Analysis of recombination in the centromere region of mouse chromosome 7 using ovarian teratoma and backcross methods

Recombination near the centromere of mouse chromosome 7 was studied using data obtained from ovarian teratomas and backcrosses. The recombination percentage for the centromere-Gpi-1 (glucose phosphate isomerase-1) interval was 13.4 +/- 2.6 using the ovarian teratoma mapping method. In a backcross using the Robertsonian translocation Rb(7.18)9Lub (Rb9) as the centromeric marker, the centromere-Gpi-1 recombination percentage was 4.5 +/- 1.3, demonstrating that Rb9 suppresses recombination near the centromere of chromosome 7. The recombination percentage for the Gpi-1-Ldh-1 (lactate dehydrogenase-1) interval was estimated on the LT/Sv mouse genetic background to be 19.0 +/- 2.9 using the ovarian teratoma mapping method, a value comparable to the 15.5 +/- 4.8 reported earlier. On the same genetic background in a backcross segregating for Rb9, the Gpi-1-Ldh-1 recombination percentage was 7.1 +/- 1.6. Another backcross, without the Rb9 translocation but utilizing a different genetic background, produced a recombination percentage for the Gpi-1-Ldh-1 interval of 10.7 +/- 1.5, a value similar to that obtained in the Rb-containing cross. These results suggest that either the recombination suppression in the centromere area caused by Rb9 does not extend to the Gpi-1-Ldh-1 genetic region or, if it does, that the differing genetic backgrounds of these two crosses influence recombination. No recombinants were detected among 410 offspring produced from a backcross mating segregating for Ldh-1 and ru-2 (ruby-eye-2). Thus, the gene order of Ldh-1 and ru-2 on chromosome 7 remains uncertain.     

Genetics and biology of human ovarian teratomas. II. Molecular analysis of origin of nondisjunction and gene-centromere mapping of chromosome I markers.

Chromosomal heteromorphisms and DNA polymorphisms have been utilized to identify the mechanisms that lead to formation of human ovarian teratomas and to construct a gene-centromere map of chromosome 1 by using those teratomas that arise by meiotic nondisjunction. Of 61 genetically informative ovarian teratomas, 21.3% arose by nondisjunction at meiosis I, and 39.3% arose by meiosis II nondisjunction. Eight polymorphic marker loci on chromosome 1p and one marker on 1q were used to estimate a gene-centromere map. The results show clear linkage of the most proximal 1p marker (NRAS) and the most proximal 1q marker (D1S61) to the centromere at a distance of 14 cM and 20 cM, respectively. Estimated gene-centromere distances suggest that, while recombination occurs normally in ovarian teratomas arising by meiosis II errors, ovarian teratomas arising by meiosis I nondisjunction have altered patterns of recombination. Furthermore, the estimated map demonstrates clear evidence of chiasma interference. Our results suggest that ovarian teratomas can provide a rapid method for mapping genes relative to the centromere.     

Estimation of gametic frequencies from F2 populations using the EM algorithm and its application in the analysis of crossover interference in rice

The gametes produced in meiosis provide information on the frequency of recombination and also on the interdependence of recombination events, i.e. interference. Using F₂ individuals, it is not possible in all cases to derive the gametes, which have fused, and which provide the information about interference unequivocally when three or more segregating markers are considered simultaneously. Therefore, a method was developed to estimate the gametic frequencies using a maximum likelihood approach together with the expectation maximisation algorithm. This estimation procedure was applied to F₂ mapping data from rice (Oryza sativa L.) to carry out a genome-wide analysis of crossover interference. The distribution of the coefficient of coincidence in dependence on the recombination fraction revealed for all chromosomes increasing positive interference with decreasing interval size. For some chromosomes this mutual inhibition of recombination was not so strong in small intervals. The centromere had a significant effect on interference. The positive interference found in the chromosome arms were reduced significantly when the intervals considered spanned the centromere. Two chromosomes even demonstrated independent recombination and slightly negative interference for small intervals including the centromere. Different marker densities had no effect on the results. In general, interference depended on the frequency of recombination events in relation to the physical length. The strength of the centromere effect on interference seemed to depend on the strength of recombination suppression around the centromere.Electronic Supplementary Material Supplementary material is available for this article at     

