Between-breed variability of stillbirth and its relationship with sow and piglet characteristics L. Canario,*1 E. Cantoni,† E. Le Bihan,‡ J. C. Caritez,* Y. Billon,* J. P. Bidanel,* and J. L. Foulley* *Unit of Applied and Quantitative Genetics, INRA, 78352 Jouy-en-Josas, France; †University of Geneva, Department of Econometrics, 1211 Geneva, Switzerland; ‡University of Luxembourg FLSHASE, 7201 Walferdange, Luxembourg; and *Genetics and Animal Production Experimental Unit, INRA, 17700 Surgères, France ABSTRACT: Litter characteristics at birth were recorded in 4 genetic types of sows with differing maternal abilities. Eighty-two litters from F1 Duroc × Large White sows, 651 litters from Large White sows, 63 litters from Meishan sows, and 173 litters from Laconie sows were considered. Statistical models included random effects of sow, litter, or both; fixed effects of sow genetic type, parity, birth assistance, and piglet sex, as well as gestation length, farrowing duration, piglet birth weight, and litter size as linear covariates. The quadratic components of the last 2 factors were also considered. For statistical analyses, GLM were first considered, assuming a binomial distribution of stillbirth. Hierarchical models were also fitted to the data to take into account correlations among piglets from the same litter. Model selection was performed based on deviance and deviance information criterion. Finally, standard and robust generalized estimating equations (GEE) procedures were applied to quantify the importance of each effect on a piglet’s probability of stillbirth. The 5 most important factors involved were, in decreasing order (contribution of each effect to variance reduction): difference between piglet birth weight and the litter mean (2.36%), individual birth weight (2.25%), piglet sex (1.01%), farrowing duration (0.99%), and sow genetic type (0.94%). Probability of stillbirth was greater for lighter piglets, for male piglets, and for piglets from small or very large litters. Probability of stillbirth increased with sow parity number and with farrowing duration. Piglets born from Meishan sows had a lower risk of stillbirth (P < 0.0001) and were little affected by the sources of variation mentioned above compared with the 3 other sow genetic types. Standard and robust GEE approaches gave similar results despite some disequilibrium in the data set structure highlighted with the robust GEE approach. Key words: Bayesian generalized linear model, birth weight, farrowing duration, robust generalized estimating equation, stillbirth ©2006 American Society of Animal Science. All rights reserved. INTRODUCTION Farrowing is a critical period in most polytocous mammalian species. In pigs, up to 8% of newborns are stillborn (van der Lende et al., 2000), predominantly as a result of perinatal asphyxiation experienced in utero or during delivery (Randall, 1978; Zaleski and Hacker, 1993). This proportion tends to increase as a correlated response to selection for litter size. Limiting or reducing the number of stillbirths requires its major determinants to be investigated. Several factors, such 1 Corresponding author: laurianne.canario@jouy.inra.fr Received December 30, 2005. Accepted July 14, 2006. J. Anim. Sci. 2006. 84:3185–3196 doi:10.2527/jas.2005-775 as sow parity, piglet birth weight, sex (SEX), and birth assistance (BA) have been shown to be associated with variations in perinatal mortality (Knol et al., 2002b; Lucia et al., 2002; Mota-Rojas et al., 2005). Significant, though limited, genetic influences on stillbirth have also been reported (Blasco et al., 1995; Knol et al., 2002a). Yet, most studies do not consider the particular distribution of stillbirth and the complexity of the relationships with its main sources of variation. The aim of the current study was to analyze breed variation in stillbirth using different models (i.e., Poisson or binomial distributions) and approaches (generalized linear models, generalized estimating equations, standard or robust, and Bayesian hierarchical models) so as to determine the most reasonable model(s) and to estimate 3185 3186 Canario et al. the combined effects of several potentially important sources of variation. MATERIALS AND METHODS Animals and Data Recording Animal care followed the general guidelines outlined in the European animal welfare regulations. Litter characteristics at birth (i.e., farrowing kinetics and the number and weight of piglets born alive or dead) were recorded in 969 litters farrowed by 511 sows of 4 genetic types (GT): Large White (LW, 651 litters), Meishan (MS, 63 litters), Laconie male line (LA, 173 litters—a synthetic line based on Hampshire, Pietrain, and LW breeds), and F1 Duroc × Large White (DU × LW, 82 litters). The data were collected in the INRA experimental herd of Le Magneraud (Charente-Maritime) from 1999 to 2003. Sows were managed under a batch farrowing system, with 3-wk intervals between successive batches. They entered the farrowing unit 1 wk before the expected date of parturition. There, they were housed in individual crates with slatted floors until weaning. Farrowing was induced with prostaglandin (Planate-doprostenol Schering-Plough Animal Health, Uxbridge, UK) on d 113 of gestation. The