Selection on MHC-linked microsatellite loci in sheep populations

Microsatellites within the major histocompatibility complex (MHC) region have received increasing attention as proxy measures of the level of polymorphism at the Mhc genes themselves. We assessed the diversity of microsatellite loci within or in close proximity of the Mhc genes in several breeds of domestic sheep (Ovis aries) and the wild Mouflon (Ovis orientalis musimon). This was compared to variation at other microsatellite loci scattered throughout the sheep genome. Significantly higher number of alleles were observed at the MHC microsatellites. The sheep breeds studied fell into high- and low-diversity group. This grouping is not related to the agricultural use of the breeds, whether for milk, meat or wool. It is, however, correlated with the geographic origins of the breeds. Southern breeds are genetically more diverse than northern breeds. The observed heterozygosity was in most cases lower than Hardy-Weinberg expectations. The potential impact of selective breeding by man on this is discussed. Neutrality tests indicated that for most of the breeds, the distribution of alleles at the MHC-linked microsatellites are more even than would be expected if the genes were neutral and sampled from populations under drift-mutation equilibrium. Hitchhiking due to tight linkage with alleles at the MHC loci that are under balancing selection is proposed as a possible explanation for this pattern.     

Is Knowing the Age-Order of Alleles in a Sample Useful in Testing for Selective Neutrality?

The most powerful, and most frequently used, test of selective neutrality, based on data consisting of observed allelic frequencies in a sample of genes at some locus, is the procedure of G. A. Watterson. This procedure uses the sample homozygosity F* as the test statistic, and in effect leads to rejection of the hypothesis of selective neutrality if the observed value of F* differs significantly from neutral theory expectations. The homozygosity statistic is invariant under relabeling of the alleles and thus cannot use any further information on the alleles which might be available. We present results which suggest that information concerning the age order of the alleles cannot be used to provide a more powerful testing procedure than that of Watterson.     

Expressed 2-5A synthetase genes and pseudogenes in the marine sponge Geodia barretti

In cattle, bovine leukocyte antigens (BoLAs) have been extensively used as markers for bovine diseases and immunological traits. In this study, we sequenced alleles of the BoLA class II loci, BoLA-DRB3 and BoLA-DQA1, from 650 Japanese cattle from six herds [three herds (507 animals) of Japanese Black cattle and three herds (143 animals) of Holstein cattle] using polymerase chain reaction-sequence-based typing (PCR-SBT) methods. We identified 26 previously reported distinct DRB3 alleles in the two populations: 22 in Japanese Black and 17 in Holstein. The number of DRB3 alleles detected in each herd ranged from 9 to 20. Next, we identified 15 previously reported distinct DQA1 alleles: 13 in Japanese Black and 10 in Holstein. The number of alleles in each herd ranged from 6 to 10. Thus, allelic divergence is significantly greater for DRB3 than for DQA1. A population tree on the basis of the frequencies of the DRB3 and DQA1 alleles showed that, although the genetic distance differed significantly between the two cattle breeds, it was closely related within the three herds of each breed. In addition, Wu-Kabat variability analysis indicated that the DRB3 gene was more polymorphic than the DQA1 gene in both breeds and in all herds, and that the majority of the hypervariable positions within both loci corresponded to pocket-forming residues. The DRB3 and DQA1 heterozygosity for both breeds within each herd were calculated based on the Hardy-Weinberg equilibrium. Only one Japanese Black herd showed a significant difference between the expected and observed heterozygosity at both loci. This is the first report presenting a detailed study of the allelic distribution of BoLA-DRB3 and -DQA1 genes in Japanese Black and Holstein cattle from different farms in Japan. These results may help to develop improved livestock breeding strategies in the future.     

Validation of 15 microsatellites for parentage testing in North American bison, Bison bison and domestic cattle

Fifteen bovine microsatellites were evaluated for use in parentage testing in 725 bison from 14 public populations, 178 bison from two private ranches and 107 domestic cattle from five different breeds. The number of alleles per locus ranged from five to 16 in bison and from five to 13 in cattle. On average, expected heterozygosity, polymorphism information content (PIC) and probability of exclusion values were slightly lower in bison than in cattle. A core set of 12 loci was further refined to produce a set of multiplexed markers suitable for routine parentage testing. Assuming one known parent, the core set of markers provides exclusion probabilities in bison of 0.9955 and in cattle of 0.9995 averaged across all populations or breeds tested. Tests of Hardy-Weinberg and linkage equilibrium showed only minor deviations. This core set of 12 loci represent a powerful and efficient method for determining parentage in North American bison and domestic cattle.     

