An autosomal genetic linkage map of the sheep genome

Introgression through rare hybridization: A genetic study of a hybrid zone between red and sika deer (genus Cervus) in Argyll, Scotland

In this article we describe the structure of a hybrid zone in Argyll, Scotland, between native red deer (Cervus elaphus) and introduced Japanese sika deer (Cervus nippon), on the basis of a genetic analysis using 11 microsatellite markers and mitochondrial DNA. In contrast to the findings of a previous study of the same population, we conclude that the deer fall into two distinct genetic classes, corresponding to either a sika-like or red-like phenotype. Introgression is rare at any one locus, but where the taxa overlap up to 40% of deer carry apparently introgressed alleles. While most putative hybrids are heterozygous at only one locus, there are rare multiple heterozygotes, reflecting significant linkage disequilibrium within both sika- and red-like populations. The rate of backcrossing into the sika population is estimated as H = 0.002 per generation and into red, H = 0.001 per generation. On the basis of historical evidence that red deer entered Kintyre only recently, a diffusion model evaluated by maximum likelihood shows that sika have increased at approximately 9.2% yr-1 from low frequency and disperse at a rate of approximately 3.7 km yr-1. Introgression into the red-like population is greater in the south, while introgression into sika varies little along the transect. For both sika- and red-like populations, the degree of introgression is 30-40% of that predicted from the rates of current hybridization inferred from linkage disequilibria; however, in neither case is this statistically significant evidence for selection against introgression.

Mapping of dentin-specific acidic phosphoprotein and integrin-binding sialoprotein in sheep defines an inversion breakpoint with respect to human chromosome 4Q

Genes from sheep chromosome 6 map to human chromosome 4 in the region extending from 4p16 to 4q26. However, there is an inversion of gene order in the central portion of the chromosome with one breakpoint close to secreted phosphoprotein 1 (SPP1). Genes for SPP1, integrin-binding sialoprotein (IBSP) and dentin-specific acidic phosphoprotein (DMP1) are located close together in a YAC contig in the human. RFLP markers were developed for DMP1 and IBSP in sheep and located on the sheep linkage map to further define the breakpoint region. There were no recombinants between SPP1 and IBSP indicating that these loci are close together in sheep, as in humans. DMP1 was located approximately 80 cM from SPP1 in sheep, 7 cM from the microsatellite BMC4203. In the human YAC contig, the order of these genes is SPP1-IBSP-DMP1 with 340 kb separating SPP1 and IBSP and 150 kb between IBSP and DMP1. Therefore, one breakpoint for the inversion in gene order between the sheep and the human has been narrowed to a region of 150 kb on the human map.

A synteny map of the horse genome comprised of 240 microsatellite and RAPD markers

To generate a domestic horse genome map we integrated synteny information for markers screened on a somatic cell hybrid (SCH) panel with published information for markers physically assigned to chromosomes. The mouse-horse SCH panel was established by fusing pSV2neo transformed primary horse fibroblasts to either RAG or LMTk mouse cells, followed by G418 antibiotic selection. For each of the 108 cell lines of the panel, we defined the presence or absence of 240 genetic markers by PCR, including 58 random amplified polymorphic DNA (RAPD) markers and 182 microsatellites. Thirty-three syntenic groups were defined, comprised of two to 26 markers with correlation coefficient (r) values ranging from 0.70 to 1.0. Based on significant correlation values with physically mapped microsatellite (type II) or gene (type I) markers, 22 syntenic groups were assigned to horse chromosomes (1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 15, 18, 19, 20, 21, 22, 23, 24, 26, 30, X and Y). The other 11 syntenic groups were provisionally assigned to the remaining chromosomes based on information provided by heterologous species painting probes and work in progress with type I markers.

High-resolution gametic map of the sheep callipyge region: linkage heterogeneity among rams detected by sperm typing

The callipyge locus (CLPG) causing muscular hypertrophy in domestic sheep has previously been mapped to the distal part of ovine chromosome 18. In this study, an accurate multipoint linkage map consisting of six microsatellite markers in this chromosomal region was constructed based on the analysis of 1145 single sperm cells. The best supported order of markers was OARHH47-ILSTS54-MCM38-CSSM18-IDVGA30-BM S1561. The log odds against the second most likely order, which has a reversal of the closely linked markers CSSM18 and IDVGA30, was 5.026. Sperm typing can be used to examine a large number of meioses in single individuals, and therefore, was exploited to study individual variability of recombination rate in rams of different callipyge genotypes. The results revealed statistically significant linkage heterogeneity among rams (P < 0.05) for marker interval OARHH47-CSSM18, with individual recombination fractions varying from 0.209 to 0.357.

