Gene order and recombination rates in the linkage group S-Phi-Hal-H-(Po2)-Pgd in pigs

Families of Czech Landrace (94 litters and 636 offspring) were tested for halothane sensitivity, A-O (S), H, PHI and PGD phenotypes. Informative matings for the estimation of recombination rates between marker loci were selected. The following recombination frequencies were established: S-Phi = 4.8 % (2.5 % -10.7 %);S-H = 6.8 % (4.3 %-11.7 %); Phi-H = 2.6 % (0.9 %-5.3 9%); H-Pgd = 4.4 % (1.6 %-8.0 %). CCCC-overs were observed also between S- Hal, Hal-H andHal - Pgd, but were not found between Phi - Hal. On the basis of these results it has been possible to revise the position of the S locus in this linkage group. The most probable gene order would be: S - Phi - Hal (or Hal - Phi) -H- (P02) - Pgd.
A striking difference was found between the number of halothane-sensitive pigs (87) and HalⁿHal ⁿ genotypes determined by haplotyping (123). Segregation rates in 19 backcross matings and experimental matings of the animals proved that this difference is mostly due to incomplete CCC or low expression of halothane sensitivity.     

Localization of the Po2 locus in the S, Phi, Hal, H, Po2, Pgd linkage group in pigs

The localization of the Po2 locus controlling a polymorphic serum postalbumin was studied in 41 families of the Czech Landrace breed. The haplotypes involving six closely linked loci (S, Phi, Hal, H, Po2, Pgd) were determined for each family member. The crossovers observed between the H, Po2 and Pgd loci indicated that Po2 is located between H and Pgd. The Po2 locus appears to be closer to H [theta = 0.54% (0.06%-1.92%)] than to Pgd [theta = 4.02% (1.67%-7.96%)]. A strong Ha-Po2S association (r = 0.96, P less than 0.001) and H-PO2 linkage disequilibrium (D = 0.2218, P less than 0.01, D/DMax = 0.98) were found.     

Polymorphism of pig serum alpha-protease inhibitor-3 (PI3) and assignment of the locus to the Pi1, Po1A, Po1B, Pi2, Igh linkage group

Polymorphism of an alpha-protease inhibitor, PI3, in pig serum samples was detected using 2D agarose gel (pH 5.4)--polyacrylamide gel (pH 9.0) electrophoresis. Evidence was obtained that the five variants observed (A, B1, B2, C and D) are under genetic control by codominant alleles (Pi3A, Pi3B1, Pi3B2, Pi3C and Pi3D) at one autosomal locus. Variants A, B1, B2 and C inhibited chymotrypsin; there was no appreciable inhibition of trypsin and papain. Variant D did not inhibit chymotrypsin, and therefore its classification as a PI3 variant was put in question. PI3 typing was not possible in about 50% of the studied pigs since in those cases the PI3 variants were either too weak or absent. On the basis of backcross matings and haplotyping in complete families for protease inhibitor loci Pi1, Po1A, Pi2 and Pi3 it was proved that the Pi3 locus belongs to the protease inhibitor gene cluster, and the position of the locus in the linkage group was proposed as being Pi1-Po1A-(Po1B)-Pi3-Pi2-(Igh1, Igh2, Igh3, Igh4).     

A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates

We constructed a genetic linkage map for a tetraploid derivative species, the rainbow trout (Oncorhynchus mykiss), using 191 microsatellite, 3 RAPD, 7 ESMP, and 7 allozyme markers in three backcross families. The linkage map consists of 29 linkage groups with potential arm displacements in the female map due to male-specific pseudolinkage arrangements. Synteny of duplicated microsatellite markers was used to identify and confirm some previously reported pseudolinkage arrangements based upon allozyme markers. Fifteen centromeric regions (20 chromosome arms) were identified with a half-tetrad analysis using gynogenetic diploids. Female map length is approximately 10 M, but this is a large underestimate as many genotyped segments remain unassigned at a LOD threshold of 3.0. Extreme differences in female:male map distances were observed (ratio F:M, 3.25:1). Females had much lower recombination rates (0.14:1) in telomeric regions than males, while recombination rates were much higher in females within regions proximal to the centromere (F:M, 10:1). Quadrivalent formations that appear almost exclusively in males are postulated to account for the observed differences.     

Sex-specific recombination rates in zebrafish (Danio rerio)

In many organisms, the rate of genetic recombination is not uniform along the length of chromosomes or between sexes. To compare the relative recombination rates during meiosis in male and female zebrafish, we constructed a genetic map based on male meiosis. We developed a meiotic mapping panel of 94 androgenetic haploid embryos that were scored for genetic polymorphisms. The resulting male map was compared to female and sex-average maps. We found that the recombination rate in male meiosis is dramatically suppressed relative to that of female meiosis, especially near the centromere. These findings have practical applications for experimental design. The use of exclusively female meiosis in a positional cloning project maximizes the ratio of genetic map distance to physical distance. Alternatively, the use of exclusively male meiosis to localize a mutation initially to a linkage group or to maintain relationships of linked alleles minimizes recombination, thereby facilitating some types of analysis.     

