Accurate mapping of the "acid meat" RN gene on genetic and physical maps of pig chromosome 15

Testing for the RN(-) gene in retail pork chops

A random sample of pork chops were purchased from local retail outlets to determine if the frequency of the RN(-) phenotype could be roughly estimated by GP measurements in fresh raw pork products or by genotyping for the nearest DNA microsatellite markers. Glycolytic potential (GP) is the estimated sum of glycogen, the intermediate metabolites of glycogenolysis, and the end product, lactate. GP has been used to identify a genetic mutation known as the RN(-) or Hampshire gene. Currently, there is no genetic test for the RN(-) allele and flanking DNA microsatellite markers were not useful at predicting the RN(-) phenotype in the random samples. Excessively high GP was found in 25% of the samples which correlated with a significant (P>0.05) drop in pH (5.8 to 5.7), a paler (L* value; 54.1 to 57.5) more yellowish (b* value; 9.6 to 11.6) color, and an increased cooking loss (9 to 18%), typical of the RN(-) phenotype. A genetic test for skin colour in swine proved that the majority (79%) of high GP pork sampled were from phenotypically white pigs. Analysis of glucose levels in post-rigor samples may be useful in progeny testing for the RN gene until a true genetic marker can be identified.

Association of porcine IGF binding protein-5 gene with meat quality

IGFBP-5 is a member of the IGF families. Using PCR-SSCP, genotypic and allelic frequencies were analyzed in 18 pig breeds (n = 600). The association between haplotypes and production performance was analyzed in a Jinhua x Pietrain population family (n = 212, total 24 traits). Two SNPs (T199C and G485A) within the gene were analyzed. The breeds had different genotypic and allelic frequencies. Typically, the Chinese native pig breeds carried a higher allele C and G frequency (over 50%) than those of the European pigs, and only Guangdong Large White and wild boar were at Hardy-Weinberg equilibrium. The pigs carrying the CG haplotype had higher hue, loin, and thigh pH1 values than pigs with the TA haplotype, and pigs with the TA haplotype had the lowest loin pH2 value and highest color-a value among the haplotypes. It is proposed that the IGFBP-5 gene is associated with the variation in meat quality, especially in pH value together with other QTLs on chromosome 15.

Chromosome location and association of haplotypes of insulin-like growth factor binding protein-2 with production performance in swine

Insulin-like growth factor binding protein-2 is a member of the insulin-like growth factor families. Using a porcine RH panel, the gene was mapped on chromosome 15q22-23. Meanwhile, using polymerase chain reaction single strand conformation polymorphism, genotypic and allelic frequencies were analyzed in 17 pig breeds (total animals 570), together with a chi-square test of Hardy-Weinberg equilibrium. Also the association between haplotypes and production performance was analyzed in a Lantang x Landrace population family (n = 133, total 43 traits). At each locus we investigated, all the breeds showed different genotypic and allelic frequency distributions. In general, the Chinese native pig breeds carried a higher allele A frequency (over 50%) than the European pigs. For production performance, pigs with the CAG haplotype had higher fore-body and rear-body weight than those with the TGT and TAG haplotypes (P < 0.05). Also, pigs with the CAG haplotype had higher bone weight of the rear-body than those with the CAT haplotype (P < 0.05); pigs with the TGT and CAG haplotypes had higher forelimb and rearlimb weight than those with the CAT haplotype (P < 0.01 and P < 0.05, respectively); pigs with the TGG haplotype had higher leaf fat weight than those with the TGT and CAG haplotypes (P < 0.05); and pigs with the CAG haplotype had more stomach weight than those with the CAT and CGT haplotypes (P < 0.01); pigs with the TGT and CAG haplotypes had more ribs and longer body than those with the CGT-TGG, and CAT-TAG haplotypes (P < 0.05). These results suggest that IGFBP-2 is associated with production performance, but our population family was small. More studies with large samples are needed before the IGFBP-2 locus will be useful for a selection program.

