Maternal and direct genetic parameters for tail length, tail lesions, and growth traits in pigs

Effects of the Prenatal Maternal Health Status on Calf Disease Prevalences and Respective Genetic Parameter Estimates in German Holstein Cattle

The aim of the present study was to infer phenotypic responses and genetic parameters of the F1 calf diseases diarrhoea (DIAR) and pneumonia (PNEU) in dependency of the prenatal maternal health status (PMHS) of the dam and of the herd-calving year. The PMHS considered diagnoses for the cow disease mastitis (MAST) and claw disorders (CD) during gestation of F0 dams. Furthermore, 305-d milk production traits of F1 offspring from either healthy or diseased dam groups were compared. The study comprised 20,045 female calves (F1 = generation 1) and their corresponding dams (F0 = parental generation 0), kept in 41 large-scale herds. All F1 calves were from their dams' 2nd parity, implying that all dam (maternal) diseases were recorded during the first lactation and dry period of the dams. The F1 calves were phenotyped for DIAR up to 30 days post-partum, and for PNEU up to 180 days of age. At least one entry for the respective disease implied a score = 1 = sick, otherwise, a score = 0 = healthy, was assigned. Production records of the 10,129 F1 cows comprised 305-d records in first lactation for milk yield (MY), protein yield (PY) and fat yield (FY). Linear and generalised linear mixed models were applied to infer phenotypic responses of F1 traits in dependency of the PMHS for CD and MAST. A diagnosis for MAST or CD in F0 cows during gestation was significantly (p ≤ 0.05) associated with an increased prevalence for DIAR and PNEU, with pairwise differences of least-squares-means between calves from healthy and diseased cow groups up to 3.61%. The effects of PMHS on 305-d production traits in offspring were non-significant (p > 0.05). In bivariate genetic analyses, DIAR and PNEU were defined as different traits according to the PMHS, i.e., DIAR-MASThealthy and DIAR-MASTdiseased, DIAR-CDhealthy and DIAR-CDdiseased, PNEU-MASThealthy and PNEU-MASTdiseased, and PNEU-CDhealthy and PNEU-CDdiseased. The direct heritabilities for DIAR and PNEU were quite similar in the healthy and respective diseased dam group. Slightly larger direct heritabilities in the diseased dam groups were due to increased genetic variances. Maternal heritabilities were quite stable and smaller than the direct heritabilities. In random regression models, genetic parameters for DIAR and PNEU were estimated along the continuous herd-calving-year prevalence scale, considering a prevalence for MAST and CD (based on the 20,045 dam records plus 16,193 herd contemporary records) in the range from 0% to 30%. Direct heritabilities for PNEU were quite stable along the herd-calving-year gradient for MAST and CD. For DIAR, we observed stronger estimate fluctuations, especially increasing direct heritabilities in dependency of the herd-calving-year prevalence for MAST from 0.13 (at a MAST prevalence of 0%) to 0.30 (at a MAST prevalence of 30%). Consequently, obvious genotype x herd-calving-year PMHS interactions were observed for DIAR on the prenatal MAST scale, with a minimal correlation of 0.48 between direct genetic effects at 0% MAST prevalence and at 30% MAST prevalence. The correlations between direct genetic and maternal genetic effects were antagonistic at all herd-calving-year prevalence levels, displaying strongest fluctuations for "DIAR-MAST." The genotype x herd-calving-year PMHS interactions for DIAR suggest consideration of specific sires according to the herd health status for CD and for MAST.

Evaluating slaughterhouse findings for lung and tail lesions in fattening pigs from secondary data

