Genome-wide association study for feed efficiency in collective cage-raised rabbits under full and restricted feeding

Feed efficiency (FE) is one of the most economically and environmentally relevant traits in the animal production sector. The objective of this study was to gain knowledge about the genetic control of FE in rabbits. To this end, GWASs were conducted for individual growth under two feeding regimes (full feeding and restricted) and FE traits collected from cage groups, using 114 604 autosome SNPs segregating in 438 rabbits. Two different models were implemented: (1) an animal model with a linear regression on each SNP allele for growth trait; and (2) a two‐trait animal model, jointly fitting the performance trait and each SNP allele content, for FE traits. This last modeling strategy is a new tool applied to GWAS and allows information to be considered from non‐genotyped individuals whose contribution is relevant in the group average traits. A total of 189 SNPs in 17 chromosomal regions were declared to be significantly associated with any of the five analyzed traits at a chromosome‐wide level. In 12 of these regions, 20 candidate genes were proposed to explain the variation of the analyzed traits, including genes such as FTO, NDUFAF6 and CEBPA previously associated with growth and FE traits in monogastric species. Candidate genes associated with behavioral patterns were also identified. Overall, our results can be considered as the foundation for future functional research to unravel the actual causal mutations regulating growth and FE in rabbits.

Daily exposure to summer temperatures affects the motile subpopulation structure of epididymal sperm cells but not male fertility in an in vivo rabbit model

High temperatures have negative effects on sperm quality leading to temporary or permanent sterility. The aim of the study was to assess the effect of long exposure to summer circadian heat stress cycles on sperm parameters and the motile subpopulation structure of epididymal sperm cells from rabbit bucks. Twelve White New Zealand rabbit bucks were exposed to a daily constant temperature of the thermoneutral zone (from 18 °C to 22 °C; control group) or exposed to a summer circadian heat stress cycles (30 °C, 3 h/day; heat stress group). Spermatozoa were flushed from the epididymis and assessed for sperm quality parameters at recovery. Sperm total motility and progressivity were negatively affected by high temperatures (P < 0.05), as were also specific motility parameters (curvilinear velocity, linear velocity, mean velocity, straightness coefficient, linearity coefficient, wobble coefficient, and frequency of head displacement; P < 0.05, but not the mean amplitude of lateral head displacement). Heat stress significantly increased the percentage of less-motile sperm subpopulations, although the percentage of the high-motile subpopulation was maintained, which is consistent with the fact that no effect was detected on fertility rates. However, prolificacy was reduced in females submitted to heat stress when inseminated by control bucks. In conclusion, our results suggest that environmental high temperatures are linked to changes in the proportion of motile sperm subpopulations of the epididymis, although fertility is still preserved despite the detrimental effects of heat stress. On the other hand, prolificacy seems to be affected by the negative effects of high temperatures, especially by altering female reproduction.

Using the product threshold model for estimating separately the effect of temperature on male and female fertility

Animals under environmental thermal stress conditions have reduced fertility due to impairment of some mechanisms involved in their reproductive performance that are different in males and females. As a consequence, the most sensitive periods of time and the magnitude of effect of temperature on fertility can differ between sexes. The objective of this study was to estimate separately the effect of temperature in different periods around the insemination time on male and on female fertility by using the product threshold model. This model assumes that an observed reproduction outcome is the result of the product of 2 unobserved variables corresponding to the unobserved fertilities of the 2 individuals involved in the mating. A total of 7,625 AI records from rabbits belonging to a line selected for growth rate and indoor daily temperature records were used. The average maximum daily temperature and the proportion of days in which the maximum temperature was greater than 25°C were used as temperature descriptors. These descriptors were calculated for several periods around the day of AI. In the case of males, 4 periods of time covered different stages of the spermatogenesis, the transit through the epididymus of the sperm, and the day of AI. For females, 5 periods of time covered the phases of preovulatory follicular maturation including day of AI and ovulation, fertilization and peri-implantational stage of the embryos, embryonic and early fetal periods of gestation, and finally, late gestation until birth. The effect of the different temperature descriptors was estimated in the corresponding male and female liabilities in a set of threshold product models. The temperature of the day of AI seems to be the most relevant temperature descriptor affecting male fertility because greater temperature records on the day of AI caused a decrease in male fertility (-6% in male fertility rate with respect to thermoneutrality). Departures from the thermal zone in temperature descriptors covering several periods before AI until early gestation had a negative effect on female fertility, with the pre- and peri-implantational period of the embryos being especially sensitive (from -5 to -6% in female fertility rate with respect to thermoneutrality). The latest period of gestation was unaffected by the temperature. Overall, magnitude and persistency of the temperatures reached in the conditions of this study do not seem to be great enough to have a large effect on male and female rabbit fertility.

