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Combining different approaches (resequencing of portions of 54 obesity candidate genes, literature mining for pig markers associated with fat deposition or related traits in 77 genes, and in silico mining of porcine expressed sequence tags and other sequences available in databases), we identified and analyzed 736 SNP within candidate genes to identify markers associated with back fat thickness (BFT) in Italian Large White sows. Animals were chosen using a selective genotyping approach according to their EBV for BFT (276 with most negative and 279 with most positive EBV) within a population of ≈ 12,000 pigs. Association analysis between the SNP and BFT has been carried out using the MAX test proposed for case-control studies. The designed assays were successful for 656 SNP: 370 were excluded (low call rate or minor allele frequency <5%), whereas the remaining 286 in 212 genes were taken for subsequent analyses, among which 64 showed a P(nominal) value <0.1. To deal with the multiple testing problem in a candidate gene approach, we applied the proportion of false positives (PFP) method. Thirty-eight SNP were significant (P(PFP) < 0.20). The most significant SNP was the IGF2 intron3-g.3072G>A polymorphism (P(nominal) < 1.0E-50). The second most significant SNP was the MC4R c.1426A>G polymorphism (P(nominal) = 8.0E-05). The third top SNP (P(nominal) = 6.2E-04) was the intronic TBC1D1 g.219G>A polymorphic site, in agreement with our previous results obtained in an independent study. The list of significant markers also included SNP in additional genes (ABHD16A, ABHD5, ACP2, ALMS1, APOA2, ATP1A2, CALR, COL14A1, CTSF, DARS, DECR1, ENPP1, ESR1, GH1, GHRL, GNMT, IKBKB, JAK3, MTTP, NFKBIA, NT5E, PLAT, PPARG, PPP2R5D, PRLR, RRAGD, RFC2, SDHD, SERPINF1, UBE2H, VCAM1, and WAT). Functional relationships between genes were obtained using the Ingenuity Pathway Analysis (IPA) Knowledge Base. The top scoring pathway included 19 genes with a P(nominal) < 0.1, 2 of which (IKBKB and NFKBIA) are involved in the hypothalamic IKKβ/NFκB program that could represent a key axis to affect fat deposition traits in pigs. These results represent a starting point to plan marker-assisted selection in Italian Large White nuclei for BFT. Because of similarities between humans and pigs, this study might also provide useful clues to investigate genetic factors affecting human obesity.

The objective of this study was to evaluate the effects of mutations in 2 genes [IGF2and 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 IGF2intron3-g.3072G>A substitution was identified as the causative mutation. In the same chromosome region, we assigned, by linkage mapping, the CTSDgene, 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 CTSDmutation 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 CTSDgene by radiation hybrid mapping, we analyzed the IGF2and the CTSDpolymorphisms 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 IGF2were highly significant for all traits when using either EBV or random residuals (e.g., using EBV: lean cuts, P= 2.2 × 10−18; ADG, P= 2.6 × 10−16; backfat thickness, P= 2.2 × 10−9; feed:gain ratio, P= 2.3 × 10−9; ham weight, P= 1.5 × 10−6). No effect was observed for meat quality traits. The IGF2intron3-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 CTSDmarker (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 IGF2mutation. The effects of the CTSDg.70G>A mutation were also confirmed in a subset of Italian Large White animals carrying the homozygous genotype IGF2intron3-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 IGF2intron3-g.3072G>A mutation is not the only polymorphism affecting fatness and muscle deposition on SSC2p. Therefore, the CTSDg.70G>A polymorphism could be used to increase selection efficiency in marker-assisted selection programs that already use the IGF2mutation. However, for practical applications, because the CTSDgene 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.