Microsatellite isolation, linkage group identification and determination of recombination frequency in the peach-potato aphid, Myzus persicae (Sulzer) (Hemiptera: Aphididae)

Fifteen polymorphic microsatellite markers were used to establish linkage groups and relative rates of recombination in male and female Myzus persicae (Sulzer) (Hemiptera: Aphididae) (peach-potato aphid). We cloned nine markers from M. persicae and for these we report primer sequences and levels of allelic diversity and heterozygosity in four Australian M. persicae populations. Of the remaining six loci, four loci, also cloned from M. persicae, were obtained from G. Malarky (Natural History Museum, London) and two loci from Sitobion miscanthi were used. Additionally, the primer sequences of locus M77, a locus monomorphic in M. persicae but polymorphic in the closely related Myzus antirrhinii, are presented. Eleven of the 15 polymorphic markers were autosomal and four were X-linked. A linkage analysis was performed on a European pedigree of aphids containing five families with between seven and 11 offspring each. There was no linkage between any loci in females. In males, several pairwise comparisons yielded no recombinant offspring. With the exception of locus M40, these observations were supported in a linkage analysis performed on larger families produced from Australian M. persicae crosses. Locus M40 showed segregation consistent with involvement in a translocation between autosomes 1 and 3 in European samples but not in the Australian samples. From the Australian crosses we report an absence of recombination in males but high recombination rates in females. One X chromosome and four autosomal linkage groups were identified and tentatively assigned to chromosomes. The relevance of achiasmate meiosis to the evolution of sex is discussed.     

Mapping of theEs-4 locus and linear order of esterase genes (linkage group V; LGV) in the rat

There are three different linear orders of esterase loci of linkage group V (LGV) in the rat (Rattus norvegicus). The first is Es-2-Es-3-Es-1, the second Es-3-(Es-2,Es-4)-Es-1, and the third Es-3-Es-2-Es-1-Es-4. We carried out mating experiments to define the order clearly. Linkage analyses of the four esterase loci, Es-1, Es-2, Es-3, and Es-4, were carried out using two inbred strains carrying different alleles at the four loci. Six locus combinations examined in this study were as follows: Es-1-Es-2, Es-1-Es-3, Es-1-Es-4, Es-2-Es-3, Es-2-Es-4, and Es-3-Es-4. The recombination frequencies of each combination were 6.3, 6.3, 6.3, 5.2, 1.8, and 3.4%, respectively. The first recombination between Es-2 and Es-4 was observed. We propose that the esterase loci of LGV be classified into three clusters according to distances between the loci. The linear order of the four loci is shown to be as follows: [Es-3] (cluster II)-3.4 +/- 2.4%-[Es-4-1.8 +/- 1.7%-Es-2] (cluster III)-6.3 +/- 6.1%-[Es-1] (cluster I).     

The position of the epistatic S locus in the halothane linkage group in pigs

The linkage of the Phi, Pgd, Po2, S, H and halothane sensitivity loci was followed in a Belgian Landrace family, heterozygous for these systems over 6 generations. Recombination next to the S locus occurred mainly in pigs belonging to this particular family. From this investigation the position of the S locus is proved to be outwith the Phi-Pgd region, next to Phi . Therefore the gene sequence S - Phi - Hal -H- Po2 -Pgd is proposed. Higher recombination rates were observed in the female parental line of the multiheterozygous family when compared to the male parental line. Additional data from animals, unrelated to this strain, confirm the evidence of close linkage of the S system to the nearest marker loci.     

The position of the epistatic S locus in the halothane linkage group in pigs

The linkage of the Phi, Pgd, Po2, S, H and halothane sensitivity loci was followed in a Belgian Landrace family, heterozygous for these systems over 6 generations. Recombination next to the S locus occurred mainly in pigs belonging to this particular family. From this investigation the position of the S locus is proved to be outwith the Phi-Pgd region, next to Phi. Therefore the gene sequence S - Phi - Hal - H - Po2 - Pgd is proposed. Higher recombination rates were observed in the female parental line of the multiheterozygous family when compared to the male parental line. Additional data from animals, unrelated to this strain, confirm the evidence of close linkage of the S system to the nearest marker loci.     

Genetic linkage between the bovine plasma protease inhibitor 2 (Pi-2) and S blood group loci

A linkage relationship has been detected between the bovine plasma protease inhibitor 2 (Pi-2) and S blood group loci by linkage study within a single pedigree. Using the sequential lodscore test, the recombination fraction (theta) with maximum likelihood has been estimated at 0.200 +/- 0.043, with a maximum lodscore value of 3.466 at theta = 0.200.     

A comparison of linkage disequilibrium patterns and estimated population recombination rates across multiple populations

Large-scale studies of linkage disequilibrium (LD) have shown considerable variation in the extent and distribution of pairwise LD within and between populations. Taken at face value, these results suggest that genomewide LD maps for one population may not be generalizable to other populations. However, at least part of this diversity is due to some undesirable features of pairwise LD measures, which are well documented for the D' and r2 measures. In this report, we compare patterns of LD derived from pairwise measures with statistical estimates of population recombination rates ( rho ) along a 10-Mb stretch of chromosome 20 in four population samples, comprising East Asians, African Americans, and U.K. and U.S. individuals of western European descent. The results reveal the expected variability of D' within and between populations but show better concordance in estimates of r2 for the same markers across the population samples. Estimates of rho correlate well across populations, but there is still evidence of population-specific spikes and troughs in rho values. We conclude that it is unlikely that a single haplotype map will provide a definitive guide for association studies of many populations; rather, multiple maps will need to be constructed to provide the best-possible guides for gene mapping.     