need for birth assistance resulted from specific indications (e.g., a lengthy interval between successive births, a lack of contractions, or both). Assistance consisted of oxytocin injections and vaginal palpation during farrowing, which accounted for 6.4 and 3.0% of parturitions, respectively. Piglet births were observed every 15 min. Farrowing duration was defined as the interval of time elapsed between the birth of the first and last piglet of the litter. Newborn piglets were individually weighed and sexed within 24 h after farrowing. The farrowing duration effect was estimated on a subset of 614 records, including 28 MS, 445 LW, 99 LA, and 42 DU × LW litters. Statistical Analyses A large number of potential sources of variation in stillbirth were investigated: sow GT, parity, BA, and SEX as fixed effects; gestation length (GEST), total number born (TNB), litter birth weight, and farrowing duration (FD) as covariates; and piglets’ dam, birth litter, or both as random effects. The effect of birth weight was investigated using the raw value (individual birth weight = IBW) or the difference (DBW) from the within-litter mean birth weight (MBW). Birth assistance was considered as a binary trait (0 = no assistance; 1 = 1 or several assistances). Parity included 5 categories: 1, 2, 3, 4, and ≥5. Statistical analyses were carried out assuming 2 different distributions for stillbirth: a binomial or a Poisson (with offset) distribution. Three approaches were used successively: GLM, Bayesian hierarchical models, and generalized estimating equations (GEE). The first modeling approach assumed independent data, whereas the last 2 took into account correlations among piglets within-litter. Moreover, in the case of GEE, a robust analysis (Cantoni, 2004) was considered in addition to the standard procedure (Liang and Zeger, 1986; Zeger and Liang, 1986) so as to investigate the incidence of outliers in the data set. The GLM (McCullagh and Nelder, 1983) analyses were applied to litter grouped data (Collett, 2003) using the GENMOD procedure (SAS Inst. Inc., Cary, NC). Analyses assuming a Poisson or a binomial distribution of stillbirth (using both logit and probit link functions) were performed. All fixed effects and their first order interactions were considered; explanatory variables were then selected using a backwise procedure according to their deviance from the complete model (significance level lower than 5%). In case of overdispersion, effects were tested using an adjusted deviance (i.e., the deviance divided by the dispersion parameter φ = D0/ [N − p0], where D0 and p0 are, respectively, the deviance and number of parameters from the full model). The adequacy of the complete and full models and the comparison of nested models were tested via F-statistics (Collett, 2003). The GLM runs can be viewed as preliminary analyses aimed at selecting sets of meaningful explanatory variables and determining their mode of action (additivity or interactions, or both) before the final statistical analysis. Then, the data were analyzed using a random logistic regression in a Bayesian hierarchical framework via the Winbugs software (Spiegelhalter et al., 2003). Model selection was performed based on deviance and deviance information criterion (DIC). Assuming for example, a binomial distribution of Yi, where Yi is the number of dead piglets in the ith litter of size ni with probability of stillbirth πi, the hierarchical model involved the following 2 steps of sampling: i) Yi | πi ∼id B(ni, πi), and ii) logit(πi) ∼id N(ηi, σ2), where ηi = β0 + β1x1i + ... + βkxki corresponded to the joint effect of explanatory variables x1i,...,xki with regression coefficients β0, β1,...,βk on litter i, and where σ2 was the variance between litters in the probability of stillbirth on the logit scale. Note that ii) can be alternatively written as logit(πi) = ηi + σzi, where zi ∼id N(0,1) is the standardized random effect of litter i. Noninformative priors were assigned to β0, β1,...,βk using normal distributions with very large variances and to σ2 via 1/σ2 ∼ Γ(ε,ε) being a gamma distribution with a very small value of ε = 10−5. Classical GEE analyses were performed with the GENMOD procedure of SAS software; this procedure allowed the contribution of each fixed effect and each covariate to the variance reduction to be evaluated using a stepwise procedure and tested with the coefficient of determination of Hosmer and Lemeshow (1989). Ad- 3187 Stillbirth in pigs Table 1. Estimates1 of dam genetic type effects (SE) Dam GT Trait2 TNB, No. NBA, No. NSB, No. PSB, % GEST, d FD, h LBW, kg MBW, kg BA,5 % Test3 b d b b b NS b c — Meishan 4a 13.3 (0.6) 12.0 (0.6)c 0.3 (0.1)c 3.0 (1.3)c 113.3 (0.12)c 2.7 17.3 (0.9) 1.32 (0.05)d 4.8 Large White Duroc × Large White Laconie 12.2 (0.2) 10.6 (0.2) 0.7 (0.1) 6.5 (0.5) 113.7 (0.04) 2.9 17.4 (0.7) 1.51 (0.04) 9.7 12.8 (0.6) 11.6 (0.6)a 0.6 (0.1) 4.8 (1.2) 113.6 (0.12) 2.9 18.9 (1.4) 1.54 (0.08) 25.6 11.3 (0.4)b 9.6 (0.4)b 0.7 (0.1) 6.8 (0.9) 113.6 (0.08) 2.7 15.3 (0.8)c 1.53 (0.04) 9.8 Not significant; aP < 0.10; bP < 0.05; cP < 0.01; dP < 0.001. Estimates from a mixed model including genetic type, parity, and farrowing batch as fixed effects, and sow as random effect. Estimates were obtained using REML methodology (Patterson and Thompson, 1971) with the MIXED procedure of SAS (SAS Inst. Inc., Cary, NC). 