Could the pale, soft, and exudative condition be explained by distinctive histological characteristics?1

Pork quality depends on various genetic and environmental factors. Despite the improvement of slaughter conditions, the PSE type is still one of the main concerns in this field. This study was conducted on nonstressed animals to evaluate the tissue characteristics of some muscles usually involved during stress compared with a reference muscle, the M. triceps brachii, which is actually not subject to stress-caused damages. Samples of M. triceps brachii, M. longissimus dorsi, M. biceps femoris, and M. semimembranosus were taken from pigs exhibiting 1 of the 3 HAL genotypes (NN, Nn, or nn) and 2 of the 3 RN genotypes (rn+rn+ or rn+RN-). Histoenzymology and immunohistochemistry were used to compare the fiber typing and capillary network in these muscles within these different stress susceptibility genotypes. In comparison with the reference muscle, M. triceps brachii, the combination of a high value of the number of type IIb fibers and a low vascular network showed a primary effect on muscles usually involved during stress. This led to the definition of a PSE index. A dramatic increase (P < 0.001) in this PSE index was systematically found in muscles usually involved in the PSE-type condition. These results show that distinctive histological characteristics were associated with the vulnerability of some muscles independently of the genotypes. Moreover, this study highlights the distinctive histological features of each genotype and is likely to suggest some interactions between them.

A genome scan for quantitative trait loci affecting resistance to Trichostrongylus colubriformis in sheep

A genome linkage scan was carried out using a resource flock of 1029 sheep in six half-sib families. The families were offspring of sires derived by crossing divergent lines of sheep selected for response to challenge with the intestinal parasitic nematode Trichostrongylus colubriformis. All animals in the resource flock were phenotypically assessed for worm resistance soon after weaning using a vaccination/challenge regime. After correcting for fixed effects using a least squares linear model the faecal egg count data obtained following the first challenge and the faecal egg count data obtained after the second challenge were designated Trait 1 and Trait 2, respectively. A total of 472 lambs drawn from the phenotypic extremes of the Trait 2 faecal egg count distribution were genotyped with a panel of 133 microsatellite markers covering all 26 sheep autosomes. Detection of quantitative trait loci (QTL) for each of the faecal egg count traits was determined using interval analysis with the Animap program with recombination rates between markers derived from an existing marker map. No chromosomal regions attained genome-wide significance for QTL influencing either of the traits. However, one region attained chromosome-wide significance and five other regions attained point-wise significance for the presence of QTL affecting parasite resistance.

Comparative analysis of a BAC contig of the porcine RN region and the human transcript map: implications for the cloning of trait loci

The poorly developed transcript maps and the limited resources for genome analysis hamper positional cloning of trait loci in farm animals. This study demonstrates that this will now be easier by the combined use of BAC contigs and the import of the near complete human transcript map. The conclusion was obtained by a comparative analysis of a 2.4-Mb BAC contig of the RN region in pigs. The contig was constructed as part of a successful positional cloning project, which identified PRKAG3 as the causative gene for the RN phenotype. A comparative map including the corresponding regions on human chromosome 2q35 and mouse chromosome 1 (region 36-44 cM) is reported. Sixteen coding sequences were mapped on the BAC contig. The majority of these were identified by BLAST searches of BAC end sequences and BAC shotgun sequences generated during the positional cloning project. Map data for the orthologues in humans were available for 12 of the 16 coding sequences, and all 12 have been assigned to 2q35. Furthermore, no evidence for any rearrangement in gene order was obtained. The extensive linkage conservation indicates that the near complete human transcript map will be an invaluable resource for positional cloning projects in pigs and other domestic animals.

