Genetic association between leg conformation in young pigs and sow longevity

Designing an early selection morphological traits index for reproductive efficiency in Pura Raza Española mares

The low rate of reproductive efficiency in horses may be linked to the equine industry's practice of maintaining breeding stock that stands out for its athletic or morphological performance but exhibits poor reproductive efficiency. In this study, the age at first foaling, age at last foaling, interval between first and second foaling, average interval between foaling, foaling number and reproductive efficiency, and their relationship with the morphological records in 19,758 Pura Raza Española (PRE) mares were analyzed. After a partial least squares analysis height at withers, lateral hock angle, dorsal-sternal diameter, perimeter of anterior cannon bone, angle of shoulder, thoracic perimeter, hip-stifle distance, and angle of croup were the most important traits related with reproductive traits in PRE mares. A multivariate animal model with both morphological and reproductive traits was applied, including age, geographical area, coat color, and average stud size in the decade of the mare's first foaling. The results indicate that reproductive selection is feasible, and is enhanced by the use of morphological traits, given the moderate to high magnitudes of heritability values in both types of traits, which oscillated between 0.1 (interval between first and second foaling) and 0.95 (height at withers). The resulting genetic parameters were used to develop a series of selection indexes based on morphological or morphological and reproductive combination traits to improve reproductive efficiency traits in PRE mares and thus compute the expected genetic response (EGR) for the different strategies. The increase in EGR, when comparing EGR using only reproductive traits as selection criteria vs. using a combined index of both morphological and reproductive traits, oscillated between 4.0% for the age at first foaling to 46.8% for the interval between first and second foaling. In addition, two precocity indexes showed positive EGR when the age at last foaling and the interval between first and second foaling, both with and without morphological traits, were used as selection criteria. Therefore, this analysis reveals that the preselection of reproductive traits based on morphological traits is possible in PRE mares. Ultimately, this knowledge will help breeders achieve genetic progress in reproductive traits, leading to healthier and more successful breeding outcomes in horses.

Genome-Wide Association Study of Body Conformation Traits in a Three-Way Crossbred Commercial Pig Population

Body conformation is the most direct production index, which can fully reflect pig growth status and is closely related to critical economic traits. In this study, we conducted a genome-wide association study (GWAS) on body conformation traits in a population of 1518 Duroc × (Landrace × Yorkshire) commercial pigs. These traits included body length (BL), body height (BH), chest circumference (CC), abdominal circumference (AC), and waist circumference (WC). Both the mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) approaches were employed for the analysis. Our findings revealed 60 significant single nucleotide polymorphisms (SNPs) associated with these body conformation traits in the crossbred pig population. Specifically, sixteen SNPs were significantly associated with BL, three SNPs with BH, thirteen SNPs with CC, twelve SNPs with AC, and sixteen SNPs with WC. Moreover, we identified several promising candidate genes located within the genomic regions associated with body conformation traits. These candidate genes include INTS10, KIRREL3, SOX21, BMP2, MAP4K3, SOD3, FAM160B1, ATL2, SPRED2, SEC16B, and RASAL2. Furthermore, our analysis revealed a novel significant quantitative trait locus (QTL) on SSC7 specifically associated with waist circumference, spanning an 84 kb interval. Overall, the identification of these significant SNPs and potential candidate genes in crossbred commercial pigs enhances our understanding of the genetic basis underlying body conformation traits. Additionally, these findings provide valuable genetic resources for pig breeding programs.

