The PiGMaP consortium cytogenetic map of the domestic pig (Sus scrofa domestica)

Classical, Molecular, and Genomic Cytogenetics of the Pig, a Clinical Perspective

The chromosomes of the domestic pig (Sus scrofa domesticus) are known to be prone to reciprocal chromosome translocations and other balanced chromosome rearrangements with concomitant fertility impairment of carriers. In response to the remarkable prevalence of chromosome rearrangements in swine herds, clinical cytogenetics laboratories have been established in several countries in order to screen young boars for chromosome rearrangements prior to service. At present, clinical cytogenetics laboratories typically apply classical cytogenetics techniques such as giemsa-trypsin (GTG)-banding to produce high-quality karyotypes and reveal large-scale chromosome ectopic exchanges. Further refinements to clinical cytogenetics practices have led to the implementation of molecular cytogenetics techniques such as fluorescent in-situ hybridization (FISH), allowing for rearrangements to be visualized and breakpoints refined using fluorescently labelled painting probes. The next-generation of clinical cytogenetics include the implementation of DNA microarrays, and next-generation sequencing (NGS) technologies such as DNA sequencing to better explore tentative genome architecture changes. The implementation of these cytogenomics techniques allow the genomes of rearrangement carriers to be deciphered at the highest resolution, allowing rearrangements to be detected; breakpoints to be delineated; and, most importantly, potential gene implications of those chromosome rearrangements to be interrogated. Clinical cytogenetics has become an integral tool in the livestock industry, identifying rearrangements and allowing breeders to make informed breeding decisions.

An improved pig reference genome sequence to enable pig genetics and genomics research

Background

The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete, and unresolved redundancies, short-range order and orientation errors, and associated misassembled genes limited its utility.

Results

We present 2 annotated highly contiguous chromosome-level genome assemblies created with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2.

Conclusions

These highly contiguous assemblies plus annotation of a further 11 short-read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

Sequencing through thick and thin: Historiographical and philosophical implications

DNA sequencing has been characterised by scholars and life scientists as an example of 'big', 'fast' and 'automated' science in biology. This paper argues, however, that these characterisations are a product of a particular interpretation of what sequencing is, what I call 'thin sequencing'. The 'thin sequencing' perspective focuses on the determination of the order of bases in a particular stretch of DNA. Based upon my research on the pig genome mapping and sequencing projects, I provide an alternative 'thick sequencing' perspective, which also includes a number of practices that enable the sequence to travel across and be used in wider communities. If we take sequencing in the thin manner to be an event demarcated by the determination of sequences in automated sequencing machines and computers, this has consequences for the historical analysis of sequencing projects, as it focuses attention on those parts of the work of sequencing that are more centralised, fast (and accelerating) and automated. I argue instead that sequencing can be interpreted as a more open-ended process including activities such as the generation of a minimum tile path or annotation, and detail the historiographical and philosophical consequences of this move.

Characterization and comparative analysis of immunoglobulin lambda chain diversity in a neonatal porcine model

To elucidate how antigen exposure and selection shape the porcine antibody repertoires, we investigated the immunoglobulin lambda light chain (IGL) gene repertoires of the binary cross-bred (Yorkshire×Landrace) pig at different developmental stages, pre-suckle neonate (0days), wean piglet (35days) and growing pig (75days) under normal farming conditions. Immunoglobulin lambda light transcript (IGLV-J-C) clones of the peripheral blood mononuclear cells (PBMCs) from these different developmental stages were assessed for IGL combination, junction and sequence diversity. Previous research has revealed that IGLV8 plays a major role in immunity during the early fetus stage and that IGLV3 accounts for 30% of the neonatal IGLV repertoires. Here, we found that the antibody profile exhibited salient features at different stages. The usage of the IGLV3-3 subclass gradually decreased during development, in contrast, the utilization of IGLV8 (IGLV8-10, IGLV8-13 and IGLV8-18), which started in the fetal stage, has increased in the growing stage. Moreover, the junction diversity, as measured by the IGLV hypervariable complementarity determining region 3 (CDR3L) lengths, was constant during the different stages. The complete junction mutation ratio clearly increased in the growing pig compared to that in the younger pig. Our data provide new insights into the postnatal porcine IGLV repertoires maturation which can lay the foundation for porcine antibody gene research.

