Cytogenetic localization of 136 genes in the horse: comparative mapping with the human genome

Paternally expressed retrotransposon Gag-like 1 gene, RTL1, is one of the crucial elements for placental angiogenesis in horses†

RTL1 (retrotransposon Gag-like 1) is an essential gene in the development of the human and murine placenta. Several fetal and placental abnormalities such as intrauterine growth restriction (IUGR) and hydrops conditions have been associated with altered expression of this gene. However, the function of RTL1 has not been identified. RTL1 is located on a highly conserved region in eutherian mammals. Therefore, the genetic and molecular analysis in horses could hold important implications for other species, including humans. Here, we demonstrated that RTL1 is paternally expressed and is localized within the endothelial cells of the equine (Equus caballus) chorioallantois. We developed an equine placental microvasculature primary cell culture and demonstrated that RTL1 knockdown leads to loss of the sprouting ability of these endothelial cells. We further demonstrated an association between abnormal expression of RTL1 and development of hydrallantois. Our data suggest that RTL1 may be essential for placental angiogenesis, and its abnormal expression can lead to placental insufficiency. This placental insufficiency could be the reason for IUGR and hydrops conditions reported in other species, including humans.

The equine mononuclear phagocyte system: The relevance of the horse as a model for understanding human innate immunity

The mononuclear phagocyte system (MPS) is a family of cells of related function that includes bone marrow progenitors, blood monocytes and resident tissue macrophages. Macrophages are effector cells in both innate and acquired immunity. They are a major resident cell population in every organ and their numbers increase in response to proinflammatory stimuli. Their function is highly regulated by a wide range of agonists, including lymphokines, cytokines and products of microorganisms. Macrophage biology has been studied most extensively in mice, yet direct comparisons of rodent and human macrophages have revealed many functional differences. In this review, we provide an overview of the equine MPS, describing the variation in the function and phenotype of macrophages depending on their location and the similarities and differences between the rodent, human and equine immune response. We discuss the use of the horse as a large animal model in which to study macrophage biology and pathological processes shared with humans. Finally, following the recent update to the horse genome, facilitating further comparative analysis of regulated gene expression between the species, we highlight the importance of future transcriptomic macrophage studies in the horse, the findings of which may also be applicable to human as well as veterinary research.

Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes

Dynamic evolutionary processes and complex structure make the Y chromosome among the most diverse and least understood regions in mammalian genomes. Here, we present an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates. The eMSY comprises single-copy, equine specific multi-copy, PAR transposed, and novel ampliconic sequence classes. The eMSY gene density approaches that of autosomes with the highest number of retained X-Y gametologs recorded in eutherians, in addition to novel Y-born and transposed genes. Horse, donkey and mule testis RNAseq reveals several candidate genes for stallion fertility. A novel testis-expressed XY ampliconic sequence class, ETSTY7, is shared with the parasite Parascaris genome, providing evidence for eukaryotic horizontal transfer and inter-chromosomal mobility. Our study highlights the dynamic nature of the Y and provides a reference sequence for improved understanding of equine male development and fertility.

Applied equine genetics

Genome sequencing of the domestic horse and subsequent advancements in the field of equine genomics have led to an explosion in the development of tools for mapping traits and diseases and evaluating gene expression. The objective of this review is to discuss the current progress in the field of equine genomics, with specific emphasis on assembly and analysis of the reference sequence and subsequent sequencing of a Quarter Horse mare; the genomic tools currently available to researchers and their implications in genomic investigations in the horse; the genomics of Mendelian and non-Mendelian traits; the genomics of performance traits and considerations regarding genetic testing in the horse. The whole-genome sequencing of a Quarter Horse mare has provided additional variants within the equine genome that extend past single nucleotide polymorphisms to include insertions/deletions and copy number variants. Equine single nucleotide polymorphism arrays have allowed for the investigation of both simple and complex genetic traits while DNA microarrays have provided a tool for examining gene expression across various tissues and with certain disease conditions. Recently, next-generation sequencing has become more affordable and both whole-genome DNA sequencing and transcriptome-wide RNA sequencing are methodologies that are being applied to equine genomic research. Research in the field of equine genomics continues to expand rapidly as the cost of genotyping and sequencing decreases, resulting in a need for quality bioinformatics software and expertise to appropriately handle both the size and complexity of these data.

