Search

A GWAS was performed using the genotypes obtained by PorcineSNP60 v2 BeadChip and 11 phenotypic traits (carcass lean meat percentage; backfat thickness; Longissimus thoracis muscle thickness; lightness; backfat thickness measured with caliper at the midline; meat pH measured at about 1h post mortem and 24h post mortem; CIE L*, a* and b* color parameters; and water-holding capacity). Three markers were associated with three of the phenotypic traits considered: M1GA0009592 (SSC7) with backfat thickness and lean meat content, DIAS0002910 (SSC6) and ALGA0109856 (SSC6) with water-holding capacity. The marker M1GA0009592, associated with backfat thickness, lies in a QTL region near the gene JARID2, which is a transcription factor also involved in the regulation of adipose-derived stem cell pluripotency. The results seem to indicate a possible role of these genomic regions in the regulation of pig carcass fatness (i.e. backfat at last rib) and water-holding capacity.

The perilipins (PLIN) belong to a family of structural proteins that play a role regulating intracellular lipid storage and mobilization. Here, PLIN1 and PLIN2 have been evaluated as candidate genes for growth, carcass and meat quality traits in pigs. A sample of 607 Duroc pigs were genotyped for two single-nucleotide polymorphisms, one in intron 2 of the PLIN1 gene (JN860199:g.173G>A) and the other at the 3' untranslated region of the PLIN2 gene (GU461317:g.98G>A). Using a Bayesian approach, we have been able to find evidence of additive, dominant and epistatic associations of the PLIN1 and PLIN2 polymorphisms with early growth rate and carcass length. However, the major effects were produced by the dominant A allele at the PLIN2 polymorphism, which also affected the carcass lean weight. Thus, pigs carrying an additional copy of the A allele at the g.98G>A PLIN2 polymorphism had a probability of at least 98% of producing carcasses with heavier lean weight (+0.41 kg) and ham weight (+0.10 kg). The results obtained indicate that the PLIN2 polymorphism could be a useful marker for lean growth. In particular, it may help to reduce the undesired negative correlated response in lean weight to selection for increased intramuscular fat content, a common scenario in some Duroc lines involved in the production of high quality pork products. This work was partially funded by national projects AGL2009-09779 and AGL2012-33529 (Ministry of Education and Innovation, Spain) and AGER-HEPI- GET grant N. 2011-0279 (Italy). S. Gol is recipient of a PhD scholarship from MINECO, Spain (BES-2014- FPU13/04975).

In livestock, skeletal muscle is a tissue of major economic importance for meat production and muscle mass is largely determined during the prenatal period by the number and the size of muscle fibres. The understanding of gene expression changes during prenatal pig muscle development is still limited. In this study, genes identified as differentially expressed in a previous microarray research and chosen for the function of the coded protein as putative candidate involved in myogenesis were considered to analyse their expression profile during foetal growth of Duroc and Pietrain pigs. The eleven genes were considered by real-time PCR for a time-course evaluation of the transcription level at six stages of prenatal longissimus dorsi development. The results suggest that the most relevant variations in mRNA levels of the analysed genes seem to follow temporal waves of gene expression. Significant changes of transcription were observed at 21–35 and 63–91 days, the two main phases of skeletal muscle development. During the early phases of Pietrain embryos’ development, 10 of the 11 genes showed an induction. In Duroc embryos, a second phase of gene up-regulation can be identified in the phase 63–77 days. These results provide new data on developmental changes of expression profile of 11 genes involved in different functional pathways related to prenatal myogenic processes in Duroc and Pietrain pigs.

The objective of this study was to determine the distribution of glycolytic potential (GP) and its relationships with meat pH and the estimated breeding values (EBVs) of some traits in Italian Large White pigs. GP was determined on samples taken from the semimembranosus muscle at 120 min postmortem. Values of GP were normally distributed around a mean value of µmol/g 103.5 ± 23.0. Increasing GP was associated with decreasing pH at 2 and 24 h postmortem. A nonlinear relationship was found between GP and pHu. GP also showed no relationship with the EBVs of daily gain and feed : gain ratio and a weak relationship with EBVs of carcass traits such as backfat thickness and lean cut weight. The positive but weak correlation between GP and EBV of ham weight loss during the first salting period may suggest a potential risk of using meat with high GP in dry-cured ham production. PRACTICAL APPLICATIONS Glycolytic potential is considered to be a determinant parameter for pork quality, especially when the meat is going to be processed. A better knowledge of its variation and its relationship with other valuable traits in vivo and postmortem is important in a breed such as the Italian Large White, largely used in the production of heavy pigs destined to produce meat for seasoned products. Data reported here on the variation of GP could suggest to breeder association the need to control this parameter in selection programs irrespectively to the presence of the RN- negative allele, as the relationship of GP with processing losses could hinder dry-cured ham producers.

