Construction of a whole-genome radiation hybrid panel for high-resolution gene mapping in pigs

The insulin-like growth factor 2 (IGF2) gene intron3-g.3072G>A polymorphism is not the only Sus scrofa chromosome 2p mutation affecting meat production and carcass traits in pigs: evidence from the effects of a cathepsin D (CTSD) gene polymorphism

The objective of this study was to evaluate the effects of mutations in 2 genes [IGF2 and cathepsin D (CTSD)] that map on the telomeric end of the p arm of SSC2. In this region, an imprinted QTL affecting muscle mass and fat deposition was reported, and the IGF2 intron3-g.3072G>A substitution was identified as the causative mutation. In the same chromosome region, we assigned, by linkage mapping, the CTSD gene, a lysosomal proteinase, for which we previously identified an SNP in the 3'-untranslated region (AM933484, g.70G>A). We have already shown strong effects of this CTSD mutation on several production traits in Italian Large White pigs, suggesting a possible independent role of this marker in fatness and meat deposition in pigs. To evaluate this hypothesis, after having refined the map position of the CTSD gene by radiation hybrid mapping, we analyzed the IGF2 and the CTSD polymorphisms in 270 Italian Large White and 311 Italian Duroc pigs, for which EBV and random residuals from fixed models were calculated for several traits. Different association analyses were carried out to distinguish the effects of the 2 close markers. In the Italian Large White pigs, the results for IGF2 were highly significant for all traits when using either EBV or random residuals (e.g., using EBV: lean cuts, P = 2.2 x 10(-18); ADG, P = 2.6 x 10(-16); backfat thickness, P = 2.2 x 10(-9); feed:gain ratio, P = 2.3 x 10(-9); ham weight, P = 1.5 x 10(-6)). No effect was observed for meat quality traits. The IGF2 intron3-g.3072G>A mutation did not show any association in the Italian Duroc pigs, probably because of the small variability at this polymorphic site for this breed. However, a significant association was evident for the CTSD marker (P < 0.001) with EBV of all carcass and production traits in Italian Duroc pigs (lean content, ADG, backfat thickness, feed:gain ratio) after excluding possible confounding effects of the IGF2 mutation. The effects of the CTSD g.70G>A mutation were also confirmed in a subset of Italian Large White animals carrying the homozygous genotype IGF2 intron3-g.3072GG, and by haplotype analysis between the markers of the 2 considered genes in the complete data set. Overall, these results indicate that the IGF2 intron3-g.3072G>A mutation is not the only polymorphism affecting fatness and muscle deposition on SSC2p. Therefore, the CTSD g.70G>A polymorphism could be used to increase selection efficiency in marker-assisted selection programs that already use the IGF2 mutation. However, for practical applications, because the CTSD gene should not be imprinted (we obtained this information from expression analysis in adult skeletal muscle), the different modes of inheritance of the 2 genes have to be considered.

Investigation of LDHA and COPB1 as candidate genes for muscle development in the MYOD1 region of pig chromosome 2

Porcine MYOD1 gene has been mapped to swine chromosome (SSC) 2p14-p17, which is involved in the regulation of the proliferation and differentiation of skeletal muscle cells. The LDHA (lactate dehydrogenase A) and COPB1 (coatomer protein complex, subunit beta 1) genes, which map close to MYOD1, are involved in energy metabolism and protein transport processes. Both genes might play important roles in muscle development. However, little is known about the porcine LDHA and COPB1 genes. In the present study, the full-length cDNA of these two genes were cloned. The mapping results demonstrated that porcine LDHA and COPB1 were all mapped to SSC 2p14-p17. In this region, there are several QTL for growth and carcass traits, including average backfat thickness, lean and fat percentage. The RT-PCR results revealed that both LDHA and COPB1 were highly expressed in porcine skeletal muscle tissues, implying their potential regulatory function of muscle development. LDHA and COPB1 were then mapped to the region and multipoint analyses generated a best sex-averaged map order of each gene between linked markers: MYOD1_75.2 cM _LDHA_79 cM _CSRP3_83.8 cM _TEF-1_86.5 cM _COPB1_90 cM. Association analyses revealed that the substitution of c.423A>G had a significant effect on average daily gain on test, average backfat thickness (BFT), loin muscle area, lumbar BFT, marbling score, tenth rib BFT, average drip loss and fiber type II ratio. The substitution of c.3096C>T had a significant effect on average BFT, lumbar BFT, tenth rib BFT, carcass weight and last rib BFT. Interestingly, both SNPs were all associated with average BFT, lumbar BFT and tenth rib BFT.

Recombinational landscape of porcine X chromosome and individual variation in female meiotic recombination associated with haplotypes of Chinese pigs

BACKGROUND

Variations in recombination fraction (theta) among chromosomal regions, individuals and families have been observed and have an important impact on quantitative trait loci (QTL) mapping studies. Such variations on porcine chromosome X (SSC-X) and on other mammalian chromosome X are rarely explored. The emerging assembly of pig sequence provides exact physical location of many markers, facilitating the study of a fine-scale recombination landscape of the pig genome by comparing a clone-based physical map to a genetic map. Using large offspring of F1 females from two large-scale resource populations (Large White male symbol x Chinese Meishan female symbol, and White Duroc male symbol x Chinese Erhualian female symbol), we were able to evaluate the heterogeneity in theta for a specific interval among individual F1 females.