Genetic analysis for sow stayability at different parities in purebred Landrace and Large White pigs

Genetic parameters for sow stayability were estimated from farrowing records of 10,295 Landrace sows and 8192 Large White sows. The record for sow stayability from parity k to parity k + 1 (k = 1, …, 6) was 0 when a sow had a farrowing record at parity k but not at parity k + 1, and 1 when a sow had both records. Heritability was estimated by using single‐trait linear and threshold animal models. Genetic correlations among parities were estimated by using two‐trait linear–linear and single‐trait random regression linear animal models. Genetic correlations with litter traits at birth were estimated by using a two‐trait linear–linear animal model. Heritability estimates by linear model analysis were low (0.065–0.119 in Landrace & 0.061–0.157 in Large White); those by threshold model analysis were higher (0.136–0.200 & 0.110–0.283). Genetic correlations among parities differed between breeds and models. Genetic correlation between sow stayability and number born alive was positive in many cases, implying that selection for number born alive does not reduce sow stayability. The results seem to be affected by decisions on culling made by farmers.

Unintended consequences of selection for increased production on the health and welfare of livestock

Modern farming technologies, including quantitative selection and breeding methods in farm animal species, resulted in increased production and efficiency. Selection for increased output in both intensive and extensive production systems has trade-offs and negative outcomes, often more pronounced in intensive systems. Animal welfare and health are often adversely affected and this influences sustainable production. The relative importance of animal welfare differs among developed and developing countries due to the level of economic development, food security and education, as well as religious and cultural practices which presents challenges for sound scientific research. Due to breeding goals in the past set on growth performance, traits such as fertility, welfare and health have been neglected. Fertility is the single most important trait in all livestock species. Reduced fertility and lameness, claw health and mastitis results in unnecessary culling and reduced longevity. Selection pressure for growth accompanied with inbreeding has resulted in a number of genetic defects in beef, sheep and pigs. This review demonstrated the importance of inclusion of animal welfare concepts into breeding objectives and selection strategies. Accurate phenotyping of welfare traits is a limiting factor in the implementation of mitigating strategies, which include diagnostic testing, control of inbreeding and genomic selection.

Genetic associations between stayability and longevity in commercial crossbred sows, and stayability in multiplier sows

Longevity in commercial sows is often selected for through stayability traits measured in purebred animals. However, this may not be justifiable because longevity and stayability may be subject to both genotype by environment interaction (G × E) and genotype by genotype interaction (G × G). This study tested the hypothesis that stayability to service after first parity is more strongly genetically correlated with longevity in commercial herds when stayability is measured in commercial herds rather than multiplier herds. The analysis was based on farrowing- and service-records from 470,824 sows (189,263 multiplier; 281,561 commercial) and 300 herds (156 multiplier; 144 commercial sows). Multiplier sows were either purebred Landrace or Yorkshire and commercial sows were mainly rotationally crossbreds between the two breeds. Commercial longevity was defined as age in days when culled (LongC), and stayability to service after first parity was defined for both commercial sows (StayC) and multiplier sows (StayM). The genetic correlations between LongC, StayC, and StayM were estimated by restricted maximum likelihood using linear mixed models. Genetic parameters were estimated separately for Landrace and Yorkshire. In Landrace, the genetic correlations between LongC and StayC, LongC and StayM, and StayC and StayM were 0.86 ± 0.02, 0.24 ± 0.05, and 0.34 ± 0.06, respectively. In Yorkshire, the genetic correlations between LongC and StayC, LongC and StayM, and StayC and StayM were 0.81 ± 0.03, 0.17 ± 0.05, and 0.18 ± 0.7, respectively. Conclusively, longevity in commercial herds is more strongly correlated with stayability when stayability is measured in commercial herds rather than multiplier herds.

Maternal effect on body measurement and meat production traits in purebred Duroc pigs