Utilization of gene mapping information in livestock animals

A number of recent advances in genomic research will change and improve livestock production in the near future. Genetic linkage maps have been developed for a number of livestock species including cattle, sheep, and pigs. These maps allow scientists to identify chromosomal regions that influence traits of economic importance. This information will lead to improved genetic selection practices by identifying animals with superior copies of the chromosomal regions that affect the selected trait. This mapping information will also be used to identify the genes controlling the trait. A number of genomic regions or loci have already been reported that affect production, carcass or disease traits, and in a few cases, a specific gene has been identified. Production of transgenic animals with sequence changes in these genes may be beneficial for evaluating the effect of the gene upon the selected trait and more specifically the effect of certain polymorphisms (mutations) within the gene.

Genetic Basis of Trypanotolerance in Cattle and Mice

Under most circumstances, certain breeds of domestic ruminants show a remarkable resistance to the effects of African trypanosomiasis: they can tolerate the presence of parasites while apparently controlling levels of parasitaemia and, crucially, not showing the severe anaemia and production loss that are characteristic of infection in susceptible hosts. As discussed here by Stephen Kemp and Alan Teale, the genetic control of this phenomenon might finally be yielding to gene mapping studies. Genetic regions determining susceptibility to trypanosomiasis in mice have been identified and parallel studies are well advanced in cattle. There is growing evidence that only modest numbers of genes are involved in determining the difference between a susceptible and a resistant animal. These observations raise a new series of important questions concerning the possible exploitation of major trypanotolerance genes and the way that they might function in different genetic and physical environments.

Nuclear transfer in mammals: recent developments and future perspectives

A clone can be defined as a set of genetically identical animals. Small clones of two or occasionally up to four identical animals can be obtained by embryo splitting or blastomere separation. Embryo cloning by nuclear transfer involves the transfer of genetic material from a donor cell (karyoplast) to the cytoplasm of an oocyte or zygote from which the genetic material has been removed (cytoplast). In farm animals, metaphase II oocytes are most widely used as cytoplasts. There are now many factors known to influence the efficiency of embryo cloning by nuclear transfer. These include stage of development and cell cycle of donor cells, the choice of the recipient cell, the methods for activation of oocytes, the cell cycle coordination between donor cell and recipient cytoplast, and the method for fusion between nuclear donor and recipient cytoplast. Recent progress in cloning embryos and animals from cultured cells of embryonic, fetal, or adult origin offers a wide spectrum of potential applications of nuclear transfer, such as the unlimited multiplication of elite embryos or animals from selected matings and the potential for precise genetic modification of farm animals for gene farming or xenotransplantation.

Comparative gene mapping: a fine-scale survey of chromosome rearrangements between ruminants and humans

A total of 202 genes were cytogenetically mapped to goat chromosomes, multiplying by five the total number of regional gene localizations in domestic ruminants (255). This map encompasses 249 and 173 common anchor loci regularly spaced along human and murine chromosomes, respectively, which makes it possible to perform a genome-wide comparison between three mammalian orders. Twice as many rearrangements as revealed by ZOO-FISH were observed. The average size of conserved fragments could be estimated at 27 and 8 cM with humans and mice, respectively. The position of evolutionary breakpoints often correspond with human chromosome sites known to be vulnerable to rearrangement in neoplasia. Furthermore, 75 microsatellite markers, 30 of which were isolated from gene-containing bacterial artificial chromosomes (BACs), were added to the previous goat genetic map, achieving 88% genome coverage. Finally, 124 microsatellites were cytogenetically mapped, which made it possible to physically anchor and orient all the linkage groups. We believe that this comprehensive map will speed up positional cloning projects in domestic ruminants and clarify some aspects of mammalian chromosomal evolution.

Ovine neuronal ceroid lipofuscinosis: a large animal model syntenic with the human neuronal ceroid lipofuscinosis variant CLN6

The neuronal ceroid lipofuscinoses (NCLs) are a group of inherited degenerative neurological diseases affecting children. A number of non-allelic variants have been identified within the human population and the genes for some of these have recently been identified. The underlying mechanism for the neuropathology remains an enigma; however, pioneering studies with the naturally occurring ovine model (OCL) have led to the proposal that these diseases represent lesions in specific hydrophobic protein degradation pathways. In this study, we show linkage between OCL and microsatellite markers on OAR 7q13-15. Using interspecies chromosome painting we establish that OAR 7q13-15 is syntenic with human chromosome 15q21-23, the region which was recently defined as the location of a newly identified late infantile variant (CLN6). We propose that our ovine model represents a mutation in the gene orthologous to that mutated in the human late infantile variant CLN6. The ovine linkage flock, consisting of 56 families, represents a powerful resource for positional cloning of this NCL gene. The availability of such a large animal model will have important implications for experimentation in downstream corrective therapies.

