Disequilibrium mapping of a quantitative-trait locus in an expanding population.

Linkage disequilibrium (LD) mapping can be successful if there is strong nonrandom association between marker alleles and an allele affecting a trait of interest. The principles of LD mapping of dichotomous traits are well understood, but less is known about LD mapping of a quantitative-trait locus (QTL). It is shown in this report that selective genotyping can increase the power to detect and map a rare allele of large effect at a QTL. Two statistical tests of the association between an allele and a quantitative character are proposed. These tests are approximately independent, so information from them can be combined. Analytic theory is developed to show that these two tests are effective in detecting the presence of a low-frequency allele with a relatively large effect on the character when the QTL is either already a candidate locus or closely linked to a marker locus that is in strong LD with the QTL. The latter situation is expected in a rapidly growing population in which the allele of large effect was present initially in one copy. Therefore, the proposed tests are useful under the same conditions as those for successful LD mapping of a dichotomous trait or disease. Simulations show that, for detection of the presence of a QTL, these tests are more powerful than a simple t-test. The tests also provide a basis for defining a measure of association, gamma, between a low-frequency allele at a putative QTL and a low-frequency allele at a marker locus.     

Tightly linked flanking microsatellite markers for the Usher syndrome type I locus on the short arm of chromosome 11.

Usher syndrome type I is an autosomal recessive disease characterized by profound congenital hearing impairment and vestibular dysfunction followed by the onset of progressive pigmentary retinopathy in childhood or early adolescence. A locus (USH1C) for one form of this disease was previously assigned to the short arm of chromosome 11 through linkage studies in the Acadian population of southwestern Louisiana. Linkage analyses of a set of microsatellite markers in 27 Acadian families provide evidence that USH1C lies between D11S861 and D11S928. Three markers (D11S419, D11S921, and D11S899) that lie between the flanking markers show no recombination with USH1C, and all 54 chromosomes with the abnormal allele at the disease locus have identical alleles for D11S419 and D11S921. This haplotype was found on only 10 of 50 chromosomes with the normal allele at the disease locus, suggesting a strong founder effect. Of the 54 chromosomes with the abnormal allele, 12 had a divergent allele at D11S899. These results suggest that USH1C is in the 2-3-cM interval between D11S861 and D11S899.     

A CA-repeat polymorphism close to the adenomatous polyposis coli (APC) gene offers improved diagnostic testing for familial APC.

Presymptomatic genetic testing for the presence of a mutant allele causing familial adenomatous polyposis coli (APC) has been difficult to perform effectively in the past because DNA markers surrounding the APC gene on chromosome 5q have not been very informative. We report results of genetic linkage studies on both research families and clinical families by using D5S346, a highly polymorphic dinucleotide (CA)-repeat locus 30-70 kb from the APC gene. Linkage analysis with this marker in a large APC pedigree showed an increase of at least 9.0 LOD units, in likelihood of linkage of the disease-causing allele to the APC locus, when compared with the highest LOD score attained with any other closely linked marker. When the first 14 APC families that requested genotypic analysis by the DNA Diagnostic Laboratory at the University of Utah were tested with D5S346, 20 of the 31 at-risk individuals were identified as either carriers or noncarriers of an APC-predisposing allele. We see this marker as an important tool for research studies and for the presymptomatic diagnosis of APC.     

Serum esterase genetics in rabbits. IV. The prealbumin and β-globulin systems

Discontinuous starch gel electrophoresis revealed a fourth allele of rabbit prealbumin serum esterase at locus Est-2. This allele is designated Est-2 ^f and appears to be silent. In addition to the prealbumin serum esterases, another serum esterase system was studied in rabbits. This system is localized in the β-globulin region. Genetic analysis indicated that one locus with two codominant alleles controls the variation in this region. Linkage of this system with Est-1 and Est-2 of the prealbumin serum esterases was demonstrated. Comparison of the arrangement of these esterase loci on linkage group VI with the esterase loci on chromosome 8 of the mouse gives additional support for the theory of evolutionary conservation of chromosomal segments coding for mammalian esterases.     