In humans, common variants in the fat mass and obesity associated (FTO) gene are associated with body mass index and obesity. Here we sequenced exon 4, parts of introns 3 and 4 and two portions of the 3'-untranslated region of the porcine FTO gene in a panel of nine pigs of different breeds and identified three SNPs. Allele frequencies of the g.276T>G (AM931150) mutation were studied in seven pig breeds. This mutation was used to linkage-map FTO to SSC6. Association analyses between the g.276T>G polymorphism and several traits [pH of semimembranosus muscle and estimated breeding values (EBV) for average daily gain, back fat thickness, lean cuts, ham weight and feed:gain ratio] were carried out in 257 sib-tested Italian Large White pigs. Only feed:gain ratio showed P

The European wild boar is an important game species, subjected to local extinctions and translocations in the past, and currently enormously and worryingly expanding in some areas where management is urgently required. Understanding the relative roles of ancient and recent events in shaping the genetic structure of this species is therefore not only an interesting scientific issue, but it represents also the basis for addressing future management strategies. In addition, several pig breeds descend from the European wild boar, but the geographical location of the domestication area(s) and the possible introgression of pig genomes into wild populations are still open questions. Here, we analysed the genetic variation in different wild boar populations in Europe. Ten polymorphic microsatellites were typed in 252 wild boars and the mtDNA control region was sequenced in a subset of 145 individuals. Some samples from different pig breeds were also analysed. Our results, which were obtained considering also 612 published mtDNA sequences, suggest that (i) most populations are similarly differentiated, but the major discontinuity is found along the Alps; (ii) except for the Italian populations, European wild boars show the signature of a postglacial demographic expansion; (iii) Italian populations seem to preserve a high proportion of preglaciation diversity; (iv) the demographic decline which occurred in some areas in the last few centuries did not produce a noticeable reduction of genetic variation; (v) signs of human-mediated gene flow among populations are weak, although in some regions the effects of translocations are detectable and a low degree of pig introgression can be identified; (vi) the hypothesis of an independent domestication centre in Italy is not supported by our data, which in turn confirm that Central European wild boar might have represented an important source for domestic breeds. We can therefore conclude that recent human activities had a limited effect on the wild boar genetic structure. It follows that areas with high variation and differentiation represent natural reservoirs of genetic diversity to be protected avoiding translocations. In this context controlling some populations by hunting is not expected to affect significantly genetic variation in this species.

Ten genes (ANK1, bR10D1, CA3, EPOR, HMGA2, MYPN, NME1, PDGFRA, ERC1, TTN), whose candidacy for meat-quality and carcass traits arises from their differential expression in prenatal muscle development, were examined for association in 1700 performance-tested fattening pigs of commercial purebred and crossbred herds of Duroc, Pietrain, Pietrain × (Landrace × Large White), Duroc × (Landrace × Large White) as well as in an experimental F2 population based on a reciprocal cross of Duroc and Pietrain. Comparative sequencing revealed polymorphic sites segregating across commercial breeds. Genetic mapping results corresponded to pre-existing assignments to porcine chromosomes or current human?porcine comparative maps. Nine of these genes showed association with meat-quality and carcass traits at a nominal P-value of ? 0.05; PDGFRA revealed no association reaching the P ? 0.05 threshold. In particular, HMGA2, CA3, EPOR, NME1 and TTN were associated with meat colour, pH and conductivity of loin 24 h postmortem; CA3 and MYPN exhibited association with ham weight and lean content (FOM) respectively at P-values of

The use of DNA markers to evaluate genetic diversity is an important component of the management of animal genetic resources. The Food and Agriculture Organisation of the United Nations (FAO) has published a list of recommended microsatellite markers for such studies; however, other markers are potential alternatives. This paper describes results obtained with a set of amplified fragment length polymorphism (AFLP) markers as part of a genetic diversity study of European pig breeds that also utilized microsatellite markers. Data from 148 AFLP markers genotyped across samples from 58 European and one Chinese breed were analysed. The results were compared with previous analyses of data from 50 microsatellite markers genotyped on the same animals. The AFLP markers had an average within-breed heterozygosity of 0.124 but there was wide variation, with individual markers being monomorphic in 3-98% of the populations. The biallelic and dominant nature of AFLP markers creates a challenge for their use in genetic diversity studies as each individual marker contains limited information and AFLPs only provide indirect estimates of the allelic frequencies that are needed to estimate genetic distances. Nonetheless, AFLP marker-based characterization of genetic distances was consistent with expectations based on breed and regional distributions and produced a similar pattern to that obtained with microsatellites. Thus, data from AFLP markers can be combined with microsatellite data for measuring genetic diversity.

