strongly for the allele and it rose to high frequency or fixation.
This would be consistent with the wide diversity of myostatin haplotypes seen in European cattle breeds Dunner et al, Under this scenario, the LD between GDF -8 and neutral markers at the beginning of the selective sweep the period where strong selection was imposed would be lower than that for a model where strong selection coincided with the introduction of the mutation. As a result, the probability of detecting a hitchhiking effect would be reduced. Our own data from a study on South Devon cattle, another breed with double-muscling, indicate that even if farmers strongly favour the DM phenotype, effective selection when the trait is rare is likely to be weak.
This is because of the difficulties in assessing the genotype on heterozygous individuals Wiener et al, Our results and previously published work on Asturiana de los Valles Dunner et al, demonstrate that selection on GDF -8 has left a stronger mark on this breed than the other two DM breeds. This indicates that the double-muscling mutation the same mutation as found in Belgian Blue has been in the Asturiana a shorter time than in the other two breeds. There could be confounding factors in the comparison of DM and non-DM breeds. If there is another gene near to GDF -8 under selection in all breeds, then differences between DM and non-DM breeds might be over-shadowed.
Alternatively, GDF -8 may itself have been under selection in the non-DM breeds, but perhaps for different alleles, for example, for those which increase the lean muscle mass of an animal Lin et al, This could help to explain the fact that beef breeds showed greater LD than dairy breeds and that beef breeds had significant and nearly significant asymptotic regression curves for heterozygosity as a function of distance from GDF In a previous study, we analysed samples from these breeds for non-synonymous sequence variants within the coding regions of GDF -8 and none were found Smith et al, and unpublished data.
However, it is possible that variants do exist in promoter regions of the gene. Alternatively, an excess of LD could be caused by population structure rather than selection. Thus, it is possible that peculiarities eg, recent admixture of previously isolated populations in the history of Aberdeen Angus and Toro de Lidia, which showed particularly high levels of LD, led to a great excess of LD throughout the genome.
The elevated number of significant LD pairs at the opposite end of chromosome 2 suggests that this may be the case for Toro de Lidia. Calculating LD for markers on other chromosomes would help to resolve this issue.
The results from our study indicate that such an approach would not have clearly identified the region of the myostatin gene at least at the density of markers used in this study. A similar approach was used more successfully in a study of natural rat populations under strong selection for resistance to anticoagulants.
In comparing several population genetic parameters, Kohn et al found large differences between rat populations where resistance had evolved to high levels and those where resistance was low or nonexistent. They used patterns of LD for 26 microsatellite markers in five rat populations to improve positioning of the anticoagulant-resistance gene in rats, which had already been localized to a 6-cM region.
These results indicate that there is a stronger hitchhiking effect than found in the DM cattle breeds. This suggests that the mutation for anticoagulant resistance is relatively recent and that selection pressure imposed by anticoagulant use is stronger than breeders' preferences for double-muscling, which is not surprising.
Our study shows that before implementing such an approach for mapping trait genes in livestock, it will be important to have information on the age and history of selection of the trait in particular breeds so that breeds can be chosen to maximize the chances of success. Alternative methods that utilize haplotype data eg, Sabeti et al, may turn out to be more powerful, but have the disadvantage of requiring additional data to infer phase.
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Detecting recent positive selection in the human genome from haplotype structure. Nature : — Story highlights A transgender man says testosterone has changed his life But finding a girlfriend gets a bit complicated. A transgender man, Gutierrez grew up as a woman.