The purpose of this study was to test the presence of LD between some microsatellite loci in and out of MHC in White Karaman, Awassi and Merinolandschaf sheep populations. It was not intended to estimate the degree of LD for the population and loci. Nor was aimed to estimate the gametic frequencies or recombination rate, as no family information was available.
LD can arise via linkage, selection, population admixture with different allele frequencies, random drift in small populations, different allele frequencies in males and females 23. Investigations of different populations showed that LD decreased with the marker distance only for closely linked loci 24,25. However, if there were not other factors, LD due to linkage would be lost after some generations depended on the recombination frequencies between loci 23. Since the samples used in this study were collected randomly from the populations, the animals were as unrelated as possible, and the breeds were old, significant LD due to linkage was not thereby expected. In this study, significant LDs have been found even between unlinked loci or loci mapped with great distance on the same chromosome and these findings agree with this suggestion. This was the case for both before and after pooling. Therefore, it seems that there is no tendency in the sheep populations studied to maintain LD even between closely linked loci in MHC, i.e. due to selection. These results contrast with those of Paterson 8, who found significant LD between MHC linked loci in a free living sheep population. Paterson 8 concluded that LD between the MHC linked loci were maintained due to selection. The populations studied here were kept under the control of human. Thus the selection pressure of diseases on the populations here might have been less than that on the sheep population studied by Paterson 8. The investigations of Ohta 26 and Farnir et al. 24 showed that selection played a less important role than other factors, i.e. inbreeding or population subdividing.
The significant LDs found between unlinked loci in this study is in accordance with the results of Farnir et al. 24 who found significant LD (at p < 0,05) between unlinked loci with a frequency of 12% (out of 281 microsatellite markers). Nevertheless, Tenesa et al. 25 could not observe any significant LDs between unlinked loci (13 loci on two chromosomes, n=50), while they found significant LDs between loci closer than 10 cM. However it is difficult to compare the results of this study with those of Farnir et al. 24 and Tenesa et al. 25 because, the frequencies of gametic genotypes were not estimated here.
After pooling significant deviations were observed between loci and the p-values decreased as low as < 0,05. These results indicate that the significant deviations observed from HWE before pooling could have been due to some rare alleles. A total of 108 tests were performed for three populations [9x(9-1)/2)x3] and seven significant deviations (6,48%) were observed in all populations. This kind of significance can be observed just by chance, if the sample size is small. Significant deviations after pooling were observed only for one or two pairs of loci in the Turkish sheep populations. Significant LDs after pooling between the locus BM1258 and others in Merinolandschaf, seem to be specific for this locus, and could be because of some null alleles. Null alleles arise due to mutations in the nucleotide sequence of the primer binding regions, so that some alleles can not be amplified by using PCR 27.
These results suggest that a population admixture did not occur between the sheep populations studied to cause significant disequilibrium between loci tested. Furthermore, the results suggest that the lack of significant LDs did not indicate a localisation of loci on different chromosomes. As a conclusion the results indicated that the populations in this study were mostly in equilibrium and that selection did not play a major role to maintain the linkage disequilibrium between MHC-linked loci in the populations studied.
Acknowledgement
This study was supported by the Deutsche Forschungsgemeinschaft (Grant No. GE-291/19).