Linkage between the H and 6-Pgd Loci in Pigs)

The designation H stands for a blood group system and its corresponding chromosomal locus in pigs. The system includes multiple alleles, but merely two of these, Ha and Hc, were involved in the present investigation. The two alleles are co-dominant and form a closed system in the Duroc breed (Andre-sen 1963, 1964). The results of the present study using pigs of the Danish landrace breed and particularly the Duroc breed have shown that electrophoretic variants of the enzyme 6-phospho-gluconate dehydrogenase (6-PGD) in the erythrocytes likewise are determined by two alternative alleles, A and B, in pigs of both breeds. Thus, in agreement with observations by Saison (1968), who studied various other breeds and their crosses, three electrophoretic patterns were observed among the pigs studied. The three patterns or types appear as bands in the starch-gel after the addition of substrate. They are designated as A, AB and B. They correspond to the genotypes AA, AB and BB.     

Gene order and recombination rate in homologous chromosome regions of the chicken and a passerine bird

Genome structure has been found to be highly conserved between distantly related birds and recent data for a limited part of the genome suggest that this is true also for the gene order (synteny) within chromosomes. Here, we confirm that synteny is maintained for large chromosomal regions in chicken and a passerine bird, the great reed warbler Acrocephalus arundinaceus, with few rearrangements, but in contrast show that the recombination-based linkage map distances differ substantially between these species. We assigned a chromosomal location based on sequence similarity to the chicken genome sequence to a set of microsatellite loci mapped in a pedigree of great reed warblers. We detected homologous loci on 14 different chromosomes corresponding to chicken chromosomes Gga1-5, 7-9, 13, 19, 20, 24, 25, and Z. It is known that 2 passerine macrochromosomes correspond to the chicken chromosome Gga1. Homology of 2 different great reed warbler linkage groups (LG13 and LG5) to Gga1 allowed us to locate the split to a position between 20.8 and 84.8 Mb on Gga1. Data from the 5 chromosomal regions (on Gga1, 2, 3, 5, and Z) with 3 or more homologous loci showed that synteny was conserved with the exception of 2 large previously unreported inversions on Gga1/LG5 and Gga2/LG3, respectively. Recombination data from the 9 chromosomal regions in which we identified 2 or more homologous loci (accounting for the inversions) showed that the linkage map distances in great reed warblers were only 6.3% and 13.3% of those in chickens for males and females, respectively. This is likely to reflect the true interspecific difference in recombination rate because our markers were not located in potentially low-recombining regions: several linkage groups covered a substantial part of their corresponding chicken chromosomes and were not restricted to centromeres. We conclude that recombination rates may differ strongly between bird species with highly conserved genome structure and synteny and that the chicken linkage map may not be suitable, in terms of genetic distances, as a model for all bird species.     

Differences in recombination rates on chromosome 23 between German Angus and German Simmental and breed specific linkage mapping

Five paternal half sib families of German Angus (GA) (n = 428) and six of German Simmental (GS) (n = 378) including dams were genotyped with 11 microsatellites (INRA132, RM033, BM1815, BM1258, BOLA-DRB1, BM1818, BM1905, BM1443, CYP21, CSSM5 and DYMS1) derived from chromosome 23. Differences in heterozygosity between the breeds were observed. Significant differences in recombination rates between GA and GS could be demonstrated for the marker intervals INRA132-CSSM5, CYP21-BOLA-DRB1 and BOLA-DRB1-BM1818. The length of the map of GA was 90.5 cM in contrast to 117.8 cM for GS. The breed specific linkage maps show differences in length but confirmation of the order of the markers.     

Combining sperm typing and linkage disequilibrium analyses reveals differences in selective pressures or recombination rates across human populations

A previous polymorphism survey of the type 2 diabetes gene CAPN10 identified a segment showing an excess of polymorphism levels in all population samples, coinciding with localized breakdown of linkage disequilibrium (LD) in a sample of Hausa from Cameroon, but not in non-African samples. This raised the possibility that a recombination hotspot is present in all populations and we had insufficient power to detect it in the non-African data. To test this possibility, we estimated the crossover rate by sperm typing in five non-African men; these estimates were consistent with the LD decay in the non-African, but not in the Hausa data. Moreover, resequencing the orthologous region in a sample of Western chimpanzees did not show either an excess of polymorphism level or rapid LD decay, suggesting that the processes underlying the patterns observed in humans operated only on the human lineage. These results suggest that a hotspot of recombination has recently arisen in humans and has reached higher frequency in the Hausa than in non-Africans, or that there is no elevation in crossover rate in any human population, and the observed variation results from long-standing balancing selection.