To identify DNA markers associated with performance, carcass, and meat production traits including muscle postmortem cathepsin activity, several porcine genes encoding for lysosomal proteinases (cathepsin B, CTSB; cathepsin D, CTSD; cathepsin F, CTSF; cathepsin H, CTSH; cathepsin L, CTSL; and cathepsin Z, CTSZ) and for a cathepsin inhibitor (cystatin B) were investigated. Single nucleotide polymorphisms were identified in CTSD, CTSH, CTSL, and CTSZgenes with a combination of in silico expressed sequence tag database mining and single-strand conformation polymorphism analysis. Sequencing and PCR-RFLP protocols were used to validate the identified polymorphisms. Allele frequencies at these loci were investigated in Italian Large White, Landrace, Duroc, Piétrain, Belgian Landrace, Hampshire, and Meishan breeds. Genotyping CTSDand CTSHmarkers made it possible to genetically map these genes to SSC 2 and 7, respectively. Markers in CTSD, CTSH, CTSL, and CTSZgenes, together with mutations we previously reported in cystatin B, CTSB, and CTSFgenes, were genotyped in an Italian Large White sib-tested population (272 or 482 animals). For these animals, meat quality traits (cathepsin B activity, pH measured at 2 h postmortem, pH measured at 24 h postmortem, glycogen, lactate, and glycolytic potential of semimembranosus muscle) and EBV for ADG, lean cuts (LC), backfat thickness (BFT), ham weight (HW), and feed:gain ratio (FGR) were determined. Analyzed markers did not show any association with muscle cathepsin B activity. Thus, it could be possible that different genes, other than these investigated candidates, affect this trait, which is correlated with the excessive softness defect of dry-cured hams. The results of association analysis confirmed the effects we already reported in another study for CTSFon ADG (P= 0.008), LC (P= 0.001), and BFT (P= 0.02). Moreover, CTSDwas associated with ADG, LC (P< 0.0001), BFT, HW, and FGR (P< 0.001); CTSHwas associated with FGR (P= 0.026); and CTSZwas associated with ADG (P= 0.006), LC (P= 0.01), HW (P= 0.024), and FGR (P= 0.029). The biochemical and physiological functions of the lysosomal proteinases, together with the results obtained in our investigation, suggest that the cathepsin gene family might play important roles affecting economic traits in pigs.

In assessing single gene effects on a quantitative trait, contrasts between the genotypes would be of primary interest. However, only the net differences over and above the contributions from polygene effects from other loci would be of practical importance. In a population of 11015 Holstein cows, the B allele of K-casein was significantly favourable for milk and protein yields and for protein %, and the A allele of β-lactoglobulin was favourable for fat % and protein yield. The degree of dominance for their effects was shown. Also shown were the independence between effects of the casein variants and those of polygene, and between effects of casein genes. Adjustment for casein gene effects made no difference to the estimates of heritability and other genetic parameters of all five dairy production traits.

AbstractThe official results of trotters in Italian harness racings have been used to get AM-BLUP estimates of genetic parameters, EBVs and rTIof three groups of traits: speed (racing time, annual best time, best time in career between 2- and 5-year old), earnings (earnings/start, annual earnings, total earnings between 2- and 5-year old) and Elo system traits (underlying performance and final rating). The Elo system has been used for half a century in chess players rating, and it has been modified and fitted to several games and sports: it has already been used for genetic evaluation of sport horses in France. The highest heritability estimates in each group of traits have been found for best time (.430±.014), total earnings (.271±.013) and Elo final rating (.270±.008). The choice of “k”, the Elo ratings updating factor, did not show a key role in affecting the results. The underlying performance heritability and repeatability have been estimated .159±.004 and .420±.007 respectively. The Elo-based systems proved to be very promising in objectively evaluating trotters.

AbstractGlycolytic Potential (GP) is an important parameter influencing pig meat quality. In order to identify genes and gene networks influencing glycolytic potential we utilized microarray analysis and studied the expression profile of skeletal muscle tissue from Italian Large White pigs with extreme high/low levels of GP. The knowledge of differentially expressed genes in groups of pigs with substantively different GP values could be a first step to understand the metabolic regulatory pathways influencing GP.The genes more expressed in the samples with low GP are mainly associated with energy metabolism while those more expressed in the samples with high GP are involved in intracellular transport. These results can give useful information to identify candidate genes for glycolytic potential level of pig meat.

