Development of 50 gene-associated microsatellite markers using BAC clones and the construction of a linkage map of swine chromosome 4

Identification of a second gene associated with variation in vertebral number in domestic pigs

Background

The number of vertebrae in pigs varies and is associated with body size. Wild boars have 19 vertebrae, but European commercial breeds for pork production have 20 to 23 vertebrae. We previously identified two quantitative trait loci (QTLs) for number of vertebrae on Sus scrofa chromosomes (SSC) 1 and 7, and reported that an orphan nuclear receptor, NR6A1, was located at the QTL on SSC1. At the NR6A1 locus, wild boars and Asian local breed pigs had the wild-type allele and European commercial-breed pigs had an allele associated with increased numbers of vertebrae (number-increase allele).

Results

Here, we performed a map-based study to define the other QTL, on SSC7, for which we detected genetic diversity in European commercial breeds. Haplotype analysis with microsatellite markers revealed a 41-kb conserved region within all the number-increase alleles in the present study. We also developed single nucleotide polymorphisms (SNPs) in the 450-kb region around the QTL and used them for a linkage disequilibrium analysis and an association study in 199 independent animals. Three haplotype blocks were detected, and SNPs in the 41-kb region presented the highest associations with the number of vertebrae. This region encodes an uncharacterized hypothetical protein that is not a member of any other known gene family. Orthologs appear to exist not only in mammals but also birds and fish. This gene, which we have named vertnin (VRTN) is a candidate for the gene associated with variation in vertebral number. In pigs, the number-increase allele was expressed more abundantly than the wild-type allele in embryos. Among candidate polymorphisms, there is an insertion of a SINE element (PRE1) into the intron of the Q allele as well as the SNPs in the promoter region.

Conclusions

Genetic diversity of VRTN is the suspected cause of the heterogeneity of the number of vertebrae in commercial-breed pigs, so the polymorphism information should be directly useful for assessing the genetic ability of individual animals. The number-increase allele of swine VRTN was suggested to add an additional thoracic segment to the animal. Functional analysis of VRTN may provide novel findings in the areas of developmental biology.

A new 4016-marker radiation hybrid map for porcine-human genome analysis

We constructed a 5000-rad comprehensive radiation hybrid (RH) map of the porcine (Sus scrofa) genome and compared the results with the human genome. Of 4475 typed markers, 4016 (89.7%) had LOD >5 compared with the markers used in our previous RH map by means of two-point analysis and were grouped onto the 19 porcine chromosomes (SSCs). All mapped markers had LOD >3 as determined by RHMAPPER analysis. The current map comprised 430 microsatellite (MS) framework markers, 914 other MS markers, and 2672 expressed sequence tags (ESTs). The whole-genome map was 8822.1 cR in length, giving an average marker density of 0.342 Mb/cR. The average retention frequency was 35.8%. Using BLAST searches of porcine ESTs against the RefSeq human nucleotide and amino acid sequences (release 22), we constructed high-resolution comparative maps of each SSC and each human chromosome (HSA). The average distance between ESTs in the human genome was 1.38 Mb. SSC contained 50 human chromosomal syntenic groups, and SSC11, SSC12, and SSC16 were only derived from the HSA13q, HSA17, and HSA5 regions, respectively. Among 38 porcine terminal regions, we found that at least 20 regions have been conserved between the porcine and human genomes; we also found four paralogous regions for the major histocompatibility complex (MHC) on SSC7, SSC2, SSC4, and SSC1.

Gene expression profiling, chromosome assignment and mutational analysis of the porcine Golgi-resident UDP-N-acetylglucosamine transporter SLC35A3

SLC35A3 encodes a Golgi-resident UDP-N-acetylglucosamine transporter. Here, the porcine SLC35A3 gene was assigned to Sus scrofa chromosome 4 (SSC4) by a combination of radiation hybrid and linkage analysis. Expression profiling using real time RT-PCR showed ubiquitous but variable transcription of SLC35A3 in a selection of tissues. The deduced 325 amino acid sequence revealed a hydrophobic protein with 10 predicted transmembrane helices and the N- and C-terminal tails facing the cytosolic side of the Golgi apparatus. In addition, mutated versions of the UDP-GlcNAc transporter were analyzed in a yeast complementation assay, which allowed us to identify important domains and amino acid residues. Thus, the N-terminal tail was inessential for activity, whereas removal of the first transmembrane domain inhibited yeast complementation. The hydrophilic C-terminus was dispensable while mutant proteins either fully or partially deprived of the last membrane-spanning helix were functionally impaired. The third luminal loop showed modest sequence conservation and appeared structurally flexible as certain deletions were acceptable. In contrast, the fourth luminal loop was more sensitive to changes since the competence of the mutant protein was lowered by mutations. Substitutions of glycines 190, 215 and 254, which are invariant positions in the SLC35A subfamilies affected activity negatively. Interestingly, inhibition of function by a valine to phenylalanine mutation, which has been associated with skeletal malformations, is likely caused by structural incompatibility of the bulky aromatic phenylalanine side chain with the integrity of the transmembrane helix, since substitutions with the smaller aliphatic side chains of leucine and isoleucine were acceptable changes.