RESULTS

Alignments between the cytogenetic map, radiation hybrid (RH) map, genetic maps and clone map of SSC-X with the physical map of human chromosome X (HSA-X) are presented. The most likely order of 60 markers on SSC-X is inferred. The average recombination rate across SSC-X is of approximately 1.27 cM/Mb. However, almost no recombination occurred in a large region of approximately 31 Mb extending from the centromere to Xq21, whereas in the surrounding regions and in the Xq telomeric region a recombination rate of 2.8-3.3 cM/Mb was observed, more than twice the chromosome-wide average rate. Significant differences in theta among F1 females within each population were observed for several chromosomal intervals. The largest variation was observed in both populations in the interval UMNP71-SW1943, or more precisely in the subinterval UMNP891-UMNP93. The individual variation in theta over this subinterval was found associated with F1 females' maternal haplotypes (Chinese pig haplotypes) and independent of paternal haplotype (European pig haplotypes). The theta between UMNP891 and UMNP93 for haplotype 1122 and 4311 differed by more than fourteen-fold (10.3% vs. 0.7%).

CONCLUSIONS

This study reveals marked regional, individual and haplotype-specific differences in recombination rate on SSC-X. Lack of recombination in such a large region makes it impossible to narrow QTL interval using traditional fine-mapping approaches. The relationship between recombination variation and haplotype polymorphism is shown for the first time in pigs.

BCL10 as a new candidate gene for immune response in pigs: cloning, expression and association analysis

BCL10 is an apoptotic regulatory molecule identified through its direct involvement in t(1; 14)(p22; q32) of mucosa-associated lymphoid tissue lymphoma, and was implicated in the pathogenesis of this and several other tumour types. BCL10 was recognized as an antigen receptor-specific regulator of NF-kappaB, which showed close association with immune responses. In this study, we cloned and characterized BCL10 from the porcine spleen and analysed its genomic structure. BCL10 was mapped to SSC4q21-q23 by the IMpRH panels, it is closely linked to the marker S0161 and SW1461. This gene has three exons and two introns. Reverse transcriptase-polymerase chain reaction analyses showed that BCL10 was widely expressed in all the examined tissues. Transient transfection indicated that porcine BCL10 was located in cytoplasm in Pig Kidney Epithelial cells. BCL10 gene displays the opposite expression trend between the two treatments mimic virus and bacteria of polyriboinosinic-polyribocytidylic acid (Poly I:C) and lipopolysaccharide (LPS). The level of the BCL10 mRNA was up-regulated during 12-24 h and peaking at 48 h when treated with LPS, whereas it was down-regulated during 0-48 h and highest at 0 h (cells without treating with Poly I:C) when treated with Poly I:C. One single nucleotide polymorphism (SNP) site was identified in the 3'-untranslated region of porcine BCL10. Association analysis revealed that this SNP was significantly associated with intermediate cell mass (eosinophile granulocyte, basophile granulocyte and histoleucocyte) percentage, absolute intermediate cell mass count and mean red blood cell volume of 0-day-old pigs, and red blood cell count of 17-day-old pigs (P < 0.05), and also had significant associations with red blood cell count and haemoglobin concentration of 32-day-old pigs (P < 0.01).

Cloning, chromosomal localization, expression profile and association analysis of the porcine WNT10B gene with backfat thickness

The Wingless-type MMTV integration site (Wnt) family encodes secreted glycoproteins that are ligands for the frizzled family of seven-transmembrane receptors and the low density lipoprotein receptor-related protein family of co-receptors. The WNT10B gene inhibits differentiation of preadipocytes in vitro and impairs adipose development in vivo. In the present study, a 1,615-bp cDNA sequence of the porcine WNT10B gene was obtained by RT-PCR. The porcine WNT10B gene was assigned to 5p11-p15 by using the somatic cell hybrid panel (SCHP) and the radiation hybrid (IMpRH) panel. One SNP in the 3'-untranslated region (3'-UTR) was found and association analysis suggested that the SNP was associated with backfat thickness. Semi-quantitative RT-PCR showed that the porcine WNT10B gene was expressed in all tissues examined in 35d and adult pigs and the mRNA expression of WNT10B in fat tissue of Tongcheng pigs was dramatically higher than that in Large White pigs.

Molecular characterization and association analysis of FBXO40 with partial hematological indexes in pig

F-box proteins are quite significant ubiquitin-proteasome pathway regulators in eukaryotic cells. FBXO40, a member of this large family, alters its expression pattern in muscle atrophy. Here we isolated most of the verified porcine FBXO40 coding sequence (CDS) (2258 bp) and assigned it to the porcine chromosome 13q4.1-4.6 by using the INRA-Minnesota porcine radiation hybrid panel, and we also explored the tissue expression distributions, which is relatively high in longissimus dorsi muscle, heart, low in kidney, small intestine, brain, hypophysis, lymphonode, thymus, spleen, large intestine, ovary, stomach, and undetectable in testis, liver, uterus and thyroid gland. Inferring phylogenetic tree was constructed to study the evolutionary implications. Moreover, a HindII (HincII)-RFLP (A/C) polymorphism in 3'-untranslated region (3'-UTR) of porcine FBXO40 gene was demonstrated by sequencing and PCR-restriction fragment length polymorphism (PCR-RFLP) analysis. Statistical analysis result of this polymorphism showed that the allele A was predominant in all detected indigenous breeds, but C in western introduced commercial breeds. The SNP was further analyzed in our experimental pig population including Tongcheng, Landrace, Large White, and crossbreds of Large White × (Landrace × Tongcheng) and Landrace × (Large White × Tongcheng). The association analysis results indicated that the A/C base substitution was associate with some hematological indexes, the hemoglobin concentration (P < 0.0001), mean corpuscular volume hemoglobin concentration (P = 0.0002) and mean corpuscular volume (P = 0.0138).