Advances in livestock genomics: Opening the barn door

Genome research in animals used in agriculture has progressed rapidly in recent years, moving from rudimentary genome maps to trait maps to gene discovery. These advances are the result of animal genome projects following closely in the footsteps of the Human Genome Project, which has opened the door to genome research in farm animals. In return, genome research in livestock species is contributing to our understanding of chromosome evolution and to informing the human genome. Enhancement of these contributions plus the much anticipated application of DNA-based tools to animal health and production can be expected as livestock genomics enters its sequencing era.

Linking porcine microsatellite markers to known genome regions by identifying their human orthologs

Microsatellites, or tandem simple sequence repeats (SSRs), have become one of the most popular molecular markers in genome mapping because of their abundance across genomes and because of their high levels of polymorphism. However, information on which genes surround or flank them has remained very limited for most SSRs, especially in livestock species. In this study, an in silico comparative mapping approach was developed to link porcine SSRs to known genome regions by identifying their human orthologs. From a total of 1321 porcine microsatellites used in this study, 228 were found to have blocks in alignment with human genomic sequences. These 228 SSRs span about 1459 cM of the porcine genome, but with uneven distributions, ranging from 2 on SSC12 to 24 on SSC14. Linking these porcine SSRs to the known genome regions in the human genome also revealed 16 new putative synteny groups between these two species. Fifteen SSRs on SSC3 with identified human orthologs were typed on a pig-hamster radiation hybrid (RH) panel and used in a joint analysis with 80 known gene markers previously mapped on SSC3 using the same panel. The analysis revealed that they were all highly linked to either one or both adjacent markers. These results indicated that assigning the porcine SSRs to known genome regions by identifying their human orthologs is a reliable approach. The process will provide a foundation for positional cloning of causative genes for economically important traits.

Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome

Based on published information, we have identified 991 genes and gene-family clusters for cattle and 764 for pigs that have orthologues in the human genome. The relative linear locations of these genes on human sequence maps were used as "rulers" to annotate bovine and porcine genomes based on a CSAM (contiguous sets of autosomal markers) approach. A CSAM is an uninterrupted set of markers in one genome (primary genome; the human genome in this study) that is syntenic in the other genome (secondary genome; the bovine and porcine genomes in this study). The analysis revealed 81 conserved syntenies and 161 CSAMs between human and bovine autosomes and 50 conserved syntenies and 95 CSAMs between human and porcine autosomes. Using the human sequence map as a reference, these 991 and 764 markers could correlate 72 and 74% of the human genome with the bovine and porcine genomes, respectively. Based on the number of contiguous markers in each CSAM, we classified these CSAMs into five size groups as follows: singletons (one marker only), small (2-4 markers), medium (5-10 markers), large (11-20 markers), and very large (> 20 markers). Several bovine and porcine chromosomes appear to be represented as di-CSAM repeats in a tandem or dispersed way on human chromosomes. The number of potential CSAMs for which no markers are currently available were estimated to be 63 between human and bovine genomes and 18 between human and porcine genomes. These results provide basic guidelines for further gene and QTL mapping of the bovine and porcine genomes, as well as insight into the evolution of mammalian genomes.

Comparative mapping of Homo sapiens chromosome 4 (HSA4) and Sus scrofa chromosome 8 (SSC8) using orthologous genes representing different cytogenetic bands as landmarks

