Gametic Associations Research Articles

Mapping Quantitative Trait Loci in a Non-Equilibrium Population

The genetic control of a complex trait can be studied by testing and mapping the genotypes of the underlying quantitative trait loci (QTLs) through their associations with observable marker genotypes. All existing statistical methods for QTL mapping assume an equilibrium population, allowing marker-QTL associations to be simply described at the gametic level. However, many mapping populations in practice may deviate from equilibrium; thus, gametic associations cannot reflect marker-QTL associations at the genotype level. We develop a robust model for mapping QTLs in a non-equilibrium natural population in which individuals are not necessarily randomly mating due to various evolutionary forces. Without use of Hardy-Weinberg equilibrium, the new model founds marker-QTL associations directly on the genotypes, specified by a group of disequilibrium parameters. Simulation studies were performed to test the statistical properties of the model, which suggests that the new model covers current mapping models and can be safely used for any data set.

Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes

BackgroundThe minor histocompatibility antigens (mHags) are self-peptides derived from common cellular proteins and presented by MHC class I and II molecules. Disparities in mHags are a potential risk for the development of graft-versus-host disease (GvHD) in the recipients of bone marrow from HLA-identical donors. Two alleles have been identified in the mHag HA-1. The correlation between mismatches of the mHag HA-1 and GvHD has been suggested and methods to facilitate large-scale testing were afterwards developed.MethodsWe used sequence specific primer (SSP) PCR and direct sequencing to detect HA-1 gene polymorphisms in a sample of 131 unrelated Italian subjects. We then set up a novel melting temperature (Tm) assay that may help identification of HA-1 alleles without oligonucleotide probes.ResultsWe report the frequencies of HA-1 alleles in the Italian population and the presence of an intronic 5 base-pair deletion associated with the immunogeneic allele HA-1H. We also detected novel variable sites with respect to the consensus sequence of HA-1 locus. Even though recombination/gene conversion events are documented, there is considerable linkage disequilibrium in the data. The gametic associations between HA-1R/H alleles and the intronic 5-bp ins/del polymorphism prompted us to try the Tm analysis with SYBR® Green I. We show that the addition of dimethylsulfoxide (DMSO) during the assay yields distinct patterns when amplicons from HA-1H homozygotes, HA-1R homozygotes, and heterozygotes are analysed.ConclusionThe possibility to use SYBR® Green I to detect Tm differences between allelic variants is attractive but requires great caution. We succeeded in allele discrimination of the HA-1 locus using a relatively short (101 bp) amplicon, only in the presence of DMSO. We believe that, at least in certain assets, Tm assays may benefit by the addition of DMSO or other agents affecting DNA strand conformation and stability.

Testing two possible mechanisms for gametic association in human: frozen haplotypes and segregation distortion.

Two possible mechanisms for the development and maintenance of gametic association have been subject to test using family studies (HLA typed) and direct analysis of two linked markers in individual sperm. The mechanisms are: (I) haplotypes frozen against recombination and (2) balanced segregation distortion. In the study of 1,320 families, 86 individuals were identified in the offspring of whom recombination was confirmed or suspected. These individuals displayed allele frequencies of HLA similar to the others in the study, but had significantly different haplotype frequencies. In general, they displayed reduced (or absent) frequencies for the more common haplotypes. Similarly, in the study of meiotic products, recombination was observed in the individual whose HLA phenotypes suggested rare haplotypes, but not in the other individual. Both results were of marginal significance. When the family data were used to test for segregation distortion at HLA-DR, only a marginally significant result was found. However, when the data were classified according to the sex of the parent, a highly significant result was found in females, but not in males. Male segregation distortion was found in the sperm analysis, but was only of marginal statistical significance. The concordant results of two different experimental systems suggest that both mechanisms remain feasible explanations of the gametic associations in this area of the genome, although of the two, segregation distortion is preferable on theoretical grounds.

Two-locus identity probabilities and identity disequilibrium in a partially selfing subdivided population.