Linkage and QTL maps of Sus scrofa chromosome 9 (SSC9) were constructed using 16 markers, with 13 to 15 used in three F2 families based on Wild Boar (W), Meishan (M) and Pietrain (P) crosses. The LPR and SLN loci were integrated into the linkage map of SSC9 for the first time. Only a few quantitative trait loci (QTLs), explaining up to 5.1% of the F2 phenotypic variance, were identified on SSC9 with chromosome-wide significant effects on growth and fattening in the W x P family and on weight of liver, growth and fat-to-meat ratio in the W x M family. No QTLs were found in the M x P family. Gene effects were mainly dominant in the W x P family. In the W x M family, Wild Boar QTL alleles for weight of liver were superior over Meishan alleles.

Summary Three informative pig F2 families based on European Wild Boar (W), Meishan (M) and Pietrain (P) crosses have been used for genome-wide linkage and quantitative trait loci (QTL) analysis. Altogether 129 microsatellites, 56 type I loci and 46 trait definitions (specific to growth, fattening, fat deposition, muscling, meat quality, stress resistance and body conformation) were included in the study. In the linkage maps of M × P, W × P and W × M families, average spacing of markers were 18.4, 19.7 and 18.8 cM, the numbers of informative meioses were 582, 534 and 625, and the total lengths of autosomes measured were 27.3, 26.0 and 26.2 Morgan units, respectively. Maternal maps were on average 1.3 times longer than paternal maps. QTLs contributing more than 3% of F2 phenotypic variance could be identified at p

Summary Linkage maps of Sus scrofa chromosome 4 (SSC4) based on 19 markers were similar in lengths for three F2-families [Wild Boar (W), Meishan (M) and Pietrain (P) crosses] and in agreement with the previously published maps. Quantitative trait loci (QTLs) on SSC4 affect mainly muscle and fat mass. Compared with others, Pietrain alleles were associated with longer carcass, higher body weight and higher meat content. In all three families, the profiles of F ratio values for these traits showed peaks close to the positions of candidate genes V-ATPase, ATP1A2 and ATP1B1. Additional more proximally mapped QTLs, significant at the p

For Sus scrofa chromosome 13 (SSC13) eleven markers were genotyped to generate linkage and QTL maps in three F 2 families based on Wild Boar (W), Meishan (M) and Pietrain (P) crosses. Results of linkage maps were similar and agreed with published maps. Quantitative trait loci (QTLs) for body weights, meat conductivity and fat deposition were mapped in the M x P family to the interval S0076-S0068 (40-80 cM) and near the locus SW38 (120-150 cM). QTLs for the same traits were observed in the W x M family in different intervals explaining up to 5.3% of the F 2 phenotypic variance. No significant QTLs for the traits under investigation were found in the W x P family. The effects of QTL alleles were mostly dominant. In the M x P and W x M families alleles inherited from Meishan were generally associated with high values of live weights, food consumption and fat deposition and low values of meat conductivity.

Excessive softness is a serious defect of dry cured hams which seems related to high activity of lysosomal cysteine proteinases, such as cathepsin B, in fresh pork muscles a few days after slaughtering. As it has been shown that cathepsin B activity has a moderate heritability in Italian Large White pigs we started a candidate gene approach to identify the gene(s) that affect(s) this parameter. Here, we studied two candidate genes: cathepsin B (CTSB) and cystatin B (CSTB). We amplified and sequenced porcine DNA fragments for these two genes that were used to identify polymorphisms by SSCP and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. Four and two alleles were detected at the CTSB and CSTB loci, respectively. Sequencing of the CSTB alleles showed a missense mutation that changes a codon for aspartic acid into a codon for asparagine in exon 3 of the gene. Allele frequencies for the two loci differed among the pig breeds studied (Large White, Landrace, Duroc, Belgian Landrace, Hampshire, Pietrain, Meishan, Cinta Senese, Casertana, Calabrese and Nero di Sicilia). Linkage, somatic cell hybrid panel and radiation hybrid panel analyses assigned CTSB to porcine chromosome (Sscr) 14 and CSTB to Sscr 13. The markers identified at the CTSB and CSTB loci were used in association studies with several traits of economic importance including parameters that may indicate the suitability of pig meat to produce dry-cured hams. Significant associations were observed between CTSB and back-fat thickness and between CSTB and average daily gain. In this study, cathepsin B activity was not associated with the polymorphisms identified at the CTSB and CSTB loci.

To identify genes with effects on meat quality and production traits we developed an adult porcine skeletal muscle cDNA library. After pre-screening this library with seven genes highly expressed in skeletal muscle, 385 non-hybridizing clones were sequenced from both ends to yield 510 expressed sequence tags (ESTs). Together with those ESTs previously generated from this library, we have produced 701 porcine skeletal muscle ESTs. These ESTs were grouped into 306 different cDNA species and compared with the human skeletal muscle transcriptional profiles obtained from different databases. Furthermore we mapped 107 of these cDNAs using a somatic cell hybrid panel with genes mapping over all the autosomes (except on chromosome 11) and on chromosome X. The mapping of these cDNAs contributed to the construction of a first genomic transcript map of the skeletal muscle tissue in pig.

