Identification of a novel QTL for lean meat percentage using imputed genotypes.

Lean meat percentage is a critical production trait in pig breeding systems with direct implications for the sustainability of the industry. In this study, we conducted a genome-wide association study for lean meat percentage using a cohort of 850 Duroc × (Landrace × Yorkshire) crossbred pigs and we identified QTL on SSC3 and SSC18. Based on the predicted effect of imputed variants and using the PigGTEx database of molecular QTL, we prioritized candidate genes and SNPs located within the QTL regions, which may be involved in the regulation of porcine leanness. Our results indicate that a nonsense mutation in ZC3HAV1L on SSC18 has a direct effect on lean meat percentage.

Genome-wide association studies for additive and dominance effects for body composition traits in commercial crossbred Piétrain pigs.

Fat depth (FD) and muscle depth (MD) are economically important traits and used to estimate carcass lean content (LMP), which is one of the main breeding objectives in pig breeding programmes. We assessed the genetic architectures of body composition traits for additive and dominance effects in commercial crossbred Piétrain pigs using both 50 K array and sequence genotypes. We first performed a genome-wide association study (GWAS) using single-marker association analysis with a false discovery rate of 0.1. Then, we estimated the additive and dominance effects of the most significant variant in the quantitative trait loci (QTL) regions. It was investigated whether the use of whole-genome sequence (WGS) will improve the QTL detection (both additive and dominance) with a higher power compared with lower density SNP arrays. Our results showed that more QTL regions were detected by WGS compared with 50 K array (n = 54 vs. n = 17). Of the novel associated regions associated with FD and LMP and detected by WGS, the most pronounced peak was on SSC13, situated at ~116-118, 121-127 and 129-134 Mbp. Additionally, we found that only additive effects contributed to the genetic architecture of the analysed traits and no significant dominance effects were found for the tested SNPs at QTL regions, regardless of panel density. The associated SNPs are located in or near several relevant candidate genes. Of these genes, GABRR2, GALR1, RNGTT, CDH20 and MC4R have been previously reported as being associated with fat deposition traits. However, the genes on SSC1 (ZNF292, ORC3, CNR1, SRSF12, MDN1, TSHZ1, RELCH and RNF152) and SSC18 (TTC26 and KIAA1549) have not been reported previously to our best knowledge. Our current findings provide insights into the genomic regions influencing composition traits in Piétrain pigs.

A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations.

BACKGROUND: Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. RESULTS: In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. CONCLUSIONS: We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

Improving the estimation of the lean meat percentage in pig carcasses using Box-Cox transformation and additional carcass parameters.

The objective of this study was to evaluate and improve the prediction models of the AutoFOM III and FOM II apparatuses (Frontmatec Group, Denmark) used to estimate the lean meat percentage (LMP) of pig carcasses in Belgium, since the current models underestimate the pig carcasses with a LMP higher than 66 %. Non-linearity in the backfat thickness (BT) parameters was identified as the main reason for this bias in prediction. Box-Cox transformation of the parameters R2P10, R2P8 and R2P4 from AutoFOM III allowed to lower the root mean squared error of prediction (RMSEP) of the model from 1.72 to 1.59, while simultaneously removing the bias of the high LMP carcasses. For the FOM II apparatus, there was no effect of the transformation of the only BT parameter on the RMSEP (2.15 before and 2.14 after transformation) and on the bias. Next to the transformation, it was investigated whether adding other information about the carcasses could also improve the RMSEP of the prediction models. The parameters hot carcass weight, carcass length, ham width, ham angle and sex were added to the original models without transformation and lowered the RMSEP from AutoFOM III and FOM II to 1.55 and 1.83 respectively. Finally, the best results were found by combining the Box-Cox transformation and adding other carcass parameters, resulting in RMSEP values of 1.50 and 1.82 for AutoFOM III and FOM II respectively, on top of the removal of the high LMP bias. IMPLICATIONS: Accurate estimation of the lean meat percentage of pig carcasses is of great economic importance for the pig production and slaughtering sector, so every opportunity to increase precision should be seized. This study shows that the current linear prediction models can be improved by taking into account non-linearity, depending on the device. An even larger increase in precision can be achieved by adding carcass information that is currently not measured or not linked to the classification device but that is partly already available at the slaughterline.