The recently published draft sequence of the human genome will provide a basic reference for the comparative mapping of genomes among mammals. In this study, we selected 214 genes with complete coding sequences on Homo sapiens chromosome 4 (HSA4) to search for orthologs and expressed sequence tag (EST) sequences in eight other mammalian species (cattle, pig, sheep, goat, horse, dog, cat, and rabbit). In particular, 46 of these genes were used as landmarks for comparative mapping of HSA4 and Sus scrofa chromosome 8 (SSC8); most of HSA4 is homologous to SSC8, which is of particular interest because of its association with genes affecting the reproductive performance of pigs. As a reference framework, the 46 genes were selected to represent different cytogenetic bands on HSA4. Polymerase chain reaction (PCR) products amplified from pig DNA were directly sequenced and their orthologous status was confirmed by a BLAST search. These 46 genes, plus 11 microsatellite markers for SSC8, were typed against DNA from a pig-mouse radiation hybrid (RH) panel with 110 lines. RHMAP analysis assigned these 57 markers to 3 linkage groups in the porcine genome, 52 to SSC8, 4 to SSC15, and 1 to SSC17. By comparing the order and orientation of orthologous landmark genes on the porcine RH maps with those on the human sequence map, HSA4 was recognized as being split into nine conserved segments with respect to the porcine genome, seven with SSC8, one with SSC15, and one with SSC17. With 41 orthologous gene loci mapped, this report provides the largest functional gene map of SSC8, with 30 of these loci representing new single-gene assignments to SSC8.

Genome-wide scan for body composition in pigs reveals important role of imprinting

The role of imprinting in body composition was investigated in an experimental cross between Chinese Meishan pigs and commercial Dutch pigs. A whole-genome scan revealed significant evidence for five quantitative trait loci (QTL) affecting body composition, of which four were imprinted. Imprinting was tested with a statistical model that separated the expression of paternally and maternally inherited alleles. For back fat thickness, a paternally expressed QTL was found on Sus scrofa chromosome 2 (SSC2), and a Mendelian-expressed QTL was found on SSC7. In the same region of SSC7, a maternally expressed QTL affecting muscle depth was found. Chromosome 6 harbored a maternally expressed QTL on the short arm and a paternally expressed QTL on the long arm, both affecting intramuscular fat content. The individual QTL explained from 2% up to 10% of the phenotypic variance. The known homologies to human and mouse did not reveal positional candidate genes. This study demonstrates that testing for imprinting should become a standard procedure to unravel the genetic control of multifactorial traits.

Expansion of the pig comparative map by expressed sequence tags (EST) mapping

We have used a PCR-based approach for the genetical and physical mapping of 34 transcripts isolated from a porcine small intestine cDNA library. All but one gene were regionally localized by using a somatic pig-rodent cell hybrid panel, and 12 genes were mapped by linkage analysis of single-stranded conformational polymorphisms developed in 3' untranslated regions of transcripts. For 20 of the transcripts, the human homolog has already been mapped. This study thus represents a significant contribution to the pig comparative map. Some important findings were that we could clarify the extent of a previously identified inversion event in a region of conserved synteny between SSC6q and HSA1p, that SSC14q does contain a region homologous to HSA1, a situation not clear from earlier ZOO-FISH studies, and that the homology between SSC17 and HSA20 includes the p-arm of HSA20.

Linkage assignment of eleven genes to the porcine genome

We report comparative linkage mapping of eleven genes in the swine genome by RFLP analysis. These genes include: Acid phosphatase type 5 (ACP5), Cholecystokinin Type B Receptor (CCKBR), Antibiotic Peptide (FALL39), Insulin-like Growth Factor 1 Receptor (IGF1R), Integrin Alpha M (ITGAM), Integrin Beta 2 (ITGbeta2), Opioid Receptor Mu-1 (OPRM1), Pro-hormone Converter (PC1/3), Retinol Binding Protein 3 (RBP3), Ribosomal DNA (RNR1), and Zona Pellucida Glycoprotein 1 (ZP1). The CCKBR and ITGbeta2 loci define the ends of the linkage groups on Chromosomes (Chro) (SSC) 9p and 13qter, respectively.

Mapping of 22 expressed sequence tags isolated from a porcine small intestine cDNA library

Complementary DNA sequences were selected from a resource of tentatively identified clones from a porcine small intestine cDNA library. Forty PCR primer pairs were designed to amplify 101-309 base pairs of the 3' untranslated region of the genes. The PCR conditions were optimized by altering both formamide and magnesium concentrations on samples of pig, mouse, and hamster DNA. Twenty primer pairs that, under stringent conditions, were pig-specific and amplified the expected fragments were chosen for regional assignment in a pig/rodent hybrid cell panel. Furthermore, 22 primer pairs were chosen to amplify DNA from the parental animals of the PiGMaP shared reference families in order to detect possible polymorphisms. Primer pairs that generated polymorphisms were used for genetic mapping. A total of 22 porcine expressed sequence tags (ESTs) were cytogenetically or genetically mapped by this approach. Twelve of the mapped ESTs could be added to the human-porcine comparative map.