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

We have developed a panel of 152 whole-genome radiation hybrids by fusing irradiated diploid pig lymphocytes or fibroblasts with recipient hamster permanent cells. The number and size of the porcine chromosome fragments retained in each hybrid clone were checked by fluorescence in situ hybridization with a SINE probe or by primed in situ labeling (PRINS) with SINE-specific primers. A strategy based on the interspersed repetitive sequence polymerase chain reaction (IRS-PCR) was developed for selected clones to determine if the large fragments painted by the SINE probe corresponded to one pig chromosome or to different fragments of several chromosomes. This strategy was buttressed by a double PRINS approach using primers specific for alpha-satellite sequences of two different groups of swine chromosomes. Genome retention frequency was estimated for each clone by PCR with 32 markers localized on different porcine chromosomes. Of the 152 hybrids produced, 126 were selected on the basis of cytogenetic content and chromosome retention frequency to construct a radiation hybrid map of swine chromosome 8. Our initial results for this chromosome indicate that the resolution of the radiation hybrid map is 18 times higher than that obtained by linkage analysis.

Cytogenetic assignment of 53 microsatellites from the USDA-MARC porcine genetic map

This study provides 53 new fluorescent in situ hybridization cytogenetic assignments for microsatellite markers linked on the swine genetic map. Forty microsatellites are physically assigned for the first time. The chromosomal locations of eight markers were either confirmed or refined, while five loci were assigned to locations different from those given in previous reports. Markers were selected to provide physical anchors based on their presumed proximity to centromeres or telomeres and at approximately 30 cM intervals across the genetic map. The number of physical anchors for pig (SSC) chromosomes 8, 15, and 18 linkage groups was significantly improved. Centromeric regions were localized to areas less than 10 cM for SSC 1, 2, 3, 6, 7, 8, and 9. Although the recombination rate was generally higher across small biarmed chromosomes and lowest for large acrocentric chromosomes, two regions with particularly low (1q2.1-->q2.9 and 13q2.3-->q4.1) and three regions with extremely high (5p1.5-->p1.2, 6p1.4-->p1.3, and 12p1.5-->p1.4) rates of recombination were detected. These assignments represent an overall 10% increase in the number of physically assigned markers in Sus scrofa and more than a 20% increase in the number of Type II loci assigned to the pig cytogenetic map.

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.

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.

Mapping of microsatellite markers developed from a flow-sorted swine chromosome 6 library

Swine Chromosome (Chr) 6-enriched libraries, generated with size-fractionated DNA isolated from chromosomes sorted by flow cytometry, have been used to develop new Chr 6 microsatellite markers. Chromosome isolation procedures were established to reproducibly prepare high quality chromosomes from phytohemagglutinin (PHA)-stimulated swine peripheral blood lymphocytes and to sort individual chromosomes after staining with Hoechst 33258 and chromomycin A3. Chromosome purity was verified by specific staining of swine Chr 6 with fluorescence in situ hybridization (FISH) by use of painting probes generated by degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) amplification of as few as 300 sorted Chr 6. For library construction, DNA was extracted from flow-sorted pools representing Chr 6, amplified, size selected for fragments from 300 to 700 bp, and ligated into pBluescript SK II+ or Lambda ZAP Express. The libraries were then screened with a radiolabeled poly-(dCA) DNA probe. Of 107 (CA)n repeat-containing clones verified by sequencing, 21 were polymorphic and used to genotype the University of Illinois swine reference families. Linkage analysis was then performed with CRIMAP 2.4 (LOD > 3.0), and the results showed that 15 of the microsatellites mapped to swine Chr 6. At least three of these new markers map to locations where there were gaps in the consensus Chr 6 map. Another four markers, because of their PIC values, should provide more informative markers in other areas of the map. Most of the new markers can also be used for automated genotyping with fluorescent labeling. This set of 15 new Chr 6 markers will, therefore, be useful in helping to define QTL associated with swine Chr 6.

