Estimation of genetic parameters for birth weight, preweaning mortality, and hot carcass weight of crossbred pigs

Genetic evaluation for production and body size traits using different animal models in purebred-Duroc pigs

Duroc pigs are popular crossbred terminal sires, and accurate assessment of genetic parameters in the population can help to rationalize breeding programmes. The principle aim of this study were to evaluate the genetic parameters of production (birth weight, BW; age at 115 kg, AGE; feed conversion ratio, FCR) and body size (body length, BL; body height, BH; front cannon circumference, FCC) traits of Duroc pigs. The second objective was to analyze the fit of different genetic assessment models. The variance components and correlations of BW (28,348 records), AGE (28,335 records), FCR (11,135 records), BL (31,544 records), BH (21,862 records), and FCC (14,684 records) traits were calculated by using DMU and AIREMLF90 from BLUPF90 package. In the common environment model, the heritability of BW, AGE, FCR, BL, BH, and FCC traits were 0.17 ± 0.014, 0.30 ± 0.019, 0.28 ± 0.024, 0.16 ± 0.013, 0.14 ± 0.017, and 0.081 ± 0.016, with common litter effect values of 0.25, 0.20, 0.18, 0.23, 0.19, and 0.16, respectively. According to the results of the Akaike information criterion (AIC) calculations, models with smaller AIC values have a better fit. We found that the common environment model with litter effects as random effects for estimating genetic parameters had a better fit. In this Model, the estimated genetic correlations between AGE with BW, FCR, BL, BH, and FCC traits were -0.28 (0.040), 0.76 (0.038), -0.71 (0.036), -0.44 (0.060), and -0.60 (0.073), respectively, with phenotypic correlations of -0.17, 0.52, -0.22, -0.13 and -0.24, respectively. In our analysis of genetic trends for six traits in the Duroc population from 2012 to 2021, we observed significant genetic trends for AGE, BL, and BH. Particularly noteworthy is the rapid decline in the genetic trend for AGE, indicating an enhancement in the pig's growth rate through selective breeding. Therefore, we believe that some challenging-to-select traits can benefit from the genetic correlations between traits. By selecting easily measurable traits, they can gain from synergistic selection effects, leading to genetic progress. Conducting population genetic parameter analysis can assist us in devising breeding strategies.

Bayesian analysis reveals the influence of maternal effect on pre-weaning body weights in Landlly piglets

The present study was undertaken to estimate the (co)variance components and genetic parameters of body weights recorded in Landlly piglets from birth to weaning at weekly intervals (w0 to w6). The data pertained to body weights of 2462 piglets, born to 91 sires and 159 dams across different generations during a 7-year period from 2014 to 2020. Five animal models (I-V), differentiated by inclusion or exclusion of maternal effects with or without covariance between maternal and direct genetic effects, were fitted on the data using the Bayesian algorithm. The analyses were implemented by Gibbs sampling in the BLUPF90 program and Markov chain Monte Carlo (MCMC) methodology was used to draw samples of posterior distribution pertaining to (co)variance components. Based on deviance information criteria (DIC), model V with inclusion of direct additive genetic, direct maternal genetic and permanent environmental effect of dam as random factors along with covariance between direct additive and maternal effects best fitted the data on pre-weaning traits (w0 to w5). Whereas, model I incorporating only the direct additive genetic effect best fitted the weaning weight (w6) data in Landlly piglets. The posterior mean estimates of direct heritability under the best models for W0 to W6 were 0.13, 0.19, 0.29, 0.13, 0.26, 0.32 and 0.46, respectively. Inclusion of the maternal component helped in better partitioning of variance for different body weights in Landlly piglets. The maternal heritability ranged from 0.06 to 0.14, while the litter heritability ranged from 0.11 to 0.15 for pre-weaning weights (W0 to W5) under the best-fit models. The influence of maternal environment was greater than maternal genetic effect from birth to 4th week of age. The results implied that variations in body weight of Landlly pigs were genetically controlled to moderate levels (especially w2 and w4) with contributions from direct additive and maternal genotype that can be exploited by designing efficient breeding programmes.

Five risk factors and their interactions of probability for a sow in breeding herds having a piglet death during days 0-1, 2-8 and 9-28 days of lactation

Background

Increasing preweaning piglet mortality is a concern for veterinarians and producers in relation to sow performance and piglet welfare. Our objectives were (1) to characterize pre-weaning piglet mortality risk for sows (PWM) during early (0–1 days), mid- (2–8 days) and late (9–28 days) lactation and (2) to quantify the following five factors and their interactions, parity, number of piglets born alive (PBA), number of stillborn piglets (SB), gestation length (GL) and season for PWM during the three lactation phases.

