Consensus and comprehensive linkage maps of bovine chromosome 24

This study describes development of a consensus genetic linkage map of bovine chromosome 24 (BTA24). Eight participating laboratories contributed data for 58 unique markers including a total of 25 409 meioses. Eighteen markers, which were typed in more than one reference population, were used as potential anchors to generate a consensus framework map. The framework map contained 16 loci ordered with odds greater than 1000:1 and spanned 79.3 cM. Remaining markers were included in a comprehensive map relative to these anchors. The resulting BTA24 comprehensive map was 98.3 cM in length. Average marker intervals were 6.1 and 2.5 cM for framework and comprehensive maps, respectively. Marker order was generally consistent with previously reported BTA24 linkage maps. Only one discrepancy was found when comparing the comprehensive map with the published USDA-MARC linkage map. Integration of genetic information from different maps provides a high-resolution BTA24 linkage map.     

Consensus and comprehensive linkage maps of bovine chromosome 7

The objective of this project was to integrate the currently available linkage maps for bovine chromosome 7 (BTA7) by combining data sets from eight research groups. A total of 54 unique markers were typed in eight pedigrees. Multilocus linkage analysis with CRI-MAP produced a bovine chromosome 7 consensus framework map of 27 loci ordered with odds greater than 1000:1. Furthermore, we present a bovine chromosome 7 comprehensive map integrating 54 loci. The locus order is in general agreement with the recently published linkage maps except for one discrepancy. The order of loci BM9289, BMS713, and ILSTS001 was reversed in the consensus framework map relative to the published USDA-MARC bovine chromosome 7 linkage map.     

Cytological and linkage maps of Drosophila virilis chromosomes

Cytological (photographic) maps of third-instar larvae Drosophila virilis salivary gland chromosomes were constructed; genetic maps of the chromosomes are also given together with the list of mutations known for this species.     

Comparison of wheat physical maps with barley linkage maps for group 7 chromosomes

Comparative genetic maps among the Triticeae or Gramineae provide the possibility for combining the genetics, mapping information and molecular-marker resources between different species. Dense genetic linkage maps of wheat and barley, which have a common array of molecular markers, along with deletion-based chromosome maps of Triticum aestivum L. will facilitate the construction of an integrated molecular marker-based map for the Triticeae. A set of 21 cDNA and genomic DNA clones, which had previously been used to map barley chromosome 1 (7H), were used to physically map wheat chromosomes 7A, 7B and 7D. A comparative map was constructed to estimate the degree of linkage conservation and synteny of chromosome segments between the group 7 chromosomes of the two species. The results reveal extensive homoeologies between these chromosomes, and the first evidence for an interstitial inversion on the short arm of a barley chromosome compared to the wheat homoeologue has been obtained. In a cytogenetically-based physical map of group 7 chromosomes that contain restriction-fragment-length polymorphic DNA (RFLP) and random amplified polymorphic DNA (RAPD) markers, the marker density in the most distal third of the chromosome arms was two-times higher than in the proximal region. The recombination rate in the distal third of each arm appears to be 8–15 times greater than in the proximal third of each arm where recombination of wheat chromosomes is suppressed.     

Molecular genetic linkage maps of mouse chromosomes 4 and 6.

We have generated a moderate resolution genetic map of mouse chromosomes 4 and 6 utilizing a (C57BL/6J x Mus spretus) F1 x Mus spretus backcross with RFLPs for 31 probes. The map for chromosome 4 covers 77 cM and details a large region of homology to human chromosome 1p. The map establishes the breakpoints in the mouse 4-human 1p region of homology to a 2-cM interval between Ifa and Jun in mouse and to the interval between JUN and ACADM in human. The map for mouse chromosome 6 spans a 65-cM region and contains a large region of homology to human 7q. These maps also provide chromosomal assignment and order for a number of previously unmapped probes. The maps should allow the rapid regional assignment of new markers to mouse chromosomes 4 and 6. In addition, knowledge of the gene order in mouse may prove useful in determining the gene order of the homologous regions in human.     