2 Total number born (TNB); number born alive (NBA); number (NSB) and proportion (PSB) of stillborn piglets per litter; birth assistance (BA); gestation length (GEST); farrowing duration (FD); litter birth weight (LBW); and mean birth weight (MBW). 3 Level of significance of breed effect test using Wald score statistics. 4 Level of significance of the test of the contrast to Large White breed. 5 No statistical comparison was performed for BA. NS 1 ditionally, interactions between GT and covariates (i.e., GEST, TNB, FD, IBW, DBW, and MBW) were included to test the homogeneity of covariate functions between GT. The within-subject correlation coefficient, associated with the implementation of an exchangeable matrix on the random effect, was tested using the GEEse procedure from the R software (Yan and Højsgaard, 2006). The classical GEE estimator for both regression and nuisance parameters can be highly influenced by deviating data points (outliers). A robust version of GEE (Cantoni, 2004) was hence used with the S-PLUS software (Insightful Corp., 2004) with routines available from E. Cantoni (http://www.unige.ch/ses/metri/cantoni/). Robust statistics (Hampel et al., 1986) consider that models are only ideal approximations and that in practice their assumptions are almost never fully met. Therefore, estimators and test statistics that are stable in a neighborhood of the postulated model are developed. The robust GEE procedure is one of these tools and can be seen as a weighted version of the standard GEE equations, with 2 types of weights, one to control for deviations on the response space on one side and another to control for deviations on the design space on the other side. Inspection of these weights from a fitted robust GEE model allows departing observations (i.e., those that have been given small weights) to be identified. A robust binary GEE model including GT, parity, and BA as fixed effects was fitted and compared with a standard GEE. A characterization of the subpopulation of down-weighted observations from this model was carried out using the GLM procedure of SAS. This analysis allowed suspected separation in the data to be identified. Given that complete separation would imply the nonexistence of the estimator, the methodology of Christmann and Rousseeuw (2001) was used (package ncomplete from R software, A. Christmann, http:// www.statistik.uni-dortmund.de/de/textonly/content/ einrichtungen/lehrstuehle/personen/christmann/soft ware.html) to compute the overlap (i.e., the smallest number of observations whose removal yielded complete separation). RESULTS Model Selection Genetic type estimations are presented in Table 1. The performance of LW, DU × LW, and LA sows did not differ for any of the traits investigated. Conversely, MS sows had a significantly larger litter size, smaller number and proportion of stillbirth, shorter farrowing duration, and lower mean birth weight than the 3 other GT. Results of the GLM analyses are shown in Table 2. Covariates selected were the same whatever the distribution (binomial or Poisson) and link function (probit or logit) hypothesized. Because no difference appeared between these 2 link functions, we chose the most common one (i.e., the logit) for the remaining analyses. The full model was rejected unless a correction for overdispersion was applied. All main effects related to the sow (i.e., GT, parity, and BA) were selected, but no interaction reached statistical significance. Results from the Bayesian analyses are given in Table 3. They clearly showed the superiority of models assuming a binomial distribution over those assuming a Poisson distribution (differences in DIC values exceeded 10). Results additionally indicated that the model with litter as a single random effect was satisfactory to take into account correlations among piglets 3188 Canario et al. Table 2. Model selection for stillbirth based on standard GLM analyses1 Binomial model Model expression2 Nested model Without correction for data dispersion (−1) = Saturated model (0) = Full model + GT + P + BA + GT × P + GT × BA + P × BA (1) = (0) − P × BA + GT + P + BA + GT × P + GT × BA (2) = (1) − GT × BA + GT + P + BA + GT × P (3) = (2) − GT × P + GT + P + BA (4) = (3) − BA + GT + P (5) = (3) − P + GT + BA (6) = (3) − GT + P + BA NP3 df Deviance Deviance difference P-value Deviance Deviance difference P-value 969 28 941 0 1,207.1 1,207.1 <0.0001 0 1,232.1 1,232.1 <0.0001 24 4 1,210.6 3.5 0.48 1,236.3 4.2 0.37 21 9 8 5 6 3 12 1 4 3 1,214.4 1,230.9 1,237.5 1,253.2 1,279.6 3.8 16.5 6.6 15.7 26.4 0.28 0.17 0.01 0.0001 <0.0001 1,241.4 1,256.9 1,269.7 1,276.8 1,314.1 5.0 15.6 12.8 7.1 37.3 0.17 0.21 0.0003 0.0005 <0.0001 With correction for data dispersion (−1) = Saturated model (0) = Full model (1) = (0) − P × BA (2) (3) (4) (5) (6) = = = = = (1) (2) (3) (3) (3) − − − − − GT × BA GT × P BA P GT + GT + P + BA + GT × P + GT × BA + P × BA + GT + P + BA + GT × P + GT × BA + GT + P + BA + GT × P + GT + P + BA + GT + P + GT + BA + P + BA Poisson model (φ = D0/[N − p0] = 1.283)4 ⌬ deviance/φ P-value 0 1,207.1 733.4 0.99 (φ = D0/[N − p0] = 1.309) 0 1,232.1 941.2 0.49 969 28 941 24 4 1,210.6 2.7 0.60 1,236.3 3.2 0.52 21 9 8 5 6 3 12 1 4 3 1,214.4 1,230.9 1,237.5 1,253.2 1,279.6 3.0 12.9 5.1 12.2 20.6 0.40 0.38 0.02 0.002 <0.0001 1,241.4 1,256.9 1,269.7 1,276.8 1,314.1 3.9 11.8 9.8 5.4 28.5 0.28 0.46 0.002 0.004 <0.0001 1 Results obtained with a logit link function. GT = Sow genetic type; P = parity; BA = birth assistance. 