Methods

Data obtained from 264,333 parity records of 55,635 sows farrowed in 2015 and 2016 from 74 Spanish herds. Three multi-level mixed-effects logistic regression models were separately applied for PWM during three lactation phases, which was analyzed as whether or not a sow had a piglet death (i.e. probability of a sow having a piglet death) in each phase.

Results

PWM during early, mid- and late lactation were 36.9, 27.0 and 15.4%, respectively. As PBA increased from 11 or less to 16 or more pigs, PWM during early and mid-lactation increased by 15.8 and 6.0%, respectively, but there was no increase during late lactation. Also, as GL decreased from 117–120 to 110–113 days, PWM during early, mid- and late lactation increased by 7.5, 6.8 and 1.5%, respectively. Additionally, PWM during the respective lactation phases increased by 8.3, 5.2 and 1.0%, as SB increased from 0 to 3 or more pigs. During early lactation, parity 1 sows had 2.1% lower PWM than parity 5 or higher sows, but during mid- and late lactation they had 4.2% higher PWM (P < 0.05). However, there was no difference between summer and winter for PWM during early lactation (P = 0.26).

Conclusion

Management practices to reduce PWM need to take account of these factors, and be modified for different phases. For example, during early lactation special care should be given to piglets born to parity 5 or higher sows farrowing 16 or more PBA, having 3 or more SB or GL 110–113 days, whereas during mid- and late lactation more care should be given to piglets born to parity 1 sows with the same PBA, GL and SB conditions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40813-021-00231-0.

A 10-year trend in piglet pre-weaning mortality in breeding herds associated with sow herd size and number of piglets born alive

BACKGROUND

Piglet pre-weaning mortality (PWM) is one of the biggest problems regarding sow performance and piglet welfare. Recently, PWM has increased in some countries, but it is not known if there are similar increases in other countries, nor whether increased PWM is related to either increased numbers of piglets born alive (PBA) or to sow herd size. So, the objectives of the present study were 1) to explore the trend in PWM in Spanish sow herds over a recent 10-year period, along with related measurements such as PBA, stillborn piglets, herd productivity and herd size; and 2) to examine the relationships between PWM and the related measurements.

METHODS

Herd-level annual data from 2007 to 2016 for 91 herds in Spain were abstracted from a sow database compiled by a veterinary consultancy firm that asked client producers to mail data files on a regular basis. The database software automatically calculated herd-level PWM (%) as follows: the total number of piglets born alive to a sow completely weaned during a year (TPBA) minus the total number of piglets weaned by the completely weaned sow during the year divided by TPBA × 100. All the statistical analyses were performed by using SAS University Edition. A growth curve model was applied to incorporate correlations for all of the observations arising from the same farm.

RESULTS

Over the 10 years, herd means of PWM (standard deviation) increased from 11.9 (4.1) % to 14.4 (3.2) %, and mean PBA increased by 1.9 pigs. Mean age of piglet death during lactation increased by 3.8 days, and later years were significantly associated with herd size and the number of piglets weaned per sow per year (PSY; P <  0.05). Higher PWM was associated with more PBA, more stillborn piglets and small-to-mid herds (lower than the median size: < 570 sows; P <  0.05). Also, there was a significant interaction between the herd size groups and PBA for PWM (P <  0.05): as PBA increased from 9 to 14 pigs, PWM increased by 9.6% in small-to-mid herds, compared with an increase of only 6.6% in large herds (> 570 sows). Furthermore, as PWM decreased from 18 to 8%, herd productivity measured as PSY increased by 2.2 pigs in large herds, compared with only 0.6 pigs in small-to-mid herds.

CONCLUSION

Large herds were better than small-to-mid herds at alleviating the association between increased PBA and increased PWM. Also, the relationship between decreased PWM and increased herd productivity was improved more in large herds than in small-to-mid herds.