Alignment of the PiGMaP and USDA linkage maps of porcine chromosomes 2 and 5

The PiGMaP and USDA porcine linkage maps for chromosomes 2 and 5 have been aligned by typing five USDA microsatellite markers from chromosomes 2 and 4 from chromosome 5 on the PiGMaP reference families. The markers in the two maps can be successfully aligned except for Sw395 on chromosome 2, which is the end-most marker in the USDA map 22 cM remote from the next marker, but which maps to a more central location and in the same position as Sw776 in the PiGMaP families. The mapping of four additional chromosome 5 markers has enabled amalgamation of the two previously separate PiGMaP linkage groups assigned to chromosome 5 and has more than doubled the length of its map. The USDA map of chromosome 5 is considerably shorter than the revised PiGMaP version, particularly between DAGK and Sw1071 , where the corresponding lengths are 9 cM versus 33 cM.     

Alignment of the PiGMaP and USDA linkage maps of porcine chromosomes 3 and 9

The European Pig Gene Mapping Project (PiGMaP) and United States Department of Agriculture (USDA) porcine linkage maps for chromosomes 3 and 9 have been aligned by typing three USDA microsatellites from chromosome 3 and five from chromosome 9 on the PiGMaP reference families. Using the crimap linkage analysis package, revised multipoint linkage maps were constructed for chromosome 3 and 9. Inclusion of these USDA markers in the multipoint analysis resulted in an increase in length of 47% and 33% respectively for these two PiGMaP linkage groups. This increase in size is mainly the result of extension of the ends of both linkage groups.     

Bovine chromosome 4 workshop: consensus and comprehensive linkage maps

The report of the bovine chromosome 4 (BTA4) workshop is presented. Six laboratories contributed a total of 30,168 informative meioses from 62 loci. Twenty-two loci were typed by at least two independent laboratories and were used to construct a consensus linkage map of BTA4. The remaining 40 loci were subsequently incorporated into a comprehensive map. The sex-averaged consensus map covered 131.4 cM. The female map was 124.3 cM in length, while the male map was 134.3 cM. The comprehensive sex-averaged map spanned 141.6 cM. The length of the female and male comprehensive maps were 123.1 cM and 156.4 cM, respectively. Average genetic distance between loci was 6 and 2.3 cM for the consensus and comprehensive linkage maps, respectively.     

Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping

High-density whole-genome maps are essential for ordering genes or markers and aid in the assembly of genome sequence. To increase the density of markers on the bovine radiation hybrid map, and hence contribute to the assembly of the bovine genome sequence, an Illumina BeadStation was used to simultaneously type large numbers of markers on the Roslin-Cambridge 3000 rad bovine-hamster whole-genome radiation hybrid panel (WGRH3000). In five multiplex reactions, 6738 sequence tagged site (STS) markers were successfully typed on the WGRH3000 panel DNA. These STSs harboured SNPs that were developed as a result of the bovine genome sequencing initiative. Typically, the most time consuming and expensive part of creating high-density radiation hybrid (RH) maps is genotyping the markers on the RH panel with conventional approaches. Using the method described in this article, we have developed a high-density whole-genome RH map with 4690 loci and a linkage map with 2701 loci, with direct comparison to the bovine whole-genome sequence assembly (Btau_2.0) in a fraction of the time it would have taken with conventional typing and genotyping methods.     

Plant sex determination and sex chromosomes

Sex determination systems in plants have evolved many times from hermaphroditic ancestors (including monoecious plants with separate male and female flowers on the same individual), and sex chromosome systems have arisen several times in flowering plant evolution. Consistent with theoretical models for the evolutionary transition from hermaphroditism to monoecy, multiple sex determining genes are involved, including male-sterility and female-sterility factors. The requirement that recombination should be rare between these different loci is probably the chief reason for the genetic degeneration of Y chromosomes. Theories for Y chromosome degeneration are reviewed in the light of recent results from genes on plant sex chromosomes.     

Reinforcement and sex linkage

We present a general model for the effect of sex linkage on the evolution of reinforcement of mating preferences on an island. We find that the level of reinforcement can vary up to 80% depending on the mode of inheritance of the female preference and male trait. When reinforcement is driven mainly by selection in the male trait and intrinsic hybrid incompatibilities are weak, sex-linked preferences and autosomal male traits are the most conducive to reinforcement, whereas autosomal preferences and X-linked traits are the least. Surprisingly, the effect of mode of inheritance on reinforcement is poorly predicted by its effect on the genetic correlation between the male trait and female preference. Sex-linkage of genetic incompatibility loci increases reinforcement, though this is not due solely to the occurrence of Haldane's rule. We find that reinforcement can lead to complete reproductive isolation in some cases but not others and that the mode of inheritance can determine which outcome occurs.     