Cloning and spatio-temporal expression of porcine CDK5 and CDK5R1(p35) genes

Cyclin-dependent kinase 5 (CDK5) is a serine/threonine kinase homologue attributed to the mitotic cyclin-dependent kinase family. Both the kinase activity and the biological effects of CDK5 in central nervous system are mainly dependent on association with its regulatory subunit 1 known as CDK5R1 (p35). In the present study, the full-length coding regions of CDK5 and CDK5R1 were cloned from pigs. Radiation hybrid mapping localized porcine CDK5 to chromosome 18q12-13, whereas CDK5R1 was electro-localized to chromosome 12q12. Real-time quantitative RT-PCR (qRT-PCR) showed that CDK5 mRNA is ubiquitously present in all porcine tissues examined, with relatively high levels in cerebral cortex, cerebellum, testicle and lung. We also examined the expression profile of porcine CDK5/CDK5R1 in various tissues at different developmental stages. The results indicated that CDK5 mRNA reaches the highest level in cerebral cortex at two months of age and in cerebellum and liver at 4 months of age, respectively, whereas the peak level of CDK5R1 was observed in both cerebral cortex and cerebellum at two months of age, indicating the pivotal role of CDK5/CDK5R1 during the development of porcine brain.

Comparison of PERV genomic locations between Asian and European pigs

Xenotransplantation from pigs provides a possible solution to the shortage of human organs for allotransplantation. Porcine endogenous retroviruses (PERVs) are a possible obstacle to using porcine organs in addition to the immunological barriers. Three main types of PERVs (A, B and C) have been previously investigated in diverse pig breeds. To examine the copy numbers of PERVs and their genomic locations in the Korean native pig genome, we screened a BAC (Bacterial Artificial Chromosome) library with PERV-specific protease primers for initial recognition of PERV-positive clones and three sets of envelope-specific primers for the identification of PERV types. A total of 45 PERV-positive clones, nine PERV-A and 36 PERV-B, have been identified from the library screening and the BAC contigs were constructed using the primers designed from BAC end sequences (BESs). These primers were also used for SCH (Somatic Cell Hybrid) and RH (Radiation Hybrid) mapping of the PERV-positive clones. The results indicate that 45 PERV-positive BAC clones belong to nine contigs and a singleton. SCH and IMpRH (INRA-Minnesota Porcine Radiation Hybrid) mapping results indicated that there are at least eight separate PERV genomic locations, consisting of three PERV-A and five PERV-B. One contig could not be mapped, and two contigs are closely located on SSC7. Southern blotting indicates there may be up to 15 additional sites. Further investigation of these clones will contribute to a general strategy to generate PERV-free lines of pigs suitable for xenotransplantation.

Molecular cloning and characterisation of heparanase mRNA in the porcine placenta throughout gestation

Heparanase (HPSE) is an endoglycosidase that specifically degrades heparan sulfate, which is an abundant glycosaminoglycan of the pig placenta. The aim of the present study was to clone cDNA encoding porcine HPSE and characterise the expression level and localisation of HPSE mRNA in porcine placentas throughout gestation. Placental tissues were collected from litters on Days 25, 45, 65, 85 and 105 of gestation. Three transcript variants similar to HPSE were identified in the pig placenta. In addition, the HPSE gene was mapped to pig chromosome 8 in close proximity to quantitative trait loci for litter size and prenatal survival. Real-time polymerase chain reaction and in situ hybridisation were used to characterise the expression of two HPSE variants, namely HPSE v1 and v2, in the pig placenta throughout gestation. The expression of HPSE v1 and v2 was elevated (P < 0.01) in placentas during very early gestation (Day 25) as well as during late gestation (Days 85 and 105). Finally, HPSE v1 and v2 mRNA were localised to the cuboidal trophoblast cells of the folded bilayer located nearest to the maternal endometrium. These findings illustrate that HPSE likely plays a role in the development and modification of the pig placenta, which has implications for litter size and prenatal survival.

Association of ZYX polymorphisms with carcass and meat quality traits in commercial pigs

Zyxin (ZYX) is one of the proteins in focal adhesions along the actin fibers playing a role in actin organization and signal transduction. By radiation hybrid and genetic mapping we assigned ZYX to porcine chromosome 18 in the area of quantitative traits loci for carcass and meat quality and muscle fiber traits and hence considered ZYX a functional positional candidate gene. Analysis of a newly detected SNPs (c.+279 C>T, c.+399 A>G, c.+522 A>G) in pigs from different commercial breeds (Pietrain [Pi], German Landrace [LR], German Large White x German Landrace [F1] and PiF1) revealed a significant association with carcass traits (including: side- and backfat thickness, loin weight and carcass lean content) and meat quality traits (including: pH, color and drip loss). However, the lack of consistent association across all pig populations in this study indicates that the association of the SNPs may be depending on causal mutations in linkage disequilibrium and/or interactions with other loci.