Structural organization and chromosomal assignment of the swine endothelin-1 gene

Cosmid clone containing swine endothelin-1 (EDN1) gene, cosEDN1, was isolated from swine cosmid library using swine EDN1 cDNA as a probe. The sequence analysis of cosEDN1 DNA revealed that the swine EDN1 gene consists of 5 exons, spanning approximately 6.5 kb. In the 5'-upstream region of the EDN1 gene, AP-1 and NF-1 elements were found, suggesting the possibility that the expression of swine EDN1 gene is controlled by protooncogene products Fos and Jun, and TGF-beta. Fluorescence in situ hybridization (FISH) using cosEDN1 DNA as a probe demonstrated that EDN1 gene resides on swine chromosome 7p13- > pter.

Characterization, chromosomal localization, and genetic variation of the porcine heart fatty acid-binding protein gene

The purpose of this study was to detect genetic variation in the porcine H-FABP gene, a candidate gene for meat quality traits in pigs. Lambda phages containing the porcine H-FABP gene were isolated by plaque hybridization with human H-FABP cDNA. The coding and flanking intronic sequences of the porcine H-FABP gene were determined as well as 1.6 kb of the 5' upstream region. The various potential regulatory sequences in this region are in accordance with the function and expression of the protein in muscle and mammary tissue. Furthermore, comparison with the homolog region of the mouse identified a highly conserved 13-bp element (CTTCCT [A/C] TTTCGG) that may be involved in regulation of expression. The porcine H-FABP gene was localized on Chromosome (Chr) 6 by porcine sequence-specific PCR on DNA from a pig/rodent cell hybrid panel. In addition, part of the H-FABP gene was screened for genetic variation by PCR-RFLP analysis. Three PCR-RFLPs were detected, one in the upstream region (HinfI) and two in the second intron (HaeIII and MspI). In most pig breeds the corresponding alleles have a variable distribution, possibly a consequence of selective breeding. This genetic variation will enable us to investigate the role of the H-FABP locus in porcine production and meat quality traits.

Genomic mapping of chemokine and transforming growth factor genes in swine

Five chemokine genes, transforming growth factors alpha, beta 2 and 3 (TGFBA, TGFB-2, and TGFB-3), interleukin 8 (IL-8), and monocyte chemoattractant protein 2 (MCP-2), were mapped to porcine linkage groups on Chromosomes 3q, 10p, 7q, 8, and 12q, respectively. Restriction fragment length polymorphisms (RFLPs) for these genes were developed by Southern blot hybridization after digestion of porcine genomic DNA with BamHI and MspI (TGFBA), BamHI and PvuII (TGFB-2), HindIII (TGFB-3), BglII (IL-8), and PstI (MCP-2) and used to genotype the USDA-MARC Swine Reference Population pigs. Sufficient informative meioses, 61 (TGFBA), 58 (TGFB-2), 28 (TGFB-3), 38 (IL-8), and 156 (MCP-2), were available to pursue two-point pairwise linkage analysis with over 1,000 existing loci in the USDA-MARC genome database to establish initial linkage (LOD > 3). Multi-point analysis with CRIMAP determined the most likely order for each new marker. The assignment of the five chemokine genes in swine concurs with previous porcine/human chromosomal homologies based on results from ZOO-FISH and chromosomal painting experiments. These findings add five new informative Type I markers within a single gene family to the swine genome and may help us understand the genetic basis for disease resistance in livestock.