Effect of intramuscular vaccination against Lawsonia intracellularis on production parameters, diarrhea occurrence, antimicrobial treatment, bacterial shedding, and lean meat percentage in two Danish naturally infected finisher pig herds.

Lawsonia intracellularis (LI) is an economically important enteric pathogen in pigs with a worldwide endemic prevalence. The objective of this study was to evaluate the effect of an intramuscularly administrated LI vaccine (Porcilis®Lawsonia Vet.) in Danish finisher pigs (30-115 kg) measured on key production figures, antimicrobial (AB) treatments, occurrence of diarrhea and LI shedding. The study was a group-randomized block-trial with parallel groups in two herds, Herd 1 and Herd 2, experiencing a natural subclinical-clinical LI infection in early finisher period. Vaccination occurred at weaning, but the study focused on the first eight weeks in the finisher period. Further, slaughterhouse data were included. In total, 52 and 50 finisher pens comprising 2184 and 2254 finisher pigs were included in each of two herds, respectively. LI vaccination significantly reduced feed conversion ratio (FCR) by 0.05 and 0.09 FU/kg (p = 0.007 and p < 0.001) alongside a significantly increased average daily weight gain (ADWG) by 31 and 43 gr/day (p = 0.001 and p < 0.001) in each of the herds, respectively. In the vaccinated group, less variation was found in ADWG compared to the control group (p < 0.001 in both herds) as an expression of a more uniform growth, which was further confirmed by less variation in lean meat percent in the vaccinated group in one herd (p = 0.007). No significant difference between groups were found in mortality and pigs excluded due to welfare reasons. AB flock treatment against diarrhea was significantly reduced in Herd 1 with all pens treated in the control group compared to 30.8 % in the vaccinated group (p < 0.001). In Herd 2, the difference was non-significant with 68.0 % in the control group compared to 50.0 % in the vaccination group (p = 0.252). Low levels of individual treatments against diarrhea were seen in both herds (≤ 5.0 %) but still significantly reduced in vaccinated pigs compared to control pigs (p < 0.050 in both herds). Mean diarrheic blot counts were significantly reduced in vaccinated pens compared to control pens (p < 0.001 in both herds). In vaccinated pigs, shedding of LI was reduced in both prevalence (p < 0.001 in both herds), excretion level in positive samples (p < 0.001 in both herds) and, in one herd, also in duration (p = 0.003) when compared to control pigs. In conclusion, pigs vaccinated with Porcilis®Lawsonia Vet against LI in both of two high-health and high-productive finisher herds had, compared to non-vaccinated pigs, significantly improved key production figures, and reduced AB treatment, occurrence of diarrhea, LI shedding, and growth variation.

Two variants of AUTS2 gene are associated with high lean meat percentage in Pekin ducks.

Duck meat is starting to receive more attention due to its unique meaty characteristics. Pekin duck is an important breed resource of meat duck, which has been used in meat production and product research. However, the study about whole genome resequencing analysis of ducks for meat production has not been reported and the underlying mechanisms of meat production remain undefined. Here, lines with high lean meat percentage (S, n = 30) and low lean meat percentage (Z, n = 30) were used to analyze. The values of body weight, breast meat weight and leg meat weight in S line (body weight: 3,071 ± 26.83 g), breast meat: 391.3 ± 6.670 g; leg meat: 121.1 ± 2.184 g) were significantly higher than those in Z line (body weight: 2,584 ± 38.53 g, breast meat: 263.9 ± 6.984 g; leg meat: 110.1 ± 3.645 g). The values of body size in Z line (26.47 ± 0.1571 cm) were significantly higher than that in S line (25.38 ± 0.2475 cm). A total of 14,220,037 SNPs were obtained from 19 individuals by whole-genome resequencing, and the separate analyses of FST (range from 0.30 to 0.52) and log2θπ ratio (range from 5.8 to 8.1) revealed 50 and 124 candidate genes in the top 0.1% regions respectively, which involved in 209 and 298 candidate regions. The integration of two approaches resulted in 7 overlapping genes. Notably, AUTS2 gene is related to activator of developmental regulator. As expected, we found that in the chr29:2.29-2.30 Mb region of AUTS2, the FST value is 0.32, and the S line (π = 7.3 × 10 -5) shows a very low level of π value compared with Z line (π = 8.8 × 10 -3). Genotyping and GWAS analysis showed that 2 candidate SNPs (chr29:2,296,787 and chr29:2,296,832) were associated with high meat percentage, which were verified by Sanger sequencing. Taken together, lean meat percentage was much higher in S line individuals by comparing with Z line. The integration of FST and θπ resulted in only 7 overlapping genes that in the top 0.1% candidate regions of them. The chr29:2,296,787 and chr29:2,296,832 in the AUTS2 gene could be important molecular markers for high lean meat adaptation selection in S line.