A primary male autosomal linkage map of the horse genome

A primary male autosomal linkage map of the domestic horse (Equus caballus) has been developed by segregation analysis of 140 genetic markers within eight half-sib families. The family material comprised four Standardbred trotters and four Icelandic horses, with a total of 263 offspring. The marker set included 121 microsatellite markers, eight protein polymorphisms, five RFLPs, three blood group polymorphisms, two PCR-RFLPs, and one single strand conformation polymorphism (SSCP). One hundred markers were arranged into 25 linkage groups, 22 of which could be assigned physically to 18 different chromosomes (ECA1, ECA2, ECA3, ECA4, ECA5, ECA6, ECA7, ECA9, ECA10, ECA11, ECA13, ECA15, ECA16, ECA18, ECA19, ECA21, ECA22, and ECA30). The average distance between linked markers was 12.6 cM and the longest linkage group measured 103 cM. The total map distance contained within linkage groups was 679 cM. If the distances covered outside the ends of linkage groups and by unlinked markers were included, it was estimated that the marker set covered at least 1500 cM, that is, at least 50% of the genome. A comparison of the relationship between genetic and physical distances in anchored linkage groups gave ratios of 0.5-0.8 cM per Mb of DNA. This would suggest that the total male recombinational distance in the horse is 2000 cM; this value is lower than that suggested by chiasma counts. The present map should provide an important framework for future genome mapping in the horse.

Quantitative trait locus mapping in dairy cattle by means of selective milk DNA pooling using dinucleotide microsatellite markers: analysis of milk protein percentage

"Selective DNA pooling" accomplishes quantitative trait locus (QTL) mapping through densitometric estimates of marker allele frequencies in pooled DNA samples of phenotypically extreme individuals. With poly(TG) microsatellites, such estimates are confounded by "shadow" ("stutter") bands. A correction procedure was developed on the basis of an observed linear regression between shadow band intensity and allele TG repeat number. Using this procedure, a selective DNA pooling study with respect to milk protein percentage was implemented in Israel-Holstein dairy cattle. Pools were prepared from milk samples of high and low daughters of each of seven sires and genotyped with respect to 11 markers. Highly significant associations with milk protein percentage were found for 5 of the markers; 4 of these markers confirmed previous reports. Selective DNA pooling accessed 80.6 and 48.3%, respectively, of the information that would have been available through individual selective genotyping or total population genotyping. In effect, the statistical power of 45,600 individual genotypings was obtained from 328 pool genotypings. This methodology can make genome-wide mapping of QTL accessible to moderately sized breeding organizations.

Microsatellite behavior with range constraints: parameter estimation and improved distances for use in phylogenetic reconstruction

A symmetric stepwise mutation model with reflecting boundaries is employed to evaluate microsatellite evolution under range constraints. Methods of estimating range constraints and mutation rates under the assumptions of the model are developed. Least squares procedures are employed to improve molecular distance estimation for use in phylogenetic reconstruction in the case where range constraints and mutation rates vary across loci. The bias and accuracy of these methods are evaluated using computer simulations, and they are compared to previously existing methods which do not assume range constraints. Range constraints are seen to have a substantial impact on phylogenetic conclusions based on molecular distances, particularly for more divergent taxa. Results indicate that if range constraints are in effect, the methods developed here should be used in both the preliminary planning and final analysis of phylogenetic studies employing microsatellites. It is also seen that in order to make accurate phylogenetic inferences under range constraints, a larger number of loci are required than in their absence.

Genetic variation within the ovine cystic fibrosis transmembrane conductance regulator gene

We report here the results of a preliminary screening programme to identify natural mutations in the ovine cystic fibrosis transmembrane conductance regulator (CFTR) gene. Nine regions of the ovine CFTR gene were screened, corresponding to human CFTR gene exons 4, 6b, 7, 9, 10, 11, 12, 17b and 20. DNA samples from up to 2000 individual sheep were examined by single-stranded conformation polymorphism (SSCP) of each exon. In addition to the mutation (R297Q) reported previously, we have found several interesting variants, including intronic DNA variants and exonic polymorphisms.

