Sex-specific recombination rates in Parus major and P. caeruleus, an exception to Huxley's rule

Huxley's rule predicts lower recombination rates in the heterogametic sex than in the homogametic one. The genotyping of Parus major and P. caeruleus families at 8 microsatellite and 4 enzyme loci yielded contradicting data. Significant genotypic disequilibrium was observed between esterase-1, esterase-2 and esterase-3 in adults of P. major and between esterase-2/esterase-3 and esterase-2/microsatellite PK-12 in P. caeruleus. Support comes from linkage analyses of nuclear families. In P. major, the recombination rate of esterase-2/esterase -3 in males is significantly lower than in females (theta(male) = 0.076, theta(female) = 0.145). The opposite is found for the recombination rates of esterase-1/esterase-2 and esterase-2/esterase-3 in P. caeruleus (EST-1/EST-2: theta(female) = 0.218, theta(male) = 0.5, EST-2/EST-3: theta(female) = 0.109, theta(male) = 0.194). We conclude that the basis of differences in recombination rates cannot be heterogamety, per se, but must have multiple genetic causes including chromosomal rearrangments that have evolved after the cladogenesis of the two species.     

Possible heterogeneity in the phosphoglycolate phosphatase (PGP)-haptoglobin alpha (HPA) linkage.

Previous investigators have reported loose linkage in both sexes for phosphoglycolate phosphatase (PGP) and haptoglobin alpha (HPA). We present results of linkage studies between PGP and HPA in two data sets, one from Houston and the other an update of an earlier report from Los Angeles. Using quadratic interpolation to estimate the male (theta m) and female (theta f) recombination values from bivariate lod tables, we found for the Houston data that theta m = 0.43 and theta f = 0.03 at the maximum lod score of z = 2.23. For the Los Angeles series, we found that theta m = 0.31, theta f = 0.48, and z = 0.27. We invoke heterogeneity in the recombination value in different families as an explanation of our findings. We also recommend that bivariate lod tables should always be generated, even though not reported. This is because the usual assumption of theta m = theta f (and, rarely, theta f = 1.8 theta f) under which lod scores are computed may be invalid in many cases.     

Homologous recombination between transferred and chromosomal immunoglobulin kappa genes.

Homologous recombination between transferred and chromosomal DNAs provides a means of introducing well-defined, predetermined changes in the chromosomal genes. Here we report that this approach can be used to specifically modify the immunoglobulin genes in mouse hybridoma cells. The test system is based on the Sp6 hybridoma, which synthesizes immunoglobulin M (kappa) specific for the hapten 2,4,6-trinitrophenyl (TNP). As recipient cells, we used the Sp6-derived mutant hybridoma igk14, which has a deletion of the kappa TNP gene and consequently does not synthesize TNP-specific immunoglobulin M. igk14 retains the mu TNP gene and two additional rearranged kappa genes, denoted kappa M21B1 and kappa M21G. As a transfer vector, we used pSV2neo bearing the functionally rearranged TNP-specific V kappa segment. Following DNA transfer by electroporation, we isolated rare transformants which produced normal amounts of the functional kappa TNP chain. Analysis of the DNA of these transformants indicated that in all cases, a functional kappa TNP gene had been formed as the result of a homologous integrative recombination event with the igk14 kappa M21B1 gene. These results suggest that homologous recombination might be used for mapping and introducing immunoglobulin gene mutations and for more conveniently engineering specifically altered immunoglobulins.     

The appropriate threshold for declaring linkage when allowing sex-specific recombination rates.

In human genetics, two loci are declared to be linked when the lod score at the maximum likelihood recombination fraction theta exceeds the threshold of 3.0. Since recombination rates differ between the sexes, one can alternatively detect linkage by estimating separate recombination rates, theta m and theta f, for male and female meiosis and examining the corresponding sex-specific lod scores. The question arises: In order to maintain the same chance of falsely declaring linkage, what is the correct threshold for declaring linkage when sex-specific lod scores are used? We show here that the appropriate threshold is about 3.5. If the restriction that theta f greater than theta m is added, the appropriate threshold falls to about 3.25. We also discuss the relative efficiency of detecting linkage by using sex-specific and sex-averaged lod scores.     