A primary genetic map of the pericentromeric region of the human X chromosome

We report a genetic linkage map of the pericentromeric region of the human X chromosome, extending from Xp11 to Xq13. Genetic analysis with five polymorphic markers, including centromeric alpha satellite DNA, spanned a distance of approximately 38 cM. Significant lod scores were obtained with linkage analysis in 26 families from the Centre d'Etude du Polymorphisme Humain, establishing estimates of genetic distances between these markers and across the centromere. Physical mapping experiments, using a panel of somatic cell hybrids segregating portions of the X chromosome due to translocations or deletions, are in agreement with the multilocus linkage analysis and indicate the order Xp11 . . . DXS7(L1.28)-TIMP- DXZ1(alpha satellite, cen)- DXS159(cpX73)-PGK1 . . . Xq13. The frequency of recombination in the two approximately 20-cM intervals flanking alpha satellite on either chromosome arm was roughly proportional to the estimated physical distance between markers; no evidence for a reduced crossover frequency was found in the intervals adjacent to the centromere. However, significant interfamilial variations in recombination rates were noted in this region. This primary map should be useful both as a foundation for a higher resolution centromere-based linkage map of the X chromosome and in the localization of genes to the pericentromeric region.     

Double recombinants in mitosis

A mathematical model for the random process of repeated cell division and recombination in two nonoverlapping genetic intervals is formulated and investigated. From this model, a test for statistical independence of recombination in the two intervals and a method of estimating the rate of double recombination are developed. Crossing over in both intervals, crossing over in one and gene conversion in the other, and gene conversion in both are treated. For markers on the same chromosome, all possible arrangements of the loci relative to the centromere are considered.Supported by National Science Foundation Grant DEB81-03530.     

Linkage analysis of the murine mos proto-oncogene on chromosome 4

A linkage analysis of the murine Mos gene, which codes for the c-mos proto-oncogene, was performed in 88 backcross progeny of an interspecies cross of laboratory mice and Mus spretus. Linkage was tested for four different genes on mouse chromosome 4: Aco-1, Mup-1, b, and Ifb. The gene order (from centromere) with intervening percentage recombination is Mos-15.9 (+/- 3.9)-Aco-1-5.6 (+/- 2.4)-Mup-1-3.4 (+/- 1.9)-b-5.6 (+/- 2.4)-Ifb. These results confirm the previous assignment of Mos to chromosome 4 on the basis of segregation in somatic cell hybrids (D. Swan et al., 1982, J. Virol. 44: 752-754) and show furthermore that Mos and the Ifa/Ifb clusters are not tightly linked as a group of intronless genes, but are separated by a map distance of 30.6 +/- 4.9 recombination units. The linkage data obtained in the present study place Mos in a region compatible with the physical map (D. W. Threadgill and J. E. Womack, 1988, Genomics 3: 82-86).     

Mapping of FMR1, the gene implicated in fragile X-linked mental retardation, on the mouse X chromosome

A genetic map of the Cf-9 to Dmd region of the mouse X chromosome has been established by typing 100 offspring from a Mus musculus x Mus spretus interspecific backcross for the four loci Cf-9, Cdr, Gabra3, and Dmd. The following order and genetic distances in centimorgans were determined: (Cf-9)-2.4 +/- 1.7-(Cdr)-2.0 +/- 1.4-(Gabra3)-4.1 +/- 2.0-(Dmd). Six backcross offspring carrying X chromosomes with recombination events in the Cdr-Dmd region were identified. These recombination events were used to define the position of Fmr-1, the murine homologue of FMR1, which is the gene implicated in the fragile X syndrome in man, and that of DXS296h, the murine homologue of DXS296. Both Fmr-1 and DXS296h were mapped into the same recombination interval as Gabra3 on the mouse X chromosome. These findings provide strong support for the concept that the order of loci lying in the Cf-9 to Gabra3 segment of the X chromosome is highly conserved between human and mouse.     

Nondisjunction of chromosome 15: origin and recombination.

Thirty-two cases of uniparental disomy (UPD), ascertained from Prader-Willi syndrome patients (N = 27) and Angelman syndrome patients (N = 5), are used to investigate the pattern of recombination associated with nondisjunction of chromosome 15. In addition, the meiotic stage of nondisjunction is inferred by using markers mapping near the centromere. Two basic approaches to the analysis of recombination are utilized. Standard methods of centromere mapping are employed to determine the level of recombination in specific pairwise intervals along the chromosome. This method shows a significant reduction in recombination for two of five intervals examined. Second, the observed frequency of each recombinant class (i.e., zero, one, two, three, or more observable crossovers) is compared with expected values. This is useful for testing whether the reduction in recombination can be attributed solely to a proportion of cases with no recombination at all (because of asynapsis), with the remaining groups showing normal recombination (or even excess recombination), or whether recombination is uniformly reduced. Analysis of maternal UPD(15) data shows a slight reduction in the multiple-recombinant classes, with a corresponding increase in both the zero- and one-recombinant classes over expected values. The majority, more than 82%, of the extra chromosomes in maternal UPD(15) cases are due to meiotic I nondisjunction events. In contrast, most paternal UPD(15) cases so far examined appear to have a postzygotic origin of the extra paternal chromosome.     