Construction of a swine YAC library allowing an efficient recovery of unique and centromeric repeated sequences

A swine DNA genomic library was constructed in yeast artificial chromosome (YAC) using the pYAC4 vector and the AB1380 strain. The DNA prepared from two Large White males was partially digested with EcoRI and size selected after both digestion and ligation. The YAC library contained 33792 arrayed clones with an average size of 280 kb as estimated by analysis of 2% of the clones, thus representing a threefold coverage of the swine haploid genome. The library was organized in pools to facilitate the PCR screening. The complexity of the library was tested both for unique and centromeric repeated sequences. In all, 20 out of 22 primer sets allowed the characterization of one to six clones containing specific unique sequences. These sequences are known to be on Chromosomes (Chrs) 1, 2, 5, 6, 7, 8, 13, 14, 15, 17, and X. Eight additional clones carrying centromeric repeat units were also isolated with a single primer set. The sequencing of 37 distinct repeat units of about 340 bp subcloned from these eight YACs revealed high sequence diversity indicating the existence of numerous centromeric repeat unit subfamilies in swine. Furthermore, the analysis of the restriction patterns with selected enzymes suggested a higher order organization of the repeat units. According to preliminary FISH experiments on a small number of randomly chosen YACs and YACs carrying specific sequences, the chimerism appeared to be low. In addition, primed in situ labeling experiments favored the idea that the YACs with centromeric repeat sequences were derived from a subset of metacentric and submetacentric chromosomes.

ZOO-FISH analysis with 7 human chromosome specific libraries detects conserved regions between human and camel (Camelus dromedarius)

Chromosomal homologies between individual human chromosomes and the camel karyotype have been established by using heterologous chromosome painting experiments called ZOO-FISH. Biotin-labelled DNA libraries from seven flow-sorted human chromosomes were used as probes for fluorescence in situ hybridization (FISH) on camel chromosomes. Human DNA libraries 3, 4, 13, 14, 15, 19 and 21 hybridized to camel chromosomes 2, 6, 7, 21, 25, 32 and 33, were used in identifying and delineating 10 segments of homology. Comparison of ZOO-FISH results with several species within the artiodactyls allowed the study of karyotype rearrangements and the transfer results from the human genome project and the animal gene maps. ZUSAMMENFASSUNG: Homologe Chromosomenregionen zwischen einzelnen Humanchromosomen und dem Kamelkaryotyp wurden mittels Verwendung der heterologen Chromosomenhybridisierung, genannt ZOO-FISH, dargestellt. Biotin-markierte DNS-Bibliotheken von sieben durchflusszytometrisch sortierten Humanchromosomen wurden als Proben für die Fluoreszenz In Situ Hybridisierung (FISH) auf Kamelchromosomen verwendet. Human DNS-Bibliotheken der Chromosomen 3, 4, 13, 14, 15, 19 und 21 hybridisierten auf die Kamelchromosomen 2, 6, 7, 21, 25, 32 und 33, und identifizierten 10 homologe Segmente zwischen Mensch und Kamel. Vergleichende Ergebnisse aus ZOO-FISH Daten unterschiedlicher Spezies innerhalb der Artiodaktilen erlauben das Studium der Karyotypenbildung und die Uebertragung von Daten aus dem Human Genom Projekt und den Genkarten der Tiere.

Construction and analysis of an hn-cDNA library derived from the p-arm of pig chromosome 12

Our aim is to find unidentified genes on specific pig chromosomes or chromosome fragments. Our approach has involved the construction of a heterogeneous nuclear complementary (hn-c) DNA library of the p-arm of pig Chromosome (Chr) 12, the only pig chromosome present in the pig x hamster hybrid cell line 8990. Total RNA was extracted from the cells and first-strand synthesis of hn-cDNA carried out with random and oligo dT primers. Pig hn-cDNA was isolated by amplification of first-strand synthesized hn-cDNA with primers specific for Short Interspersed Repeat Elements (SINEs) via the polymerase chain reaction (PCR). Hn-cDNAs were size selected and cloned in E. coli XL-1 blue cells with PCR-Script as the vector. The library consisted of 6000 clones. Clone inserts were amplified by PCR with vector-specific primers, and randomly picked inserts greater than 600 bp were sequenced. Homology searches were carried out with the FASTA search program on the GenEmbl database. Thirty clones were sequenced, and of these three showed strong homologies to GenEmbl sequences: (1) to sheep, mouse, human, and rat mammary gland factor (MGF); (2) to MLN-50, a gene that is amplified in human familial breast cancer and is present on human Chr 17; the latter is homologous to pig chromosome 12; (3) to a family of unassigned overlapping human ESTs. Of the other sequenced clones, seven were over 80% homologous with pig SINE sequences; three were over 75% homologous to human LINE sequences; six displayed open reading frames over a mean distance equivalent to 50 amino acids, although these showed no significant similarities with sequences in the databases. Using this approach, we have been able to identify several new genes on the p-arm of pig Chr 12. This is the first report of gene isolation from a library derived from a pig chromosome fragment.