Molecular characterization and association analysis of porcine PANE1 gene

The proliferation associated nuclear element 1 (PANE1) is a novel gene that is involved in immune response besides its primary role in centromere assembly. Different PANE1 transcripts show a distinct expression patterns in resting and activated CD19+ cells. In this study, we cloned and characterized the cDNA sequence of porcine PANE1, which shares high sequence identity with their mammalian counterparts. Chromosome localization by INRA IMpRH panel assigned this gene to SSC 5p14-p15, and it was closely linked to porcine ACO2 and CYP25 genes (61cR, LOD score 4.91). The reverse transcriptase-polymerase chain reaction revealed that porcine PANE1 gene was differently expressed in seven diverse tissues, showed highest expression level in lymph node, but lowest in kidney. A single nucleotide polymorphism (SNP) (C>A) which can be digested by restriction enzyme BssHII was identified in intron 1 of porcine PANE1, allele frequencies determination in different pig breeds and association analysis were performed on this SNP BssHII by PCR-restriction fragment length polymorphism assay. Allele frequencies varied greatly among different pig breeds, and the association results indicated that piglet individuals with the AA genotype had significantly higher levels of lymphocyte percentage (LYMPH%) (17 days) (P = 0.0218), mean corpuscular volume (32 days) (P = 0.0314) and absolute value of lymphocyte (LYMPH#) (32 days) (P = 0.0356), but lower (P < 0.0001) birth weight than those with other two genotypes.

The chromosomal localization, expression pattern and polymorphism analysis of porcine FSCN1 gene differently expressed from LongSAGE library

Fascin homologue 1 (FSCN1) has established roles in cell adhesion, motility, and cell-cell interactions. Our LongSAGE analysis suggested that FSCN1 was potentially differentially expressed in prenatal pig skeletal muscle. We have cloned the genomic DNA and mRNA sequence of FSCN1 gene and mapped it to SSC3p16-p17. The FSCN1 gene was differently expressed during prenatal skeletal muscle development and exhibited different expression pattern between Tongcheng and Landrace pigs. In Tongcheng pigs, FSCN1 expression was similar at 33 and 65 days post conception (dpc), and then sharply increased to a peak at 90 dpc. In Landrace pigs, however, expression increased between 33 and 65 dpc, peaked at 65 dpc, and was down-regulated thereafter. Significantly different expression levels between Tongcheng and Landrace were observed at 65 and 90 dpc. In postnatal pigs, it was strongly expressed only in the brain, but weakly in skeletal muscle and other tissues. We initially identified 32 SNPs through genomic DNA of FSCN1 gene. Association analysis suggested that the 6840(C/T) mutation was significantly associated with the age at market weight (AGE) (p = 0.0004), average day gain from birth to market (ADG1) (p = 0.0002), and average day gain at testing period (ADG2) (p < 0.0001). Our study suggested that FSCN1 gene plays an in prenatal skeletal muscle development and was a candidate gene for meat production trait.

A single nucleotide polymorphism in the porcine cathepsin K (CTSK) gene is associated with back fat thickness and production traits in Italian Duroc pigs

Cathepsin K (CTSK) was selected as a candidate gene for fat deposition in pigs because recently, in human and mouse, it was shown that this lysosomal proteinase is an obesity marker. A single nucleotide polymorphism (SNP) was identified in intron 4 of the porcine CTSK gene (g.15G>A; FM209043). Allele frequencies of this polymorphism were analysed in seven pig breeds. Radiation hybrid mapping confirmed the localization of CTSK to porcine chromosome 4, close to the FAT1 QTL region. Three populations of pigs (one Italian Large White and two Italian Duroc groups of pigs) were selected for association analysis. In the Italian Large White breed the g.15G>A SNP was not informative. Association analysis including all Italian Duroc pigs showed that the CTSK marker was associated with back fat thickness and lean cuts (P < 0.01), and average daily gain and feed:gain ratio (P < 0.05) estimated breeding values.

Confirmed association between a single nucleotide polymorphism in the FTO gene and obesity-related traits in heavy pigs

We recently showed that a polymorphism in the fat mass and obesity associated (FTO) gene (AM931150: g.276T > G) is associated with fat deposition traits in pigs. To confirm this result, we genotyped this polymorphism in an Italian Duroc population made up by 313 performance tested pigs with known estimated breeding values (EBVs) for average daily gain, back fat thickness (BFT), feed:gain ratio, lean cuts (LC), and visible intermuscular fat (VIF, a measure of intermuscular fat in the hams). In addition, we genotyped 148 commercial heavy pigs for which several fat deposition traits and lean meat percentage were measured. The results of the association analyses confirmed the effect of the FTO mutation on obesity-related traits (VIF, BFT and LC) in the Italian Duroc pigs (P < 0.01) and in the commercial pigs (intramuscular fat content of different muscles, P < 0.05 or P < 0.10; lean meat content, P < 0.05; BFT, P < 0.05; intermuscular fat content in the hams, P < 0.05).

Characterization analysis and polymorphism detection of the porcine Myd88 gene

The myeloid differentiation primary response protein 88 (Myd88) is an essential adaptor protein, which mediates in all Toll-like receptor (TLR) members signal transduction, except for TLR3. In this study, the 4464 bp genomic sequence of porcine Myd88 was first isolated, whereupon tissue distribution, chromosome mapping and single nucleotide polymorphism (SNP) were analyzed. Our results revealed that porcine Myd88 gene, which was located at chromosome 13 linked with marker S0288 (distance = 40 cR; LOD = 8.66), was widely expressed in all the examined tissues. There were 16 potential SNPs in the isolated genome fragment. SNP 797T/C in the first intron was studied, with no significant association being found between the genotype and immune traits in pigs (p > 0.05). The porcine Myd88 protein contained both the death domain (DD) and the Toll/IL-1 receptor domain (TIR). Leu residues, essential for its structure, were the most abundant encountered in the DD. The TIR contained two conserved motifs which may play important roles in the Myd88 function.