Multilocus Analysis for Gene-Centromere Mapping Using First Polar Bodies and Secondary Oocytes

Polar body and oocyte typing is a new technique for gene-centromere mapping and for generating female linkage maps. A maximum likelihood approach is presented for ordering multiple markers relative to the centromere and for estimating recombination frequencies between markers and between the centromere and marker loci. Three marker-centromere orders are possible for each pair of markers: two orders when the centromere flanks the two markers and one order when the centromere is flanked by the two markers. For each possible order, the likelihood was expressed as a function of recombination frequencies for two adjacent intervals. LOD score for recombination frequency between markers or between the centromere and a marker locus was derived based on the likelihood for each gene-centromere order. The methods developed herein provide a general solution to the problem of multilocus genecentromere mapping that involves all theoretical crossover possibilities, including four-strand double crossovers.     

Genetic variation in alkaline phosphatase of the house mouse (Mus musculus) with emphasis on a manganese-requiring isozyme

Genetic variation among inbred strains is described for electrophoretic migration of alkaline phosphatase from intestine, kidney, blood plasma, and three isozymes of liver. A manganese-requiring isozyme of liver and kidney unaffected by neuraminidase is described, and the locus controlling variation in this isozyme is designated Akp-1. Data from recombinant inbred strains place the locus on chromosome 1 at a distance of 3.6 +/- 2.9 cM from the M1s locus on the side distal to the centromere. Test-cross data show the following gene order and recombination percentages: Dip-1 19.0 +/- 3.8% Lp 7.4 +/- 2.2% Akp-1.     

Shiverer gene maps near the distal end of chromosome 18 in the house mouse

Several mouse mutations cause unstable locomotion, tremor, seizures, and a reduced lifespan because of deficient myelin formation in the central nervous system. Mutant alleles at the shiverer (shi) locus are the only ones in this series with a selective molecular defect, namely, in myelin basic proteins (MBPs), which are virtually absent in shi homozygotes and 50% reduced in heterozygotes. In the present study, backcross and intercross matings indicate recombination of 21.2 +/- 3.3% between myelin deficient, shimld, and fused phalanges, syfp, a marker near the middle of chromosome 18. Recombination of shimld with twirler (Tw), a marker near the centromere, is 45.7 +/- 4.9%. Thus, the shi locus maps near the distal end of mouse chromosome 18 and is the first available marker for this region. Given the evidence of other workers that an MBP locus maps to the same mouse chromosome, and that part of this chromosome may be syntenic with an MBP-PEPA region on human chromosome 18, it is likely that shi is in or near an MBP gene.     

Hph-1: A Mouse Mutant with Hereditary Hyperphenylalaninemia Induced by Ethylnitrosourea Mutagenesis

Ethylnitrosourea mutagenesis of spermatogonial stem cells and a three-generation breeding scheme were used to screen for recessive mutations that cause defects in phenylalanine metabolism leading to elevated serum levels of this amino acid. This paper describes the isolation of such a mutation, hph-1, causing a heritable hyperphenylalaninemia in the neonate and weanling and an inability to effectively clear a phenylalanine challenge in the adult. Micro-pedigree analysis of the original mutant mouse and data obtained from crosses of affected and unaffected animals indicate that the mutation segregates in an autosomal recessive manner. An interspecies mouse backcross mapping experiment places the mutant gene locus on mouse chromosome 14 very near Np-1 and a backcross experiment with a conventional inbred mouse strain involving a nearby locus confirms the chromosome 14 assignment. The initial symptomatology of the mutant phenotype suggests this mutant may represent a useful animal model for the study of hyperphenylalaninemia in man.     