3 NP = Number of parameters. 4 φ = Dispersion parameter. 2 (1,882 vs. 1,884 DIC for litter + mother model and litter model, respectively). Results from classical GEE analyses (Table 4) were in agreement with Bayesian analyses; a greater betweensubject correlation coefficient (α) was obtained from the model including the litter as random effect in comparison to a sow random effect (α = 0.042 vs. 0.021). Both coefficients were highly significant (P < 0.0001). Sources of Variation for Stillbirth Substituting dam GT with piglet GT gave very similar results (difference of deviance: 4,498.81 − 4,490.56 = 8.25 for 11 − 4 = 7 df; P = 0.311). No difference in probability of stillbirth between purebred and crossbred piglets was observed (P = 0.473). The reduction in residual sum of squares due to the successive addition of each explanatory variable demonstrated that birth weight (per se as IBW or as a Table 3. Model comparison for stillbirth based on deviance information criterion (DIC) Model Model Model Model 1 2 3 4 Distribution Random effect(s) DIC Binomial Binomial Binomial Poisson Litter + mother Litter — Litter 1,881.7 1,884.2 2,028.6 1,931.8 difference DBW from the mean of the litter) was the main determinant of piglet survival (+2.25 and +2.36% in variance reduction, respectively), followed by SEX, FD, sow GT, and parity (1.01, 0.99, 0.94, and 0.50%, respectively) and the quadratic components of IBW (0.30%) and DBW (0.23%; Table 5). The remaining effects made lower contributions (<0.21%). Results from GEE analyses also demonstrated the strong influences of GT, SEX, and DBW on probability of stillbirth (P < 0.0001; Table 6). Genetic type × covariate interactions were not significant, except those involving birth weight (i.e., IBW and DBW). Piglets from MS sows had a 86% lower probability of stillbirth than piglets born from LW sows (P < 0.0001), whereas piglets from DU × LW or LA sows had a similar probability as those from LW sows. Probability of stillbirth did not significantly differ from parity 1 to 4 but was 1.6 times greater in the fifth (or later) parity (P < 0.05 to P < 0.001). A clearer view of parity × GT effects on probability of stillbirth is shown in Figure 1. Probability of stillbirth decreased slightly from the first to the second parity, and then progressively increased up to the fifth parity, except for MS sows, where it remained at consistently low values. Male piglets had an approximately 1.8 times greater probability of stillbirth than female piglets (P < 0.0001; Table 6). Piglets from litters with assistance during parturition had a 1.4 times greater probability of stillbirth than litters without assistance (P = 0.03). 3189 Stillbirth in pigs Table 4. Generalized estimating equations estimates (SE) assuming a binary distribution and global test of sow vs. litter random effects on probability of piglet stillbirth Model 1 (Sow effect) Effect1 Intercept GT DU × LW GT MS GT LA Parity 2 Parity 3 Parity 4 Parity 5 GEST BA α Global effect (χ2)2 23.80e 12.87b 0.46NS 3.54a Model 2 (Litter effect) Level effect (SE)3 1.00 (5.94) −0.19 (0.19) −1.71 (0.41)e 0.13 (0.15) −0.25 (0.14)a 0.13 (0.16) 0.16 (0.17) 0.41 (0.17)b −0.04 (0.05) 0.34 (0.16)b 0.021 Global effect (χ2)2 43.25e 12.32b 0.894b 7.19c Level effect (SE)3 1.19 (5.99) −0.14 (0.18) −1.86 (0.41)e 0.10 (0.14) −0.23 (0.15) 0.12 (0.17) 0.14 (0.17) 0.42 (0.17)b −0.04 (0.05) 0.50 (0.15)c 0.042 1 Estimates were expressed as deviations from a piglet born from a Large White sow in first parity receiving birth assistance. Genetic type (GT) of the sow with Duroc × Large White F1 (DU × LW), Meishan (MS), and Laconie (LA); gestation length (GEST), birth assistance (BA); α: within-subject correlation coefficient. 2 Level of significance for χ2 statistic: NS = not significant; aP < 0.10 ; bP < 0.05 ; cP < 0.01; dP < 0.001; e P < 0.0001. 3 Figures correspond to the log odds ratio. Odds ratio can be obtained with an exponential transformation. Level of significance for z statistic: same as in footnote 2. Litter size had a nonlinear effect on probability of stillbirth, except for litters from MS sows, where the probability remained almost constant (Figure 2). In the 3 other GT, piglets from small and large litters were more susceptible to die at farrowing with a minimum probability for intermediate litters of 12 piglets. When a global adjustment for IBW was made, the risk of stillbirth increased in extreme litters, particularly in small ones (Figure 2a vs. 2b). Piglet birth weight affected probability of stillbirth in an inverse exponential fashion (Figure 3) but with a different magnitude in each GT, which resulted in a significant GT × BW interaction. The increase in probability of stillbirth with decreasing birth weights was highest in LW and lowest in MS litters. Differences in probability of stillbirth were larger when the data were adjusted for DBW instead of IBW (Figure 4 vs. Figure 3). The risk of stillbirth grew rapidly when piglet Table 5. Reduction of deviance (GLM model)1 due to the addition of each explanatory variable Data set 13 Data set 23 Model2 Deviance Reduction, % Deviance Reduction, % (0) = intercept (1) = (0) + GT (2) = (1) + P (3) = (2) + SEX (4) = (3) + GEST (5) = (4) + BA (6) = (5) + TNB (7) = (6) + TNB2 (8) = (7) + IBW (9) = (8) + IBW2 (8) = (7) + MBW (9) = (8) + MBW2 (10) = (9) + DBW (11) = (10) + DBW2 (12) = (7) + FD 4,571.90 4,528.84 4,506.09 4,460.40 4,459.73 4,453.03 4,447.89 4,438.54 4,338.68 4,325.88 4,427.42 4,427.11 4,322.56 4,312.50 — 0.94 0.50 1.01 0.06 0.15 0.12 0.21 2.25 0.30 0.25 0.007 2.36 0.23 — 2,783.33 2,755.93 2,741.06 2,741.81 2,711.11 2,707.46 2,703.90 2,698.20 — — — — — — 2,671.37 0.98 0.54 0.96 0.14 0.13 0.13 0.21 — — — — — — 0.99 1 Modeling was realized with litter as subject for the correlation structure. Sow genetic type (GT) with Duroc × Large White F1 (DU × LW), Meishan (MS), and Laconie (LA) sows; parity (P), sex of the piglet (SEX), gestation length (GEST), birth assistance (BA), total number born (TNB), individual birth weight (IBW), mean birth weight (MBW), difference from the within-litter mean birth weight (DBW), and farrowing duration (FD). 3 Data set 1 included all factors of variation but FD and included 969 litter records. Data set 2 is a subsample of data set 1 including 614 litter records with information on FD. 2 3190 Canario et al. Table 6. Generalized estimating equations estimates of log odds ratio (SE) and global tests on probability of piglet stillbirth Model 1 Effect1 Intercept GT DU × LW GT MS GT LA Parity 2 Parity 3 Parity 4 Parity 5 SEX GEST BA TNB TNB2 IBW IBW2 MBW MBW2 DBW DBW2 FD α Global effect (χ2)2 44.08e 11.06b 47.37e 0.54NS 4.04b 4.94b 5.54b — — −1.07NS 0.17NS 52.75e 3.58a — Model 2 Level effect (SE)3 3.25 (6.09) −0.06 (0.19) −2.05 (0.42)e 0.12 (0.14) −0.11 (0.15) 0.19 (0.17) 0.15 (0.18) 0.48 (0.17)c 0.64 (0.09)e −0.04 (0.05) 0.38 (0.17)b −0.22 (0.08)c 0.01 (0.00)c — — −0.99 (0.92) 0.11 (0.27) −1.11 (0.21)e 0.88 (0.38)b — 0.036 Global effect (χ2)2 24.38d 10.22b 23.66d 3.71a 1.18NS 2.22NS 2.54NS — — — — — — 8.10c Level effect (SE)3 12.60 (7.80) −0.06 (0.26) −3.18 (0.98)c 0.12 (0.16) −0.30 (0.19)a 0.14 (0.21) 0.05 (0.21) 0.39 (0.19)c 0.58 (0.12)e −0.13 (0.07) 0.23 (0.20)a −0.17 (0.09)a 0.01 (0.00)b — — — — — — 0.20 (0.05)e 0.025 1 Estimates were expressed as deviations from a male piglet born from a Large White sow in first parity without birth assistance. Sow genetic type (GT) with Duroc × Large White F1 (DU × LW), Meishan (MS), and Laconie (LA) sows; parity, sex of the piglet (SEX), gestation length (GEST), birth assistance (BA), total number born (TNB), individual birth weight (IBW), mean birth weight (MBW), difference from the withinlitter mean birth weight (DBW), and farrowing duration (FD). α: Within-litter correlation coefficient. 2 Level of significance for χ2 statistic: NSNot significant; aP < 0.10; bP < 0.05; cP < 0.01; dP < 0.001; e P < 0.0001. 3 Figures correspond to the log odds ratio. Odds ratio can be obtained with an exponential transformation. Level of significance for z statistic: same as in footnote 2. weights fell below the litter average; piglets from LW sows weighing 500 g less than the litter average weight had a 7.8 times greater probability of stillbirth than Figure 1. Parity effect on probability of stillbirth of piglets according to sow genetic type. Probability was estimated with gestation length = 114 d, total number born = 12, sex of the piglet = female, and birth assistance = 0. LW = Large White; MS = Meishan; DU × LW = Duroc × Large White; LA = Laconie. piglets from MS sows. Additional adjustments for mean birth weight and litter size had limited effects on DBW pattern. Farrowing duration positively influenced probability of stillbirth (Table 6, model 2; P < 0.01) with a 23% greater risk for each supplementary hour elapsed (Figure 5), except for litters from MS sows, where FD had little effect. It should be emphasized that, except for birth weight, the difference between MS and the 3 other GT was a consequence of the nonlinear relationship between probability of stillbirth and its explanatory variables; interactions with GT were not significant. The results obtained with the robust GEE approach were very similar to standard GEE results, the only difference being the quadratic term of regression on birth weight, which became nonsignificant. However, an analysis of variance of the weights attributed to the data clearly demonstrated that the data with weights lower than 1 were allocated to nearly all stillborn piglets (562 among 568). This means that we must be cautious in interpreting the results because of the unbalanced experimental design. Weight allocation was dependent on GT (P < 0.0001), sow parity (P < 0.0001), and the square of total number born (P < 0.016); lower weights Stillbirth in pigs 3191 Figure 3. Relationships between individual weight at birth effect and probability of stillbirth of piglets according to sow genetic type. Probability was estimated with gestation length = 114 d, sex of the piglet = female, birth assistance = 0, parity = 2, and total number born = average per sow genetic type. LW = Large White; MS = Meishan; DU × LW = Duroc × Large White; LA = Laconie. regression approach of Rousseeuw and Christmann (2003), which can be computed even when separation is present, provided similar estimates to those obtained from the robust GEE procedure. Figure 2. Patterns of litter size effect on probability of stillbirth of piglets according to sow genetic type. Probability was estimated with gestation length = 114 d, parity = 2, sex of the piglet = female, and birth assistance = 0, (a) without or (b) with correction for individual birth weight being equivalent (1.2 kg). LW = Large White; MS = Meishan; DU × LW = Duroc × Large White; LA = Laconie. were attributed to MS litters and to parities 1, 2, and 4. The particularly low stillbirth rate in MS sows (Table 1) is likely to have promoted this variable as a cause of separability. We also found that the overlap between the y = 0 and y = 1 observations only involved 8 of the 11,735 observations. However, the hidden logistic Figure 4. Effect of the difference in individual birth weight from the litter mean on probability of stillbirth of piglets according to sow genetic type. Probability was estimated with gestation length = 114 d, sex of the piglet = female, birth assistance = 0, parity = 2, total number born = 12, and mean birth weight = 1.2 kg. LW = Large White; MS = Meishan; DU × LW = Duroc × Large White; LA = Laconie. 3192 Canario et al. because of the small sample of MS farrowings, their low (3%) stillbirth, and above all, the fact that stillborn piglets often have extreme characteristics (e.g., the lightest or heaviest within a litter). However, the separation issue arises only with binary regression, when parameters are estimated via classical (e.g., GLM, GEE) and robust (e.g., robust GEE) techniques. On the contrary, Rousseeuw and Christmann’s (2003) estimation procedure and Poisson GLM and GEE models do not suffer from this problem. Given that we have obtained consistent results throughout the different modeling approaches, we can be confident about these results. Sow Characteristics Influencing Stillbirth Figure 5. Effect of farrowing duration on probability of stillbirth of piglets according to sow genetic type. Probability was estimated with gestation length = 114 d, sex of the piglet = female, birth assistance = 0, parity = 2. LW = Large White; MS = Meishan; DU × LW = Duroc × Large White; LA = Laconie. DISCUSSION Methodological Aspects Like other reproductive traits, stillbirth has so far been essentially studied as a trait of the sow. The influence of piglet characteristics on their own survival has only been investigated recently. Leenhouwers et al. (1999), Roehe and Kalm (2000), and Knol et al. (2002a) estimated the risk factors of preweaning mortality in pigs using logistic regression or generalized mixed models. The current study used a similar approach but complemented it by advanced methodologies, which were more efficient in model selection and parameter inference. A first set of analyses based on generalized linear models allowed the major factors of variation to be identified and different distributions and link functions to be tested. Contrary to Roehe and Kalm (2000), the sire effect was not considered because most sires produced only 1 litter, and its effect would have been poorly estimated. The Bayesian analysis was very helpful in model selection via calculation of the DIC, which highlighted the superiority of models based on a binomial distribution over those assuming a Poisson distribution. We also established that the model including litter as a single random effect was as efficient as the more complicated one involving dam effect. The existence of correlated data implied use of GEE. This procedure was not a repetition of the previous method because it relied on a marginal approach, giving estimates at the population level, in contrast to the Bayesian hierarchical approach, which applies at the subject level (here, litter). The robustness of the analysis is an important issue, often neglected. The use of a robust GEE procedure enabled us to demonstrate unbalance of the data set The average litter size at birth (TNB) and the number of stillborn piglets were slightly greater than the values reported in Leenhouwers et al. (1999) analysis of stillbirth. They were similar for MS, but somewhat larger for LW sows, to the figures reported by Bidanel (1993) in a comparison of MS and LW sow reproductive performance. Genetic Type. Most studies have shown that sow GT is a major determinant of reproductive traits in pigs, the influence of piglet genotype being much more limited (Bidanel et al., 1989; Haley et al., 1995). Yet, differences in stillbirth number or proportion are limited between most GT. For instance, Leenhouwers et al. (1999) did not find any difference among a variety of purebred and crossbred genotypes. Here, the lack of difference among LA, LW, and DU × LW confirmed those results. The MS Chinese breed shows totally different characteristics at birth, and in the current study, had a much lower probability of stillbirth than standard genotypes, in agreement with Bidanel et al. (1989), Bidanel (1993), and Haley et al. (1995). The vascularity of the placenta and the within litter homogeneity in placenta