The Application of Zoo-Fish Technique for Analysis of Chromosomal Rearrangements in the Equidae Family

Genome analysis is necessary to trace evolutionary rearrangements and relationships between species. Initially, to this end, the tools of classical cytogenetics were used but along with the development of molecular cytogenetics methods it became possible to analyse the genome more thoroughly. One of the widely used methods is fluorescence in situ hybridization (FISH) and its different types. Zoo-FISH, or cross-species chromosome painting, which uses painting probes specific for whole chromosomes, enables detecting homologous synteny blocks, the occurrence of which is evidence that species share a common ancestry and are related. Zoo-FISH technique is complemented by FISH with probes specific to chromosome arms or repetitive sequences (telomeres, centromeres), which provide additional information about karyotype organization, as well as karyotype polymorphism and conservation. Another method used is FISH with gene-specific probes, which enable the localization of single loci, thus making it possible to determine linkages between genes and verify data obtained after using painting probes in Zoo-FISH technique. Because of its diverse karyotype and rapid karyotypic evolution, the Equidae family is an ideal object of study using a number of methods based on in situ hybridization, which, in turn, enables information to be obtained at many levels of DNA organization.

Gene expression profiling in equine muscle tissues using mouse cDNA microarrays

REASONS FOR PERFORMING STUDY

Progress could be achieved by using microarrays to understand metabolic adaptations and disorders in equine muscle in response to exercise.

OBJECTIVES

To test the feasibility of using mouse cDNA microarrays to analyse gene expression profile in normal equine muscles.

METHODS

Muscular biopsies of dorsal gluteus medius and longissimus lumborum were done in 4 healthy Standardbreds. Total RNA was extracted from the muscle samples. The concentration and quality of RNA were measured before and after amplification. Gene expression profiles were measured using mouse cDNA microarrays including 15,264 unique genes representing about 11,000 documented genes. Three hybridisation tests were performed to check interspecificity, reproducibility and to compare gene expression in these muscles. For each test, a dye-swap hybridisation with Cy3 and Cy5 fluoromarkers were done and the gene list filtered according the signal level.

RESULTS

According to the specificity test, the mouse cDNA microarrays were correctly hybridised by equine muscle cDNA. All positive control genes (GAPDH, HPRT and beta-Actin) and no negative control gene (yeast, plant) hybridised. The reproducibility test demonstrated a good linearity between the duplicate hybridisations: 99.99% of the significant expressed genes have an expression ratio between 1.4 and 1/1.4 = 0.71. These limits can be considered as the thresholds to qualify as up-regulated (ratio >1.4) or downregulated (ratio <0.71). In the muscle comparison test between gluteus medius vs. longissimus lumborum, 63 genes were found up-regulated and 8 genes down-regulated. The range of gene expression ratios in the gluteus medius was 0.61-8.31 x the longissimus lumborum. This list of modulated genes was classified by functions using a gene ontology data basis.

CONCLUSION

Mouse microarrays could be used to hybridise equine RNA extracted from muscle tissues. For many genes there are large sequence identities that allowed interspecific cDNA hybridisation. The sensitivity of the method allowed quantification of up- and down-regulated genes after applying appropriate filters.

POTENTIAL RELEVANCE

Expression profiling could be used to explore the muscle metabolism changes related to exercise, training, pathology and illegal medication in horses.

FISH mapping of six genes responsible for development of the nervous and skeletal systems on donkey (Equus asinus) chromosomes

The results obtained in the present study made it possible to place selected markers responsible for development of the nervous and skeletal systems on the physical map of the donkey genome. Fluorescence in situ hybridization (FISH) was used to localize genes such as GDF5 (15q13), FRZB (4q23.1), TWIST (1q31), PAX6 (20q25), SALL1 (24q15) and SHH (1q35) on donkey chromosomes. The identification of their localization confirmed previously proposed homologies using ZOO-FISH technique, except for FRZB and SALL1 genes. This suggests that they were affected by rearrangements that changed their localization compared to horse, and in the case of the SALL1 gene also compared to human.