The Kiel RN experiment: final porcine chromosome 15 mapping results

SUMMARY

A marker experiment with pigs from commercially selected lines is described. One important goal of the experiment was to map the porcine RN locus, a major gene responsible for lowered terminal pH and increased glycogen level in muscle tissue. Experimental families comprised 15 Piétrain × Hampshire boars, of which 14 were heterozygous at the RN locus, 61 homozygous rn(+) /rn(+) sows (five Landrace, 12 Large White, and 44 Landrace × Large White crossbreds), and 509 progenies, 496 of them from heterozygous boars, in total 585 animals. Genotyping was done for seven chromosome 15 microsatellite loci: Sw919, Sw964, S0088, Sw120, Sw906, Sw936, and Sw312. Genotype assignment for the RN locus was based on musculus longissimus dorsi glycogen content. The heterozygosity of markers ranged from 0.47 to 1 in boars and from 0.71 to 0.88 in sows. RN was mapped to the centre of an interval, flanked by Sw120 and the marker pair Sw906/Sw936. Male multipoint distances between RN and Sw120, Sw906, and Sw936 were estimated as 5 cM, 5 cM, and 6.9 cM, respectively. Two-point recombination rates between these markers and RN were 0.05 in all cases, with corresponding lod scores of 52.09, 29.30, and 42.53. Concordances and disconcordances of mapping results in the RN region from different studies are discussed. The male map length of the chromosome region covered was 68.8 cM, in contrast to the female map length of 124.7 cM. Significant differences in recombination rates between sexes were found in intervals Sw919-Sw964, Sw964-S0088, and Sw936-Sw312, but not in the neighbourhood of the RN gene. ZUSAMMENFASSUNG: Es wird ein Kartierungsexperiment mit Schweinen aus kommerziell genutzten Linien beschrieben. Vordringliches Ziel dieses Experimentes war es, das RN-Gen zu kartieren, das für einen erniedrigten End-pH-Wert und einen erhöhten Glykogengehalt im Musklegewebe verantwortlich ist. Die Daten stammen von 15 Hampshire × Piétrain Ebern, von denen 14 am RN Locus heterozygot waren, 61 homozygoten rn(+) /rn(+) Sauen (5 Landrasse-, 12 Large White und 44 Landrasse × Large White Kreuzungssauen) sowie 509 Nachkommen, 496 davon von heterozygoten Ebern, insgesamt also 585 Tiere. Für sieben Mikrosatellitenmarker auf Chromosom 15 wurden die Tiere typisiert: Sw919, Sw964, S0088, Sw120, Sw906 und Sw312. Die Bestimmung der Genotypen am RN-locus erfolgte anhand des Glykogenghalts im Musculus longissimus dorsi. Der Heterozygotiegrad der Marker lag zwischen 0, 47 und 1 bei Ebern und zwischen 0, 71 und 0, 88 bei den Sauen. Als Position des RN-Gens wurde die Mitte eines Intervalles bestimmt, der von dem Marker Sw120 sowie dem Markerpaar Sw906/Sw936 begrenzt wird. Für das männliche Geschlect wurden die Kartenabstände zwischen RN und Sw120, Sw906 und Sw936 in einer Mehrpunktanalyse auf 5 cM, 5 cM und 6, 9 cM geschätzt. Paarweise Schätzungen der Rekombinationsraten zwischen diesen Markern und RN betrugen in allen Fällen 0, 5, mit zugehörigen lod scores vol 52, 09, 29, 30 und 42, 53. übereinstimmungen und Diskrepanzen zwischen Kartierungsergebnissen verschiedener Arbeitsgruppen werden diskutiert. Die Kartenlänge des mit Markern abgedeckten Teils von Chromsom 15 betrug beim männlichen Geschlecht 68, 8 cM, im Gegensatz zu einer Länge von 124, 7 cM beim weiblichen Geschlecht. Signifikante Unterschiede in den Rekombinationsraten beider Geschlechter wurden in den Intervallen Sw919-Sw964, Sw964-S0088 und Sw936-Sw312 gefunden, nicht jedoch in der Umgebung des RN-Genes.

Livestock genomics comes of age

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