A microsatellite genetic linkage map for zebrafish (Danio rerio)

We have constructed a zebrafish genetic linkage map consisting of 705 simple sequence-length polymorphism markers (SSLPs). The map covers 2350 centimorgans (cM) of the zebrafish genome with an average resolution of 3.3 cM. It is a complete map in genetic mapping terms (there is one linkage group for each of the 25 chromosomes), and it has been confirmed by somatic-cell hybrids and centromere-mapping using half-tetrad analysis. The markers are highly polymorphic in the zebrafish strains used for genetic crosses and provide a means to compare genetic segregation of developmental mutations between laboratories. These markers will provide an initial infrastructure for the positional cloning of the nearly 600 zebrafish genes identified as crucial to vertebrate development,and will become the anchor for the physical map of the zebrafish genome.

Major histocompatibility complex variation associated with juvenile survival and parasite resistance in a large unmanaged ungulate population

Antagonistic coevolution between hosts and parasites has been proposed as a mechanism maintaining genetic diversity in both host and parasite populations. In particular, the high levels of genetic diversity widely observed at the major histocompatibility complex (MHC) of vertebrate hosts are consistent with the hypothesis of parasite-driven balancing selection acting to maintain MHC genetic diversity. To date, however, empirical evidence in support of this hypothesis, especially from natural populations, has been lacking. A large unmanaged population of Soay sheep (Ovis aries L.) is used to investigate associations between MHC variation, juvenile survival, and parasite resistance. We show in an unmanaged, nonhuman population that allelic variation within the MHC is significantly associated with differences in both juvenile survival and resistance to intestinal nematodes. Certain MHC alleles are associated with low survivorship probabilities and high levels of parasitism or vice versa. We conclude that parasites are likely to play a major role in the maintenance of MHC diversity in this population.

A second-generation linkage map of the sheep genome

A genetic map of Ovis aries (haploid n = 27) was developed with 519 markers (504 microsatellites) spanning approximately 3063 cM in 26 autosomal linkage groups and 127 cM (female specific) of the X Chromosome (Chr). Genotypic data were merged from the IMF flock (Crawford et al., Genetics 140, 703, 1995) and the USDA mapping flock. Seventy-three percent (370/504) of the microsatellite markers on the map are common to the USDA-ARS MARC cattle linkage map, with 27 of the common markers derived from sheep. The number of common markers per homologous linkage group ranges from 5 to 22 and spans a total of 2866 cM (sex average) in sheep and 2817 cM in cattle. Marker order within a linkage group was consistent between the two species with limited exceptions. The reported translocation between the telomeric end of bovine Chr 9 (BTA 9) and BTA 14 to form ovine Chr 9 is represented by a 15-cM region containing 5 common markers. The significant genomic conservation of marker order will allow use of linkage maps in both species to facilitate the search for quantitative trait loci (QTLs) in cattle and sheep.

Construction and extensive characterization of a goat bacterial artificial chromosome library with threefold genome coverage

A goat Bacterial Artificial Chromosome (BAC) library of 61,440 independent clones was constructed and characterized. The average size of the inserts was estimated at 153 kilobases by analyzing almost 500 clones using Not1 digestion followed by FIGE (Field Inverted Gel Electrophoresis) analysis. The library represents about three genome equivalents, which yields a theoretical probability of 0.95 of isolating a particular DNA sequence. After individual growth, the clones were arrayed in 40 superpools, which were organized in three dimension pools. A rapid technique for pool DNA preparation by microwave treatment was set up. This technique was compatible with PCR analysis. Primer pairs from 166 sequences (microsatellites, coding sequences from goat, and conserved Expressed Sequence Tags (ESTs) from humans) enabled the library to be successfully searched in 165 cases, with an average of 3.52 positive superpools. Only one sequence could not be found. The degree of chimerism was evaluated by FISH analysis with DNA from over 110 clones and was estimated at 4%. This BAC library will constitute an invaluable tool for positional cloning in ruminants, as well as for more general comparative mapping studies in mammals.

Localization and genomic organization of sheep antimicrobial peptide genes

Antimicrobial peptides are an abundant and diverse component of animal innate immunity. Within mammalian species, defensins and cathelicidins are the two principal antimicrobial peptide families. We identified and sequenced ten new sheep genes which encode potential antimicrobial peptides including two beta-defensins and eight cathelicidins. We mapped the two-exon beta-defensin genes to sheep chromosome 26 and the four-exon cathelicidin genes to sheep chromosome 19 using sheep-hamster somatic cell hybrids in conjunction with flow-sorted sheep chromosomes. These assignments confirm homology between sheep, cattle, mouse, and human antimicrobial peptide gene families. Contig construction for the sheep cathelicidin gene family demonstrates that three genes, OaDodeA, OaDodeB, and OaMAP-34, are present head-to-tail in a 14.5 kb region, and that four proline/arginine-rich genes, OaBac5, OaBac7.5, OaBac11, and OaBac6, are arranged head-to-tail in a region covering 30.5 kb. This richly diverse family of sheep cathelicidin peptides is encoded in a gene array which may reflect the mechanism of its evolution.