Crossbreeding parameters for growth and feed consumption traits from a five diallel mating scheme in rabbits

Twenty-five genetic groups of young rabbits originated from a diallel-crossbreeding scheme among 5 selected lines: 3 maternal and 2 terminal sire lines belonging to 2 Spanish research institutions. A sample of 2,773 young rabbits from 525 litters was controlled during the fattening period lasting from 5 to 9 wk. Growth and feed consumption traits were evaluated throughout different biweekly batches. A Bayesian approach was used for inference from an animal model with common litter effects. On average, genetic groups coming from lines selected for growth rate were heavier (+58.9 g at 32 d and +315.5 g at 60 d), had greater growth rate (9.24 and 8.15 g/d from individual or cage analysis, respectively) and feed intake (+13.24 g/d), and showed better feed conversion ratio (-0.21 g of intake/g of gain), than the genetic groups originated from crosses among lines selected for litter size. Crossbreeding parameters were estimated from the samples of the marginal posterior distribution of the genetic group effect according to the Dickerson model. Maternal genetic and individual heterosis effects were null or very low. Direct genetic effects mainly regulated the expression of growth traits.

Individual efficiency for the use of feed resources in rabbits

A Bayesian procedure, which allows consideration of the individual variation in the feed resource allocation pattern, is described and implemented in 2 sire lines of rabbit (Caldes and R). The procedure is based on a hierarchical Bayesian scheme, where the first stage of the model consists of a multiple regression model of feed intake on metabolic BW and BW gain. In a second stage, an animal model was assumed including batch, parity order, litter size, and common environmental litter effects. Animals were reared during the fattening period (from weaning at 32 d of age to 60 d of age) in individual cages on an experimental farm, and were fed ad libitum with a commercial diet. Body weight (g) and cumulative feed intake (g) were recorded weekly. Individual BW gain (g) and average BW (ABW, g) were calculated from these data for each 7-d period. Metabolic BW (g(0.75)) was estimated as ABW(0.75). The number of animals actually measured was 444 and 445 in the Caldes and R lines, respectively. Marginal posterior distributions of the genetic parameters were obtained by Gibbs sampling. Posterior means (posterior SD) for heritabilities for partial coefficients of regression of feed intake on metabolic BW and feed intake on BW gain were estimated to be 0.35 (0.17) and 0.40 (0.17), respectively, in the Caldes line and 0.26 (0.19) and 0.27 (0.14), respectively, in line R. The estimated posterior means (posterior SD) for the proportion of the phenotypic variance due to common litter environmental effects of the same coefficients of regression were respectively, 0.39 (0.14) and 0.28 (0.13) in the Caldes line and 0.44 (0.22) and 0.49 (0.14) in line R. These results suggest that efficiency of use of feed resources could be improved by including these coefficients in an index of selection.