Using slaughterhouse findings to monitor animal health and welfare is not a new idea. The German Federal Veterinary Surgeon's Association even calls for the establishment of an animal health database that combines slaughterhouse findings with health and farm data from already existing monitoring programs to create a comprehensive monitoring and surveillance tool. In an attempt to combine secondary health data from slaughterhouse findings, antibiotic use monitoring as well as biosecurity and husbandry evaluations into an integrated dataset, data from 18,593 fattening pig farms across Germany participating in the private sector Quality scheme for food (from 2018 to 2020) were harmonized at the half-year level and combined. As an example, the combined data was used to evaluate lung and tail lesion findings from abattoirs as indicators of animal health and welfare with descriptive analysis and mixed model approaches. Differences between abattoirs due to different data collection methods were taken into account by either considering the abattoir as a random effect or standardizing the prevalence data using abattoir means. The mean prevalence of lung lesions per half-year varied between 8.69 % and 9.78 %. The mean prevalence of tail lesion increased continuously from 0.65 % in the first half of 2018-1.04 % in the second half of 2020. Farm size, agricultural region, half-year and antibiotic treatment frequency were found to be associated (p < 0.000001) with the prevalence of both lung and tail lesions. A lack of variance and specificity of the secondary biosecurity and husbandry evaluation data restricts the use of individual assessment criteria as well as biosecurity and husbandry indices (calculated from a subset of assessment criteria) in our analyses. We therefore used the data for a broad categorization of farms and it could be found, that the occurrence of a lower rating in any assessment criteria during farm evaluations is associated (p < 0.000001) with a higher prevalence of lung and tail lesions, but the interpretation remains uncertain. The already existing data in the fattening pig sector can be used for the evaluation of animal health and welfare indicators to a large extent. Nonetheless, missing information, differences and changes (over time) in data collection methods introduce biases into the dataset. By improving the data quality and harmonizing collection methods, secondary animal health data could prove to be a useful tool in promoting animal health and welfare.

Pig tail length is associated with the prevalence of tail malformations but not with inflammation of the tail

BACKGROUND

Assuming that tail length is associated with the prevalence of tail biting, attempts are being made to shorten tails by genetic selection in order to avoid the painful procedure of docking. However, undesirable side effects such as kinky tails and inflammatory changes may occur. The aim of the present study was to clinically quantify in a population with known segregation of tail length, i) its variability, ii) possible associations with kinked tails and iii) possible associations of tail length and kinks with inflammation of the tail using 348 piglets at day 3 (undocked) and 39 (docked tails) of life.

RESULTS

The relative tail length (tail tip to tail base/tail tip to ear base × 100) varied between 20.3 and 31.3%. A reduced tail length was associated with kinked tails. Piglets with the shortest tails had 28% kinked tails, 5.6 times more than the piglets with the longest tails. The tails showed high prevalence of inflammation both on day 3 and on the docked tails on day 39. Overall, these were not associated with tail length or kinked tails. Only necrosis of the tail was significantly more frequent in the kinked tails than in the normal tails. Sow line, sow ID and boar ID significantly affected relative tail length, which may suggest a genetic cause.

CONCLUSION

Based on the phenotypic variation found in the present study, it seems possible to influence tail length through breeding. It remains to be seen whether the available potential is sufficient to actually reduce tail biting. At the same time, a higher incidence of kinked tails and necrosis is to be expected.

Genome-Wide Association Study Reveals Single Nucleotide Polymorphisms Associated with Tail Length and Tail Kinks in Piglets

Tail docking is still used in pigs to reduce the prevalence of tail biting, although it is purely symptomatic and contrary to animal welfare. Genetic selection for shorter tails might, however, help to avoid tail docking and has therefore been proposed. A genetic basis for tail length is known for many species. Variability in tail length, including moderate heritability, has also been demonstrated in pigs. The aim of the present study was to identify genetic markers for tail length and to define candidate genes. To this end, 140 piglets were phenotyped and genotyped at 3 days of age and a genome-wide association study was performed. Seven SNPs were mapped on chromosomes 1, 2, 6, 11, and 15. Two linked SNPs on chromosome 2 resulted in a functional amino acid exchange. The genotypes at the SNPs were only associated with small differences in relative tail length of up to 16.5% (short genotype versus long genotype at SSC15), but at the same time with the occurrence of malformations in the form of tail kinks. The small effect size and the association between tail length and tail kinks, together with the generally pure symptomatic effect on tail biting, argue against the applicability of selection for shorter tails in pigs.

Genetic parameter estimation for pork production and litter performance traits of Landrace, Large White, and Duroc pigs in Japan