Protein kinase C: a new linkage marker for growth hormone and for COL1A1

An expanded linkage group on the long arm of human chromosome 17 is reported. Using the CEPH panel of DNAs and restriction fragment length polymorphism (RFLP) markers for the centromere locus (D17Z1), growth hormone (GH1), collagen type I alpha 1 (COL1A1), and protein kinase C-alpha polypeptide (PKCA) loci, theta values of 0.03, 0.11, and 0.23 were found between PKCA and GH1, PKCA and COL1A1, and PKCA and D17Z1, respectively. The theta values calculated for GH1 versus COL1A1 or D17Z1 were 0.11 and 0.23, respectively. Sex-specific recombination rates were calculated for the best likelihood order and demonstrate female recombination greater than male recombination. Therefore, the loci studied span a map region of approximately 30 cm between 17cen and 17q24, with the most likely gene order being D17Z1-COL1A1-PKCA-GH1.     

A gene for pyridoxine-dependent epilepsy maps to chromosome 5q31

Pyridoxine-dependent epilepsy (PDE) is a rare autosomal recessive disorder characterized by generalized seizures in the first hours of life and responding only to pyridoxine hydrochloride. The pathogenesis of PDE is unknown, but an alteration in the binding of pyridoxal 5-phosphate to glutamic acid decarboxylase (GAD) has been postulated in patients with PDE. Results are reported for genetic linkage analyses in four families with consanguineous parents and in one family with nonconsanguineous parents. The GAD1 (2q31) and GAD2 genes (10p23) were tested and excluded. A genomewide search was subsequently performed, using microsatellite markers at an average distance of 10 cM, and the search revealed linkage of the disease-causing gene to markers on chromosome 5q31.2-q31.3 (maximum LOD score [Z(max)] 8.43 at recombination fraction [theta] 0 and Zmax=7.58 at straight theta=0 at loci D5S2017 and D5S1972, respectively). A recombination event, between loci D5S638 and D5S463, in one family defined the distal boundary, and a second recombination event between loci D5S2011 and D5S2017 in another family defined the proximal boundary of the genetic interval encompassing the PDE gene (5.1 cM). Ongoing studies may lead to the identification of the disease-causing gene.     

Hindered convection of macromolecules in hydrogels

Hindered convection of macromolecules in gels was studied by measuring the sieving coefficient (theta) of narrow fractions of Ficoll (Stokes-Einstein radius, r(s) = 2.7-5.9 nm) in agarose and agarose-dextran membranes, along with the Darcy permeability (kappa). To provide a wide range of kappa, varying amounts of dextran (volume fractions < or = 0.011) were covalently attached to agarose gels with volume fractions of 0.040 or 0.080. As expected, theta decreased with increasing r(s) or with increasing concentrations of either agarose or dextran. For each molecular size, theta plotted as a function of kappa fell on a single curve for all gel compositions studied. The dependence of theta on kappa and r(s) was predicted well by a hydrodynamic theory based on flow normal to the axes of equally spaced, parallel fibers. Values of the convective hindrance factor (K(c), the ratio of solute to fluid velocity), calculated from Theta and previous equilibrium partitioning data, were unexpectedly large; although K(c) < or = 1.1 in the fiber theory, its apparent value ranged generally from 1.5 to 3. This seemingly anomalous result was explained on the basis of membrane heterogeneity. Convective hindrances in the synthetic gels were quite similar to those in glomerular basement membrane, when compared on the basis of similar solid volume fractions and values of kappa. Overall, the results suggest that convective hindrances can be predicted fairly well from a knowledge of kappa, even in synthetic or biological gels of complex composition.     

Mapping autosomal recessive vitamin D dependency type I to chromosome 12q14 by linkage analysis.

Linkage analysis in French-Canadian families with vitamin D dependency type I (VDD1) demonstrated that the gene responsible for the disease is linked to polymorphic RFLP markers in the 12q14 region. We studied 76 subjects in 14 sibships which included 17 affected individuals and 17 obligate heterozygotes. Significant results for linkage were obtained with the D12S17 locus at the male recombination fraction (theta m) .018 (Z[theta m theta f] = 3.20) and with D126 at (theta m = .025 (Z[theta m theta f] = 3.07). Multipoint linkage analysis and studies of haplotypes and recombinants strongly suggest the localization of the VDD1 locus between the collagen type II alpha 1 (COL2A1) locus and clustered loci D12S14, D12S17, and D12S6, which segregate as a three-marker haplotype. Linkage disequilibrium between VDD1 and this three-marker haplotype supports the notion of a founder effect in the studied population. The current status of the localization of the disease allows for carrier detection in the families at risk.     