Protected denomination of origin (PDO) dry cured hams, like Parma and San Daniele hams, are produced from the hind legs of heavy pigs, according to Consortia rules. Seasoning of the legs lasts at least 12 mo with the only addition of salt. This simple production technology cannot correct possible original defects of the green legs. A specific breeding program able to produce animals with the requested characteristics of the meat and legs is therefore needed. For this reason, two specific traits, linked to the quality of the final products, have been defined by ANAS and used in the selection programs of Italian heavy pigs: visible intermuscular fat (VIF) and ham weight loss at first salting (HWLFS). VIF is a subjective evaluation of the level of fat deposition between leg muscles. An excess in intermuscular fat negatively affects the acceptability of hams by consumers and depreciates the final product. HWLFS is correlated to total weight loss of the hams during the entire seasoning period. In this study we performed genome-wide association studies (GWAS) for these two traits in the Italian Large White and Italian Duroc pig breeds. About 1350 and 430 performance tested pigs of these two breeds respectively were genotyped by the PorcineSNP60 BeadChip. Results of the GWAS identified quite a large number of QTL regions affecting these traits in both breeds with poor overlapping between traits and breeds. These results suggest that VIF and HWLFS are mainly affected by different genetic factors supporting their combined use in the definition of a Total Merit Genetic Index in Italian heavy pigs.

AbstractThe data collected in the first seven years of the 100-day Station Test for Italian Saddle Horse stallions have been used to estimate EBVs by single trait - repeatability AM-BLUP. There were 9449 scores for “character”and “gaits”, and 3564 for “jumping ability”in the training period; 344 scores for each trait were also available from the final evaluations assigned by two well-known professional riders; in the pedigree file of the 180 tested horses there were 2837 animals. Heritability estimates were .38±.02 and .23±.14 for “character”, .60±.02 and .58±.04 for “gaits”, and .48±.02 and .52±.04 for “jumping”, in the training period and in the final evaluation, respectively. The training period and the final evaluation were weighted 90% and 10% in each trait index, and the weights for “character”, “gaits”and “jumping”were 25%, 25% and 50% in the overall index. The genetic index was correlated .97 with the current official index, both linearly and in rank: therefore, the 82 licensed stallions give a selection intensity of .85, instead of the theoretical maximum of .87. Although the difference in the response to selection that the switching to BLUP could assure is low, the breeders could make comparisons between stallions approved in different editions.

AbstractFatty acid synthase (FASN) is a multifunctional enzyme that plays a central role in fatty acid biosynthesis catalysing the conversion of acetyl-CoA and malonyl-CoA into long-chain saturated fatty acids and has an important role in energy homeostasis. Pig FASNgene has been assigned to chromosome 12p1.5 and a T>C polymorphism in the fourth exon was found. Adiponectin (ADN) is a fat-derived hormone involved in insulin sensitivity, in lipid and glucose metabolism. In literature is reported that the gene was mapped on chromosome 13 at 53.6 cM, in a region containing QTL for intramuscolar fat (IMF). In this gene several SNPs were identified and one of these polymorphisms (a G>A missense mutation within the 60thcodon) determining the Val-Ile substitution in the protein, has been previously reported.The aim of this work is to analyse the variability of polymorphisms of fatty acid synthase described by Munoz et al., 2003 (Anim. Genet. 34:234) and adiponectin genes, candidates for meat and carcass quality, in Italian Duroc pigs. Up to now researches on these functional genes in this pig breed have not been performed.In order to estimate allele frequencies, the FASNT>C polymorphism and the ADNG>A mutation were studied by PCR-RFLP in 134 and 257 Italian Duroc, respectively. At the FASNlocus the allele frequency was 0.041 for T allele; at the ADNlocus the frequency of the alleles A was 0.136. We investigated the effect of FASNand ADNpolymorphisms on Estimated Breeding Values (EBVs) for single traits (average daily gain, feed to gain ratio, weight of lean cuts, ham weight, backfat thickness and visible intermuscular fat) and for selection indexes (Total Index and Terminal Index) estimated by ANAS. The analyses were performed using the GLM procedure of SAS System and a model with the genotype at FASNor ADNlocus as fixed factor.At the FASNlocus only few pigs carried the T allele; therefore, we tried to perform the analysis comparing the pigs with both genotypes T/T plus C/T versus those genotyped C/C at this locus. The results didn’t show any association of the polymorphism with the examined traits.The same model was used for the ADNlocus and the G/A genotyped pigs versus the G/G ones showed a significant higher estimated mean value for Total Index (P= 0.0114).For both the analysed genes the obtained results should be verified on a larger sample even if the present findings could suggest a possible role of ADNon the traits included in Total Index in the Duroc breed.