Measures of association of genes at different loci (linkage disequilibrium) are widely used to determine whether the structure of natural populations is clonal or not, to map genes from population data, or to test for the homogeneity of response of molecular markers to background selection, for example. However, the usual definitions of parameters for gametic associations may not be suitable for all these purposes. In this paper, we derive the recursion equations for one- and two-locus identity probabilities in an infinite island model. We study the role of drift, gene flow, partial selfing and mutation model on the expected association of genes across loci. We define the 'within-subpopulation identity disequilibrium' as the difference between the joint two-locus probability of identity in state and the expected product of one-locus identity probabilities. We evaluate this parameter as a function of recombination rate, effective size, gene flow and selfing rate. Within-subpopulation identity disequilibrium attains maximum values for intermediate immigration rates, whatever the selfing rate. Moreover, identity disequilibrium may be very small, even for high selfing rates. We discuss the implications of these findings for the analysis of data from natural populations.

Microsatellites in the HLA region: 1999 update.

In this third update of a series of reviews on microsatellites in the HLA region or close to it we report 155 microsatellites, corresponding to 51 newly described markers, in addition to the 103 reported in the 1997 and 1998 reviews. This work is based both on a literature review and on data publicly available in molecular databases on the internet (http://www.gdb.org; http://bioinfo.weizmann.ac.il/cards/; http://cedar.genetics.soton.ac.uk/) up to September 1999. Thanks to numerous studies involving major histocompatibility complex (MHC) microsatellites, documentation on HLA region is proposed, including information on microsatellites described through MHC sequence projects and presenting documented location, polymorphism and amplification condition, together with additional information on previously described microsatellites when available and information on data in the literature regarding gametic associations between HLA region loci and alleles and microsatellite alleles. As basic information are presented various documents: i) a table showing the following characteristics of the 155 microsatellites: name, localisation, polymorphism, primer sequences, reference; ii) an integrated map of some HLA region genes and the 155 microsatellites considered; and iii) a summary table on HLA and microsatellites association patterns. In addition, an overview on HLA microsatellite analysis application is presented, with a special focus on disease genetics studies in the form of recent references where the use of microsatellites of the HLA region was a key tool. This review aims at providing the human immunogenetics community with a tool for helping optimal choice of microsatellites to be used in various studies.

Extensive genome-wide linkage disequilibrium in cattle.

A genome-wide linkage disequilibrium (LD) map was generated using microsatellite genotypes (284 autosomal microsatellite loci) of 581 gametes sampled from the dutch black-and-white dairy cattle population. LD was measured between all marker pairs, both syntenic and nonsyntenic. Analysis of syntenic pairs revealed surprisingly high levels of LD that, although more pronounced for closely linked marker pairs, extended over several tens of centimorgan. In addition, significant gametic associations were also shown to be very common between nonsyntenic loci. Simulations using the known genealogies of the studied sample indicate that random drift alone is likely to account for most of the observed disequilibrium. No clear evidence was obtained for a direct effect of selection ("Bulmer effect"). The observation of long range disequilibrium between syntenic loci using low-density marker maps indicates that LD mapping has the potential to be very effective in livestock populations. The frequent occurrence of gametic associations between nonsyntenic loci, however, encourages the combined use of linkage and linkage disequilibrium methods to avoid false positive results when mapping genes in livestock.

HLA-B44 subtypes and the chance of finding HLA compatible donor/recipient pairs for bone marrow transplantation: a haplotype study of 303 Italian families.

A total of 1176 HLA-A,B,DR haplotypes were reconstructed by typing 303 unrelated families referred to our laboratory during the last seven years for the search of HLA identical sibs in view of bone marrow transplantation. A total of 614 different three-locus haplotypes were found. Most of them (83.6%) were present only once or twice, whereas 24/614 (3.9%) were found 6-28 times each. HLA-B44 was present in 4 of these most frequent haplotypes. HLA-B44 has been implicated as the molecular target for bone marrow allograft rejection. Therefore, a better knowledge of the HLA-B44 haplotype relationships might prove useful for the programming of registries of unrelated bone marrow donors. Eighty five serologically defined HLA-B44 unrelated subjects, either one or both parents from the above families, were subtyped by a high-resolution sequence-specific oligonucleotide probing approach. Moreover, 34 unrelated potential donors recruited for those patients that did not find a suitable donor among their siblings were subtyped also for HLA-B44. B*4403, which accounted for 47/85 (55.3%) serologically defined B44 alleles, appeared in strong, statistically significant, linkage disequilibrium with HLA-A29, -A23 and -DR7. On the other hand, B*4402, which covered virtually all other B44 alleles, showed prevalent gametic associations with HLA-A2 and HLA-A24. The linkage disequilibrium between HLA alleles is the key for the low frequency of HLA-B44 mismatches in donors selected as HLA-A,B,DRB1 identical to patients waiting for unrelated bone marrow transplantation. If a given patient presents unusual haplotypes, the chance of finding HLA-B44 mismatches may be higher because of the presence of different haplotype relationships in the donors.