A comparative study of major histocompatibility complex antigens in East African and European cattle breeds

An account is given of the serologically defined class I specificities encoded by the bovine MHC (expressed as the BoLA system) in two populations of African cattle and in European breeds. The BoLA typing was performed using alloantisera raised against tissue antigens of both European and African breeds of cattle. All of the specificities agreed in the first two international BoLA workshops were found in the African cattle, although there were significant differences in the frequency of some specificities between the African and European animals. Many of the European antisera, which are operationally monospecific in Bos taurus cattle, were multispecific in the African animals. Subgroups of two specificities (w8 and w10) were demonstrated. Five new BoLA-A locus alleles were detected by means of antisera raised against alloantigens of African cattle. Two of these occurred at an extremely high frequency in the African populations; one being unique to these cattle. Monoclonal antibodies proved to be useful typing reagents, particularly in the elucidation of subgroups.     

Increased heterozygosity and allele variants are seen in Texel compared to Suffolk sheep

In this study, the Suffolk and Texel sheep breeds were compared for microsatellite marker heterozygosity throughout seven chromosomal regions in the sheep genome. A total of 623 Texel animals and 489 Suffolk animals in five and three half-sib families, respectively, were genotyped for microsatellite markers across the seven different chromosomes. Using the observed allele frequencies, the expected levels of heterozygosity were calculated for each family. The expected levels of heterozygosity did not significantly differ between the breeds across all regions studied. However, levels of expected heterozygosity were 32% higher in Texel animals on chromosome 4 due to a region of increased heterozygosity between BMS648 and BM3212. The number of allelic variants significantly differed between the breeds, solely due to a region of increased number of alleles on chromosome 20. This region of higher numbers of allele variants in the Texel breed extended from the MHC to c. 15 cM distal to the MHC region incorporating markers OMHC1, CSRD226, TGLA387 and BM1818, which had 3.30, 7.02, 3.09 and 6.75 more alleles in Texel than in Suffolk animals, respectively. No difference was observed in the variance of allele frequency between the two breeds. It is proposed that previous selective sweeps may have reduced numbers of alleles and levels of heterozygosity in the Suffolk breed.     

Heterozygosity excess at the cattle DRB locus revealed by large scale genotyping of two closely linked microsatellites

A method for MHC DRB typing in cattle based on two closely linked and highly polymorphic microsatellites is described. The two microsatellites DRBP1ms and DRB3ms are located in intron 2 of the corresponding DRB gene. The very strong linkage disequilibrium between the two loci made it possible to establish DRB microsatellite haplotypes. The typing results with this method on reference samples followed closely that obtained with RFLP and direct sequence analysis of DRB3 exon 2. The method is well suited for large scale genotyping and was successfully applied for typing more than 600 unrelated animals representing 23 breeds. The data were used to test whether the observed DRB allele frequency distributions were consistent with that expected for selectively neutral alleles in populations at mutation-drift equilibrium. A significant heterozygosity excess was detected and there was an obvious trend across breeds towards a more even allele frequency distribution than expected. The deviation may be due to balancing selection acting on the DRB locus or by recent population bottlenecks.     

Contrasting patterns of variation in MHC loci in the Alpine newt

Major histocompatibility complex (MHC) genes are essential in pathogen recognition and triggering an adaptive immune response. Although they are the most polymorphic genes in vertebrates, very little information on MHC variation and patterns of evolution are available for amphibians, a group known to be declining rapidly worldwide. As infectious diseases are invoked in the declines, information on MHC variation should contribute to devising appropriate conservation strategies. In this study, we examined MHC variation in 149 Alpine newts ( Mesotriton alpestris ) from three allopatric population groups in Poland at the northeastern margin of the distribution of this species. The genetic distinctiveness of the population groups has previously been shown by studies of skin graft rejection, allozymes and microsatellites. Two putative expressed MHC II loci with contrasting levels of variation and clear evidence of gene conversion/recombination between them were detected. The Meal-DAB locus is highly polymorphic (37 alleles), and shows evidence of historical positive selection for amino acid replacements and substantial geographical differentiation in allelic richness. On the contrary, the Meal-DBB locus exhibits low polymorphism (three alleles differing by up to two synonymous substitutions) and a uniform distribution of three alleles among geographical regions. The uniform frequencies of the presumptively neutral Meal-DBB alleles may be explained by linkage to Meal-DAB . We found differences in allelic richness in Meal-DAB between regions, consistent with the hypothesis that genetic drift prevails with increasing distance from glacial refugia. Pseudogene loci appear to have evolved neutrally. The level of DAB variation correlated with variation in microsatellite loci, implying that selection and drift interplayed to produce the pattern of MHC variation observed in marginal populations of the Alpine newt.     