Chromosomal assignments are reported for fourteen porcine expressed sequence tags (ESTs)--CALM1, CRYAB, MYH7, MYL1, PDK4, PGAM2, PYGM, REV3L, RFC1, SLN, SPTBN1, SRM160, TPM1 and YWHAG. The ESTs were derived from our porcine skeletal muscle cDNA library. The ESTs sequences selected for mapping included the presence of the 3'-untranslated region. The assignments were performed using two independent somatic cell hybrid panels providing the possibility of confirmation of the results obtained. The observed localizations are compared with the locations predicted from heterologous (human-pig, pig-human) chromosome painting data and knowledge of the map locations of the human homologues. These results add new information to the porcine genome transcript map.

Information is presented on the frequency of the Msp I (-) allele in the third intron of the bovine growth hormone gene in a large number of cattle breeds. Consideration of the breed frequencies in relation to their geographic origin shows a low frequency for breeds originating in Northern Europe, moderate frequencies for breeds originating in Eastern Europe or the countries surrounding the Mediterranean basin, and very high frequencies for breeds originating in the Indian subcontinent. Consideration of breed frequencies in relation to breed type, shows low to moderate frequencies for the humpless breeds, high frequencies for the humped breeds. Various explanations for this distribution are discussed, among them the possibility that the Msp I (-) allele originated in the Bos indicus breeds of the Indian subcontinent, from which it diffused through the humpless Bos taurus breeds of Eastern Europe, the Mediterranean basin, eventually reaching Western, Northern Europe, Western Africa in low frequencies.

Two expressed sequence tags were isolated from a porcine skeletal muscle cDNA library and identified as the putative partial cDNAs of the porcine Na+, K(+)-ATPase subunit alpha 2 (ATP1A2) and muscle phosphofructokinase (PFKM) genes after sequencing and homology search. Results of analysis of a pig-rodent somatic cell hybrid panel by PCR allowed the assignments of ATP1A2 to porcine chromosome (chr) 4 and of PFKM to porcine chr 5. These assignments support previously observed conservation of syntenic relationships between human chr 1 and porcine chr 4 and between human chr 12 and porcine chr 5.

A partial cDNA clone encoding the porcine proteasome subunit A4 (PSMA4 or proteasome subunit C9) has been isolated from a porcine muscle cDNA library and sequenced. A biallelic TaqI RFLP was identified in Large White, Landrace and Duroc breeds. Moreover, the 3'-untranslated region of the gene showed a triallelic SSCP. By linkage analysis the PSMA4 locus was assigned to pig chromosome 7 and by radioactive in situ hybridization this locus was mapped to the region 7q13-q14.

An Alw 26I PCR-RFLP in exon 1 of the porcine SKI oncogene and mapping the gene to the RYR1 (CRC ) linkage group on chromosome 6

Sources/description: Expressed sequence tags, European Molecular Biology Laboratory (EMBL) accession numbers AJ301262, AJ301107, and AJ301170, corresponding respectively to portions of the porcine muscle creatine kinase (CKM), peroxisomal enoyl coenzyme A hydratase 1 (ECH1), and skeletal slow troponin T1 (TNNT1) genes were isolated from an adult porcine skeletal muscle cDNA library. Polymerase chain reaction primers for CKM and ECH1 were designed in the 3¢-untranslated region to amplify fragments of 207 bp and 104 bp, respectively. For TNNT1, primers were designed in the coding sequence, each on a different exon, according to the organization of the human and mouse TNNT1 gene. Partial sequencing confirmed that the obtained amplicon of about 490 bp contained portions of exons 8 and 9 and the intervening intron of the porcine TNNT1 gene (EMBL accession number AJ495809).

Description: A recombinant clone was isolated at random from a skeletal muscle cDNA library1. The sequence of the resulting 598 bp insert (EMBL accession number X94253) was compared in EMBL and GenBank databases using BLASTN2. The comparisons showed the highest matches with mouse and human PCBP2 cDNAs3−5 (mouse X75947, mouse X97982, human X78136and mouse L19661; BLASTN probability were 1·9e-182, 1·1e-176, 1·6e-174 and 4·7 e-172, respectively). Excluding two gaps that could be due to alternative splicing, the deduced porcine protein sequence revealed the complete identity with corresponding human ( X78136) and mouse ( L19661) sequences. The mouse sequences X75947and X97982showed only one amino acid difference (Arg instead of Gly) with the deduced amino acid sequence of the porcine cDNA clone isolated.