An integrated RH map of porcine chromosome 10

BACKGROUND

Whole genome radiation hybrid (WG-RH) maps serve as "scaffolds" to significantly improve the orientation of small bacterial artificial chromosome (BAC) contigs, order genes within the contigs and assist assembly of a sequence-ready map for virtually any species. Here, we report the construction of a porcine: human comparative map for pig (Sus scrofa) chromosome 10 (SSC10) using the IMNpRH2(12,000-rad) porcine WG-RH panel, integrated with the IMpRH(7000-rad) WG-RH, genetic and BAC fingerprinted contig (FPC) maps.

RESULTS

Map vectors from the IMNpRH2(12,000-rad) and IMpRH(7,000-rad) panels were merged to construct parallel framework (FW) maps, within which FW markers common to both panels have an identical order. This strategy reduced map discrepancies between the two panels and significantly improved map accuracy. A total of 216 markers, including 50 microsatellites (MSs), 97 genes and ESTs, and 69 BAC end sequences (BESs), were ordered within two linkage groups at two point (2 pt) LOD score of 8. One linkage group covers SSC10p with accumulated map distances of 738.2 cR(7,000) and 1814.5 cR(12,000), respectively. The second group covers SSC10q at map distances of 1336.9 cR(7,000) and 3353.6 cR(12,000), yielding an overall average map resolution of 16.4 kb/cR(12,000) or 393.5 kb per marker on SSC10. This represents an approximately 2.5-fold increase in map resolution over the IMpRH(7,000-rad) panel. Based on 127 porcine markers that have homologous sequences in the human genome, a detailed comparative map between SSC10 and human (Homo sapiens) chromosome (HSA) 1, 9 and 10 was built.

CONCLUSION

This initial comparative RH map of SSC10 refines the syntenic regions between SSC10 and HSA1, 9 and 10. It integrates the IMNpRH2(12,000-rad) and IMpRH(7,000-rad), genetic and BAC FPC maps and provides a scaffold to close potential gaps between contigs prior to genome sequencing and assembly. This map is also useful in fine mapping of QTLs on SSC10.

A pig-human comparative RH map comprising 20 genes on pig chromosome 13q41 that harbours the ETEC F4ac receptor locus

The enterotoxigenic Escherichia coli (ETEC) F4ac is a major cause of diarrhoea in newborn and young pigs. The locus for the intestinal ETEC F4ac receptor (F4acR) has been mapped to pig chromosome (SSC) 13q41 with known homology to human chromosome (HSA) 3q21 and q29. However, the causative gene and mutation(s) remain unknown. The aim of this study was to characterize gene-derived markers on SSC13q41 for fine mapping of the F4acR locus, and construct a high-resolution pig-human comparative map to select positional candidate genes for F4acR. Pig-specific sequence-tagged site markers were developed for 20 genes that are located in a 6.8-Mb region on HSA3q21 and q29, and a total of 34 single-nucleotide polymorphisms (SNPs) were identified in 14 of 20 markers developed. Eighteen markers were mapped to SSC13q41, while the other two markers (PLXNA1 and KLF15) were assigned to SSC13q32 and SSC7q13, respectively, by radiation hybrid mapping. This result showed that there was a small conserved segment on SSC7 corresponding to HSA3q21. A framework map comprising 18 markers on SSC13q41 was established, refining the synteny breakpoint on SSC13q41 to a region of 12.3 centiRay. The comparative radiation hybrid (RH) map revealed three interesting candidate genes for F4acR from the human genome, viz. MUC4, MUC13 and MUC20. Linkage analysis with six marker polymorphisms revealed that MUC4 had the most significant linkage with the F4acR locus.

A robust linkage map of the porcine autosomes based on gene-associated SNPs

BACKGROUND

Genetic linkage maps are necessary for mapping of mendelian traits and quantitative trait loci (QTLs). To identify the actual genes, which control these traits, a map based on gene-associated single nucleotide polymorphism (SNP) markers is highly valuable. In this study, the SNPs were genotyped in a large family material comprising more than 5,000 piglets derived from 12 Duroc boars crossed with 236 Danish Landrace/Danish Large White sows. The SNPs were identified in sequence alignments of 4,600 different amplicons obtained from the 12 boars and containing coding regions of genes derived from expressed sequence tags (ESTs) and genomic shotgun sequences.

RESULTS

Linkage maps of all 18 porcine autosomes were constructed based on 456 gene-associated and six porcine EST-based SNPs. The total length of the averaged-sex whole porcine autosome was estimated to 1,711.8 cM resulting in an average SNP spacing of 3.94 cM. The female and male maps were estimated to 2,336.1 and 1,441.5 cM, respectively. The gene order was validated through comparisons to the cytogenetic and/or physical location of 203 genes, linkage to evenly spaced microsatellite markers as well as previously reported conserved synteny. A total of 330 previously unmapped genes and ESTs were mapped to the porcine autosome while ten genes were mapped to unexpected locations.

CONCLUSION

The linkage map presented here shows high accuracy in gene order. The pedigree family network as well as the large amount of meiotic events provide good reliability and make this map suitable for QTL and association studies. In addition, the linkage to the RH-map of microsatellites makes it suitable for comparison to other QTL studies.