No evidence for major histocompatibility complex-dependent mating patterns in a free-living ruminant population

Conventionally, the extraordinary diversity of the vertebrate major histocompatibility complex (MHC is thought to have evolved in response to parasites and pathogens affecting fitness. More recently, reproductive mechanisms such as disassortative mating have been suggested as alternative mechanisms maintaining MHC diversity. A large unmanaged population of Soay sheep (Ovis aries L.) was used to investigate reproductive mechanisms in the maintenance of MHC diversity. Animals were sampled as new-born lambs and between 887 and 1209 individuals were typed at each of five microsatellite markers located either within or flanking the ovine MHC. All loci were in Hardy-Weinberg proportions. A novel likelihood-based approach was developed to analyse mating patterns using paternity data. No evidence for non-random mating with respect to MHC markers was found using this technique. We conclude that MHC diversity in the St Kildan Soay sheep population is unlikely to be maintained by mating preferences and that, in contrast with evidence from experimental mice populations, MHC variation plays no role in the mating structure of this population.

A linkage map of the canine genome

A genetic linkage map of the canine genome has been developed by typing 150 microsatellite markers using 17 three-generation pedigrees, composed of 163 F2 individuals. One hundred and thirty-nine markers were linked to at least one other marker with a lod score > or = 3.0, identifying 30 linkage groups. The largest chromosome had 9 markers spanning 106.1 cM. The average distance between markers was 14.03 cM, and the map covers an estimated 2073 cM. Eleven markers were informative on the mapping panel, but were unlinked to any other marker. These likely represent single markers located on small, distinct canine chromosomes. This map will be the initial resource for mapping canine traits of interest and serve as a foundation for development of a comprehensive canine genetic map.

Comparative genomics: lessons from cats

The genomics era, spear headed by dazzling technological developments in human and mouse gene mapping, has additionally provoked extensive comparative gene mapping projects for domestic species of several vertebrate orders. As the human genome project promises a one dimensional string of 100,000 genes and sequences, comparative mapping will extend that inference to a second dimension representing index species of the 20 living mammalian orders and to a third dimension by phylogenetic description of the genomes of mammal ancestors. We review here the remarkable extent of genome homology conservation among mammals illustrated by technology applications in the feline genome project.

A two-stage half-sib design for mapping quantitative trait loci in food animals

Daughter and granddaughter half-sib designs for mapping quantitative trait loci were modified to increase experimental power. This new design includes a two-stage procedure, in contrast to conventional one-step half-sib designs. In stage 1, a few progeny of each sire are genotyped for marker loci. Based on the analyses of stage 1 data, some sires are chosen to continue genotyping more progeny for stage 2. When multiple chromosomes are under investigation, chromosomes and sires for stage 2 are selected based on the analysis of stage 1 data. Sire selection results in increased frequency of heterozygous genotypes of interest in stage 2 if the markers are linked to those genes. Chromosome selection can increase the proportion of chromosomes with segregating quantitative trait loci in stage 2 if not all of the chromosomes evaluated in stage 1 have segregating quantitative trait loci. Numerical results indicated that two-stage half-sib designs are generally more powerful than conventional designs when 1) the noncentrality parameter is moderate or larger, 2) larger quantitative trait loci are mapped using tightly linked markers in larger families, and 3) variation is large in numbers and sizes of segregating quantitative trait loci among the chromosomes evaluated in stage 1.

Physical and linkage mapping of human chromosome 17 loci to dog chromosomes 9 and 5