Linkage maps of human chromosomes

Finding the chromosomal location of human genes that heretofore have been defined solely by phenotypes, in particular clinical phenotypes that are transmitted in Mendelian fashion in families, is an early and often crucial step in the process of identifying the molecular basis of a disease. Recent progress in construction of chromosomal maps of genetically linked DNA markers has made almost the entire human genome accessible to linkage studies in families that are segregating genetic defects. Construction of linkage maps requires a panel of three-generation families for genotyping, a large number of polymorphic markers, and sophisticated computer programs for analysis of genotypic data. After a locus harboring a deleterious mutation has been identified by linkage to a mapped marker, a high-resolution map of the region can be constructed with new markers derived from cosmid libraries, to narrow the search for the gene in question. For example, this strategy has been pursued in the effort to characterize the gene responsible for familial adenomatous polyposis. When a target region has been narrowed to about 1 centiMorgan, corresponding to roughly a million base pairs in physical distance, other techniques of molecular biology can be brought to bear to isolate and clone the actual gene.     

The chromosomes and linkage groups ofPisum

By appropriate genetical studies using reciprocal translocation stocks it has been possible to confirmLamprecht's evidence that inPisum there are seven linkage groups. Lamm's evidence for six linkage groups has been shown to be due to incomplete knowledge of the chromosomal structure of certain interchange lines.It is suggested thatLamprecht's system of chromosomal nomenclature should be universally adopted forPisum.Lamm &Miravelle's extended tester set has been accordingly renumbered and the intercrossing of the interchange lines completed in order to extend the confirmatory evidence as to their chromosomal constitution.     

Ethnicity and human genetic linkage maps

Human genetic linkage maps are based on rates of recombination across the genome. These rates in humans vary by the sex of the parent from whom alleles are inherited, by chromosomal position, and by genomic features, such as GC content and repeat density. We have examined--for the first time, to our knowledge--racial/ethnic differences in genetic maps of humans. We constructed genetic maps based on 353 microsatellite markers in four racial/ethnic groups: whites, African Americans, Mexican Americans, and East Asians (Chinese and Japanese). These maps were generated using 9,291 subjects from 2,900 nuclear families who participated in the National Heart, Lung, and Blood Institute-funded Family Blood Pressure Program, the largest sample used for map construction to date. Although the maps for the different groups are generally similar, we did find regional and genomewide differences across ethnic groups, including a longer genomewide map for African Americans than for other populations. Some of this variation was explained by genotyping artifacts--namely, null alleles (i.e., alleles with null phenotypes) at a number of loci--and by ethnic differences in null-allele frequencies. In particular, null alleles appear to be the likely explanation for the excess map length in African Americans. We also found that nonrandom missing data biases map results. However, we found regions on chromosome 8p and telomeric segments with significant ethnic differences and a suggestive interval on chromosome 12q that were not due to genotype artifacts. The difference on chromosome 8p is likely due to a polymorphic inversion in the region. The results of our investigation have implications for inferences of possible genetic influences on human recombination as well as for future linkage studies, especially those involving populations of nonwhite ethnicity.     

Genomics of sex chromosomes

Sex chromosomes in plants and animals are distinctive, not only because of their gender-determining role but also for genomic features that reflect their evolutionary history. The genomic sequences in the ancient sex chromosomes of humans and in the incipient sex chromosomes of medaka, stickleback, papaya, and poplar exhibit unusual features as consequences of their evolution. These include the enormous palindrome structure in human MSY, a duplicated genomic fragment that evolved into a Y chromosome in medaka, and a 700 kb extra telomeric sequence of the W chromosome in poplar. Comparative genomic analysis of ancient and incipient sex chromosomes highlights common features that implicate the selection forces that shaped them, even though evolutionary origin, pace, and fate vary widely among individual sex-determining systems.