Genetics of octanol and α-glycerophosphate dehydrogenases in the mosquito Aedes (Finlaya) togoi

Genetic studies were performed on octanol dehydrogenase (EC 1.1.1.73) and alpha-glycerophosphate dehydrogenase (EC 1.1.1.8) in the mosquito Aedes (Finlaya) togoi by agar gel electrophoresis. The electrophoretic survey revealed two octanol dehydrogenase loci (Odh-1, Odh-2) and one alpha-glycerophosphate dehydrogenase locus (alpha-Gpdh) in this species. Five alleles were observed at the Odh-2 locus in seven laboratory strains, whereas the alpha-Gpdh locus was completely monomorphic in six of seven strains examined and the second allele at this locus was detected in only one strain at a frequency of 0.14. Both loci code for dimeric enzymes. Linkage studies on Odh-2 and alpha-Gpdh suggested that the gene arrangement and recombination units were Odh-2--(25.8)--M (sex locus)--(30.5)--s (strawcolored larva) and M--(25.6)--alpha-Gpdh--(15.4)--s. These results, together with linkage data previously reported, give the following gene linkage on the sex chromosome: Odh-2--Est-3 (carboxylesterase)--Acph (acid phosphatase)--M--alpha-Gpdh--s--Est-2 (carboxylesterase). The total map length of this arrangement is approximately 75 map units.     

Polymorphism at the ovine major histocompatibility complex class II loci

Southern hybridization analysis of the ovine major histocompatibility complex (MHC) ( MhcOvar ) class II region, using sheep-specific probes for the DQA1, DQA2, DQB and DRA loci, has revealed extensive polymorphism. DQA1 and DQAP had eight and 16 alleles respectively, DQB had six and DRA had three alleles. Little information was derived from the DRB locus owing to extensive cross-hybridization between the DRB probe and the DQB locus. Differences in allele frequency between breeds were revealed. At the DQA1 locus a null allele (DQA1-N) was observed with a frequency of between 27% and 45%, making this the most common DQA1 allele in all breeds examined. The frequency of DQA1-N homozygotes was between 11% and 18%, raising questions as to the functional significance of the DQA1 gene. Linkage analysis between the DQA1, DQA2, DQB and DRA loci did not reveal any recombination.     

The tyrosinase-positive oculocutaneous albinism gene shows locus homogeneity on chromosome 15q11-q13 and evidence of multiple mutations in southern African negroids.

Tyrosinase-positive oculocutaneous albinism (ty-pos OCA) is an autosomal recessive disorder of the melanin pigmentary system. South African ty-pos OCA individuals occur with two distinct phenotypes, with or without darkly pigmented patches (ephelides, or dendritic freckles) on exposed areas of the skin. These phenotypes are concordant within families, suggesting that there may be more than one mutation at the ty-pos OCA locus. Linkage studies carried out in 41 families have shown linkage between markers in the Prader-Willi/Angelman syndrome (PWS/AS) region on chromosome 15q11-q13 and ty-pos OCA. Analysis showed no obligatory crossovers between the alleles at the D15S12 locus and ty-pos OCA, suggesting that the D15S12 locus is very close to or part of the disease locus, which is postulated to be the human homologue, P, of the mouse pink-eyed dilution gene, p. Unlike caucasoid "ty-pos OCA" individuals, negroid ty-pos OCA individuals do not show any evidence of locus heterogeneity. Studies of allelic association between the polymorphic alleles detected at the D15S12 locus and ephelus status suggest that there was a single major mutation giving rise to ty-pos OCA without ephelides. There may, however, be two major mutations causing ty-pos OCA with ephelides, one associated with D15S12 allele 1 and the other associated with D15S12 allele 2. The two loci, GABRA5 and D15S24, flanking D15S12, are both hypervariable, and many different haplotypes were observed with the alleles at the three loci on both ty-pos OCA-associated chromosomes and "normal" chromosomes.(ABSTRACT TRUNCATED AT 250 WORDS)     

Evidence for Linkage Disequilibrium Maintained by Selection in Two Natural Populations of DROSOPHILA SUBOBSCURA

One island and one mainland population of Drosophila subobscura were found polymorphic at the XDH (xanthine dehydrogenase) and the AO (aldehyde oxidase) loci. It was observed that one allele at the XDH locus, which has a low frequency in both populations, is nonrandomly associated with the alleles at the AO locus. Two lines of evidence support the thesis that this linkage disequilibrium is due to epistasis rather than random drift: (1) D or r, measures of the disequilibrium, have the same sign and magnitude in both populations. (2) The linkage disequilibrium is not due to inversions. Inversions segregating on the chromosome carrying XDH and AO have been separated into two classes, between which exchange of alleles at the two loci is suppressed. Linkage disequilibrium for XDH and AO was observed within each class. In the absence of any exchange of alleles, these disequilibria must have arisen and been maintained independently. The suggestion is made that the epistatic disequilibrium results from the close structural and physiological relationship which exists between the two enzymes.     