We estimated genetic parameters for two pork production and six litter performance traits of Landrace, Large White, and Duroc pigs reared in Japan. Pork production traits were average daily gain from birth to end of performance testing and backfat thickness at end of testing (46,042 records for Landrace, 40,467 records for Large White, and 42,920 records for Duroc). Litter performance traits were number born alive, litter size at weaning (LSW), number of piglets dead during suckling (ND), survival rate of piglets during suckling (SV), total piglet weight at weaning (TWW), and average piglet weight at weaning (AWW) (27,410, 26,716, and 12,430 records for Landrace, Large White, and Duroc, respectively). ND was calculated as the difference between LSW and litter size at start of suckling (LSS). SV was calculated as LSW/LSS. AWW was calculated as TWW/LSW. Pedigree data for Landrace, Large White, and Duroc breeds contained 50,193, 44,077, and 45,336 pigs, respectively. Trait heritability was estimated via single-trait analysis and genetic correlation between two traits was estimated via two-trait analysis. When considering the linear covariate of LSS in the statistical model for LSW and TWW, for all breeds, the heritability was estimated to be 0.4-0.5 for pork production traits and below 0.2 for litter performance traits. Estimated genetic correlation between average daily gain and backfat thickness was small, ranging from 0.057 to 0.112, and those between pork production traits and litter performance traits were negligible to moderate, ranging from -0.493 to 0.487. A wide range of genetic correlation values among the litter performance traits was estimated, while that between LSW and ND could not be obtained. The results of genetic parameter estimation were affected by whether the linear covariate of LSS was included in the statistical model for LSW and TWW or not. This finding implies the necessity of carefully interpreting the results according to the choice of statistical model. Our results could give fundamental information on simultaneously improving productivity and female reproductivity for pigs.

Multiple-trait and structural equation modelling approaches to infer genetic relationships between tail length and weight traits in Merinoland sheep

Tail docking is routinely conducted in long-tailed sheep breeds to prevent flystrike infections, but it is not in agreement with legal guidelines and animal welfare issues. Selection on short tails is a sustainable alternative in this regard, but side effects on other breeding goal traits are unclear. In consequence, the present study aimed to estimate genetic parameters for tail length (TL) at birth, birth weight (BW), weaning weight (WW) and postweaning weight (PWW) at the slaughtering date considering single-trait (STM), multiple-trait (MTM) and structural equation models (SEM) with different random effects, and accordingly, different covariance structures. The SEM considered time-lagged recursive relationships among response variables in three different pathways. The first path pertained to the effect of TL on WW and of WW on PWW. The second path reflected the effect of BW on WW and of WW on PWW. The third path was the recursive effect of TL on PWW. The phenotypic data consisted of 2803 records for TL, 13,042 records for BW, 1556 records for WW and 3986 records for PWW from Merinoland lambs. Lambs were born in the period from 1995 to 2021 and kept at the university Gießen research station, Germany, with their naturally long tails. Genetic statistical model evaluation based on Bayesian and Akaike's information criteria suggested models simultaneously considering direct genetic, maternal genetic and maternal permanent environmental effects and respective covariances. For statistical models including the same random effects and covariance structures, SEM were superior over MTM. The direct heritability for TL from the best-fitting STM was 0.60 ± 0.08, indicating the potential for genetic reduction of tail length within a few generations. For growth traits, the direct heritabilities ranged from 0.16 ± 0.03 for BW to 0.31 ± 0.09 for PWW. The maternal heritabilities were 0.03 ± 0.03 for TL, 0.12 ± 0.02 for BW, 0.04 ± 0.03 for WW and 0.07 ± 0.03 for PWW, reflecting small, but the non-significant influence of uterine characteristics on the tail development. The direct genetic correlations between TL and all weight traits were positive and very similar to MTM and SEM but reflected antagonistic genetic relationships from a breeding perspective. Oppositely, the structural equation coefficients reflecting trait associations phenotypically were negative (favourable) for the time-lagged effects of TL on WW and on PWW. As an explanation, lambs with long and woolly tails have an increased risk for contamination with dirt and dust causing infections, which in turn impairs the body weight development. In conclusion, breeding on short tails should consider trait-associated environmental risk factors, for example, disease susceptibility, which can be mimicked via SEM approaches.

Genetic parameters for linear conformation, stayability, performance and reproduction traits in German local Swabian-Hall landrace sows