Using lod scores to detect sex differences in male-female recombination fractions

Human recombination fraction (RF) can differ between males and females, but investigators do not always know which disease genes are located in genomic areas of large RF sex differences. Knowledge of RF sex differences contributes to our understanding of basic biology and can increase the power of a linkage study, improve gene localization, and provide clues to possible imprinting. One way to detect these differences is to use lod scores. In this study we focused on detecting RF sex differences and answered the following questions, in both phase-known and phase-unknown matings: (1) How large a sample size is needed to detect a RF sex difference? (2) What are "optimal" proportions of paternally vs. maternally informative matings? (3) Does ascertaining nonoptimal proportions of paternally or maternally informative matings lead to ascertainment bias? Our results were as follows: (1) We calculated expected lod scores (ELODs) under two different conditions: "unconstrained," allowing sex-specific RF parameters (theta(female), theta(male)); and "constrained," requiring theta(female) = theta(male). We then examined the DeltaELOD (identical with difference between maximized constrained and unconstrained ELODs) and calculated minimum sample sizes required to achieve statistically significant DeltaELODs. For large RF sex differences, samples as small as 10 to 20 fully informative matings can achieve statistical significance. We give general sample size guidelines for detecting RF differences in informative phase-known and phase-unknown matings. (2) We defined p as the proportion of paternally informative matings in the dataset; and the optimal proportion p(circ) as that value of p that maximizes DeltaELOD. We determined that, surprisingly, p(circ) does not necessarily equal (1/2), although it does fall between approximately 0.4 and 0.6 in most situations. (3) We showed that if p in a sample deviates from its optimal value, no bias is introduced (asymptotically) to the maximum likelihood estimates of theta(female) and theta(male), even though ELOD is reduced (see point 2). This fact is important because often investigators cannot control the proportions of paternally and maternally informative families. In conclusion, it is possible to reliably detect sex differences in recombination fraction.     

Recombination between kappa chain genetic markers and the Lyt-3 locus

Recombination has been detected for the first time between chromosome 6 loci controlling kappa chain expression in normal mouse serum immunoglobulin and the Lyt-3 locus. The recombination event occurred at the 26th or 27th backcross generation during the derivation of the Lyt-2a, Lyt-3a-congenic line B6.PL(85NS). The line is now homozygous for the Lyt-2a, Lyt-3a allele(s) at N30F13 and homozygous animals express the Igk-Ef1b allele derived from C57BL/6. The frequency of recombination has been estimated to be 0.30% based on the present results and previous studies in which no recombination was detected. The results rule out the hypothesis that the Lyt-3 locus itself controls the light chain phenotype observed in normal serum immunoglobulin.     

Homozygosity mapping of a Weill-Marchesani syndrome locus to chromosome 19p13.3-p13.2

Weill-Marchesani syndrome (WMS) is a rare disease characterized by short stature, brachydactyly, joint stiffness, and characteristic eye abnormalities, including microspherophakia, ectopia lentis, and glaucoma. Both autosomal recessive and autosomal dominant modes of inheritance have been described in association with WMS. We have performed a genome-wide search in two large consanguineous families of Lebanese and Saudian origin consistent with an autosomal recessive mode of inheritance. Here, we report the linkage of the disease gene to chromosome 19p13.3-p13.2 (Zmax=5.99 at theta=0 at locus D19S906). A recombination event between loci D19S905 and D19S901 defines the distal boundary, and a second recombination event between loci D19S221 and D19S840 defines the proximal boundary of the genetic interval encompassing the WMS gene (12.4 cM). We hope that our ongoing studies will lead to the identification of the disease-causing gene.     

A structural locus for coagulation factor XIIIA (F13A) is located distal to the HLA region on chromosome 6p in man

Linkage between the locus for coagulation factor XIIIA (F13A) and HLA-region genes has been revealed during a linkage study between F13A and approximately 40 other polymorphic marker genes. In males, the maximum lod score between F13A and HLA-region genes (HLA-A, -C, -B, -DR; C4A, -B; Bf; and/or C2) is 7.60 at theta 1 = .18. To GLO, the maximum lod score is 2.37 at theta 1 = .19; to PGM3, .22 at theta 1 = .35. Female data indicate a clear sex difference in recombination frequency between F13A and HLA. The present findings, in combination with earlier knowledge of PGM3/GLO/HLA localization and gene distances, show that F13A is distal to HLA on the short arm of chromosome 6 in man. It is thus likely that by including FXIIIA typing in linkage studies, the whole male 6p is within mapping distance of highly polymorphic, classical marker genes. Earlier findings that the Hageman factor gene (F12) is located in the same chromosomal region may indicate the presence of a coagulation factor gene cluster in this region.     

The gene for X-linked hydrocephalus maps to Xq28, distal to DXS52.