Joint Report of the Third International Bovine Lymphocyte Antigen (BoLA) Workshop, Helsinki, Finland, 27 July 1986

Summary. Two hundred and eighty-two alloantisera were submitted by 20 participating laboratories from 13 countries and tested against lymphocytes of 1298 cattle. The cell panel consisted of samples from 38 Bos taurus breeds, 11 Bos taurus crossbreeds, 4 Bos indicus breeds, 6 Bos taurus X Bos indicus , and a variety of other crossbred populations. Using a standardized lymphocytotoxicity test, all 17 previously identified BoLA specificities were confirmed. The workshop produced agreement on 16 new lymphocyte alloantigenic specificities. Three of the new specificities behaved as splits of previously identified BoLA specificities. Four of the new specificities behaved as alleles at the agreed BoLA-A locus. Seven new specificities are tentatively assigned to the BoLA-A locus but require further definition. Two new specificities may represent products of a second closely-linked BoLA locus.     

Microsatellite DNA typing for assessment of genetic variability in Tharparkar breed of Indian zebu (Bos indicus) cattle, a major breed of Rajasthan

The present study estimates genetic variability with a set of 25 microsatellite markers in a random sample of 50 animals of Tharparkar breed of Indian zebu (Bos indicus) cattle. Tharparkar is a dual-purpose breed, valued for its milk as well as draught utility, and is adapted to the inhospitable Thar desert conditions of Rajasthan typified by summer temperature hovering above 50 degrees C, sparse rainfall and vegetation, and scarcity of even drinking water. The observed number of alleles ranged from 4 (ETH3, ILSTS030, INRA5, INRA63 and MM8) to 11 (HEL9 and ILSTS034), with allelic diversity (average number of observed alleles per locus) of 6.20. Observed and expected heterozygosity ranged from 0.25 (INRA63) to 0.77 (ETH10), and from 0.51 (HEL5 and HAUT27) to 0.88 (HEL9) respectively. Wide range of genetic variability supported the utility of these microsatellite loci in measurement of genetic diversity indices in other Indian cattle breeds too. Various average genetic variability measures, namely allele diversity (6.20), observed heterozygosity (0.57), expected heterozygosity (0.67) and mean polymorphism information content (0.60) values showed substantial within-breed genetic variability in this major breed of Rajasthan, despite accumulated inbreeding as reflected by high average inbreeding coefficient (F(IS) = 0.39). The Tharparkar population has not experienced a bottleneck in the recent past.     

Breed differences in the distribution of BoLA-A locus antigens in American cattle

A total of 627 cattle representing seven breeds from south central Nebraska, USA were tested for 37 BoLA antigens which behave as products of 37 distinct alleles of the class I BoLA-A locus. Four antigens were absent from all breeds tested. The other antigens showed marked and statistically significant differences in breed distribution. There was no evidence for blank (null) alleles. The number of alleles in each breed ranged from 10 to 20. The Hereford and Simmental populations tested were less polymorphic than the Angus, Brown Swiss, Charolais, Gelbvieh and Limousin populations.     

Indigenous domestic breeds as reservoirs of genetic diversity: the Argentinean Creole cattle