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

Tail length and tail lesions are the major triggers for tail biting in pigs. Against this background, 2 datasets were analyzed to estimate genetic parameters for tail characteristics and growth traits. Dataset 1 considered measurements for trait tail length (T-LEN) and for the growth traits birth weight (BW), weaning weight (WW), postweaning weight (PWW), and average daily gain (ADG) from 9,348 piglets. Piglets were born in the period from 2015 to 2018 and kept on the university Gießen research station. Dataset 2 included 4,943 binary observations from 1,648 pigs from the birth years 2016 to 2019 for tail lesions (T-LES) as indicators for nail necrosis, tail abnormalities, or tail biting. T-LES were recorded at 30 ± 7 d after entry for rearing (T-Les-1), at 50 ± 7 d after entry for rearing (end of the rearing period, T-LES-2), and 130 ± 20 d after entry for rearing (end of fattening period, T-LES-3). Genetic statistical model evaluation for dataset 1 based on Akaike's information criterion and likelihood ration tests suggested multiple-trait animal models considering covariances between direct and maternal genetic effects. The direct heritability for T-LEN was 0.42 (±0.03), indicating the potential for genetic selection on short tails. The maternal genetic heritability for T-LEN was 0.05 (±0.04), indicating the influence of uterine characteristics on morphological traits. The negative correlation between direct and maternal effects for T-LEN of -0.35 (±0.13), as well as the antagonistic relationships (i.e., positive direct genetic correlations in the range from 0.03 to 0.40) between T-LEN with the growth traits BW, WW, PWW, and ADG, complicate selection strategies and breeding goal definitions. The correlations between direct effects for T-LEN and maternal effects for breeding goal traits, and vice versa, were positive but associated with a quite large SE. The heritability for T-LES when considering the 3 repeated measurements was 0.23 (±0.04) from the linear (repeatability of 0.30) and 0.21 (±0.06; repeatability of 0.29) from the threshold model. The breeding value correlations between T-LES-3 with breeding values from the repeatability models were quite large (0.74 to 0.90), suggesting trait lesion recording at the end of the rearing period. To understand all genetic mechanisms in detail, ongoing studies are focusing on association analyses between T-LEN and T-LES, and the identification of tail biting from an actor's perspective.

Effects of sire line, birth weight and sex on growth performance and carcass traits of crossbred pigs under standardized environmental conditions

A variety of available terminal sire lines makes the choice of terminal sire line complex for the pig producer. Higher birth weights are important for subsequent growth performance and selection for this trait is also necessary in sire lines. The aim was to investigate the effect of sire line, birth weight and gender on growth performance, carcass traits and meat quality. In total 3844 crossbred pigs from Camborough Pig Improvement Company (PIC) dams matched with either a Synthetic (A) or Piétrain (B) sire line were used. Pigs from line A grew faster (p<0.01), showed higher feed intake (p<0.01) and reached a higher final body weight (p≤0.01), but they had a similar efficiency (p=0.179). Leaner carcasses and heavier primal cuts (p<0.001) were observed in pigs from line B. Carcasses from pigs sired by line A had higher meat quality (p<0.001). Males had a higher growth rate (p≤0.05) but had a poorer feed efficiency (p<0.01). Heavier birth weight pigs and females had leaner, higher value carcasses with heavier primal cuts (p<0.001) compared to middle and low birth weight females or males. Sire line by sex interactions was significant for growth (p≤0.05) and carcass traits (p<0.001). Interaction between sire line and birth weight classes were only detected for loin depth (p<0.01). Line A is preferable if the numbers of fatting pigs per fattening place and year should be improved, and line B is an option to increase leanness and carcass primal cuts.

Postweaning mortality in commercial swine production. I: review of non-infectious contributing factors

Postweaning mortality is a complex causal matrix involving animal, environment, and infectious etiologic factors. Despite advances in swine productivity such as total pigs born, growth rate, feed intake, and efficiency, there have been modest to no improvements in postweaning mortality rates over the last several years. Industry averages for postweaning mortality range from four to eight percent for each the nursery, grow-finish, or wean-finish stages. Retrospective mortality causal analyses of individual databases have been performed. However, little information derived from meta-analysis, systematic review, or comprehensive literature reviews are available. In order to develop and evaluate strategies to comprehensively manage and reduce postweaning mortality, addressing the complexity and range of impact that factors have on mortality is necessary to identify and prioritize such contributing factors. Our objective is to describe the current state of knowledge regarding non-infectious causes of postweaning mortality, focusing on estimates of frequency and magnitude of effect where available. Postweaning mortality can be generalized into non-infectious and infectious causes, with non-infectious factors further classified into anatomic abnormalities, toxicity, animal factors, facility factors, nutritional inadequacies, season, and management factors. Important non-infectious factors that have been identified through review of literature include birth weight, pre-weaning management, weaning age and weight, and season. Additionally, reasons for mortality with a low incidence but a high magnitude include abdominal organ torsion/volvulus, sodium ion or ionophore toxicosis, or dietary imbalance due to feed formulation or manufacture error. Many interactive effects are present between and among infectious and non-infectious factors, but an important trend is the impact that non-infectious factors have on the incidence, severity, and resolution of infectious disease. Strategies to reduce postweaning mortality must consider the dynamic, complex state that forms the causal web. Control of postweaning mortality through understanding of the complexity, evaluation of mortality reduction strategies through rigorous scientific evaluation, and implementation remains an area of opportunity for continued growth and development in the global swine industry.