Molecular cloning and characterization of equine thymic stromal lymphopoietin

Thymic stromal lymphopoietin (TSLP) is a novel cytokine that plays a central role in T helper 2 (Th2) cell differentiation and allergic inflammation. It is predominantly expressed by epithelial cells, and its expression is increased in patients with atopic dermatitis and asthma. Mice overexpressing TSLP in the skin develop allergic dermatitis and mice overexpressing TSLP in lungs develop asthma-like disease. However, it is not known whether TSLP plays an important role in equine allergies. Therefore, we cloned and sequenced the complete translated region of equine TSLP gene and measured its expression in various tissues. The equine TSLP gene is organized in 4 exons and encodes a protein of 143 amino acids, which has 62% amino acid identity with human TSLP.

Interleukin 4 receptor alpha (IL4R) and calcium-activated chloride channel 1 (CLCA1) genes map to donkey chromosome

The results obtained in the present study enabled the physical map of the donkey genome to be extended with markers associated with recurrent airway obstruction (RAO), a major performance-limiting disease of Equidae. The equine BAC clone containing the IL4R and CLCA1 genes were localized to EAS 14q13 and EAS 6q15 respectlivy by fluorescent in situ hybridization. Identification of their locus confirmed the distribution of syntenic regions between the domestic horse and the domestic donkey within the chromosomes analysed.

Partial deletion of the LAMA3 gene is responsible for hereditary junctional epidermolysis bullosa in the American Saddlebred Horse

Laminin 5 is a heterotrimeric basement membrane protein integral to the structure and function of the dermal-epidermal junction. It consists of three glycoprotein subunits: the alpha3, beta3 and gamma2 chains, which are encoded by the LAMA3, LAMB3 and LAMC2 genes respectively. A mutation in any of these genes results in the condition known as hereditary junctional epidermolysis bullosa (JEB). A 6589-bp deletion spanning exons 24-27 was found in the LAMA3 gene in American Saddlebred foals born with the skin-blistering condition epitheliogenesis imperfecta. The deletion confirms that this autosomal recessive condition in the American Saddlebred Horse can indeed be classified as JEB and corresponds to Herlitz JEB in humans. A diagnostic test was developed and nine of 175 randomly selected American Saddlebred foals from the 2007 foal crop were found to be carriers of the mutation (frequency of 0.026).

A 4,103 marker integrated physical and comparative map of the horse genome

A comprehensive second-generation whole genome radiation hybrid (RH II), cytogenetic and comparative map of the horse genome (2n = 64) has been developed using the 5000rad horse x hamster radiation hybrid panel and fluorescence in situ hybridization (FISH). The map contains 4,103 markers (3,816 RH; 1,144 FISH) assigned to all 31 pairs of autosomes and the X chromosome. The RH maps of individual chromosomes are anchored and oriented using 857 cytogenetic markers. The overall resolution of the map is one marker per 775 kilobase pairs (kb), which represents a more than five-fold improvement over the first-generation map. The RH II incorporates 920 markers shared jointly with the two recently reported meiotic maps. Consequently the two maps were aligned with the RH II maps of individual autosomes and the X chromosome. Additionally, a comparative map of the horse genome was generated by connecting 1,904 loci on the horse map with genome sequences available for eight diverse vertebrates to highlight regions of evolutionarily conserved syntenies, linkages, and chromosomal breakpoints. The integrated map thus obtained presents the most comprehensive information on the physical and comparative organization of the equine genome and will assist future assemblies of whole genome BAC fingerprint maps and the genome sequence. It will also serve as a tool to identify genes governing health, disease and performance traits in horses and assist us in understanding the evolution of the equine genome in relation to other species.