Is there selection in favour of heterozygotes in families with merosin-deficient congenital muscular dystrophy?

Merosin-deficient congenital muscular dystrophy is an autosomal recessive neuromuscular disorder caused by partial or total absence of laminin-2 (merosin) in the skeletal muscle. Affected children have severe weakness, hypotonia at birth, high creatine kinase (CK) levels (more than 10 times normal) and are not able to walk or stand unsupported. Linkage and mutation analysis demonstrated that the gene encoding for the laminin-alpha2 chain, mapped on chromosome 6q22-23, is invariably responsible for this form of congenital muscular dystrophy. We investigated the pattern of inheritance of the haplotypes associated with the mutated allele in 29 informative merosin-deficient families, using tightly linked informative polymorphic microsatellite markers. This allowed us to identify heterozygous individuals from normal homozygotes, who are clinically, pathologically and biochemically indistinguishable. By linkage analysis, we found a statistically significant increase in the number of heterozygous individuals carrying either the paternal or the maternal haplotypes associated with the mutated allele. This could suggest a selection in favour of the alleles carrying mutations at the laminin alpha2-chain locus.     

Adenosine deaminase,Ada, is in mouse chromosome 2H3, and is not allelic with wasted,wst

The adenosine deaminase locus (Ada) in the mouse has been localized by in situ hybridization to band 2H3. Linkage analysis of backcross data has shown that Ada is 13.8 +/- 2.7 cM from the coat texture mutant, ragged, Ra. From the results of earlier work (Abbott, C. M., et al., Proc. Natl. Acad. Sci. USA 83:693, 1986), it had been suggested that wst was a low-activity allele of Ada, but this cannot be so because Ada and wst have been found to be nonallelic.     

A new variant of the Es-4 locus in the rat

A new variant of kidney esterase in the DK/Nac rat strain is reported. The new esterase was tentatively named ES-4C determined by a third allele of the Es-4 locus of Linkage Group V (LGV). Strain distribution was surveyed using 17 inbred strains, but no strain except for the DK/Nac strain possessed the ES-4C type. Although we surveyed outbred stocks (Jcl: Wistar and Jcl: SD) we could not find rats carrying the ES-4C type. Genetic analysis of the ES-4C type was carried out using mating experiments between DK/Nac and BUF/Nac (ES-4B). The results indicated that the new variant was controlled by the Es-4 locus and it was named the Es-4c allele.     

Population genetics of modifiers of meiotic drive. I. The solution of a special case and some general implications

This is a study of the formal population genetics of a two locus model where the alleles at one locus are subject to meiotic drive and zygotic selection and the only effect of the other locus is the modification of drive intensity. A complete analytic solution is obtained for a biologically reasonable special case. It is then argued, partially with the aid of computer analysis, that with moderate relaxation of assumptions of the special case, the conclusions derived from that case still hold. These conclusions are that if there is linkage a stable two locus polymorphism can result. There is permanent linkage disequilibrium with the loosing allele at the drive locus in coupling with the suppressor allele at the modifier locus, and the driven allele coupled with the modifier allele which enhances drive. It is suggested that this result explains how the SD system in Drosophila maintains its integrity in natural populations.     

GDF5 is a second locus for multiple-synostosis syndrome

Multiple-synostosis syndrome is an autosomal dominant disorder characterized by progressive symphalangism, carpal/tarsal fusions, deafness, and mild facial dysmorphism. Heterozygosity for functional null mutations in the NOGGIN gene has been shown to be responsible for the disorder. However, in a cohort of six probands with multiple-synostosis syndrome, only one was found to be heterozygous for a NOGGIN mutation (W205X). Linkage studies involving the four-generation family of one of the mutation-negative patients excluded the NOGGIN locus, providing genetic evidence of locus heterogeneity. In this family, polymorphic markers flanking the GDF5 locus were found to cosegregate with the disease, and sequence analysis demonstrated that affected individuals in the family were heterozygous for a novel missense mutation that predicts an R438L substitution in the GDF5 protein. Unlike mutations that lead to haploinsufficiency for GDF5 and produce brachydactyly C, the protein encoded by the multiple-synostosis-syndrome allele was secreted as a mature GDF5 dimer. These data establish locus heterogeneity in multiple-synostosis syndrome and demonstrate that the disorder can result from mutations in either the NOGGIN or the GDF5 gene.     

Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana

Linkage disequilibrium in highly selfing organisms is expected to extend well beyond the scale of individual genes. The pattern of polymorphism in such species must thus be studied over a larger scale. We sequenced 14 short (0.5-1 kb) fragments from a 400-kb region surrounding the flowering time locus FRI in a sample of 20 accessions of Arabidopsis thaliana. The distribution of allele frequencies, as quantified by Tajima's D, varies considerably over the region and is incompatible with a standard neutral model. The region is characterized by extensive haplotype structure, with linkage disequilibrium decaying over 250 kb. In particular, recombination is evident within 35 kb of FRI in a haplotype associated with a functionally important allele. This suggests that A. thaliana may be highly suitable for linkage disequilibrium mapping.     

Genetic variants of the Bombyx mori silkworm encoding sericin proteins of different lengths

A variant sericin polypeptide originally found by acid gel electrophoresis in the Nd-s mutant strain of the silkworm, Bombyx mori, has been analyzed genetically. The vriant polypeptide (called S-2^v) is encoded by a gene which behaves as a codominant allele of the gene encoding the standard S-2 sericin polypeptide. Linkage analysis locates these alleles at 0.0 map unit on chromosome 11. SDS-polyacrylamide gel electrophoresis shows that the molecular weight of the S-2^v variant polypeptide is lower by approximately 62,500 than that of the S-2 polypeptide. Amino acid analysis indicates that the two sericin polypeptides have similar compositions. These results are consistent with the idea that the variant allele arose by deletion within the S-2 coding sequence in the Src-2 gene locus as the result of unequal recombination.     

Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in admixed populations, by conditioning on parental admixture.

Genes that underlie ethnic differences in disease risk can be mapped in affected individuals of mixed descent if the ancestry of the alleles at each marker locus can be assigned to one of the two founding populations. Linkage can be detected by testing for association of the disease with the ancestry of alleles at the marker locus, by conditioning on the admixture (defined as the proportion of genes that have ancestry from the high-risk population) of both parents. With regard to exploiting the effects of admixture, this test is more flexible and powerful than the transmission-disequilibrium test. Under the assumption of a multiplicative model, the statistical power for a given sample size depends only on parental admixture and the risk ratio r between populations that is generated by the locus. The most informative families are those in which mean parental admixture is .2-.7 and in which admixture is similar in both parents. The number of markers required for a genome search depends on the number of generations since admixture and on the information content for ancestry (f) of the markers, defined as a function of allele frequencies in the two founding populations. Simulations using a hidden Markov model suggest that, when admixture has occurred 2-10 generations earlier, a multipoint analysis using 2,000 biallelic markers, with f values of 30%, can extract 70%-90% of the ancestry information for each locus. Sets of such markers could be selected from libraries of single-nucleotide polymorphisms, when these become available.     

Genetic linkage between Huntington disease and the D4S10 locus in South African families: further evidence against non-allelic heterogeneity

Summary A study of genetic linkage between Huntington disease (HD) and the D4S10 locus (G8) has been undertaken in 10 South African (SA) families originating from the black, white and mixed acestry population groups. Allele frequencies at the D4S10 locus have been established in the non-Caucasoid population groups. There are significant differences in the allele frequencies at the D4S10 locus between the various SA populations. Clearly, information about population-specific frequencies for all polymorphisms is essential prior to the implementation of predictive testing in different population groups. Linkage has been demonstrated within this mixed group of HD families in SA using the HindIII, EcoRI and MspI polymorphisms, detected by G8. A maximum lod score of 8.14 at a recombination fraction of 0.00 (confidence limit 0–0.058) has been calculated using a combined haplotype of the HindIII and MspI polymorphisms. Taking into account the diverse ethnic backgrounds of the different SA population groups in this investigation, the data obtained from the study provide further evidence that there is probably only a single HD locus.     

Linkage relationship between incontinentia pigmenti (IP2) and nine terminal X long arm markers

Summary Linkage data for familial incontinentia pigmenti (IP2) and nine X chromosomal markers are reported. Previously found linkage between IP2 and the DXS52 locus is confirmed with the maximum lod score of 6.19 at a recombination fraction of 0.03. Linkage is also established with loci DXS134, DXS15 and DXS33. Multipoint analysis allows us to localize the IP2 locus outside a block of seven linked markers of the Xq28 region.