Genome-Wide Association Study and Fine Mapping Reveals Candidate Genes for Birth Weight of Yorkshire and Landrace Pigs

Birth weight of pigs is an important economic factor in the livestock industry. The identification of the genes and variants that underlie birth weight is of great importance. In this study, we integrated two genotyping methods, single nucleotide polymorphism (SNP) chip analysis and restriction site associated DNA sequencing (RAD-seq) to genotype genome-wide SNPs. In total, 45,175 and 139,634 SNPs were detected with the SNP chip and RAD-seq, respectively. The genome-wide association study (GWAS) of the combined SNP panels identified two significant loci located at chr1: 97,745,041 and chr4: 112,031,589, that explained 6.36% and 4.25% of the phenotypic variance respectively. To reduce interval containing causal variants, we imputed sequence-level SNPs in the GWAS identified regions and fine-mapped the causative variants into two narrower genomic intervals: a ∼100 kb interval containing 71 SNPs and a broader ∼870 kb interval with 432 SNPs. This fine-mapping highlighted four promising candidate genes, SKOR2, SMAD2, VAV3, and NTNG1. Additionally, the functional genes, SLC25A24, PRMT6 and STXBP3, are also located near the fine-mapping region. These results suggest that these candidate genes may have contribute substantially to the birth weight of pigs.

Genetic evaluation including maternal effects in Large White Yorkshire × desi crossbred pigs under hot and humid conditions of India

A study was conducted to evaluate the individual and sow performance traits of Large White Yorkshire × desi crossbred pigs at All India Co-ordinated Research Project on Pigs (AICRP), Kattupakkam. The genetic groups studied were 50% LWY (100% LWY × 100% desi), 50% LWY inter se (50% LWY 50% desi × 50% LWY 50% desi), 75% LWY (100% LWY × 50% LWY 50% desi) and 75% LWY inter se (75% LWY 25% desi × 75% LWY 25% desi). The (co)variance components for different traits were estimated by restricted maximum likelihood method (REML). The average inbreeding in the whole population was 5.4%. Maternal genetic and common litter effects were important random sources of variation in individual traits. The least-squares mean for birth weight (BW), weaning weight (WW), average daily gain up to weaning (ADG), market weight (MW), pre-weaning mortality (PWM), age at first farrowing (AFF), litter size at birth (LSAB), litter weight at birth (LWAB), litter size at weaning (LSAW), litter weight at weaning (LWAW) and farrowing interval (FI) were 1.079 kg, 7.906 kg, 142.238 g, 8.4%, 62.208 kg, 456.829 days, 197.994 days, 6.792, 8.174 kg, 6.347 and 60.649 kg, respectively, and the direct heritability obtained through the best model were 0.069, 0.015, 0.012, 0.031, 0.291, 0.019, 0.173, 0.257, 0.076 and 0.157, respectively. The repeatability estimates for LWAB, LSAW, LWAW and FI were 0.265, 0.258, 0.263 and 0.762, respectively. The 75% LWY were better in terms of production and reproduction traits and the high heritability for litter traits provided good scope for improvement.

Estimation of direct and maternal genetic parameters for individual birth weight, weaning weight, and probe weight in Yorkshire and Landrace pigs

As a result of selecting for increased litter size, newborn piglets are being born lighter and have a lower chance of survival. Raising fewer pigs to market weight would have a negative impact on the industry and farmer profitability; thus, understanding the genetics of individual growth performance traits will determine whether these traits will play an important role in pig breeding schemes. This study aimed to estimate genetic parameters for individual birth weight (BW), weaning weight (WW), and probe weight (PW) in Canadian-purebred Yorkshire and Landrace pigs. PW is a live weight taken at the time of the ultrasound measurements, when pigs weigh about 100 kg. Data were collected from 2 large and related breeding herds from 2003 to 2015. Four linear animal models were used, which included the following: Model 1-direct additive genetic effect; Model 2-direct additive genetic and maternal genetic effect; Model 3-direct additive genetic and common litter effect; and Model 4-direct additive genetic, maternal genetic, and common litter effect. The model which included all 3 random effects (Model 4) was determined to be the best fit to the data. Low to moderate direct heritability estimates were observed as follows: 0.15 ± 0.03 for BW, 0.04 ± 0.01 for WW, and 0.33 ± 0.03 for PW for the Yorkshire breed; and 0.05 ± 0.01 for BW, 0.01 ± 0.01 for WW, and 0.27 ± 0.03 for PW in the Landrace breed. As expected, the direct heritability estimates increased with age as a result of decreased maternal influence on the trait. Bivariate animal models were also used to estimate genetic and environmental correlations between traits. Strong direct genetic correlations were observed between BW and WW in both breeds. Based on the estimates of genetic parameters, individual BW could be evaluated and considered in breeding programs aiming to increase BW and improve subsequent performance. Different selection emphasis could also be applied on direct and maternal additive genetic effects on BW to optimize the breeding programs and improve selection efficiency.