weight (Ford, 1997; Wilson et al., 1999; Vallet et al., 2002), which would correspond to a particular ability to limit conceptus growth and limit uterine crowding (Ashworth et al., 1996; Vonnahme et al., 2002), have been hypothesized as possible reasons for the low stillbirth proportion of MS sows. The greater body inertia (fewer contractions) and the lower activity of MS sows might also favor their shorter and more regular farrowings (Canario et al., 2004), which are likely to limit hypoxia, stress, or premature rupture of the umbilical cord. Parity. The increase in probability of stillbirth in later parities is in agreement with the literature (Leenhouwers et al., 1999; Knol et al., 2002a; Borges et al., 2005). This increase might result from excessive fatness of old sows; from aging of the uterus, which, having reduced muscular tone, becomes less efficient for the farrowing process (Pejsak, 1984); or from both of these. The tendency toward a greater probability of stillbirth in the first parity, though nonsignificant, is in line with other studies (Cutler et al., 1992; Leenhouwers et al., 1999) and might be related to insufficient size of the Stillbirth in pigs birth canal in young gilts (Pejsak, 1984; Cutler et al., 1992). Gestation Length. The lack of effect of GL on probability of stillbirth does not agree with the results of Zaleski and Hacker (1993) and Leenhouwers et al. (1999), who both found a negative effect of GL on the number of stillborn piglets per litter and attributed it to the immaturity of piglets born after short gestations. The lack of effect in the current study was not related to a lower variability of gestation length, which ranged from 107 to 116 d in our study vs. 108 to 119 d in Leenhouwers et al. (1999). Including birth weight as a maturity criterion in the model had no effect on results regarding gestation length. Birth Assistance. The positive association between birth assistance and probability of stillbirth is somewhat expected because assistance is given when farrowing problems occur. A positive association between vaginal palpations and stillbirth was also reported by Lucia et al. (2002). Some authors (Alonso-Spilsbury et al., 2004; Mota-Rojas et al., 2005, 2006) have recently suggested that oxytocin treatment per se might be associated with a greater probability of stillbirth. The effect might be due to an increase in sow myometrial activity resulting in deterioration in blood and gaseous maternal-fetal exchanges (Lucia et al., 2002; Mota et al., 2002; Mota-Rojas et al., 2005). Yet, due to the lack of a welldesigned experiment with random treatments, causality relationships between probability of stillbirth and farrowing treatments remain unclear. Litter Size. The positive influence of litter size on stillbirth is well documented (Kerr and Cameron, 1995; Leenhouwers et al., 1999; Knol et al., 2002a). A major reason remains that, in most cases, large litters are associated with longer farrowings and greater risks of hypoxia (Herpin et al., 2001). In the current study, a greater probability of stillbirth was also found in small litters, as previously reported in several studies (Fahmy et al., 1978; Kerr and Cameron, 1995; Knol et al., 2002a). This increased mortality might result from physiological inabilities or difficulties of sows to have a normal gestation (Dziuk, 1979). The optimal value of 12 piglets per litter found in the current study is somewhat greater than the value of 9 piglets reported by Zaleski and Hacker (1993). This difference in optimal litter size may be due to management; to GT differences, which may, in the case of the LW breed, result from selection for litter size carried out over the last decade (Tribout et al., 2003); or to both of these. Mean Birth Weight. Literature results regarding the relationship of MBW with stillbirth are rather conflicting; positive (Leenhouwers et al., 2003) and negative (Zaleski and Hacker, 1993; Leenhouwers et al., 1999) effects of MBW have been reported. Betweenbreed differences in piglet survival were attributed to a between-breed difference in mean birth weight (Leenhouwers et al., 1999). Once more, Meishan sows, which have piglets with a much lower average birth weight than the other GT, appear as an exception. Their low 3193 probability of stillbirth may be due to a greater maturity of piglets at birth (Herpin et al., 1996) and possibly better ability of sows to expel their piglets. Piglet Characteristics Influencing Stillbirth Sex. Female piglets have been shown to have a greater birth to weaning survival probability than males (Lay et al., 2002). The study of Knol et al. (2002a) showed a 2 to 4% lower probability of survival for male than female piglets. The impact of sex on farrowing survival has been more controversial (Svendsen et al., 1986; Daza et al., 1999). The underlying mechanisms responsible for this sexual dimorphism have not been elucidated. Lay et al. (2002) hypothesized a greater susceptibility of males to farrowing stress due to a greater basal cortisol. Individual Birth Weight. Birth weight is considered to be the most important factor influencing piglet survival from birth to weaning (e.g., Roehe and Kalm, 2000; Knol et al., 2002a; Leenhouwers et al., 2003). Our