Fine mapping of a swine quantitative trait locus for number of vertebrae and analysis of an orphan nuclear receptor, germ cell nuclear factor (NR6A1)

The number of vertebrae in pigs varies and is associated with meat productivity. Wild boars, which are ancestors of domestic pigs, have 19 vertebrae. In comparison, European commercial breeds have 21-23 vertebrae, probably owing to selective breeding for enlargement of body size. We previously identified two quantitative trait loci (QTL) for the number of vertebrae on Sus scrofa chromosomes (SSC) 1 and 7. These QTL explained an increase of more than two vertebrae. Here, we performed a map-based study to define the QTL region on SSC1. By using three F2 experimental families, we performed interval mapping and recombination analyses and defined the QTL within a 1.9-cM interval. Then we analyzed the linkage disequilibrium of microsatellite markers in this interval and found that 10 adjacent markers in a 300-kb region were almost fixed in European commercial breeds. Genetic variation of the markers was observed in Asian local breeds or wild boars. This region encoded an orphan nuclear receptor, germ cell nuclear factor (NR6A1, formerly known as GCNF), which contained an amino acid substitution (Pro192Leu) coincident with the QTL. This substitution altered the binding activity of NR6A1 to its corepressors, nuclear receptor-associated protein 80 (RAP80) and nuclear receptor corepressor 1 (NCOR1). In addition, somites of mouse embryos demonstrated expression of NR6A1 protein. Together, these results suggest that NR6A1 is a strong candidate for one of the QTL that influence number of vertebrae in pigs.

A polymerase chain reaction screening method for rapid detection of microsatellites in bacterial artificial chromosomes

Standard protocols aimed at identifying subclones of interest from bacterial artificial chromosomes (BACs) include the use of hybridization methods that are time consuming and often require the use of radioactive isotopes. Through our efforts to identify microsatellites in BACs from rainbow trout (Oncorhynchus mykiss) we have developed a nonradioactive polymerase chain reaction (PCR)-based screening technique to select microsatellites containing subclones for marker development. Two BACs were subcloned and screened by PCR using a vector-specific primer and a mix of microsatellite repeat primers. The subclones were then sequenced to evaluate the efficiency of the PCR screening method. Correlation between positive PCR amplification and presence of microsatellites varied between the two BACs (21.9% and 71.4%), but still a sufficient number of subclones were identified to enable design and optimization of microsatellite markers.

Targeted oligonucleotide-mediated microsatellite identification (TOMMI) from large-insert library clones

Background

In the last few years, microsatellites have become the most popular molecular marker system and have intensively been applied in genome mapping, biodiversity and phylogeny studies of livestock. Compared to single nucleotide polymorphism (SNP) as another popular marker system, microsatellites reveal obvious advantages. They are multi-allelic, possibly more polymorphic and cheaper to genotype. Calculations showed that a multi-allelic marker system always has more power to detect Linkage Disequilibrium (LD) than does a di-allelic marker system [1]. Traditional isolation methods using partial genomic libraries are time-consuming and cost-intensive. In order to directly generate microsatellites from large-insert libraries a sequencing approach with repeat-containing oligonucleotides is introduced.

Results

Seventeen porcine microsatellite markers were isolated from eleven PAC clones by targeted oligonucleotide-mediated microsatellite identification (TOMMI), an improved efficient and rapid flanking sequence-based approach for the isolation of STS-markers. With the application of TOMMI, an average of 1.55 (CA/GT) microsatellites per PAC clone was identified. The number of alleles, allele size distribution, polymorphism information content (PIC), average heterozygosity (H_T), and effective allele number (N_E) for the STS-markers were calculated using a sampling of 336 unrelated animals representing fifteen pig breeds (nine European and six Chinese breeds). Sixteen of the microsatellite markers proved to be polymorphic (2 to 22 alleles) in this heterogeneous sampling. Most of the publicly available (porcine) microsatellite amplicons range from approximately 80 bp to 200 bp. Here, we attempted to utilize as much sequence information as possible to develop STS-markers with larger amplicons. Indeed, fourteen of the seventeen STS-marker amplicons have minimal allele sizes of at least 200 bp. Thus, most of the generated STS-markers can easily be integrated into multilocus assays covering a broader separation spectrum. Linkage mapping results of the markers indicate their potential immediate use in QTL studies to further dissect trait associated chromosomal regions.