The horse genome derby: racing from map to whole genome sequence

The map of the horse genome has undergone unprecedented expansion during the past six years. Beginning from a modest collection of approximately 300 mapped markers scattered on the 31 pairs of autosomes and the X chromosome in 2001, today the horse genome is among the best-mapped in domestic animals. Presently, high-resolution linearly ordered gene maps are available for all autosomes as well as the X and the Y chromosome. The approximately 4350 mapped markers distributed over the approximately 2.68 Gbp long equine genome provide on average 1 marker every 620 kb. Among the most remarkable developments in equine genome analysis is the availability of the assembled sequence (EquCab2) of the female horse genome and the generation approximately 1.5 million single nucleotide polymorphisms (SNPs) from diverse breeds. This has triggered the creation of new tools and resources like the 60K SNP-chip and whole genome expression microarrays that hold promise to study the equine genome and transcriptome in ways not previously envisaged. As a result of these developments it is anticipated that, during coming years, the genetics underlying important monogenic traits will be analyzed with improved accuracy and speed. Of larger interest will be the prospects of dissecting the genetic component of various complex/multigenic traits that are of vital significance for equine health and welfare. The number of investigations recently initiated to study a multitude of such traits hold promise for improved diagnostics, prevention and therapeutic approaches for horses.

Three autosomal chromosome translocations associated with repeated early embryonic loss (REEL) in the domestic horse (Equus caballus)

Repeated early embryonic loss (REEL) represents a considerable economic loss to the horse industry. Mares that experience REEL may be overlooked as potential carriers of a chromosome abnormality. Here we report three different autosomal translocations in Thoroughbred mares presented for chromosome analysis because of REEL. The karyotypes were 64,XX,t(1;21), 64,XX,t(16;22), and 64,XX,t(4;13), respectively. In order to confirm the chromosomes involved in the translocations, to map the breakpoints, and to determine if the translocations were reciprocal, genes surrounding the breakpoints were identified using existing maps and from the newly assembled horse genome sequence. Bacterial artificial chromosomes containing the genes of interest were identified and mapped to the translocation chromosomes by fluorescence in situ hybridization (FISH). FISH confirmed that the t(16;22) and t(4;13) translocations were reciprocal, while the t(1;21) was not. The breakpoints on horse chromosomes 1 and 16 appear to be the same or near breakpoints previously identified in translocations. These breakpoints are at the fusion boundary of human chromosomes 10 and 15 on horse chromosome 1 and at human chromosome 3p and 3q on horse chromosome 16. These sites may represent ancient breakpoints reused during equid evolution. Overall, chromosome abnormalities may have a greater influence on mare fertility than previously known. Thus, it is important to karyotype subfertile mares exhibiting REEL.

Genome-wide search for markers associated with osteochondrosis in Hanoverian warmblood horses

A genome-wide scan was performed to detect quantitative trait loci (QTLs) for osteochondrosis (OC) and osteochondrosis dissecans (OCD) in horses. The marker set comprised 260 microsatellites. We collected data from 211 Hanoverian warmblood horses consisting of 14 paternal half-sib families. Traits used were OC (fetlock and/or hock joints affected), OCD (fetlock and/or hock joints affected), fetlock OC, fetlock OCD, hock OC, and hock OCD. The first genome scan included 172 microsatellite markers. In a second step 88 additional markers were chosen to refine putative QTLs found in the first scan. Genome-wide significant QTLs were located on equine chromosomes 2, 4, 5, and 16. QTLs for fetlock OC and hock OC partly overlapped on the same chromosomes, indicating that these traits may be genetically related. QTLs reached the chromosome-wide significance level on eight different equine chromosomes: 2, 3, 4, 5, 15, 16, 19, and 21. This whole-genome scan was a first step toward the identification of candidate genome regions harboring genes responsible for equine OC. Further investigations are necessary to refine the map positions of the QTLs already identified for OC.

Characterization of the equine glycogen debranching enzyme gene (AGL): Genomic and cDNA structure, localization, polymorphism and expression

Glycogen debranching enzyme (AGL) is a multifunctional enzyme acting in the glycogen degradation pathway. In humans, the AGL activity deficiency causes a type III glycogen storage disease (Cori-Forbes disease). One particularity of AGL gene expression lies in the multiple alternative splicing in its 5' region. The AGL gene was localized on ECA5q14-q15. The sequence of the equine cDNA was determined to be 7.5 kb in length with an open reading frame of 4602 bp. The gene is 69 kb long and contains 35 exons. The equine AGL gene has an ubiquitous expression and presents five tissue-dependent cDNA variants arising from alternative splicing of the first exons. The equine skeletal muscle and heart contain four out of six variants previously described in humans and the equine liver express three of these four human variants. We identified a new alternative splicing variant expressed in equine skeletal and heart muscles. All these mRNA variants most probably encode only two different protein isoforms of 1533 and 1377 amino-acids. Four SNPs were detected in the mRNA. The equine in silico promoter sequence reveals a structure similar to those of other mammalian species. The disposition of the transcription factor biding sites does not correlate to the transcription start sites of tissue-specific variants.