results confirm that IBW also plays an important role in farrowing survival, as suggested by the lower birth weight of stillborn piglets as compared with live-born piglets reported in several studies (e.g., Leenhouwers et al., 1999, 2003; Knol et al., 2002a). Light piglets have lower hemoglobin levels (Zaleski and Hacker, 1993), as well as greater plasma cortisol concentrations, and larger adrenal weight in proportion to their BW than heavy piglets. There are signs of an altered adrenal function responsible for subnormal tissue differentiation and growth (Klemcke et al., 1993); the piglets are consequently more susceptible to death during the birth process. Roehe and Kalm (2000) suggested that increasing IBW could be a way to decrease stillbirth. Our results, which show a trend toward greater probability of stillbirth in heavy piglets, suggest that it might not be a good solution, as also shown by Fahmy et al. (1978). Indeed, heavy piglets, though having better vitality, have increased difficulties to engage in the vaginal canal and a greater risk of being blocked, which generally results in severe hypoxia and a greater risk of dying (Fahmy et al., 1978). Several authors have recently suggested that relative birth weight [i.e., departure from litter average birth weight (DBW)] might be a more important risk factor than IBW (Quiniou et al., 2002; Roehe, 2003). The larger reduction of deviance when including DBW instead of IBW in our study tends to support this hypothesis. Hence, more homogeneous litters would be associated with a lower risk of stillbirth and birth to weaning mortality, as suggested by some recent results (e.g., Damgaard et al., 2003; Huby et al., 2003; Roehe, 2003). Farrowing Duration. An unfavorable positive relationship between farrowing duration and probability of stillbirth was clearly outlined, in accordance with many previous studies (e.g., Randall, 1972; Dial et al., 1992; van Dijk et al., 2005). Borges et al. (2005) showed that sows with a farrowing duration longer than 3 h had 2 3194 Canario et al. times greater probability of stillbirth than those with shorter farrowing durations. Probability of stillbirth would be particularly increased in piglets born late in the farrowing (Randall, 1972; Zaleski and Hacker, 1993), due to a greater risk of asphyxiation on, detachment of the placenta, occlusion, or rupture of the umbilical cord (Herpin et al., 1996). Perspectives for Breeding Our results confirm that between-breed variation in stillbirth is rather limited, with the notable exception of the MS breed. Although interest in the MS has mainly been justified by its high prolificacy (e.g., Bidanel, 1993; Haley et al., 1995), this breed has been shown to have additional interesting characteristics such as a low proportion of stillbirth and high birth to weaning survival. Development of Chinese × European synthetic lines has been the most widely used strategy to take advantage of the high reproductive performance of MS sows (e.g., Bidanel et al., 1991; Zhang et al., 2000). Synthetic lines allow partial benefits from the favorable additive effects of the MS breed, as well as from direct and maternal heterosis on litter size at birth, and also on farrowing and birth to weaning survival, provided that recombination losses are limited, as suggested by Bidanel (1993). Recent results from several MS based synthetic lines suggest that sows from these lines have better preweaning survival than Large White or Landrace sows (J. P. Bidanel, unpublished data). This study did not intend to analyze within breed variation and to find the most suitable selection criterion in order to reduce perinatal mortality. Yet the modeling strategy employed and the results showing the advantages of models assuming a binomial distribution of probability of stillbirth may be used in the future to establish the best genetic evaluation model for stillbirth. Finally, the impact of the difference from the withinlitter mean birth weight on probability of stillbirth supports the hypothesis of a detrimental effect of litter birth weight heterogeneity on perinatal survival. Litter heterogeneity in weights has also been shown to be positively associated with birth to weaning mortality. Selection for more homogeneous litters has been proposed as a method of improving piglet survival. Such canalizing selection could be considered, as suggested by the genetic parameter estimates obtained by Damgaard et al. (2003) and Huby et al. (2003), as well as by the results of a selection experiment carried out in rabbits, where promising results have been obtained on direct responses on the homogeneity of within litter birth weights and correlated responses on preweaning survival (Garreau et al., 2004). IMPLICATIONS Use of different complementary statistical methodologies in the analysis of complex unbalanced (field) data with particular distributions was put forward. Indeed, such methodologies allow more efficient model selection and parameter inference, as well as avoidance of potential problems associated with unbalanced data. The important role of birth weight and within-litter piglet birth weight homogeneity on probability of stillbirth was pointed out. 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