We investigated maternal effect on nine body measurement traits (body height, body length, front width (FW), chest width (CW), hind width (HW), chest depth, chest girth (CHG), front cannon circumference (FCC) and rear cannon circumference (RCC)) measured at the end of performance testing and five meat production traits (ages at the start and end of performance testing (D30 and D105), average daily gain (ADG), backfat thickness and loin muscle area) in purebred Duroc pigs. Genetic parameters for each trait were estimated by using six single-trait models with and without common litter environmental effect, maternal genetic effect and direct-maternal genetic correlation. The value of Akaike's information criterion was lowest with the model including direct additive genetic and common litter environmental effects for 10 traits. The estimated proportion of common litter environmental variance to phenotypic variance was approximately ≥0.1 for D30, D105, ADG, FW, CW, HW, CHG, FCC and RCC. Using a model without common litter environmental effect would overestimate the direct heritability of most traits. Standard errors of estimated genetic parameters tended to be larger in models including maternal genetic effect. The results indicate that a compromise could be made for accurate genetic parameter estimation for body measurement traits, as well as meat production traits, in pigs by considering common litter environmental effect.

Livestock Handling at the Abattoir: Effects on Welfare and Meat Quality

Low-stress handling that uses behavioral principles can help reduce bruises and improve meat quality in cattle, pigs, and sheep. Short-term stressors before stunning, such as electric prod use or jamming in the race, may increase Pale, Soft, Exudative meat in pork and reduce tenderness in beef. Longer term stresses may increase Dark, Firm and Dry meat. Continuous assessment of livestock handling practices is recommended. Handlers should be trained to move small groups of livestock. They also need to understand behavioral principles. The most important ones are flight zone and the point of balance at the shoulder. Calm animals will be easier to handle. Simple economical improvements in races and lairages can help facilitate animal movement through the facility. The movement of livestock can often be improved by (1) installation of a light at a dark stun box entrance, (2) moving lamps to reduce reflections on shiny metal, (3) installation of solid shields to prevent incoming animals from seeing people on moving conveyors, (4) redirection of air flow at the stun box entrance, or (5) in elevated conveyor restrainers, use of a false floor to prevent entering animals from seeing the “visual cliff ” effect. Continuous assessment and supervision are required to maintain low-stress handling methods.

Genome-wide association study and genomic predictions for exterior traits in Yorkshire pigs1

The objectives of this study were to identify informative genomic regions that affect the exterior traits of purebred Korean Yorkshire pigs and to investigate and compare the accuracy of genomic prediction for response variables. Phenotypic data on body height (BH), body length (BL), and total teat number (TTN) from 2,432 Yorkshire pigs were used to obtain breeding values including as response variable the estimated breeding value (EBV) and 2 types of deregressed EBVs-one including the parent average (DEBVincPA) and the other excluding it (DEBVexcPA). A final genotype panel comprising 46,199 SNP markers was retained for analysis after quality control for common SNPs. The BayesB and BayesC methods-with various π and weighted response variables (EBV, DEBVincPA, or DEBVexcPA)-were used to estimate SNP effects, through the genome-wide association study. The significance of genomic windows (1 Mb) was obtained at 1.0% additive genetic variance and was subsequently used to identify informative genomic regions. Furthermore, SNPs with a high model frequency (≥0.90) were considered informative. The accuracy of genomic prediction was estimated using a 5-fold cross-validation with the K-means clustering method. Genomic accuracy was measured as the genomic correlation between the molecular breeding value and the individual weighted response variables (EBV, DEBVincPA, or DEBVexcPA). The number of identified informative windows (1 Mb) for BH, BL, and TTN was 4, 3, and 4, respectively. The number of significant SNPs for BH, BL, and TTN was 6, 4, and 5, respectively. Diversity π did not influence the accuracy of genomic prediction. The BayesB method showed slightly higher genomic accuracy for exterior traits than BayesC method in this study. In addition, the genomic accuracy using DEBVincPA as response variable was higher than that using other response variables. Therefore, the genomic accuracy using BayesB (π = 0.90) with DEBVinPA as a response variable was the most effective in this study. The genomic accuracy values for BH, BL, and TTN were calculated to be 0.52, 0.60, and 0.51, respectively.