Genome mapping in the dog is in its early stages. Here we illustrate an approach to combined physical and linkage mapping of type 1 anchor (gene) loci in the dog using information on syntenic homology from human and mouse, an interbreed cross/backcross, and a strategy for isolation of dog genomic clones containing both gene-specific sequences and simple sequence repeat polymorphisms. Eleven gene loci from human chromosome 17q (HSA17q) were mapped to the centromeric two-thirds of dog chromosome 9 (CFA9), an acrocentric chromosome of medium size: P4HB, GALK1, TK1, GH1, MYL4, BRCA1, RARA, THRA1, MPO, NF1, and CRYBA1. Eight of these were also positioned on a linkage map spanning 38.6 cM. Based on combined fluorescence in situ hybridization and linkage mapping, the gene order on CFA9 is similar to that of the homologous genes on HSA17q and mouse chromosome 11 (MMU11), but in the dog the gene order is inverted with respect to the centromere. Canine loci, GALK1, TK1, GH1, MYL4, THRA1, and RARA constitute a closely linked group near the centromeric end of CFA9, spanning a genetic distance of only 4.7 cM. Canine NF1 and CRYBA1 lie distally, near the lower border of the Giemsa band adjacent to the distal one-third of CFA9. NF1 and CRYBA1 are loosely linked to the more centromeric group (31.2 cM). No HSA17 genes were found on the telomeric one-third of CFA9. Painting of dog chromosomes with a human whole chromosome 17 probe showed hybridization with only the proximal two-thirds of CFA9, consistent with the conclusion that the distal one-third corresponds to a segment or segments of other human chromosomes. Two loci, GLUT4 and PMP22, located on HSA17p, were mapped by FISH to dog chromosome 5 in a region also identified by the whole human chromosome 17 paint, indicating disruption of HSA17 syntenic homology at the centromere.

Genetical and physical assignments of equine microsatellites--first integration of anchored markers in horse genome mapping

Twenty equine microsatellites were isolated from a genomic phage library, and their genetical and physical localization was sought by linkage mapping and fluorescent in situ hybridization (FISH). Nineteen of the markers were found to be polymorphic with, in most cases, heterozygosities exceeding 50%. The markers were mapped in a Swedish reference family for gene mapping, comprising eight half-sib families from Standardbred and Icelandic horse sires. Segregation was analyzed against a set of 35 other markers typed in the pedigree. Thirteen of the microsatellites showed linkage to at least one other marker, with a total of 21 markers being involved in these linkages. In parallel, 18 of the microsatellites could be assigned to their chromosomal region by FISH. These assignments involved eight equine autosomes: ECA1, 2, 4, 6, 9, 10, 15, and 16. The genetical and physical mappings revealed by this study represent a significant extension of the current knowledge of the equine genome map.

A second-generation linkage map of the bovine genome

We report a bovine linkage map constructed with 1236 polymorphic DNA markers and 14 erythrocyte antigens and serum proteins. The 2990-cM map consists of a sex-specific, X chromosome linkage group and 29 sex-averaged, autosomal linkage groups with an average interval size of 2.5 cM. The map contains 627 new markers and 623 previously linked markers, providing a basis for integrating the four published bovine maps. Orientation and chromosomal assignment of all the linkage groups, except BTA20 and BTA22, was provided by 88 markers that were assigned previously to chromosomes. This map provides sufficient marker density for genomic scans of populations segregating quantitative trait loci (QTL) and subsequent implementation of marker-assisted selection (MAS) mating schemes.

Genetic mapping of 21 genes on mouse chromosome 11 reveals disruptions in linkage conservation with human chromosome 5

We report a high-resolution genetic map of 21 genes on the central region of mouse Chr 11. These genes were mapped by segregation analysis of more than 1650 meioses from three interspecific backcrosses. The order of these genes in mouse was compared to the previously established gene order in human. Eighteen of the 21 genes map to human Chr 5, and 2 of the genes define a proximal border for the region of homology between mouse Chr 11 and human Chr 17. Our results indicate a minimum of four rearrangements within the 10-cM region of synteny homology between mouse Chr 11 and human Chr 5. In addition, the linkage conservation is disrupted by groups of genes that map to mouse Chrs 13 and 18. These data demonstrate that large regions of conserved linkage can contain numerous chromosomal microrearrangements that have occurred since the divergence of mouse and human ancestors. Comparison of the mouse and human maps with data for other species provides an emerging picture of mammalian chromosome evolution.

Cosmid-derived markers anchoring the bovine genetic map to the physical map

The mapping strategy for the bovine genome described in this paper uses large insert clones as a tool for physical mapping and as a source of highly polymorphic microsatellites for genetic typing, and was one objective of the BovMap Project funded by the European Union (UE). Eight-three cosmid and phage clones were characterized and used to physically anchor the linkage groups defining all the bovine autosomes and the X Chromosome (Chr). By combining physical and genetic mapping, clones described in this paper have led to the identification of the linkage groups corresponding to Chr 9, 12, 16, and 25. In addition, anchored loci from this study were used to orient the linkage groups corresponding to Chr 3, 7, 8, 9, 13, 16, 18, 19, and 28 as identified in previously published maps. Comparison of the estimated size of the physical and linkage maps suggests that the genetic length of the bovine genome may be around 4000 cM.

Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes

Precise comparisons of mammalian gene maps require common anchor loci as landmarks for conserved chromosomal segments. Using a computer script that automates DNA sequence database alignments, we designed 410 evolutionarily conserved primer pair sequences which are specific for anchor locus gene amplification from any mammalian species' DNA. Primer pairs were designed to span introns for polymorphism ascertainment, and to include sufficient exonic sequence (25-400 bp) to allow for gene identification. A total of 318 primer pairs were optimized for domestic cats, and 86% of the sequenced feline PCR products showed homology to the gene of primer origin. A screen of 20 mammals from 11 orders revealed that 35-52% of the 318 primers yielded a single PCR product without further optimization suggesting that nearly 75% can be optimized for any eutherian mammal.

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 DQA2 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.

Livestock genomics comes of age

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A genetic linkage map of the male goat genome

This paper presents a first genetic linkage map of the goat genome. Primers derived from the flanking sequences of 612 bovine, ovine and goat microsatellite markers were gathered and tested for amplification with goat DNA under standardized PCR conditions. This screen made it possible to choose a set of 55 polymorphic markers that can be used in the three species and to define a panel of 223 microsatellites suitable for the goat. Twelve half-sib paternal goat families were then used to build a linkage map of the goat genome. The linkage analysis made it possible to construct a meiotic map covering 2300 cM, i.e., > 80% of the total estimated length of the goat genome. Moreover, eight cosmids containing microsatellites were mapped by fluorescence in situ hybridization in goat and sheep. Together with 11 microsatellite-containing cosmids previously mapped in cattle (and supposing conservation of the banding pattern between this species and the goat) and data from the sheep map, these results made the orientation of 15 linkage groups possible. Furthermore, 12 coding sequences were mapped either genetically or physically, providing useful data for comparative mapping.

A test of the double-strand break repair model for meiotic recombination in Saccharomyces cerevisiae

We tested predictions of the double-strand break repair (DSBR) model for meiotic recombination by examining the segregation patterns of small palindromic insertions, which frequently escape mismatch repair when in heteroduplex DNA. The palindromes flanked a well characterized DSB site at the ARG4 locus. The "canonical" DSBR model, in which only 5' ends are degraded and resolution of the four-stranded intermediate is by Holliday junction resolvase, predicts that hDNA will frequently occur on both participating chromatids in a single event. Tetrads reflecting this configuration of hDNA were rare. In addition, a class of tetrads not predicted by the canonical DSBR model was identified. This class represented events that produced hDNA in a "trans" configuration, on opposite strands of the same duplex on the two sides of the DSB site. Whereas most classes of convertant tetrads had typical frequencies of associated crossovers, tetrads with trans hDNA were parental for flanking markers. Modified versions of the DSBR model, including one that uses a topoisomerase to resolve the canonical DSBR intermediate, are supported by these data.

Mutations in sheep microsatellites

During the construction of a primary linkage map of the sheep genome, a total of 46,225 parent-offspring transfer of microsatellite alleles were examined through the genotyping of the AgResearch International Mapping Flock. Any observations of mutations were thoroughly rechecked, including examination of new DNA samples, to yield five bona fide mutations from the study. This gave us an observed spontaneous mutation rate for microsatellites in sheep of 1.1 +/- 0.5 x 10(-4) mutations/gamete per locus. Untransformed lymphocytes were used as the source of DNA. Two of the mutations could have happened at either meiosis or during mitotic growth of the male germ cells. The other three mutations probably occurred early in the mitotic generation of the female germ cells. All of the mutations consisted of a 2-bp insertion and occurred in individuals heterozygous at the mutant locus.

Phenotypic markers for selection of nematode-resistant sheep

Nematode-resistance of an animal can be defined as an enhanced natural ability, relative to its peers, to both prevent establishment of larval nematodes and evict any that do establish. These parameters are not measurable in a practical sense and consequently nematode-resistance has usually been defined in terms of low faecal nematode egg counts (FEC). Studies in New Zealand and Australia have demonstrated that nematode-resistance, as measured by FEC, has a heritability of about 0.3 in Romney and Merino sheep. However as a selection trait FEC has practical limitations and its use may incur production penalties through withholding drench treatment for prolonged periods or from a need for artificial challenge. FEC is influenced by the level and composition of a natural nematode challenge and especially the expression of the immune response. Thus immunological parameters which reflect the underlying genetic resistance could potentially be used as phenotypic markers. Ideally, a useful phenotypic marker would be easy to sample and its assay would be inexpensive and able to be automated, in addition to being strongly correlated with nematode-resistance. Results from several New Zealand trials have indicated that antibody levels (particularly IgG1) to excretory/secretory antigens of L3 nematodes such as Trichostrongylus colubriformis may meet these criteria. Levels of antibody against L3 antigens are also independent of on-farm drenching strategies. Blood eosinophil count has also been considered for use as a selection parameter but a high degree of sample variability reduces its potential. Other immunological parameters associated with nematode-resistance which have potential as phenotypic markers include serum nematode-specific IgE and products of mucosal mast cells such as proteinases. It is likely that as the critical immune responses of sheep to nematodes become more clearly defined, new immunological parameters with potential for use as phenotypic markers will be found. The definition of these immune responses will also assist in the identification and characterization of genetic markers.