Conclusion

The sequencing strategy described in this study provides a targeted, inexpensive and fast method to develop microsatellites from large-insert libraries. It is well suited to generate polymorphic markers for selected chromosomal regions, contigs of overlapping clones and yields sufficient high quality sequence data to develop amplicons greater than 250 bases.

Interspecific chromosome-wide transcription profiles reveal the existence of mammalian-specific and species-specific chromosome domains

A long-range exploration of expression levels through wide chromosome territories was carried out in three species (pig, cattle, and chicken) by aligning EST counts against the human genome. This strategy made it possible to produce expression profiles that were very similar between pig and cattle and that were significantly correlated with chicken levels of expression. In parallel with these alignments, we developed a statistical approach enabling us to screen genomic regions for both underexpression and overexpression at the chromosome level within a given species, as well as interspecifically. The observed correlations are indicative of the existence of interspecifically conserved domains of gene expression, not only for housekeeping genes (which are highly expressed), but also for regions where genes are significantly underexpressed. Furthermore, our strategy made it possible to point out regions that are differentially regulated between species. These expression data were crossed with available comparative mapping information for pigs and cattle, suggesting that coregulated regions are syntenic in various mammals.

Comparative analysis and development of microsatellite markers on swine (Sus scrofa) chromosome 1qter

Several quantitative trait loci (QTL) have been detected on SSC1qter (Sus scrofa chromosome 1qter), including QTL for the number of vertebrae, as reported in our previous study. To provide the tools for analysis of QTLs on SSC1qter, we constructed a comparative map of swine and human. In addition, we identified 26 swine STSs and mapped 16 of them on SSC1qter using the INRA - University of Minnesota porcine radiation hybrid (IMpRH) panel. We screened a BAC library using these swine STSs and developed 35 new polymorphic microsatellite markers from the BAC clones, of which 26 were informative in our reference family. We also mapped nine microsatellite markers we had isolated previously. Consequently a total of 44 new polymorphic microsatellite markers were located within a 60-cM region of SSC1qter, spanning from SW1092 to the telomere.

High-resolution comparative mapping of pig Chromosome 4, emphasizing the FAT1 region

The first quantitative trait locus (QTL) in pigs, FAT1, was found on Chromosome 4 (SSC4) using a Wild Boar intercross. Further mapping has refined the FAT1 QTL to a region with conserved synteny to both human Chromosomes 1 and 8. To both improve the comparative map of the entire SSC4 and to define the specific human chromosome region with conserved synteny to FAT1, we have now mapped 103 loci to pig Chromosome 4 using a combination of radiation hybrid and linkage mapping. The physical data and linkage analysis results are in very good agreement. Comparative analysis revealed that gene order is very well conserved across SSC4 compared to both HSA1 and HSA8. The breakpoint in conserved synteny was refined to an area of about 23 cR on the q arm of SSC4 corresponding to a genetic distance of less than 0.5 cM. Localizations of the centromeres do not seem to have been conserved between the two species. No remnants of the HSA1 centromere were detected on the corresponding region on SSC4 and traces from the centromeric region of SSC4 cannot clearly be revealed on the homologous region on HSA8. This refined SSC4 map and the comparative analysis will be a great aid in the search for the genes underlying the FAT1 locus.

Conservation of the syntenies between porcine chromosome 7 and human chromosomes 6, 14 and 15 demonstrated by radiation hybrid mapping and linkage analysis

Comparative mapping studies facilitate the identification of genes located in quantitative trait locus (QTL) regions in domestic animals by utilizing information from the human genome. Radiation hybrid (RH) mapping is effective for this purpose because of its high resolution in ordered gene mapping on chromosomes. We constructed an RH map of pig chromosome 7, by adding 23 markers associated with genes. This RH map clearly demonstrated the mosaic of homology between pig chromosome 7 (SSC7) and human chromosomes 6, 14 and 15 at a 'gene' level, and was confirmed by linkage analysis. Clarification of the homology of SSC7 to human chromosomes will contribute to the elucidation of the gene(s) responsible for QTL detected on this chromosome.