Improvements of longevity in sows are of overriding importance from an animal welfare as well as from an economic perspective, also in the local Swabian-Hall Landrace (SHL) breed. Consequently, the aim of the present study was a detailed assessment of linear conformation traits in the context of early predictions of sow stayability and to infer genetic (co)variance components between conformation traits with reproduction and performance traits. In this regard, we implemented a linear 9-point scoring system for conformation traits reflecting the body morphology and feet and leg characteristics in gilts. Linear conformation trait scoring included body length (BLEN), body height (BHEI), hind leg angularity (HLANG), hind leg pastern (HLPAS), hind cannon bone strength (HCBS), hind leg position (HLPOS), front leg position (FLPOS), claw length (CLEN) and muscling (MUSC) from 6042 SHL gilts before first insemination at the age of 180-200 days. For the same gilts, performance traits included average daily gain (ADG) and back fat thickness (BF) measured via ultrasound, reproduction traits included the number of piglets born alive (NBA) and the number of piglets weaned (NWEAN), and stayability was a binary trait reflecting sow survival after parity 2 (STAY_12), 3 (STAY_13) and 4 (STAY_14). For the estimation of variance components and heritabilities, single-trait linear animal models were defined for conformation, performance and reproduction traits, and single-trait generalized linear mixed models with a logit link function for binary stayability traits. Genetic covariances and correlations were inferred in series of bivariate runs for all combinations of conformation and remaining traits. The distribution of the assigned conformation scores reflected a Gaussian distribution, but a large fraction of records was assigned to the intermediate score classes 4, 5 and 6. Accordingly, the restricted utilization of the 9-point scale might explain the small genetic variances and small heritabilities for feet and leg traits in the range from 0.06 to 0.17. Heritabilities were larger for the linear traits reflecting body morphology, i.e., for BLEN (0.21) and BHEI (0.20). For conformation traits, the common litter environment explained up to 17% of the phenotypic trait variation. Genetic and especially phenotypic correlations between linear conformation traits with the reproduction traits NBA and NWEAN were close to zero. Heritabilities for STAY_12, STAY_13 and STAY_14 were 0.08, 0.07 and 0.05, respectively. Moderate genetic relationships were estimated between STAY_14 with some conformation traits. Especially high scores for BHEI and BLEN (i.e., long and large gilts) implied a decline in STAY_14 genetically (r_g  = -0.24 and -0.53, respectively). Moderate genetic correlations were estimated between HLANG with STAY_14 (0.28), and between HCBS with STAY_12 (0.23). For most of the conformation traits with intermediate optimum, genetic correlations with STAY were close to zero, indicating improved longevity for gilts representing the population average with scores 4, 5 or 6, and suggesting the development of appropriate selection indices in this regard.

Estimation of direct and maternal genetic effects and annotation of potential candidate genes for weight and meat quality traits in a genotyped outdoor dual-purpose cattle breed

With regard to potential applications of genomic selection in small numbered breeds, we evaluated genomic models and focused on potential candidate gene annotations for weight and meat quality traits in the local Rotes Höhenvieh (RHV) breed. Traits included 6,003 birth weights (BWT), 5,719 200 d-weights (200dw), 4,594 365 d-weights (365dw), and 547 records for intramuscular fat content (IMF). A total of 581,304 SNP from 370 genotyped cattle with phenotypic records were included in genomic analyses. Model evaluations focused on single- and multiple-trait models with direct and with direct and maternal genetic effects. Genetic relationship matrices were based on pedigree (A-matrix), SNP markers (G-matrix), or both (H-matrix). Genome-wide association studies (GWASs) were carried out using linear mixed models to identify potential candidate genes for the traits of interest. De-regressed proofs (DRP) for direct and maternal genetic components were used as pseudo-phenotypes in the GWAS. Accuracies of direct breeding values were higher from models based on G or on H compared to A. Highest accuracies (> 0.89) were obtained for IMF with multiple-trait models using the G-matrix. Direct heritabilities with maternal genetic effects ranged from 0.62 to 0.66 for BWT, from 0.45 to 0.55 for 200dW, from 0.40 to 0.44 for 365dW, and from 0.48 to 0.75 for IMF. Maternal heritabilities for BWT, 200dW, and 365dW were in a narrow range from 0.21 to 0.24, 0.24 to 0.27, and 0.21 to 0.25, respectively, and from 0.25 to 0.65 for IMF. Direct genetic correlations among body weight traits were positive and favorable, and very similar from different models but showed a stronger variation with 0.31 (A), −0.13 (G), and 0.45 (H) between BWT and IMF. In gene annotations, we identified 6, 3, 1, and 6 potential candidate genes for direct genetic effect on BWT, 200dW, 365dW, and IMF traits, respectively. Regarding maternal genetic effects, four (SHROOM3, ZNF609, PECAM1, and TEX2) and two (TMEM182 and SEC11A) genes were detected as potential candidate genes for BWT and 365dW, respectively. Potential candidate genes for maternal effect on IMF were GRHL2, FGA, FGB, and CTNNA3. As the most important finding from a practical breeding perspective, a small number of genotyped RHV cattle enabled accurate breeding values for high heritability IMF.