Contrary to highly selected commercial breeds, indigenous domestic breeds are composed of semi-wild or feral populations subjected to reduced levels of artificial selection. As a consequence, many of these breeds have become locally adapted to a wide range of environments, showing high levels of phenotypic variability and increased fitness under natural conditions. Genetic analyses of three loci associated with milk production (alpha(S1)-casein, kappa-casein and prolactin) and the locus BoLA-DRB3 of the major histocompatibility complex indicated that the Argentinean Creole cattle (ACC), an indigenous breed from South America, maintains high levels of genetic diversity and population structure. In contrast to the commercial Holstein breed, the ACC showed considerable variation in heterozygosity (H(e)) and allelic diversity (A) across populations. As expected, bi-allelic markers showed extensive variation in He whereas the highly polymorphic BoLA-DRB3 showed substantial variation in A, with individual populations having 39-74% of the total number of alleles characterized for the breed. An analysis of molecular variance (AMOVA) of nine populations throughout the distribution range of the ACC revealed that 91.9-94.7% of the total observed variance was explained by differences within populations whereas 5.3-8.1% was the result of differences among populations. In addition, the ACC breed consistently showed higher levels of genetic differentiation among populations than Holstein. Results from this study emphasize the importance of population genetic structure within domestic breeds as an essential component of genetic diversity and suggest that indigenous breeds may be considered important reservoirs of genetic diversity for commercial domestic species.     

Gene Frequency Distribution of the BoLA-DRB3 Locus in Saavedreño Creole Dairy Cattle

The objective of this study is to describe the gene frequency distribution of the bovine lymphocyte antigen (BoLA)-DRB3 locus in Saavedreño Creole dairy cattle and to compare it with previously reported patterns in other cattle breeds. One hundred and twenty-five Saavedreño Creole dairy cattle were genotyped for the BoLA-DRB3.2 allele by polymerase chain reaction and restriction fragment length polymorphism. Twenty-two out of 53 previously identified BoLA-DRB3.2 alleles were detected, with gene frequencies ranging from 0.4 to 16.8%. Seventy percent of the variation corresponded to the seven most frequent alleles (BoLA-DRB3.2*7, *8, *11, *16, *27, *36, and *37). The studied population exhibits a high degree of expected heterozygosity (h _e = 0.919). The F _IS index did not show significant deviation from Hardy-Weinberg equilibrium. However, the neutrality test showed an even gene frequency distribution. This result could be better explained assuming balancing selection instead of neutral or positive selection for one or a few alleles. In conclusion, the results of this study demonstrated that BoLA-DRB3.2 is a highly polymorphic locus in Saavedreño Creole dairy cattle, with significant variation in allele frequency among cattle breeds.     

Isolation and characterization of new polymorphic microsatellite loci in the mixotrophic orchid Limodorum abortivum L. Swartz (Orchidaceae)

Here, we report the isolation and characterization of 11 polymorphic microsatellites in Limodorum abortivum. Allele variability has been characterized in three populations from Southern Italy and France. The number of alleles ranged from one to six per locus with an average of 3.8 alleles per locus. Observed and expected heterozygosity values ranged from 0.000 to 1.000 and from 0.492 to 0.806, respectively, with striking differences among populations. These microsatellites should be valuable tools for studying fine-scale genetic structure of scattered Limodorum abortivum populations, patterns of relationship with closely related taxa and the evolutionary ecology of its mycorrhizal interactions.     

Microsatellite polymorphism in locus OMHC1 (MHC Class I) in Polish Heath Sheep and Polish Lowland Sheep (Zelazna variety)

Our study aimed at comparative analysis of microsatellite polymorphism in locus OMHC1 (MHC Class I) in Polish Heath Sheep and Polish Lowland Sheep (Zelazna variety). The study was conducted on 100 ewes of each breed. We identified 13 alleles of the gene in Polish Heath Sheep and 9 in Polish Lowland Sheep. We found marked differences in frequency of OMHC1 alleles between both breeds. The heterozygosity coefficient and PIC, amounting to 0.79 and 0.77 for Polish Heath Sheep, and 0.82 and 0.80 for Polish Lowland Sheep, respectively, suggest considerable variability in both breeds. Additionally, the values of both coefficients indicate that OMHC1 locus can be used as a genetic marker.     

Selective pressures on MHC class II genes in the guppy (Poecilia reticulata) as inferred by hierarchical analysis of population structure

Genes of the major histocompatibility complex, which are the most polymorphic of all vertebrate genes, are a pre‐eminent system for the study of selective pressures that arise from host–pathogen interactions. Balancing selection capable of maintaining high polymorphism should lead to the homogenization of MHC allele frequencies among populations, but there is some evidence to suggest that diversifying selection also operates on the MHC. However, the pattern of population structure observed at MHC loci is likely to depend on the spatial and/or temporal scale examined. Here, we investigated selection acting on MHC genes at different geographic scales using Venezuelan guppy populations inhabiting four regions. We found a significant correlation between MHC and microsatellite allelic richness across populations, which suggests the role of genetic drift in shaping MHC diversity. However, compared to microsatellites, more MHC variation was explained by differences between populations within larger geographic regions and less by the differences between the regions. Furthermore, among proximate populations, variation in MHC allele frequencies was significantly higher compared to microsatellites, indicating that selection acting on MHC may increase population structure at small spatial scales. However, in populations that have significantly diverged at neutral markers, the population‐genetic signature of diversifying selection may be eradicated in the long term by that of balancing selection, which acts to preserve rare alleles and thus maintain a common pool of MHC alleles.     