On-farm prevalence of and potential risk factors for boar taint.

Boar taint is an unpleasant taste and odor that can occur in entire male pigs and is caused by androstenone, skatole, and to a lesser extent indole accumulating in fat tissue. In the present observational study, we evaluated an extensive list of such potential risk factors which influence boar taint: social hierarchy and puberty attainment, housing, health, preslaughter conditions, season, feed, carcass composition, slaughter weight or age, and breed. Details on these factors were collected by interviews with the participating farmers, observations on each farm by trained observers and farmers, as well as slaughterhouse data. Twenty-two farms (in West- and East-Flanders, ranging from 160 to 600 sows, selected on suitability) raising entire male pigs were included in the study to evaluate the link between boar taint and potential risk factors related to the farm and slaughter batch (114 slaughter batches and 16 791 entire male pigs in total). Average olfactory boar taint prevalence was 1.8 ±â€¯0.8%. Boar taint prevalence varied also within farms up to a maximum range between slaughter batches of 9.1% which suggests an effect of factors varying between slaughter batches such as season or other variables varying between slaughter batches. Less aggressive behavior at the end of fattening as well as lower skin lesion scores at fattening as well as at slaughter could be associated with less boar taint. The same might be said for sexual behavior, though less convincingly from this study. Measures that reduce aggression and stress have therefore have the potential to lower boar taint prevalence. The same might be said for sexual behavior, though less convincingly from this study. Furthermore, boar taint prevalence was generally higher in winter than in summer, which is relevant from a planning perspective for the slaughterhouses to seek alternative markets. Finally, increased CP gave significantly lower boar taint prevalences. This may to some extent be explained by the negative association between boar taint and lean meat percentage, as increased dietary CP levels promote the carcass lean meat percentages which can then be associated with lower boar taint levels.

Monitoring lean meat percentage predictions from optical grading probes by a commercial cutting pattern.

The lean meat percentage (LMP) classification in Norwegian slaughterhouses is obtained by Hennessy Grading Probe 7 (HGP7), an optical tool. Even though the HGP7 method is validated frequently, there is industrial and legislative demand to reconsider the applied LMP equation, typically due to the introduction of new breeds. A deboning pilot plant generates precise yield data using cutting and deboning stratified pork carcasses by a specific commercial cutting pattern (CCP) at an annual rate of approximately 250 slaughter pigs. This paper shows how results obtained by CCP can be used to measure LMP in pork and how these results can be used for monitoring the quality of LMP predicted by HGP7. The effect of gender, maternal- and paternal lines on validity of HGP7 predictions was evaluated. The effect of introducing a new maternal line (TN70) seems to be substantial, whereas the effects of the tested paternal lines are small to negligible.

Nondestructive Estimation of Lean Meat Yield of South Korean Pig Carcasses Using Machine Vision Technique.