Survival analysis in two lines of rabbits selected for reproductive traits

The objective of the study was to analyze the reproductive longevity of 2 selected lines of rabbits. The first one was the Prat line, a line selected in Spain on litter size at weaning, and raised in overlapping generations. The second one was a French line, the A1077 line, selected on litter size at birth and individual weight at 63 d of age, managed in batches, and artificially inseminated with discrete generations. Reproductive longevity was measured beginning at the first successful mating, assessed by a pregnancy diagnosis in the Prat line, and at the first kindling in the A1077 line. In the A1077 line, culling for infertility occurred after 3 unsuccessful artificial inseminations. The trait analyzed, defined as the doe length of productive life (LPL), was the time in days between date of the first positive pregnancy diagnosis and date of culling or death in the Prat line. In the A1077 line, the trait was the number of AI after the first kindling. Effects included in the model were year-season, litter size at birth, reproductive cycle or physiological status x cycle interaction, age at first mating, batch (only for the A1077 line), and additive genetic value of the animal as a random effect. Survival analyses were carried out with a Cox model for the Prat line and a discrete model for the A1077 line. The estimated heritability values for LPL were around 0.16 in the Prat and A1077 lines with a model including physiological status x cycle interaction effect. Removing this effect from the model led to an increase in estimated genetic variance with h2 = 0.24 and 0.19 in the Prat and A1077 lines, respectively. Including the traits LPL and number of AI from first fertile mating or AI in selection programs could increase reproductive longevity and decrease the replacement rate.

Genetics of litter size in three maternal lines of rabbits: Repeatability versus multiple-trait models

Variance components were estimated in 3 lines of rabbits selected for litter size at weaning (A, Prat, and V) to test one of the assumptions of the models used for selection: that litter size data at different parities are repeated measurements of the same trait. Multiple-trait analyses were performed for the total number of kits born (TB), the number of kits born alive (BA), and the number of kits weaned (NW) per litter. Estimates were obtained by REML in multivariate analyses, including all of the information of the selection criteria, under a repeatability model or a multiple-trait model, considering litter size at the first, second, and subsequent parities as different traits. Models included the fixed effects of the physiological status of the female and the year-season of mating day, buck and doe random permanent environmental effects, and doe additive genetic effects. Results indicated that prolificacy was determined mainly by doe components and that the service sire had a very small effect. Heritabilities for the first and second parities were greater than the estimates obtained under the repeatability model (0.04 to 0.14 for the repeatability model). In the A and V lines, similar values of heritability were found at the first and second parities, but in the Prat line heritability at the second parity was always greater than at the first and greater parities (values of 0.21, 0.17, and 0.15 for TB, BA, and NW, respectively, in second parities of the Prat line). Genetic correlations between the same traits at different parities were approximately 0.8 for all traits in line A, but much lower in the other 2 lines. On average, the values were 0.64 for TB, 0.48 for BA, and 0.39 for NW between the first and second parities, and 0.65 for TB, 0.56 for BA, and 0.45 for NW between the first and third and greater parities. Genetic correlations between the second and greater parities showed the greatest values (approximately 0.8) in lines A and Prat for all traits, but they were lower in line V (0.63 for BA and 0.37 for NW). The heterogeneity of heritabilities and genetic correlations between parities lower than 0.9 suggests that litter size at different parities could be considered as different traits when genetic evaluations are performed. However, when the accuracies of predicted breeding values under a multiple-trait and a repeatability model were calculated, assuming the first to be the true model, the values obtained were nearly the same for all traits in all lines.

Crossbreeding parameter estimation for functional longevity in rabbits using survival analysis methodology

A complete diallel cross involving 3 maternal lines of rabbit was performed to estimate cross-breeding parameters for functional longevity. This trait was defined as the ability to delay involuntary culling. The lines considered, A, V, and Prat, had all been selected by litter size at weaning for a long period. Data were related to a total of 653 does belonging to the 9 genetic types from the diallel cross; does were reared and bred on the same commercial farm. Survival analysis was performed using a Cox proportional hazard model. The model incorporated time-dependent factors, such as year-season, litter size, and the interaction between cycle and physiological status of the female; time-independent factors, such as the genetic type of the doe; and sire and dam random factors. Crossbreeding parameters were estimated from the solutions obtained for the type of doe and its estimated variance-covariance matrix, using a generalized least squares procedure. The estimated parameters were the differences between lines in direct genetic effects and maternal genetic effects and individual heterosis. Relevant differences were observed in direct genetic effects between lines A and Prat but not in any maternal effects. Heterosis was found to be significant and favorable between lines A and Prat, and between the lines V and Prat. The magnitude of this effect was variable but important, especially in the first cross. Results stress the importance of using crosses between specialized lines to produce does for intensive meat rabbit production.