On Fisher's exact test for detecting gametic disequilibrium between DNA polymorphisms.

Nonrandom associations between DNA polymorphisms are commonly tested by Fisher's exact test in spite of it is seriously conservative. Theoretical statistical studies have shown that the exact test with Tocher's correction does not present this problem but Tocher's correction is never used by experimentalists for detecting gametic associations. We have examined the practical consequences of using these two alternative tests for the detection of nonrandom associations in populations. A total of 1566 pairs of RFLPs of eleven gene regions and sixteen populations from previously published human and Drosophila disequilibrium data were examined. The analysis reveals remarkable differences between the two tests for detecting gametic associations. In some gene regions, the exact test with Tocher's correction detects a percentage of significant associations between RFLPS which is twice or three times higher than that detected by the exact test without correction. Therefore, the widely used exact test can be seriously underestimating disequilibrium in populations. In addition, the study shows that the standard chi-square test for independence in 2 x 2 tables detects a similar percentage of significant associations between RFLPs than Tocher's test.

PCR typing of DNA fragments of the two short tandem repeat (STR) systems upstream of the human myelin basic protein (MBP) gene in Danes and Greenland Eskimos

DNA from the double short tandem repeat (STR) system MBP (locus 18q23-pter) was amplified by the polymerase chain reaction (PCR) and the two polymorphic repeat systems were separated by cutting with the restriction enzyme NlaIII. The lengths of the DNA fragments of the two MBP STR systems MBP-A and MBP-B were analyzed by vertical electrophoresis in polyacrylamide gels followed by silver staining. DNA samples from 112 unrelated Danes, 140 unrelated Greenland Eskimos, and 88 Danish mother/child pairs were analyzed. The distributions of MBP phenotypes were in Hardy-Weinberg equilibrium in both the Eskimo and Danish populations. Significant differences were observed between the distribution of fragments (‘alleles’) in Greenland Eskimos and in Danes. The allele MBP-A7 was considerably more frequent in Eskimos (0.2214) than in Danes (0.0775) and also the allele MBP-B9 was considerably more frequent in Eskimos (0.225) than in Danes (0.06). Strong gametic associations were found between fragments from the MBP-A and MBP-B series in both Danes and Eskimos. Some of the associations were different in Danes and Eskimos. In the 88 Danish mother/child pairs, the segregation of the MBP genotypes were in accordance with a genetic model of co-dominant inheritance and no mutation was found. Two MBP STR regions with irregular structures were sequenced. One fragment had a single base G to A transition at position 124 in the primer binding region between the MBP-A and MBP-B regions. In the other fragment, a deletion starting at position 117 and including the primer binding region between the MBP-A and MBP-B regions was found.

Immune-genetic study of the new populations of Sierra Morena (Spain) through HLA polymorphisms of class I

We have studied the HLA antigenes of class I in 50 families from Andalusia and in 50 families from some towns of Sierra Morena (La Carolina among others), in which an important settlement took place by individuals from Central Europe over 200 years ago, by comparing the allele frequencies with the German population. The obtained results allowed us to conclude that a real mixture of population has occurred. The frequencies of some HLA alleles of class I in the population of Sierra Morena are intermediate to those observed in the original populations, though some phenomena of drifting have been noticed. The study of gametic associations also shows that the population of Sierra Morena behaves as an intermediate population between the two original populations. This is evident in relation to the A1-B8 haplotype, in which the population of Sierra Morena is similar to the original Andalusian population, regarding the frequency of the haplotype, and the German population, because of the intensity of disequilibrium. The study of the genetic distances shows that the ones existing between the populations of Andalusia, Germany and Sierra Morena are small, although they reveal that these populations are clearly defined.