In this paper, we report the development of a nondestructive prediction model for lean meat percentage (LMP) in Korean pig carcasses and in the major cuts using a machine vision technique. A popular vision system in the meat industry, the VCS2000 was installed in a modern Korean slaughterhouse, and the images of half carcasses were captured using three cameras from 175 selected pork carcasses (86 castrated males and 89 females). The imaged carcasses were divided into calibration (n=135) and validation (n=39) sets and a multilinear regression (MLR) analysis was utilized to develop the prediction equation from the calibration set. The efficiency of the prediction equation was then evaluated by an independent validation set. We found that the prediction equation-developed to estimate LMP in whole carcasses based on six variables-was characterized by a coefficient of determination (Rv 2 ) value of 0.77 (root-mean square error [RMSEV] of 2.12%). In addition, the predicted LMP values for the major cuts: ham, belly, and shoulder exhibited Rv 2 values≥0.8 (0.73 for loin parts) with low RMSEV values. However, lower accuracy (Rv (2) =0.67) was achieved for tenderloin cuts. These results indicate that the LMP in Korean pig carcasses and major cuts can be predicted successfully using the VCS2000-based prediction equation developed here. The ultimate advantages of this technique are compatibility and speed, as the VCS2000 imaging system can be installed in any slaughterhouse with minor modifications to facilitate the on-line and real-time prediction of LMP in pig carcasses.

Chicory fructans in pig diet reduce skatole in back fat of entire male pigs.

Androstenone, skatole and indole are main compounds responsible for boar taint, an off-odour in meat of some entire male pigs. Several feed ingredients derived from chicory have been reported to reduce fat skatole levels, while results for indole are more contradictory. The skatole-reducing effect is probably based on the prebiotic effects described for fructan compounds. Inulin and oligofructose have a high and low degree of polymerization, respectively. The fermentation rate decreases with an increasing degree of polymerization, which may result in differing effects of the compounds on skatole and/or indole levels. In this study we evaluated the effect of the inclusion of 5% inulin or 5% oligofructose during the last 3weeks before slaughter on carcass quality, concentration of skatole and indole in back fat as well as on the olfactory evaluation of boar taint in fat. Carcass weight did not differ between treatment groups but lean meat percentage increased when feeding oligofructose (P=0.019) compared to the control group, which is relevant for further research. Inclusion of 5% inulin or 5% oligofructose in the finisher diet of entire male pigs significantly reduced the back fat skatole concentration, without influence on indole. Olfactory score for boar taint tended to decrease when oligofructose was added to the diet.

A review of computed tomography and manual dissection for calibration of devices for pig carcass classification - Evaluation of uncertainty.

Online pig carcass classification methods require calibration against a reference standard. More than 30years ago, the first reference standard in the EU was defined as the total amount of lean meat in the carcass obtained by manual dissection. Later, the definition was simplified to include only the most important parts of the carcass to obtain a better balance between accuracy and cost. Recently, computed tomography (CT) obtained using medical X-ray scanners has been proposed as a reference standard. The error sources of both traditional (manual) dissection methods and the new methods based on images from CT scanning of pig carcasses are discussed in this paper. The uncertainty resulting from the effect of various error sources is estimated. We conclude that, without standardisation, the uncertainty is considerable for all the methods. However, methods based on volume estimation using CT and image analysis might lead to higher accuracy if necessary precautions are taken with respect to measuring protocol and reference materials.

Genome-wide SNP scan in a porcine Large White×Minzhu intercross population reveals a locus influencing muscle mass on chromosome 2.

A high-density single nucleotide polymorphism (SNP) array containing 62 163 markers was employed for a genome-wide association study (GWAS) to identify variants associated with lean meat in ham (LMH, %) and lean meat percentage (LMP, %) within a porcine Large White×Minzhu intercross population. For each individual, LMH and LMP were measured after slaughter at the age of 240±7 days. A total of 557 F2 animals were genotyped. The GWAS revealed that 21 SNPs showed significant genome-wide or chromosome-wide associations with LMH and LMP by the Genome-wide Rapid Association using Mixed Model and Regression-Genomic Control approach. Nineteen significant genome-wide SNPs were mapped to the distal end of Sus Scrofa Chromosome (SSC) 2, where a major known gene responsible for muscle mass, IGF2 is located. A conditioned analysis, in which the genotype of the strongest associated SNP is included as a fixed effect in the model, showed that those significant SNPs on SSC2 were derived from a single quantitative trait locus. The two chromosome-wide association SNPs on SSC1 disappeared after conditioned analysis suggested the association signal is a false association derived from using a F2 population. The present result is expected to lead to novel insights into muscle mass in different pig breeds and lays a preliminary foundation for follow-up studies for identification of causal mutations for subsequent application in marker-assisted selection programs for improving muscle mass in pigs.