Variability, repeatability and phenotypic relationships of several characteristics of production and semen quality in rabbit

A total of 2140 ejaculates from 156 adult males pertaining to four groups of bucks were analysed and the following traits were recorded: pH, ejaculate volume (V), mass motility (Mm), individual motility (Mi), concentration (Cn), total number of spermatozoa per ejaculate (TSE), percentage of sperm viability (Vi), percentage of sperm with acrosome integrity (NAR), percentage of sperm normalcy (Nr), percentage of sperm morphological abnormalities of head (H), neck-midpiece (Nm) and tail (T) and presence of proximal and distal cytoplasmic droplet (Dp, Dd). Principal component (PC) analysis and phenotypic correlations were performed in order to examine the relationships between qualitative and quantitative traits of rabbit semen. The repeatability of the traits measured was also estimated. Phenotypic correlations between sperm traits were estimated as the residual correlation from an analysis of variance, including the effects of: genetic type of the male, order of the ejaculate, day of collection and the permanent non-additive random effect of the male to which the observation corresponds. The repeatability of these traits was analysed separately, in a set of univariate analyses, using VCE software. The previously defined mixed model was used for this analysis. The principal component analysis was performed using the Princomp procedure of the SAS v.8 package. The first four PC explained 62% of total variation: 23%, 18%, 12% and 8%, respectively. Percentage of sperm viability, NAR, Nr, T and Nm were the predominant variables in the first PC. Mass motility, Mi, pH, Cn and TSE were located in the second. Percentage of sperm with the presence of proximal and distal cytoplasmic droplet, NAR, Vi and Nr were the predominant traits in the third and V defined the fourth. Repeatability of semen quality traits was moderate for most of the traits. The highest values (about 0.45) corresponded to V, Cn, Nr and Dp and the lowest (about 0.10) to H and Nm. Repeatability of the first ejaculate was greater than that of the second for pH, Mm, Mi, H, Dp and Dd.

Elliptical selection experiment for the estimation of genetic parameters of the growth rate and feed conversion ratio in rabbits1

Two elliptical selection experiments were performed in two contemporary sire lines of rabbits (C and R) in order to optimize the experimental design for estimating the genetic parameters of the growth rate (GR) and feed conversion ratio (FCR). Twelve males and 19 females from line C, and 13 males and 23 females from line R, were selected from an ellipse defined by a quadratic index based on these traits. Data from 160 rabbits of each of the parental generations of lines C and R and their offspring (275 and 266 animals, respectively) were used for the analysis. A Bayesian framework was adopted for inference. Marginal posterior distributions of the genetic parameters were obtained by Gibbs sampling. An animal model including batch, parity order, litter size, and common environmental litter effects was assumed. Posterior means (posterior standard deviations) for heritabilities of GR and FCR were estimated to be 0.31 (0.10) and 0.31 (0.10), respectively, in line C and 0.21 (0.08) and 0.25 (0.12) in line R. Posterior means of the proportion of the variance due to common litter environmental effects were 0.14 (0.06) and 0.21 (0.06) for GR and FCR, respectively, in line C and 0.17 (0.06) and 0.22 (0.06) in line R. Posterior means of genetic correlation between both traits were -0.49 (0.25) in line C and -0.47 (0.32) in line R, indicating that selection for GR was expected to result in a similar correlated response in FCR in both lines.