Investigation of crossover interference in barley ( Hordeum vulgare L.) using the coefficient of coincidence

Interference, the interaction between recombination events, was analysed in seven mapping populations of barley (Hordeum vulgare L.). The coefficient of coincidence was applied to investigate the type and position of interference within the genome. Interference was analysed with respect to dependence on the recombination fraction, and simulations were used to obtain test statistics which consider the small sample size of 71-150 double haploid lines. In addition to positive interference in intermediate intervals, strong negative interference, i.e. encouraged double recombination, was found in short intervals. The relationship between recombination fraction and interference could not be described with a uniform function, neither for the entire genome nor for individual chromosomes. The analysis of the position of interference within the genome revealed that interference does not act in the same way in the whole genome. Intervals spanning the centromere exhibited significantly higher means for the coefficient of coincidence than intervals within the chromosome arms, especially with regard to small intervals. In general, positive interference was found in the chromosome arms and no or negative interference in the genetically small but physically large centromeric region.     

Linkage analysis of the murine Hyal-1 locus on chromosome 9

We have recently described a new locus, Hyal-1, which determines hyaluronidase variants in mouse serum. On the basis of segregation in recombinant inbred and congenic strains, Hyal-1 was tentatively assigned to chromosome 9 (Fiszer-Szafarz and De Maeyer, '89). In the present study we have performed a linkage analysis of Hyal-1 using 156 backcross progeny of an interspecies cross of laboratory mice and Mus Spretus. Linkage was tested to two anchor loci on chromosome 9: d (dilute, a coat color locus) and Bgl-s (a locus controlling beta-galactosidase activity). The gene order (from centromere) with intervening percentage recombination is d-16.6 (+/- 2.9)-Hyal-1-10.9 (+/- 2.4)-Bgl-s, indicating close linkage to H-7 and Fv-2.     

Tomato chromosome 6: effect of alien chromosomal segments on recombinant frequencies.

Variation in recombinant frequencies at two adjacent intervals on chromosome 6 of tomato (Lycopersicon esculentum Mill.) has been studied in seven lines that differ in the amount and origin of introgressed segments from wild species. These lines were all crossed to a genotype homozygous recessive for the markers tl, yv, and c, which define the centromere spanning region tl-yv and the long arm region yv-c. Recombinants were identified in large F2, populations consisting of over 30 000 plants in total. Application of molecular markers provided additional information on the distribution of crossover events within the centromere-containing interval tl-yv. A decrease in recombination at the marked intervals correlated with the presence of an alien segment. Suppression of recombination was up to sixfold in the centromere spanning interval tl-yv depending on the source and size of the introgression, and was restricted to the alien segments with no strong effect on the neighbouring intervals. Key words : recombinant frequency, Lycopersicon esculentum, morphological markers, introgressions, centromere.     

Genetic and physical mapping of two centromere-proximal regions of chromosome IV in Aspergillus nidulans

Chromosome IV is the smallest chromosome of Aspergillus nidulans. The centromere-proximal portion of the chromosome was mapped physically using overlapping clones of a cosmid genomic library. Two contiguous segments of a physical map, based on restriction mapping of cosmid clones, were generated, together covering more than 0.4 Mb DNA. A reverse genetic mapping approach was used to establish a correlation between physical and genetic maps; i.e., marker genes were integrated into physically mapped segments and subsequently mapped by mitotic and meiotic recombination. The resulting data, together with additional classical genetic mapping, lead to a substantial revision of the genetic map of the chromosome, including the position of the centromere. Comparison of physical and genetic maps indicates that meiotic recombination is low in subcentromeric DNA, its frequency being reduced from 1 crossover per 0.8 Mb to approximately 1 crossover per 5 Mb per meiosis. The portion of the chromosome containing the functional centromere was not mapped because repeat-rich regions hindered further chromosome walking. The size of the missing segment was estimated to be between 70 and 400 kb.     

Mapping of nucleoside phosphorylase (Np-1) and esterase 10 (Es-10) on mouse chromosome 14

A method for detecting two alleles at Np-1 (nucleoside phosphorylase) and three alleles at Es-10 (esterase 10) from mouse blood by cellulose acetate electrophoresis is described. The allelic constitution at these loci for 44 inbred strains and stocks was determined. The location of Np-1 on chromosome 14 was established by backcross experiments in which alleles at Np-1 and Robertsonian translocations were segregating. Es-10 was shown to be linked to Np-1, and the following genetic map of Chr 14 was constructed: centromere-(8.9±4.0 cM)-[Np-1, Wc]-(10.2±1.9 cM)-Es-10-(15.5±3.7 cM)-s. The homologous human loci, NP and ES-D, are not linked.This work was supported by Contract E(11-1)-3267 with the Energy Research and Development Administration, by Contracts NO1-ES4-2156 and NO1-ES4-2159 with the National Institute of Environmental Health Sciences, and by Grants GM 19656 and GM 20919 from the National Institute of General Medical Sciences. D. A. K. was a participant in the 1975 Summer Program for College, Graduate, and Medical Students, which was supported, in part, by the Clark Foundation. The Jackson Laboratory is fully accredited by the American Association for Accreditation of Laboratory Animal Care.     