Identification and genetic mapping of random amplified polymorphic DNA (RAPD) markers to the sheep genome

The random amplified polymorphic DNA (RAPD) assay utilizes the polymerase chain reaction (PCR) and short primers of arbitrary nucleotide sequence to amplify DNA. In this study, the RAPD assay was used to identify and map polymorphic markers in the AgResearch International Mapping Flock (IMF) sheep pedigrees. Sires and dams of eight of the full-sib IMF pedigrees were screened with 131 different 10-mer oligonucleotide primers. An average of 85 RAPD polymorphisms was identified between each parental pair, and 53 markers were contributed to the AgResearch IMF collaboration. Forty-five of the RAPD markers were mapped in the AgResearch IMF genetic linkage map, and at least one marker was located on 17 of the 26 autosomes and both sex chromosomes. Three lines of evidence were used to check for the homology of scored polymorphisms in different pedigrees, pedigree evaluation, segregation analysis, and Southern blot analysis. These results demonstrate that the RAPD assay is a powerful approach for identifying polymorphisms that can be used as markers for constructing a sheep genetic linkage map.

Physical mapping confirms that sheep chromosome 10 has extensive conserved synteny with cattle chromosome 12 and human chromosome 13

The following loci, on human chromosome 13, have been newly assigned to sheep chromosome 10 using chromosomally characterized sheep-hamster cell hybrids: gap junction protein, beta 2, 26 kDa (connexin 26) (GJB2); gap junction protein, alpha 3, 46 kDa (connexin 46) (GJA3), and esterase D/formylglutathione hydrolase (ESD). This assignment of ESD is consistent with comparative mapping evidence, but not with an earlier report of it on sheep chromosome 3p26-p24. Cell hybrid analysis confirmed the location of another chromosome 13 locus, retinoblastoma 1 (including osteosarcoma) (RB1), and the anonymous ovine genomic sequence RP11 on sheep chromosome 10. Isotopic in situ hybridization was used to regionally localize RP11 on to sheep 10q15-q22. The location of microsatellites AGLA226, OarDB3, OarHH41, OarVH58, and TGLA441, previously assigned to sheep chromosome 10 by linkage analysis, was confirmed by polymerase chain reaction using the cell hybrid panel. These mapping data provide further evidence that sheep chromosome 10 is the equivalent of cattle chromosome 12, and that these chromosomes show extensive conserved synteny with human chromosome 13.

A linkage map of the ovine X chromosome

A genetic linkage map of the ovine X chromosome containing type I and type II markers has been constructed. The map contains 7 known gene markers and 14 microsatellite markers with a recombination length of 141.9 cM. Segregation of polymorphic markers was observed in a three-generation pedigree containing 480 animals. The maximum number of informative meioses was 912. Additional information was obtained for some markers by following segregation in the AgResearch International Mapping Flock, consisting of nine three-generation full-sib pedigrees. A pseudoautosomal region containing two markers has been identified at one end of the linkage map. Comparisons with mouse and human X chromosomes confirms the observation of Ohno (1973) that the gene content of the mammalian X chromosome is retained. In particular, the conserved grouping of the genes PHKA1, ATP7A, and XIST observed in both the human and the mouse X chromosome appears to be conserved in the sheep X chromosome, and XIST has been mapped to near the center of the chromosome. This study provides the first reported genetic linkage map combining both type I and type II markers for any ruminant X chromosome.

Prospects for development of genetic markers for resistance to gastrointestinal parasite infection in sheep

Selection of sheep for resistance to internal parasites represents a viable option for future parasite control. Many phenotypic measures are available for determining the level of infection in individual sheep, although no phenotypic markers are available which allow prediction of an individual's resistance status. Genetic markers are therefore the best way to incorporate parasite resistance into selection programmes. With the recent development of genetic maps, several experiments are underway to search for markers linked to parasite-resistance genes in sheep. It can be predicted confidently that markers associated with resistance will be discovered within 12 months. Markers useful as selection criteria will be available within 5 years, although considerable quantitative genetic analysis needs to be done to find the best way to utilise marker information in selection programmes. In future, methods for differential DNA analysis or mRNA expression will lead to isolation of the genes involved.