Effects of supplementing organic microminerals and methionine with or without limiting growth during the rearing phase of replacement gilts on lameness, growth, and body composition

Previous research suggested that lameness in growing pigs could be reduced using feeding strategies, such as limiting growth rate and supplementing trace minerals (TM) and (or) methionine (Met). The present study evaluates effects of 1) TM and Met and 2) limiting total lysine (Lys) during the rearing phase (90 d) of gilts (as a means to limit growth rate) on lameness, performance, and sow claw health and productivity (to first parity). Gilts (n = 240; 58.0 ± 11.1 kg body weight [BW]) were blocked, distributed into pens of 10 gilts, and pens were allocated to a 2 × 2 factorial arrangement. Factors were: 1) control or TM plus Met, which provided additional 10, 20, and 50 mg/kg of chelated copper, manganese, and zinc, respectively (0.1%, Aplomotec Plus, Tecnología & Vitaminas, S.L.; Alforja, Spain), and a 1.01 Met:Lys ratio and 2) standard Lys was formulated to meet growth requirements or low Lys to 19% below growth requirements. Feeding was provided through two phases, first between 119 and 163 d of age (phase I) and the second between 163 and 209 d of age (phase II). Diets had 2.43 and 2.31 Mcal net energy/kg for phases I and II, respectively, and were offered ad libitum. Low Lys did not affect feed intake but rather reduced average daily gain (ADG) by 6.35% and the final BW by 3.80% compared with standard Lys (P < 0.001). Low Lys reduced ADG (P < 0.001) and gain:feed (P = 0.012) during phase I but not during phase II. Lameness prevalence was 7.92% during rearing and increased with time (P < 0.001). Final BW (151 kg) and ADG (989 g) were similar (P > 0.05) whether gilts displayed lameness or not. Lameness was low in severity and not affected by dietary factors. However, TM- plus Met-fed gilts were 19.2 kg heavier (P = 0.016) than were control at lameness detection. On the sow farm, there was no evidence for differences in lameness or claw lesions among previous dietary treatments. In conclusion, lameness prevalence during the rearing phase was similar, independent of TM plus Met supplement, low Lys, or the interaction. Insufficient reduction of ADG and low severity in lameness may have limited the potential of dietary treatments. Moreover, a greater deficiency of Lys would be needed to achieve the degree of growth reduction previously reported to lessen lameness through feed restriction.

Genetic association between sow longevity and social genetic effects on growth in pigs

Objective

Sow longevity is important for efficient and profitable pig farming. Recently, there has been an increasing interest in social genetic effect (SGE) of pigs on stress-tolerance and behavior. The present study aimed to estimate genetic correlations among average daily gain (ADG), stayability (STAY), and number of piglets born alive at the first parity (NBA1) in Korean Yorkshire pigs, using a model including SGE.

Methods

The phenotypic records of ADG and reproductive traits of 33,120 and 11,654 pigs, respectively, were evaluated. The variances and (co) variances of the studied traits were estimated by a multi-trait animal model applying the Bayesian with linear-threshold models using Gibbs sampling.

Results

The direct and SGEs on ADG had a significantly negative (−0.30) and neutral (0.04) genetic relationship with STAY, respectively. In addition, the genetic correlation between the social effects on ADG and NBA1 tended to be positive (0.27), unlike the direct effects (−0.04). The genetic correlation of the total effect on ADG with that of STAY was negative (−0.23) but non-significant, owing to the social effect.

Conclusion

These results suggested that total genetic effect on growth in the SGE model might reduce the negative effect on sow longevity because of the growth potential of pigs. We recommend including social effects as selection criteria in breeding programs to obtain satisfactory genetic changes in both growth and longevity.