We report the study of five independent X-linked hydrocephalus (HSAS1) families with polymorphic DNA markers of the Xq28 region. A total of 58 individuals, including 7 living affected males and 22 obligate carriers, have been studied. Maximum lod score was 7.21 at theta = 2.40% for DXS52 (St14-1). A single recombination event was observed between this marker and the HSAS1 locus. Other markers studied were DXS296 (Z = 2.02 at theta = 2.5%), DXS304 (Z = 4.37 at theta = 7.8%), DXS74 (Z = 3.50 at theta = 0%), DXS15 (Z = 1.96 at theta = 5.7%), DXS134 (Z = 3.31 at theta = 0%), and F8C (Z = 5.79 at theta = 0%). These data confirm the localization of the HSAS1 gene to Xq28 and provide evidence for genetic homogeneity of this syndrome. In addition, examination of two obligate recombinant meioses along with multipoint linkage analysis supports the distal localization of the HSAS1 locus with respect to the DXS52 cluster. These observations are of potential interest for future studies aimed at HSAS1 gene characterization.     

Deletion of the immunoglobulin kappa chain intron enhancer abolishes kappa chain gene rearrangement in cis but not lambda chain gene rearrangement in trans.

Immunoglobulins (Ig) secreted from a plasma cell contain either kappa or lambda light chains, but not both. This phenomenon is termed isotypic kappa-lambda exclusion. While kappa-producing cells have their lambda chain genes in germline configuration, in most lambda-producing cells the kappa chain genes are either non-productively rearranged or deleted. To investigate the molecular mechanism for isotypic kappa-lambda exclusion, in particular the role of the Ig kappa intron enhancer, we replaced this enhancer by a neomycin resistance (neoR) gene in embryonic stem (ES) cells. B cells heterozygous for the mutation undergo V kappa-J kappa recombination exclusively in the intact Ig kappa locus but not in the mutated Ig kappa locus. Homozygous mutant mice exhibited no rearrangements in their Ig kappa loci. However, splenic B cell numbers were only slightly reduced as compared with the wild-type, and all B cells expressed lambda chain bearing surface Ig. These findings demonstrate that rearrangement in the Ig kappa locus is not essential for lambda gene rearrangement. We also generated homozygous mutant mice in which the neoR gene was inserted at the 3' end of the Ig kappa intron enhancer. Unexpectedly, mere insertion of the neoR gene showed some suppressive effect on V kappa-J kappa recombination. However, the much more pronounced inhibition of V kappa-J kappa recombination by the replacement of the Ig kappa intron enhancer suggests that this enhancer is essential for V kappa-J kappa recombination.     

Aberrant recombination events in B cell lines derived from a kappa-deficient human.

We have analyzed the structure of Ig kappa chain genes in B cell lines derived from a human individual who cannot synthesize any kappa chains, and whose Igs all contain lambda chains (1). We have characterized secondary DNA recombination events at two kappa alleles which have undergone misaligned V-J recombinations. One such secondary recombination has joined the flanking sequences of a V kappa and a J kappa 2 gene segment as if it were the reciprocal product of a V-J kappa 2 recombination, and resulted in the displacement of the recombined VJ kappa 1 gene segments from the C kappa locus. The non-rearranged form of the V kappa fragment which had recombined with the J kappa 2 flank was cloned. Nucleotide sequencing of this fragment identified a V kappa gene that differed by at least 38% from all previously sequenced human V kappa genes. The other V-J kappa segment analyzed has undergone a secondary recombination at a different site from that described above, at a site within the intervening sequence between the J kappa and C kappa gene segments, similar to the location of secondary recombinations which have occurred in lambda + B cell lines from mice and humans (2,3). These results prove that multiple recombinations can occur at one J kappa-C kappa locus.     

Congenital motor nystagmus linked to Xq26-q27.

Congenital motor nystagmus (CMN) is a hereditary disorder characterized by bilateral ocular oscillations that begin in the first 6 mo of life. It must be distinguished from those genetic disorders-such as ocular albinism (OA), congenital stationary night blindness (CSNB), and blue-cone monochromatism (BCM)-in which nystagmus accompanies a clinically apparent defect in the visual sensory system. Although CMN is presumed to arise from a neurological abnormality of fixation, it is not known whether the molecular defect is located in the eye or in the brain. It may be inherited in an autosomal dominant, autosomal recessive, or X-linked pattern. Three families with CMN inherited in an X-linked, irregularly dominant pattern were investigated with linkage and candidate gene analysis. The penetrance among obligate female carriers was 54%. Evaluation of markers in the region of the genes for X-linked OA, CSNB, and BCM revealed no evidence of linkage, supporting the hypothesis that CMN represents a distinct entity. The gene was mapped to chromosome Xq26-q27 with the following markers: GATA172D05 (LOD score 3.164; recombination fraction [theta] = 0.156), DXS1047 (LOD score 10.296; theta = 0), DXS1192 (LOD score 8.174; theta = 0.027), DXS1232 (LOD score 6.015; theta = 0.036), DXS984 (LOD score 6.695; theta = 0), and GATA31E08 (LOD score 4.940; theta = 0.083). Assessment of haplotypes and multipoint linkage analysis, which gave a maximum LOD score of 10.790 with the 1-LOD-unit support interval spanning approximately 7 cM, place the gene in a region between GATA172D05 and DXS1192. Evaluation of candidate genes CDR1 and SOX3 did not reveal mutations in affected male subjects.     