Fluorescent in situ hybridization mapping of the epidermal growth factor receptor gene in donkey

The physical localization of the epidermal growth factor receptor (EGFR) gene was performed on donkey chromosomes. Bacterial artificial chromosome DNA containing the equine EGFR gene was used to map this gene by fluorescent in situ hybridization on donkey metaphase chromosomes. The gene was mapped on donkey 1q21.1 region.

An advanced sheep (Ovis aries, 2n = 54) cytogenetic map and assignment of 88 new autosomal loci by fluorescence in situ hybridization and R-banding

Presented herein is an updated sheep cytogenetic map that contains 452 loci (291 type I and 161 type II) assigned to specific chromosome bands or regions on standard R-banded ideograms. This map, which significantly extends our knowledge of the physical organization of the ovine genome, includes new assignments for 88 autosomal loci, including 74 type I loci (known genes) and 14 type II loci (SSRs/microsatellite marker/STSs), by FISH-mapping and R-banding. Comparison of the ovine map to the cattle and goat cytogenetic maps showed that common loci were located within homologous chromosomes and chromosome bands, confirming the high level of conservation of autosomes among ruminant species. Eleven loci that were FISH-mapped in sheep (B3GAT2, ASCC3, RARSL, BRD2, POLR1C, PPP2R5D, TNRC5, BAT2, BAT4, CDC5L and OLA-DRA) are unassigned in cattle and goat. Eleven other loci (D3S32, D1S86, BMS2621, SFXN5, D5S3, D5S68, CSKB1, D7S49, D9S15, D9S55 and D29S35) were assigned to specific ovine chromosome (OAR) bands but have only been assigned to chromosomes in cattle and goat.

A high-resolution comparative radiation hybrid map of equine chromosome 4q12-q22

In this study, we present a comprehensive 5000-rad radiation hybrid map of a 40-cM region on equine chromosome 4 (ECA4) that contains quantitative trait loci for equine osteochondrosis. We mapped 29 gene-associated sequence tagged site markers using primers designed from equine expressed sequence tags or BAC clones in the ECA4q12-q22 region. Three blocks of conserved synteny, showing two chromosomal breakpoints, were identified in the segment of ECA4q12-q22. Markers from other segments of HSA7q mapped to ECA13p and ECA4p, and a region of HSA7p was homologous to ECA13p. Therefore, we have improved the resolution of the human-equine comparative map, which allows the identification of candidate genes underlying traits of interest.

High-resolution gene maps of horse chromosomes 14 and 21: additional insights into evolution and rearrangements of HSA5 homologs in mammals

High-resolution physically ordered gene maps for equine homologs of human chromosome 5 (HSA5), viz., horse chromosomes 14 and 21 (ECA14 and ECA21), were generated by adding 179 new loci (131 gene-specific and 48 microsatellites) to the existing maps of the two chromosomes. The loci were mapped primarily by genotyping on a 5000-rad horse x hamster radiation hybrid panel, of which 28 were mapped by fluorescence in situ hybridization. The approximately fivefold increase in the number of mapped markers on the two chromosomes improves the average resolution of the map to 1 marker/0.9 Mb. The improved resolution is vital for rapid chromosomal localization of traits of interest on these chromosomes and for facilitating candidate gene searches. The comparative gene mapping data on ECA14 and ECA21 finely align the chromosomes to sequence/gene maps of a range of evolutionarily distantly related species. It also demonstrates that compared to ECA14, the ECA21 segment corresponding to HSA5 is a more conserved region because of preserved gene order in a larger number of and more diverse species. Further, comparison of ECA14 and the distal three-quarters region of ECA21 with corresponding chromosomal segments in 50 species belonging to 11 mammalian orders provides a broad overview of the evolution of these segments in individual orders from the putative ancestral chromosomal configuration. Of particular interest is the identification and precise demarcation of equid/Perissodactyl-specific features that for the first time clearly distinguish the origins of ECA14 and ECA21 from similar-looking status in the Cetartiodactyls.