Effects of supplementing organic microminerals and methionine during the rearing phase of replacement gilts on lameness, growth, and body composition

Lameness is a primary reason for culling and mortality within a sow herd. This study evaluated the impact of feeding organic trace minerals and methionine (Met) to growing gilts (134 d) on lameness, performance, body composition and claw health (to first parity), productivity (to second parity), and reproductive performance through 2 parities. Young gilts (28.8 ± 8.8 kg of body weight [BW], n = 360) were BW blocked (10 gilts/pen) and randomly allotted to 1 of 4 dietary treatments: control (CON, basal diet); CON plus organic minerals (MIN, at 10, 20, and 50 mg/kg of Cu, Mn, and Zn, respectively; Aplomotec Plus, Tecnología & Vitaminas, S.L, Alforja, Spain); additional Met (MET, at 102% Met: Lys); and MET plus MIN (MM). Feed was provided ad libitum. Lameness, BW, and body composition were measured 7 times during rearing, at gilt service, day 109 of gestation, and first weaning. Gilts fed the MM diet had lower average daily feed intake (5.1%) and final BW (2.1%) than CON gilts (P < 0.05), whereas MIN and MET were intermediate and not different from each other. Similarly, final backfat (BF) was greatest in CON (P < 0.05), whereas CON and MIN increased final loin depth compared with MM (P < 0.05) with MET not being different. During rearing, 7.7% of all gilts presented lameness, which appeared between 106.8 and 129.7 kg BW confidence interval. Gilts that had been or were lame had reduced BW and average daily gain compared with never lame gilts (P < 0.05). Lameness during rearing was highest (P < 0.01) in gilts fed CON diet (14.8%), with no differences amongst MIN (2.0%), MET (5.3%), or MM (6.5%). In the sow herd, 21% of sows showed lameness and 24% of those were associated with claw lesions. At weaning, gilts fed CON diet had highest (P < 0.01) prevalence of lameness (20.8%) with no differences amongst MIN (6.5%), MET (11.1%), or MM (7.6%). Over the first 2 parities, 27.3% of gilts were culled. On farm, lameness was associated with 0.7 more stillborn piglets (P < 0.10), 1 mm more BF loss in first lactation (P < 0.05), and increased weaning-to-estrus by 3 d (P < 0.05). In conclusion, lameness during rearing was decreased by supplementing organic trace minerals, methionine, and their combination, which also reduced lameness during lactation.

Modeling the Costs of Postpartum Dysgalactia Syndrome and Locomotory Disorders on Sow Productivity and Replacement

Postpartum dysgalactia syndrome (PPDS) and locomotory disorders are common health problems in sows. Previous research suggests that they can cause substantial losses, reduce sow welfare, and result in premature removal of the sow from the herd. However, economic consequences of PPDS and locomotory disorders have not been investigated thoroughly. The goal of this study was to examine economic losses caused by PPDS and locomotory disorders and their impacts on sow longevity. A stochastic dynamic programming model, which maximizes return on sow space unit and assesses sow replacement under several scenarios, was developed. The state variables were litter size, parity number, and sow's health status. The model describes changes in the production parameters such as the number of piglets born and piglet mortality. Herd data originating from commercial sow herds and from a research farm were used to parameterize the model. Sow longevity, health, and economic results are related to each other. Eliminating the risk of PPDS from the model increased the value of sow space unit by €279 when compared to the baseline scenario. Eliminating the risk of locomotory disorders increased value by €110. Results suggest that these estimates correspond to about €29.1 and €11.5 in economic costs per housed sow during her lifetime. The estimated magnitude of losses was €300-€470 per affected sow for PPDS and €290-€330 per affected sow for locomotory disorders. However, realistically speaking, not all of these costs are avoidable. Due to premature replacement associated with these two disorders, the average number of litters that the sow would deliver during her lifetime is decreased by about 0.1-0.4 litters depending on the scenario. We also observed that the optimal lifetime of a sow is not a fixed number, but it depends on her productivity level as well as health status. In general, a healthy sow could stay in the herd until she has produced 6-10 litters. Research is needed to understand the structures and interactions underlying health impairments, performance, replacement policies, and farm economics, and to provide pork producers with management recommendations.