Assignment of 128 genes localized on human chromosome 14q to the IMpRH map

To provide a gene-based comparative map and to examine a porcine genome assembly using bacterial artificial chromosome-based sequence, we have attempted to assign 128 genes localized on human chromosome 14q (HSA14q) to a porcine 7000-rad radiation hybrid (IMpRH) map. This study, together with earlier studies, has demonstrated the following. (i) 126 genes were incorporated into two SSC7 RH linkage groups by CarthaGene analysis. (ii) In the remaining two genes, TOX4 linked to TCRA located in SSC7 by two-point analysis, whereas SIP1 showed no significant linkage with any gene/marker registered in the IMpRH Web Server. (iii) In the two groups, the gene clusters located from 19.9 to 36.5 Mb on HSA14q11.2-q13.3 and from 64.0 to 104.3 Mb on HSA14q23-q32.33 respectively were assigned to SSC7q21-q26. (iv) Comparison of the gene order between the present RH map and the latest porcine sequence assembly revealed some inconsistencies, and a redundant arrangement of 16 genes in the sequence assembly.

A first generation whole genome RH map of the river buffalo with comparison to domestic cattle

Background

The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH₅₀₀₀) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species.

Results

A total of 3990 markers were typed on the BBURH₅₀₀₀ panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD ≥ 8. The estimated total length of the WG-RH map is 36,933 cR₅₀₀₀. Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score ≥ 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0).

Conclusion

We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome.

Molecular characterization, chromosomal localization and association analysis with back-fat thickness of porcine LPIN2 and LPIN3

The products of mammalian LPIN2 and LPIN3 are phosphatidate phosphatase type 1 enzymes, which play an important role in the de novo biosynthesis of triacylglycerol, phosphatidylcholine and phosphatidylethanolamine. In this study, we obtained a 2,985-bp cDNA sequence of porcine LPIN2, which contains a 2,676-bp open reading frame flanked by an 11-bp 5'UTR and a 298-bp 3'UTR, and a 2,843-bp cDNA sequence of porcine LPIN3, which contains a 111-bp 5'UTR, a 2,580-bp open reading frame and a 152-bp 3'UTR. RT-PCR analysis showed that both LPIN2 and LPIN3 mRNA were ubiquitously expressed with a very high level in liver. By using the somatic cell hybrid panel (SCHP) and the radiation hybrid (IMpRH) panel, porcine LPIN2 and LPIN3 were assigned to 6q24-(1/2)q31 and 17(1/2)q21-q23, respectively. One T2193C single nucleotide polymorphism in LPIN2 was identified and was detected by Hin6I PCR-RFLP. Association analysis showed that different genotypes of LPIN2 were associated with back-fat thickness between the 6th and 7th ribs (P < 0.01).

Molecular cloning, expression analysis and chromosome localization of the Tpt1 gene coding for the pig translationally controlled tumor protein (TCTP)

This work describes the cloning and structural analysis of a Tpt1 cDNA coding for the porcine translationally controlled tumor protein (TCTP) molecule and its expression in porcine cells and tissues. Pig Tpt1 cDNA is 842-pb long that displays typical features of translationally controlled mRNAs, including a 5'-UTR containing a 5'-terminal oligopyrimidine tract (5'-TOP), and a 3'-UTR with a high CG-content and one AU rich element (ARE). Both 5'-UTR and 3'-UTR are highly conserved when they are compared with those of other mammals. The pig Tpt1 cDNA contains a 516-b open reading frame that encodes a predicted TCTP protein composed of 172 amino acids that exhibits extensive conservation compared with TCTP sequences from other species and a common structural feature with all the other TCTP proteins analyzed in mammals. Expression analysis demonstrated that Tpt1 mRNA is ubiquitously expressed in normal porcine tissues and cells, showing a higher expression in spleen, lymph nodes and lung, and a lower one in skin and heart. The pig Tpt1 gene localizes on the porcine chromosome 11, region p11.

Characterization of the porcine Kisspeptins receptor gene and evaluation as candidate for timing of puberty in sows

Kisspeptins receptor (KISS1R), also called GPR54, is a key regulator of puberty in many species. KISS1R and its genetics in pigs remain unexplored. The objective of this study was to characterize the porcine KISS1R gene and evaluate the association of KISS1R mutations with age at puberty in sows. KISS1R was assigned to pig chromosome 2q21-24 by radiation hybrid mapping. It has a 1438 bp full-length cDNA and spans 3349 bp genomic sequence consisting of five exons and four introns. Semi-quantitative RT-PCR showed that KISS1R transcripts was particularly abundant in the adrenal, prostate, testis, thymus, pituary and hypothalamus. KISS1R mRNA content in the hypothalamus was determined by real-time quantitative RT-PCR, and it fluctuated during the oestrous cycle with the highest level in the luteal phase. Anoestrus sows had markedly lower hypothalamic KISS1R mRNA content than cyclic animals. Seven KISS1R SNPs were identified in the founder animals of a White Duroc x Erhualian intercross. One missense mutation (T/C(245)) showed quite different allele distribution in Chinese and Western breeds. All F(0), F(1) animals and 367 detailed phenotyped cyclic F(2) sows in the White Duroc x Erhualian intercross were genotyped for three KISS1R polymorphisms. No significant association of KISS1R haplotypes and haplotype pairs with age at puberty was observed in the resource population, indicating that mutations in KISS1R are not responsible for divergent age at puberty in White Duroc and Erhualian pigs.