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.

A comprehensive linkage map of the pig based on a wild pig-Large White intercross

A comprehensive linkage map, including 236 linked markers with a total sex-average map length of about 2300 cM, covering nearly all parts of the pig genome has been established. Linkage groups were assigned to approximately all 18 autosomes, the X chromosome and the X/Y pseudoautosomal region. Several new gene assignments were made including the assignment of linkage group U1 (EAK-HPX) to chromosome 9. The linkage map includes 77 types I loci informative for comparative mapping and 72 in situ mapped markers physically anchoring the linkage groups on chromosomes. A highly significant heterogeneity in recombination rates between sexes was observed with a general tendency towards an excess of female recombination. The average ratio of female to male recombination was estimated at 1.4:1 but this parameter varied between chromosomes as well as between regions within chromosomes. An intriguing finding was that blood group loci were overrepresented at the distal ends of linkage groups.

Porcine linkage and cytogenetic maps integrated by regional mapping of 100 microsatellites on somatic cell hybrid panel

Recently two main genetic maps [Rohrer et al. Genetics 136, 231 (1994); Archibald et al. Mamm. Genome 6, 157 (1995)] and a cytogenetic map [Yerle et al. Mamm. Genome 6, 175 (1995)] for the porcine genome were reported. As only a very few micro-satellites are located on the cytogenetic map, it appears to be important to increase the relationships between the genetic and cytogenetic maps. This document describes the regional mapping of 100 genetic markers with a somatic cell hybrid panel. Among the markers, 91 correspond to new localizations. Our study enabled the localization of 14 new markers found on both maps, of 54 found on the USDA map, and of 23 found on the PiGMaP map. Now 21% and 43% of the markers on the USDA and PiGMaP linkage maps respectively are physically mapped. This new cytogenetic information was then integrated within the framework of each genetic map. The cytogenetic orientation of the USDA linkage maps for Chromosomes (Chrs) 3, 8, 9, and 16 and of PiGMaP for Chr 8 was determined. USDA and PiGMaP linkage maps are now oriented for all chromosomes, except for Chrs 17 and 18. Moreover, the linkage group "R" from the USDA linkage map was assigned to Chr 6.

Integration of the PiGMaP and USDA maps for porcine chromosome 14

In order to align two previously published genetic linkage maps, a set of four of the United States Department of Agriculture (USDA) microsatellite linkage markers was mapped in the International Pig Gene Mapping Project (PiGMaP) reference families. Two-point linkage analysis was used between these USDA markers and the set of genes and markers previously mapped on the PiGMaP chromosome 14 map. Markers with threshold lod scores of three or greater were used for multipoint map construction. The USDA and PigGMaP linkage maps of chromosome 14 were aligned using the four USDA microsatellite markers along with three markers that are common to both maps. The PiGMaP genetic linkage map order for chromosome 14 was confirmed and the map was expanded to 193 cM with addition of the new markers.

Physical assignments of 68 porcine cosmid and lambda clones containing polymorphic microsatellites

Two lambda phage and 66 cosmids containing informative porcine microsatellites were assigned to 17 of 18 porcine autosomes and the X Chromosome (Chr) by fluorescence in situ hybridization (FISH). These assignments provide additional physically anchored markers to integrate the porcine physical and genetic maps.