The evolutionary history of Drosophila buzzatii. XXXII. Linkage disequilibrium between allozymes and chromosome inversions in two colonizing populations

Chromosome polymorphism in Drosophila buzzatii is under selection but the genes responsible for the effect of the inversions of fitness are unknown. On the other hand, there is evidence for selection on several allozyme loci but the presence of paracentric inversions on the second chromosome, where most of the polymorphic loci are located, complicates the interpretation. Studies of the associations between allozymes and inversions are thus necessary to help understand the effect of selection at both the chromosomal and allozymic level. Until now this kind of information has only been available in D. buzzatii for two loci, Est-1 and Est-2, in Australian populations. Here we describe the genetic constitution of two Old World populations, Carboneras and Colera. Emphasis has been placed on the analysis of the linkage disequilibria between the second chromosome arrangements and three allozyme loci, Est-2, Pept-2 and Aldox, located on this chromosome. In addition, the recombination frequencies between the loci, and between the loci and the inversion breakpoints, have been estimated and a genetic map of the three loci has been produced. The two populations differ in allele and arrangement frequencies, as well as in the pattern of one-locus disequilibria. Est-2 and Aldox are associated with the second chromosome arrangements in both populations. On the other hand, Pept-2 is associated with the inversions in Colera but not in Carboneras. The gametic associations among the three loci are discussed taking into account the position of these loci on the chromosome map and the lack of recombination in the heterokaryotypes.

Gametic association of HSP70‐1 promoter region alleles and their inclusion in extended HLA haplotypes

Abstract: Gametic associations of a three‐allele polymorphism of the HSP70‐1 promoter region were analyzed in a random North Italian population, in 69 HLA homozygous cell lines and in 29 families in Boston, all typed for HLA class I, class II and complement alleles. Significant phenotypic associations were detected in the random population between HSP70‐1 alleles and several HLA markers carried by extended haplotypes. The inclusion of HSP70‐1 alleles in extended haplotypes, suggested by population analysis, was confirmed in genotyped cells, including 10W HLA homozygous cell lines and families, selected for the presence of the whole set of alleles reported for conserved extended haplotypes. Every tested extended haplotype was exclusively associated with a given HSP70‐1 allele, except those carrying DR1. HSP70‐1 C was included in both [HLA‐B8, SC01, DR3] and [HLA‐B18, F1C30, DR3] extended haplotypes, accounting for the previously observed strong association with DR3. In addition the same allele was found on the [HLA‐B13, SC31, DR7], on the [HLA‐B62, SB42, DR4] and on the [HLA‐B60, SC02, DR13] extended haplotypes. The HSP70‐1 A allele was carried by all DR4+ extended haplotypes except the one above cited. HSP70‐1 B correlated with DR10, DQB1*0501 and BF*F. Thus the HSP70‐1 promoter alleles provide new precisely located markers of extended haplotypes.

Association among quantitative, chromosomal and enzymatic traits in a natural population of Drosophila melanogaster

Summary - A sample of 1359 males and 1 259 females from a natural population of Drosophila melanogaster of the Canary Islands was simultaneously examined for wing length, inversion polymorphisms, and gene variation at 10 allozyme loci. Correlations and nonrandom associations between those genetic traits were estimated. In contrast to previous studies, large amounts of linkage disequilibrium have been found. Frequencies of significant gametic associations between linked and unlinked elements were 100% and 25%, respectively, for chromosome inversions, 81% 6nd 4% for chromosome inversions, and allozymes, and 36% and 0% for pairs of allozymes. Temporal stability in chromosome and allozyme frequencies and the average number of alleles per locus rule out a recent bottleneck effect. Mean and coefficient of variation of wing length are correlated with the degree of heterokaryotypy (both negatively) and with the degree of heterozygosis (positively for the mean, negatively for the coefficient of variation), mainly implying chromosome 3 elements. Individuals with wing length above (or below) a standard deviation from the population mean showed characteristics for the other genetic traits which resembled those of northern (or southern) populations of the species.