Cytogenetic mapping of immunity-related genes in the domestic horse

Chromosomal locations of 19 horse immunity-related loci (CASP1, CD14, EIF5A, FCER1A, IFNG, IL12A, IL12B, IL12RB2, IL1A, IL23A, IL4, IL6, MMP7, MS4A2, MYD88, NOS2A, PTGS2, TFRC and TLR2) were determined by fluorescence in situ hybridization. For IFNG and PTGS2, this study is a confirmation of their previously reported position. In addition, microsatellite (HMBr1) was localized in the same region as IFNG. All genes were assigned to regions of conserved synteny and the data obtained in this study enhance the comparative human-horse map. Cytogenetic localization of IL6 to ECA4q14-q21.1 suggested a new breakage point that changes the order of loci compared with HSA7. The map assignments of these loci serve as anchors for other loci and will aid in the search for candidate genes associated with traits in the horse.

Evolutionary movement of centromeres in horse, donkey, and zebra

Centromere repositioning (CR) is a recently discovered biological phenomenon consisting of the emergence of a new centromere along a chromosome and the inactivation of the old one. After a CR, the primary constriction and the centromeric function are localized in a new position while the order of physical markers on the chromosome remains unchanged. These events profoundly affect chromosomal architecture. Since horses, asses, and zebras, whose evolutionary divergence is relatively recent, show remarkable morphological similarity and capacity to interbreed despite their chromosomes differing considerably, we investigated the role of CR in the karyotype evolution of the genus Equus. Using appropriate panels of BAC clones in FISH experiments, we compared the centromere position and marker order arrangement among orthologous chromosomes of Burchelli's zebra (Equus burchelli), donkey (Equus asinus), and horse (Equus caballus). Surprisingly, at least eight CRs took place during the evolution of this genus. Even more surprisingly, five cases of CR have occurred in the donkey after its divergence from zebra, that is, in a very short evolutionary time (approximately 1 million years). These findings suggest that in some species the CR phenomenon could have played an important role in karyotype shaping, with potential consequences on population dynamics and speciation.

Sequence analysis of a 212 kb defensin gene cluster on ECA 27q17

Defensins are a family of evolutionary ancient antimicrobial peptides consisting of three sub-families: alpha-, beta- and theta-defensins. This investigation was focused on the genomic characterization of equine beta-defensins and the investigation of the potential clustering of beta-defensin genes in the equine genome. Six genomic BAC clones were isolated from the CHORI-241 library and one of these was mapped by FISH to ECA 27q17. This location was confirmed by RH-mapping. The contiguous 212 kb sequence of this clone was determined. Sequence analysis revealed the identification of ten pseudogenes and nine genes, six of which were highly homologous to human beta-defensin DEFB4. Clustering of the beta-defensin genes was confirmed and the order of the genes on the analyzed BAC was related to the corresponding defensin cluster on HSA 8. The knowledge about the sequence and the genomic structure of the equine beta-defensin genes will improve the classification of different paralogous defensin genes and is a prerequisite for subsequent functional studies. Additionally, the first alpha-defensin-like sequence outside the groups of primates, lagomorphs and rodents (glires) was identified.

Construction of a medium-density horse gene map

A medium-density map of the horse genome (Equus caballus) was constructed using genes evenly distributed over the human genome. Three hundred and twenty-three exonic primer pairs were used to screen the INRA and the CHORI-241 equine BAC libraries by polymerase chain reaction and by filter hybridization respectively. Two hundred and thirty-seven BACs containing equine gene orthologues, confirmed by sequencing, were isolated. The BACs were localized to horse chromosomes by fluorescent in situ hybridization (FISH). Overall, 165 genes were assigned to the equine genomic map by radiation hybrid (RH) (using an equine RH(5000) panel) and/or by FISH mapping. A comparison of localizations of 713 genes mapped on the horse genome and on the human genome revealed 59 homologous segments and 131 conserved segments. Two of these homologies (ECA27/HSA8 and ECA12p/HSA11p) had not been previously identified. An enhanced resolution of conserved and rearranged chromosomal segments presented in this study provides clarification of chromosome evolution history.