Molecular cloning, mapping, and polymorphism of the porcine SCG2 gene

The secretogranin II (SCG2) gene is associated with the synthesis and secretion of follicle-stimulating hormone and luteinizing hormone. In the present study, we have determined the complete cDNA sequence of pig SCG2, which was submitted to GenBank with accession no. AY870646. Its complete open reading frame of 1,851 nucleotides encodes 616 amino acids. The predicted protein shares 80-87% identity with mouse, human, and bovine SCG2 proteins, and all four species share almost complete identity in the secretoneurin and EM66 domains. Pig SCG2 is a protein of 589 amino acids and 68,132 Da, preceded by a signal peptide of 27 residues. It contains nine pairs of dibasic residues, which are used as potential cleavage sites for generation of physiologically active peptides. Analysis of the SCG2 gene across the INRA-Minnesota porcine radiation hybrid panel indicates close linkage with microsatellite marker SW2608, located on Sus scrofa chromosome 15 (SSC15) q25, which harbors several QTL for ovulation rate and meat quality. Comparative sequencing and EST analysis revealed nine SNPs in porcine SCG2 cDNA, including seven SNPs in the coding region and two SNPs in the 3' UTR. Four nonsynonymous SNPs (G622A, G1671T, C1718T, and A1790C) resulted in amino acid substitutions of Ala-->Thr, Glu-->Asp, Pro-->Leu, and Asn-->Thr, respectively.

Molecular characterization and expression pattern of the porcine STARS, a striated muscle-specific expressed gene

STARS (striated muscle activator of Rho signaling) promotes the nuclear localization of MRTFs and mediates SRF transcription, which provides a potential muscle-specific mechanism for linking changes in the actin cytoskeleton structure with muscle gene expression. In this study, the full-length cDNA of the porcine STARS was cloned. The open reading frame of this gene contains 1,155 bp and encodes a protein of 384 amino acids, which is 79, 73, and 77% identical with human, mouse, and rat STARS genes, respectively. RT-PCR revealed that STARS is specifically expressed in heart and skeletal muscles. STARS is also distinctly different in different muscle developmental stages. The result indicates that its expression increased gradually from 33 dpc (days postcoitum) to postnatal muscles, and peaked 28 days postnatal. The porcine STARS was mapped to SSC4p13 using the somatic cell hybrid panel and the radiation hybrid panel IMpRH (LOD score 11.98). The data show that STARS is closely linked to marker SW871. A T/G single nucleotide polymorphism in the coding sequence, detected as Bsh1236I PCR-RFLP, displays allele frequency differences in six pig breeds.

Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits

Background

In a previous screen to identify differentially expressed genes associated with embryonic development, the porcine PNAS-4 gene had been found. Considering differentially expressed genes in early stages of muscle development are potential candidate genes to improve meat quality and production efficiency, we determined how porcine PNAS-4 gene regulates meat production. Therefore, this gene has been sequenced, expression analyzed and associated with meat production traits.

Results

We cloned the full-length cDNA of porcine PNAS-4 gene encoding a protein of 194 amino acids which was expressed in the Golgi complex. This gene was mapped to chromosome 10, q11–16, in a region of conserved synteny with human chromosome 1 where the human homologous gene was localized. Real-time PCR revealed that PNAS-4 mRNA was widely expressed with highest expression levels in skeletal muscle followed by lymph, liver and other tissues, and showed a down-regulated expression pattern during prenatal development while a up-regulated expression pattern after weaning. Association analysis revealed that allele C of SNP A1813C was prevalent in Chinese indigenous breeds whereas A was dominant allele in Landrace and Large White, and the pigs with homozygous CC had a higher fat content than those of the pigs with other genotypes (P < 0.05).

Conclusion

Porcine PNAS-4 protein tagged with green fluorescent protein accumulated in the Golgi complex, and its mRNA showed a widespread expression across many tissues and organs in pigs. It may be an important factor affecting the meat production efficiency, because its down-regulated expression pattern during early embryogenesis suggests involvement in increase of muscle fiber number. In addition, the SNP A1813C associated with fat traits might be a genetic marker for molecular-assisted selection in animal breeding.

Investigation of Lpin1 as a candidate gene for fat deposition in pigs

Lpin1 deficiency prevents normal adipose tissue development and remarkably reduces adipose tissue mass, while overexpression of the Lpin1 gene in either skeletal muscle or adipose tissue promotes adiposity in mice. However, little is known about the porcine Lpin1 gene. In the present study, a 5,559-bp cDNA sequence of the porcine Lpin1 gene was obtained by RT-PCR and 3'RACE. The sequence consisted of a 111-bp 5'UTR, a 2,685-bp open reading frame encoding a protein of 894 amino acids and a 2,763-bp 3'UTR. Semi-quantitative RT-PCR analysis revealed that Lpin1 had a high level of expression in the liver, spleen, skeletal muscle and fat, a low level of expression in the heart, lung and kidney. The porcine Lpin1 gene was assigned to 3q21-27 by using the somatic cell hybrid panel (SCHP) and the radiation hybrid (IMpRH) panel. One C93T single nucleotide polymorphism (SNP) was identified and genotyped using the TaqI PCR-RFLP method. Association analysis between the genotypes and fat deposition traits suggested that different genotypes of the Lpin1 gene were associated with percentage of leaf fat and intramuscular fat.