Variation at four enzyme loci in natural populations of Drosophila melanogaster: factor analyses of genotypic and gametic associations.

Variation at four enzyme loci in natural populations of Drosophila melanogaster: factor analyses of genotypic and gametic associations.

Variation at four enzyme loci in natural populations of Drosophila melanogaster : factor analyses of genotypic and gametic associations

Variation at four enzyme loci in natural populations of Drosophila melanogaster : factor analyses of genotypic and gametic associations

Variation at four enzyme loci in natural populations of Drosophila melanogaster : factor analyses of genotypic and gametic associations

Variation at four enzyme loci in natural populations of Drosophila melanogaster : factor analyses of genotypic and gametic associations

Genetic coadaptation in the chromosomal polymorphism of Drosophila subobscura II. Changes of gametic disequilibrium in experimental populations

Experimental populations were examined for temporal changes of gametic disequilibria between allozyme loci (Lap and Pept-1) and gene arrangements of the O chromosome of Drosophila subobscura (O st and O 3+4+7) under several environmental conditions. In the foundation of the experimental populations a genetic perturbation was carried out in order to test the relevance of the current hypotheses used to explain the allozyme-inversion associations observed in natural populations. Differential changes of gametic disequilibria were detected over generations under the different environmental conditions. Mere mechanical or stochastic factors cannot explain the results and natural selection is probably the major agent generating the detected gametic associations. The observations are interpreted as a proof of coadaptation of D. subobscura inversions.

Haplotype study on C4 polymorphism in Japanese. Associations with MHC alleles, complotypes, and HLA-complement haplotypes.

Genetic polymorphism of the fourth component of human complement (C4) was investigated in 83 Japanese families which have been typed for HLA-A,-B,-C,-DR, C2, and BF. Four common C4A alleles and four common C4B alleles were observed. The allele frequencies estimated from unrelated parents were as follows: C4A3, 0.686; A4, 0.132; A2, 0.106; AQ0, 0.067; ARares, 0.009; C4B1, 0.587; B2, 0.167; B5, 0.088; and BQ0, 0.158. Eight different C4 haplotypes were observed with frequencies of more than 0.01. The estimated haplotype frequencies were as follows: C4A3-B1, 0.513; A4-B2, 0.114; A2-BQ0, 0.106; A3-B5, 0.088; AQ0-B1, 0.059; A3-BQ0, 0.047; A3-B2, 0.038; A4-B1, 0.015; and Rares, 0.021. Strong positive gametic associations were found in the following C4-HLA haplotypes: C4A2BQ0-A24, C4A2BQ0-Bw52, C4A3B5-Bw54, C4A3B5-Bw59, C4A4B2-Bw46, C4A3B5-Cw1, C4A2BQ0-DR2, and C4A3B5-DR4. Eleven complotypes were observed with frequencies of more than 0.01. C4A2BQ0 and C4A3B5 were exclusively associated with BFS-C2C. BFF was associated with C4A3B1. C2AT, C2B, and C2BH were associated with C4A3B1, A4B2, and C4A3B1, respectively. Eight different HLA-complement haplotypes were found to be characteristic of Japanese. These combinations are considerably different from those reported in Caucasoid populations.

Gametic non-random associations in North-West African populations ofDrosophila melanogaster

Three North-west African populations ofDrosophila melanogaster were analyzed for chromosomal and enzyme polymorphism as well as for gametic associations between non allelic elements mapped on the same chromosome arm. Strong geographic heterogeneity was found between populations, both for enzyme and chromosomal polymorphism. Out of the 43 possible comparisons for gametic association, 14 (32.5%) were statistically significant.

HLA-A, B and C markers in the Portuguese population.

The frequencies of most HLA‐A, ‐B and ‐C alleles known at present were determined in a random sample which is considered to be representative of the Portuguese population. Its most distinctive paii wise gametic associations are also presented.