A comparative map of the porcine and human genomes demonstrates ZOO-FISH and gene mapping-based chromosomal homologies

ZOO-FISH with chromosome-specific DNA libraries (CSLs) from individual flow-sorted human chromosomes was applied on porcine metaphase chromosomes to establish segment homology between the pig and human karyotypes. Forty-seven porcine chromosomal segments corresponding to all human chromosomes except the Y were delineated, resulting in a nearly complete coverage of the porcine karyotype. The syntenic segments detected were further confirmed by the gene mapping information available in the two species. A map demarcating physical boundaries of human homologies on individual pig chromosomes is complemented with a detail survey of the physical and genetic linkage mapping data in the two species. The resultant map, thus, provides a comprehensive and updated comparative status of the human and porcine genomes.

Chromosomal assignment of porcine EAD, EAO, LPR and P3 genes by linkage analysis

A two-point linkage analysis was performed between blood group (14), allotype (8), polymorphic protein (11), DNA type I (2), and microsatellite (2) loci in Wild Boar x Pietrain and Meishan x Pietrain three-generation families. The following new pairwise linkages were detected: LPR-EAN (Zmax = 60.68, theta = 0.055), EAD-GH1 (Zmax = 17.43, theta = 0.246), EAO-P3 (Zmax = 15.81, theta = 0.239), and P3-S0003 (Zmax = 5.43, theta = 0.312). This study and published mapping data enabled the localization of LPR (LPR allotype) to chromosome 9, EAD (erythrocyte antigen D) to chromosome 12, and EAO (erythrocyte antigen O) and P3 (P3 allotype) to the q arm of chromosome 6 with gene order S0003-P3-EAO, EAO being the most distal.

Construction of a cytogenetically characterized porcine somatic cell hybrid panel and its use as a mapping tool

A new panel of cytogenetically characterized pig-rodent somatic cell hybrids was constructed and tested for twelve microsatellite markers with PCR. Cytogenetic characterization of hybrids was accomplished by fluorescence painting and GTG-banding of metaphase chromosomes. The panel consists of 15 independent pig-hamster and 6 independent pig-mouse cell lines. In the panel, all pig autosomes and the X Chromosome (Chr) are represented, and it is informative for all chromosome pairs except 2-14, 2-15, 3-9, 14-15, 14-16, and 16-17. The microsatellites tested were S0022, S0023, S0084, S0098, S0112, S0113, S0114, S0115, S0117, S0118, S0119, and S0120. The PCR results obtained in the 21 hybrids were compared with the cytogenetic data and analyzed for concordancy and correlation. Eight microsatellites could be assigned to specific pig chromosomes, confirming seven assignments based on linkage analysis.

Assignment of 19 porcine type I loci by somatic cell hybrid analysis detects new regions of conserved synteny between human and pig

Nineteen so-called type I-loci, including ACO2, ADRA2, CAST, CCK, CHAT, IGKC, IGLV, IL4, IL6, INHA, LIF, MX1, PTH, RBP2, TCRA, TCRB, TGFB2, TGFB3, and UOX have been mapped in the pig with an informative somatic cell hybrid panel. By analyzing these new assignments in the knowledge of heterologous chromosome painting (Zoo-FISH) data for the porcine genome, it is possible to predict subchromosomal locations for most of these loci. Previously defined regions of conserved synteny were confirmed, and the extent of six of these regions was refined. These improvements in the porcine gene map facilitate the transfer of gene mapping data from "map-rich" species such as humans and mice.

Chromosomal localization of homeobox genes and associated markers on porcine chromosomes 3, 5, 12, 15, 16 and 18: comparative mapping study with human and mouse

Four homeobox genes that belong to the four homeobox gene clusters known in mammals have been regionally assigned to four distinct porcine chromosomes in conserved regions between human and pig. HOXA11, HOXB6, HOXC8, and HOXD4 genes were mapped by radioactive in situ hybridization to porcine Chromosomes (Chrs) 18q21-24 (with a secondary signal in 16q14-21), 12p11-12, 5p11-12, and 15q22-23 respectively. Besides, we have also revealed the presence of a porcine homeobox (pig Hbx24) which, although showing DNA sequence homology with a mouse gene of HOXB cluster, was located on porcine Chr 3 (3p14-13) outside the Hox clusters. To support the identity of the homeobox gene clusters analyzed and in the light of the high sequence similarity among homeobox genes, we also localized markers known to be mapped near each Hox cluster in human. In this way, four genes were also mapped in pig: GAPD (5q12-21), GAD1 (15q21-22), INHBA (18q24), and IGFBP3 (18q24). Mapping of HOXA11, INHBA, and IGFBP3 on pig Chr 18 constitutes the first assignments of genes on this small chromosome. These new localizations extend the information on the conservation of four human chromosomal regions in the pig genome.