A gene for dominant nonspecific X-linked mental retardation is located in Xq28.

A large family (MRX48) with a nonspecific X-linked mental retardation condition is described. An X-linked semidominant inheritance is suggested by the segregation in three generations of a moderate to severe mental retardation in seven males and by a milder intellectual impairment in two females, without any specific clinical, radiological, or biological feature. Two-point linkage analysis demonstrated significant linkage between the disorder and several markers in Xq28 (maximum LOD score [Zmax] = 2.71 at recombination fraction [theta] = 0); multipoint linkage analyses confirmed the significant linkage with a Zmax of 3.3 at theta = 0, at DXS1684. A recombination event observed with the flanking marker DXS8011 delineates a locus between this marker and the telomere. The approximate length of this locus is 8-9 cM, corresponding to 5.5-6 Mb. In an attempt to explain the variable intellectual impairment in females, we examined X-chromosome inactivation in all females of the family. Inactivation patterns in lymphocytes were random or moderately skewed, and no correlation between the phenotypic status and a specific inactivation pattern was observed. The interval of assignment noted in this family overlaps with five MRX loci previously reported in Xq28.     

DNA sequence variation and the recombinational landscape in Drosophila pseudoobscura: a study of the second chromosome.

The relationship between rates of recombination and DNA sequence polymorphism was analyzed for the second chromosome of Drosophila pseudoobscura. We constructed integrated genetic and physical maps of this chromosome using molecular markers at 10 loci spanning most of its physical length. The total length of the map was 128.2 cM, almost twice that of the homologous chromosome arm (3R) in D. melanogaster. There appears to be very little centromeric suppression of recombination, and rates of recombination are quite uniform across most of the chromosome. Levels of sequence variation (theta(W), based on the number of segregating sites) at seven loci (tropomyosin 1, Rhodopsin 3, Rhodopsin 1, bicoid, Xanthine dehydrogenase, Myosin light chain 1, and ribosomal protein 49) varied from 0.0036 to 0.0167. Generally consistent with earlier studies, the average estimate of theta(W) at total sites is 1.5-fold higher than that in D. melanogaster, while average theta(W) at silent sites is almost 3-fold higher. These estimates of variation were analyzed in the context of a background selection model under the same parameters of mutation rate and selection as have been proposed for D. melanogaster. It is likely that a significant fraction of the higher level of sequence variation in D. pseudoobscura can be explained by differences in regional rates of recombination rather than a larger species-level effective population size. However, the distribution of variation among synonymous, nonsynonymous, and noncoding sites appears to be quite different between the species, making direct comparisons of neutral variation, and hence inferences about effective population size, difficult. Tajima's D statistics for 6 out of the 7 loci surveyed are negative, suggesting that D. pseudoobscura may have experienced a rapid population expansion in the recent past or, alternatively, that slightly deleterious mutations constitute an important component of standing variation in this species.     

Murine lambda gene rearrangements: the stochastic model prevails over the ordered model.

The ontogeny of the immunoglobulin (Ig) gene rearrangement in mammalian B cells seems to be ordered. Heavy chain gene segments rearrange first, followed by light chain gene segments, kappa before lambda. The genomic organization of murine lambda locus does not preclude the simultaneous expression of two subtypes from the same chromosome. In order to distinguish between an ordered and a stochastic model of rearrangement, a panel of 67 B cell hybridomas secreting either lambda 1, lambda 2, lambda 3 or lambda x (recently described) were analysed for V lambda J lambda rearrangements. The results show that in 97% of cases, a single rearrangement occurred, favouring the stochastic model over the ordered one. Strikingly, the possibility of having a productive rearrangement if the first try results in an aberrant one is rare. We propose therefore, that the lambda Ig is not necessarily required to ensure allelic and subtypic exclusion mechanisms. Moreover, in 97% of the cases, at least one kappa allele is rearranged. Furthermore, the RS recombination has been detected in 77% of the cases. This suggests that, although the stimulation of kappa precedes that of lambda locus, the RS recombination acts as a transacting albeit dispensable lambda activator.