Assessment of AFLP marker behaviour in enriching STS radiation hybrid maps

Radiation hybrid (RH) mapping provides a powerful tool to build high-resolution maps of genomes. Here, we demonstrate the use of the AFLP technique for high-throughput typing of RH cell lines. Cattle were used as the model species because an RH panel was available to investigate the behaviour of AFLP markers within the microsatellite- and STS-based maps of this species. A total of 747 AFLP markers were typed on the TM112 RH radiation panel and 651 of these were assigned by two-point analysis to the 29 bovine autosomes and sex chromosomes. AFLP markers were added to the 1222 microsatellite and STS markers that were included in earlier RH maps. Multipoint maps were constructed for seven example chromosomes, which retained 248 microsatellite and STS markers, and added 123 AFLP markers at LOD 4. The addition of the AFLP markers increased the number of markers by 42.1% and the map length by 10.4%. The AFLP markers showed lower retention frequency (RF) values than the STS markers. The comparison of RF values in AFLP markers and their corresponding AFLP-derived STSs demonstrated that the lower RF values were due to the lower detection sensitivity of the AFLP technique. Despite these differences, AFLP and AFLP-derived STS markers mapped to identical or similar positions. These results demonstrate that it is possible to merge AFLP and microsatellite markers in the same map. The application of AFLP technology could permit the rapid construction of RH maps in species for which extensive genome information and large numbers of SNP and microsatellite markers are not available.

Porcine TEF1 and RTEF1: molecular characterization and association analyses with growth traits

TEA domain transcription factors play vital roles in myogenesis by binding the M-CAT motif in the promoter of the muscle-specific genes. In the present study, we cloned two porcine TEA domain family genes, TEF1 and RTEF1, and identified two different variants respectively. RT-PCR revealed that the TEF1-a variant was highly expressed and up-regulated with the development of the porcine skeletal muscle, indicating its potential regulatory function for muscle development. Promoter analysis revealed porcine TEF1 was regulated, in a TATA-independent manner, by a specific intact initiator element, and numerous binding motifs of multiple transcription factors, including SP1, CREB/ATF and AREB6. A substitution G93A was identified in the 5'-flanking sequence and used for the linkage mapping of TEF1. Association analyses in a BerkshirexYorkshire F(2) population revealed that the substitution of G93A has a significant effect on average daily gain from birth to weaning (p<0.05) and 16-day weight (p<0.05), and a suggestive effect on loin eye area (p<0.06), average back fat (p<0.07) and lumbar back fat (p<0.08). The association analyses results are in agreement with the gene's localization demonstrated by linkage analysis, SCHP and RH mapping to the QTL region of growth and carcass traits on chromosome 2p14-17.

A muscle transcriptome analysis identifies positional candidate genes for a complex trait in pig

Muscle tenderness is an important complex trait for meat quality and thus for genetic improvement through animal breeding. However, the physiological or genetic control of tenderness development in muscle is still poorly understood. In this work, using transcriptome analysis, we found a relationship between gene expression variability and tenderness. Muscle (longissimus dorsi) samples from 30 F(2) pigs were characterized by Warner-Bratzler Shear Force (WBSF) on cooked meat as a measurement of muscle tenderness. Gene expression levels were measured using microarrays for 17 muscle samples selected to represent a range of WBSF values. Using a linear regression model, we determined that samples with WBSF values above 30 N could be effectively analysed for genes exhibiting a significant association of their expression level on shear force (false discovery rate <0.05). These genes were shown to be involved in three functional networks: cell cycle, energy metabolism and muscle development. Twenty-two genes were mapped on the pig genome and 12 were found to be located in regions previously reported to contain quantitative trait loci (QTL) affecting pig meat tenderness (chromosomes 2, 6 and 13). Some genes appear therefore as positional candidate genes for QTL.

High-resolution comprehensive radiation hybrid maps of the porcine chromosomes 2p and 9p compared with the human chromosome 11

We are constructing high-resolution, chromosomal 'test' maps for the entire pig genome using a 12,000-rad WG-RH panel (IMNpRH2(12,000-rad))to provide a scaffold for the rapid assembly of the porcine genome sequence. Here we present an initial, comparative map of human chromosome (HSA) 11 with pig chromosomes (SSC) 2p and 9p. Two sets of RH mapping vectors were used to construct the RH framework (FW) maps for SSC2p and SSC9p. One set of 590 markers, including 131 microsatellites (MSs), 364 genes/ESTs, and 95 BAC end sequences (BESs) was typed on the IMNpRH2(12,000-rad) panel. A second set of 271 markers (28 MSs, 138 genes/ESTs, and 105 BESs) was typed on the IMpRH(7,000-rad) panel. The two data sets were merged into a single data-set of 655 markers of which 206 markers were typed on both panels. Two large linkage groups of 72 and 194 markers were assigned to SSC2p, and two linkage groups of 84 and 168 markers to SSC9p at a two-point LOD score of 10. A total of 126 and 114 FW markers were ordered with a likelihood ratio of 1000:1 to the SSC2p and SSC9p RH(12,000-rad) FW maps, respectively, with an accumulated map distance of 4046.5 cR(12,000 )and 1355.2 cR(7,000 )for SSC2p, and 4244.1 cR(12,000) and 1802.5 cR(7,000) for SSC9p. The kb/cR ratio in the IMNpRH2(12,000-rad) FW maps was 15.8 for SSC2p, and 15.4 for SSC9p, while the ratio in the IMpRH(7,000-rad) FW maps was 47.1 and 36.3, respectively, or an approximately 3.0-fold increase in map resolution in the IMNpRH(12,000-rad) panel over the IMpRH(7,000-rad) panel. The integrated IMNpRH(12,000-rad) andIMpRH(7,000-rad) maps as well as the genetic and BAC FPC maps provide an inclusive comparative map between SSC2p, SSC9p and HSA11 to close potential gaps between contigs prior to sequencing, and to identify regions where potential problems may arise in sequence assembly.