Mapping of the porcine urate oxidase and transforming growth factor beta 2 genes by fluorescence in situ hybridization

We have mapped two genes from human chromosome 1, urate oxidase (UOX) and transforming growth factor beta 2 (TGFB2), by fluorescence in situ hybridization (FISH) in the pig genome. Porcine-specific polymerase chain reaction (PCR) primers for both genes were designed from the porcine cDNA sequence. With the help of these primers yeast artificial chromosome (YAC) clones for UOX and TGFB2 were isolated from a pig YAC library. These DNA probes were used for FISH analysis. TGFB2 was localized to SSC 10p16. With the YAC probe for UOX two porcine chromosome regions 6q26 and 6q32, revealed specific signals. These results, help to refine the comparative mapping data between human and pig.

First international workshop on porcine chromosome 6. Report and abstracts

Recent advances in the use of microsatellite markers and the development of comparative gene mapping techniques have made the construction of high resolution genetic maps of livestock species possible. Framework and comprehensive genetic linkage maps of porcine chromosome 6 have resulted from the first international effort to integrate genetic maps from multiple laboratories. Eleven highly polymorphic genetic markers were exchanged and mapped by four independent laboratories on a total of 583 animals derived from four reference populations. The chromosome 6 framework map consists of 10 markers ordered with high local support. The average marker interval of the framework map is 15.1 cM (sex averaged). The framework map is 135, 175 and 109 cM in length (for sex averaged, female and male maps, respectively). The comprehensive map includes a total of 48 type I and type II markers with a sex averaged interval of 3.5 cM and is 166, 196 and 126 cM (for sex averaged, female and male maps, respectively). Additional markers within framework map marker intervals can thus be selected from the comprehensive map for further analysis of quantitive trait loci (QTL) located on chromosome 6. The resulting maps of swine chromosome 6 provide a valuable tool for analysing and locating QTL.

Genetic differences in recombination frequency in the pig (Sus scrofa)

A comparison has been performed on 3 recently published linkage maps of the pig, hereafter designated as the American (A), European (E), and Swedish (S) maps. The cumulated distances between common markers in these 3 maps were in the ratio 1.00 (A):0.88 (E):0.77 (S), in keeping with the ratio of the percentages of domestic genome in the reference families used to build the corresponding maps, i.e., 1.00 (A):0.81 (E):0.50 (S). From further recombination frequencies reported in wild boars (in the S report), the wild pig genome length (in centimorgans) is expected to represent 66% of the domestic pig genome length. These observations tend to confirm a general result of Burt and Bell (Nature (London), 326: 803-805 (1987)), showing higher chiasma frequencies in domestic mammalian species compared with wild species. Consequences for mapping studies are discussed.

Directed integration of the physical and genetic linkage maps of swine chromosome 7 reveals that the SLA spans the centromere

The first integrated physical and genetic linkage map encompassing the entire swine chromosome 7 (SSC7) reveals that the porcine MHC (SLA) spans the centromere. A SLA class II antigen gene lies on the q arm, whereas class I and III genes lie on the p arm, suggesting that the presence of a centromere within the SLA does not preclude a functional complex. The SLA appears smaller than other mammalian MHC, as the genetic distance across two class I, three class II, and three class III SLA gene markers is only 1.1 cM. There are significant variations in recombination rates as a function of position along the chromosome, and the SLA lies in the region with the lowest rate. Furthermore, the directed integration approach used in this study was more efficient than previous efforts that emphasized the screening of large insert libraries for random microsatellites.