Population fragmentation and major histocompatibility complex variation in the spotted suslik,Spermophilus suslicus

The fragmentation of populations typically enhances depletion of genetic variation, but highly polymorphic major histocompatibility complex (MHC) genes are thought to be under balancing selection and therefore retain polymorphism despite population bottlenecks. In this study, we investigate MHC DRB (class II) exon 2 variation in 14 spotted suslik populations from two regions differing in their degree of habitat fragmentation and gene flow. We found 16 alleles that segregated in a sample of 248 individuals. The alleles were highly divergent and revealed the hallmark signs of positive selection acting on them in the past, showing a significant excess of nonsynonymous substitutions. This excess was concentrated in putative antigen‐binding sites, which suggests that past selection was driven by pathogens. MHC diversity was significantly lower in fragmented western populations than in the eastern populations, characterized by significant gene flow. In contrast to neutral variation, amova did not reveal genetic differentiation between the two regions. This may indicate similar selective pressures shaping MHC variation in both regions until the recent past. However, MHC allelic richness within a population was correlated with that for microsatellites. F_ST outlier analyses have shown that population differentiation at DRB was neither higher nor lower than expected under neutrality. The results suggest that selection on MHC is not strong enough to counteract drift that results from recent fragmentation of spotted suslik populations.     

HLA polymorphism in the Havasupai: evidence for balancing selection.

The characterization and analysis of genetic variation at the HLA loci provides important insight for population geneticists trying to understand the evolutionary forces that have shaped human populations. This study describes the HLA-A and HLA-B loci serotyping and statistical analysis on an isolated Native American population, the Havasupai of Arizona. Four alleles at the HLA-A locus were identified, while eight alleles were found at the HLA-B locus. These variants were present as 20 of 32 potential two-locus haplotypes, with five of the six most common haplotypes exhibiting high positive linkage disequilibrium. Significant homozygote deficiency (heterozygosity excess) was detected both at HLA-A and at HLA-B. This deviation from Hardy-Weinberg proportions was not attributable to nonselective causes such as different allele frequencies in males and females or avoidance of consanguineous matings. In addition, the distribution of alleles at both HLA-A and HLA-B was more even than expected from neutrality theory; that is, the observed Hardy-Weinberg homozygosity was only 62.4% of that expected under neutrality. These observations suggest that balancing selection is of major importance in maintaining genetic variation at HLA-A and HLA-B.     

A comparison of variability and population structure for major histocompatibility complex and microsatellite loci in California coastal steelhead (Oncorhynchus mykiss Walbaum)

The major histocompatibility complex (MHC) contains genes integral to immune response in vertebrates. MHC genes have been shown to be under selection in a number of vertebrate taxa, making them intriguing for population genetic studies. We have conducted a survey of genetic variation in an MHC class II gene for steelhead trout from 24 sites in coastal California and compared this variation to that observed at 16 presumably neutral microsatellite loci. A high amount of allelic variation was observed at the MHC when compared to previously published studies on other Pacific salmonids. Elevated nonsynonymous substitutions, relative to synonymous substitutions, were detected at the MHC gene, indicating the signature of historical balancing selection. The MHC data were tested for correlations to and deviations from the patterns found with the microsatellite data. Estimates of allelic richness for the MHC gene and for the microsatellites were positively correlated, as were estimates of population differentiation (F(ST)). An analysis for F(ST) outliers indicates that the MHC locus has an elevated F(ST) relative to the neutral expectation, although a significant result was found for only one particular geographical subgroup. Relatively uniform allele frequency distributions were detected in four populations, although this finding may be partially due to recent population bottlenecks. These results indicate that, at the scale studied here, drift and migration play a major role in the observed geographical variability of MHC genes in steelhead, and that contemporary selection is relatively weak and difficult to detect.