Female site-specific transposase-induced recombination: a high-efficiency method for fine mapping mutations on the X chromosome in Drosophila

P-element transposons in the Drosophila germline mobilize only in the presence of the appropriate transposase enzyme. Sometimes, instead of mobilizing completely, P elements will undergo site-specific recombination with the homologous chromosome. Site-specific recombination is the basis for male recombination mapping, since the male germline does not normally undergo recombination. Site-specific recombination also takes place in females, but this has been difficult to study because of the obscuring effects of meiotic recombination. Using map functions, I demonstrate that it is possible to employ female site-specific transposase-induced recombination (FaSSTIR) to map loci on the X chromosome and predict that FaSSTIR mapping should be more efficient than meiotic mapping over short genetic intervals. Both FaSSTIR mapping and meiotic mapping were used to fine map the crossveinless locus on the X chromosome. Both techniques identified the same 10-kb interval as the probable location of the crossveinless mutation. Over short intervals (< approximately 7.6 cM), FaSSTIR produces more informative recombination events than does meiotic recombination. Over longer intervals, FaSSTIR is not always more efficient than meiotic mapping, but it produces the correct gene order. FaSSTIR matches the expectations suggested by the map functions and promises to be a useful technique, particularly for mapping X-linked loci.     

Linkage of Nat and Es-1 in the mouse and development of strains congenic for N-acetyltransferase

The human polymorphism in the hepatic enzyme N-acetyltransferase (NAT) affects the rate at which individuals acetylate, and in many cases detoxify, aromatic amine and hydrazine drugs and xenobiotics. Differences in NAT activity are known to affect individual susceptibility to drug toxicities and are thought to play a part in some spontaneous disorders. A mouse model for the human acetylation polymorphism has been previously characterized and involves the A/J (slow acetylator) and C57BL/6J (rapid acetylator) inbred strains. Strain distribution analysis of 40 A x B and B x A recombinant inbred (RI) strains indicated linkage between the N-acetyltransferase gene (Nat) and the esterase 1 (Es-1) gene, located on mouse chromosome 8. A double backcross involving 107 animals confirmed the recombination frequency between Nat and Es-1 to be 12 +/- 3% (mean +/- SE). The information obtained in the backcross and RI studies was combined, yielding a 13 +/- 2.8% (mean +/- SD) recombination frequency. The Es-1 genotype was determined in our newly developed congenic strains A.B6-Natr and B6.A-Nats. The B6.A-Nats strain has the Es-1 genotype of its inbred partner, the B6 strain, and the A.B6-Natr strain has the Es-1 genotype of the donor strain. These congenic strains will be important in determining the role of the NAT genotype in susceptibility to arylamine-induced cancer and other disorders.     

Comparative gene mapping in Arabidopsis lyrata chromosomes 6 and 7 and A. thaliana chromosome IV: evolutionary history, rearrangements and local recombination rates

We have increased the density of genetic markers on the Arabidopsis lyrata chromosomes AL6 and AL7 corresponding to the A. thaliana chromosome IV, in order to determine chromosome rearrangements between these two species, and to compare recombination fractions across the same intervals. We confirm the two rearrangements previously inferred (a reciprocal translocation and a large inversion, which we infer to be pericentric). By including markers around the centromere regions of A. thaliana chromosomes IV and V, we localize the AL6 centromere, and can localize the breakpoints of these chromosome rearrangements more precisely than previously. One translocation breakpoint was close to the centromere, and the other coincided with one end of the inversion, suggesting that a single event caused both rearrangements. At the resolution of our mapping, apart from these rearrangements, all other markers are in the same order in A. lyrata and A. thaliana. We could thus compare recombination rates in the two species. We found slightly higher values in A. thaliana, and a minimum estimate for regions not close to a centromere in A. lyrata is 4-5 centimorgans per megabase. The mapped region of AL7 includes the self-incompatibility loci (S-loci), and this region has been predicted to have lower recombination than elsewhere in the genome. We mapped 17 markers in a region of 1.23 Mb surrounding these loci, and compared the approximately 600 kb closest to the S-loci with the surrounding region of approximately the same size. There were significantly fewer recombination events in the closer than the more distant region, supporting the above prediction, but showing that the low recombination region is very limited in size.