Genome-wide association study for conformation traits in three Danish pig breeds

Background

Selection for sound conformation has been widely used as a primary approach to reduce lameness and leg weakness in pigs. Identification of genomic regions that affect conformation traits would help to improve selection accuracy for these lowly to moderately heritable traits. Our objective was to identify genetic factors that underlie leg and back conformation traits in three Danish pig breeds by performing a genome-wide association study followed by meta-analyses.

Methods

Data on four conformation traits (front leg, back, hind leg and overall conformation) for three Danish pig breeds (23,898 Landrace, 24,130 Yorkshire and 16,524 Duroc pigs) were used for association analyses. Estimated effects of single nucleotide polymorphisms (SNPs) from single-trait association analyses were combined in two meta-analyses: (1) a within-breed meta-analysis for multiple traits to examine if there are pleiotropic genetic variants within a breed; and (2) an across-breed meta-analysis for a single trait to examine if the same quantitative trait loci (QTL) segregate across breeds. SNP annotation was implemented through Sus scrofa Build 10.2 on Ensembl to search for candidate genes.

Results

Among the 14, 12 and 13 QTL that were detected in the single-trait association analyses for the three breeds, the most significant SNPs explained 2, 2.3 and 11.4% of genetic variance for back quality in Landrace, overall conformation in Yorkshire and back quality in Duroc, respectively. Several candidate genes for these QTL were also identified, i.e. LRPPRC, WRAP73, VRTN and PPARD likely control conformation traits through the regulation of bone and muscle development, and IGF2BP2, GH1, CCND2 and MSH2 can have an influence through growth-related processes. Meta-analyses not only confirmed many significant SNPs from single-trait analyses with higher significance levels, but also detected several additional associated SNPs and suggested QTL with possible pleiotropic effects.

Conclusions

Our results imply that conformation traits are complex and may be partly controlled by genes that are involved in bone and skeleton development, muscle and fat metabolism, and growth processes. A reliable list of QTL and candidate genes was provided that can be used in fine-mapping and marker assisted selection to improve conformation traits in pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0289-2) contains supplementary material, which is available to authorized users.

Lameness in piglets - should pain killers be included at treatment?

Background

Joint swelling and lameness are the most obvious and persistent clinical signs of infectious arthritis in piglets. For a positive treatment effect of piglets with arthritis, early initiated treatments with antibiotics are desired. Hitherto pain-reducing drugs have rarely been used within veterinary medicine, but the potential of non steroid anti-inflammatory drugs (NSAID) are interesting from an animal welfare perspective. Therefore, the aim of this study was to compare the long term efficiency of treating lameness with and without pain relief. Further, the incidences of affected joints in lame piglets were analysed.

Results

In total 415 of the 6,787 liveborn piglets included in the study were diagnosed with lameness (6.1 %). Around 86 % of these diagnoses took place during the first 3 weeks of life. There was no difference in the incidence of lameness between the sexes, but lameness was most commonly diagnosed in the offspring to old sows (>4 parturitions). Lameness was diagnosed in about every second litter and on average about two pigs were diagnosed in the affected litters. The incidence of affected litters as well as affected piglets increased with ageing of the sows.

Treatments with antibiotics solely and in combination with NSAID improved (P < 0.01 to 0.001) the clinical status from day to day, but the clinical response did not differ between the two treatment groups.

Piglets that remained healthy were 1.1 and 1.7 kg heavier (P < 0.001) than piglets diagnosed with lameness at 5 and 9 weeks of age, respectively. There were no differences in piglet body weights between the treatment strategies at any time.

Conclusions

The clinical response to penicillin was good. It was neither improved nor reduced by a concurrent administration of NSAIDs. Nevertheless NSAIDs may improve the animal welfare due to pain relief. An important finding of this study was that decreasing pain due to lameness not was negative in a long term perspective, i.e. reducing pain did not lead to overstrain of affected joints and no clinical signs of adverse effects were noted. Therefore the use of NSAIDs ought to be considered to improve the animal welfare, at least in severe cases.