A 1.3-Mb interval map of equine homologs of HSA2

A comparative approach that utilizes information from more densely mapped or sequenced genomes is a proven and efficient means to increase our knowledge of the structure of the horse genome. Human chromosome 2 (HSA2), the second largest human chromosome, comprising 243 Mb, and containing 1246 known genes, corresponds to all or parts of three equine chromosomes. This report describes the assignment of 140 new markers (78 genes and 62 microsatellites) to the equine radiation hybrid (RH) map, and the anchoring of 24 of these markers to horse chromosomes by FISH. The updated equine RH maps for ECA6p, ECA15, and ECA18 resulting from this work have one, two, and three RH linkage groups, respectively, per chromosome/chromosome-arm. These maps have a three-fold increase in the number of mapped markers compared to previous maps of these chromosomes, and an increase in the average marker density to one marker per 1.3 Mb. Comparative maps of ECA6p, ECA15, and ECA18 with human, chimpanzee, dog, mouse, rat, and chicken genomes reveal blocks of conserved synteny across mammals and vertebrates.

Single linkage group per chromosome genetic linkage map for the horse, based on two three-generation, full-sibling, crossbred horse reference families

A genetic linkage map of the horse consisting of 742 markers, which comprises a single linkage group for each of the autosomes and the X chromosome, is presented. The map has been generated from two three-generation full-sibling reference families, sired by the same stallion, in which there are 61 individuals in the F2 generation. Each linkage group has been assigned to a chromosome and oriented with reference to markers mapped by fluorescence in situ hybridization. The average interval between markers is 3.7 cM and the linkage groups collectively span 2772 cM. The 742 markers comprise 734 microsatellite and 8 gene-based markers. The utility of the microsatellite markers for comparative mapping has been significantly enhanced by comparing their flanking sequences with the human genome sequence; this enabled conserved segments between human and horse to be identified. The new map provides a valuable resource for genetically mapping traits of interest in the horse.

Equine FISH mapping of 36 genes known to locate on human chromosome ends

The INRA and the CHORI-241 horse BAC libraries were screened by hybridization with DNA probes and/or directly by PCR with primers designed in consensus sequences of genes localized at the end of each human chromosome. BAC clones were retrieved and 36 could be FISH mapped after the expected gene was confirmed in each BAC by sequencing. Our results show that 16 BACs can be considered to be at telomeric or centromeric positions in the horse and 15 were found at the boundary of actually defined conserved segments even-though often located within conserved syntenic fragments between horse and human. There is no straightforward relation between the end position of a marker in human and its end position in the horse. A gene was first anchored to ECA27 by FISH mapping. The localization of these markers expands the cytogenetic map of the horse and will serve as anchors for the integrated and future physical maps. It should also help to better understand the different chromosomal rearrangements that occurred during evolution of genomes derived from a common ancestral karyotype.

A high-resolution physical map of equine homologs of HSA19 shows divergent evolution compared with other mammals

A high-resolution (1 marker/700 kb) physically ordered radiation hybrid (RH) and comparative map of 122 loci on equine homologs of human Chromosome 19 (HSA19) shows a variant evolution of these segments in equids/Perissodactyls compared with other mammals. The segments include parts of both the long and the short arm of horse Chromosome 7 (ECA7), the proximal part of ECA21, and the entire short arm of ECA10. The map includes 93 new markers, of which 89 (64 gene-specific and 25 microsatellite) were genotyped on a 5000-rad horse x hamster RH panel, and 4 were mapped exclusively by FISH. The orientation and alignment of the map was strengthened by 21 new FISH localizations, of which 15 represent genes. The approximately sevenfold-improved map resolution attained in this study will prove extremely useful for candidate gene discovery in the targeted equine chromosomal regions. The highlight of the comparative map is the fine definition of homology between the four equine chromosomal segments and corresponding HSA19 regions specified by physical coordinates (bp) in the human genome sequence. Of particular interest are the regions on ECA7 and ECA21 that correspond to the short arm of HSA19-a genomic rearrangement discovered to date only in equids/Perissodactyls as evidenced through comparative Zoo-FISH analysis of the evolution of ancestral HSA19 segments in eight mammalian orders involving about 50 species.