Breeding for robustness: investigating the genotype-by-environment interaction and micro-environmental sensitivity of Genetically Improved Farmed Tilapia (Oreochromis niloticus).

Robustness has become a highly desirable breeding goal in the globalized agricultural market. Both genotype-by-environment interaction (G × E) and micro-environmental sensitivity are important robustness components of aquaculture production, in which breeding stock is often disseminated to different environments. The objectives of this study were (i) to quantify the degree of G × E by assessing the growth performance of Genetically Improved Farmed Tilapia (GIFT) across three countries (Malaysia, India and China) and (ii) to quantify the genetic heterogeneity of environmental variance for body weight at harvest (BW) in GIFT as a measure of micro-environmental sensitivity. Selection for BW was carried out for 13 generations in Malaysia. Subsets of 60 full-sib families from Malaysia were sent to China and India after five and nine generations respectively. First, a multi-trait animal model was used to analyse the BW in different countries as different traits. The results indicate a strong G × E. Second, a genetically structured environmental variance model, implemented using Bayesian inference, was used to analyse micro-environmental sensitivity of BW in each country. The analysis revealed the presence of genetic heterogeneity of both BW and its environmental variance in all environments. The presence of genetic variation in residual variance of BW implies that the residual variance can be modified by selection. Incorporating both G × E and micro-environmental sensitivity information may help in selecting robust genotypes with high performance across environments and resilience to environmental fluctuations.

Comparison of repeatability and multiple trait threshold models for litter size in sheep using observed and simulated data in Bayesian analyses.

Bayesian analyses were used to estimate genetic parameters on 5580 records of litter size in the first four parities from 1758 Mule ewes. To examine the appropriateness of fitting repeatability (RM) or multiple trait threshold models (MTM) to litter size of different parities, both models were used to estimate genetic parameters on the observed data and were thereafter compared in a simulation study. Posterior means of the heritabilities of litter size in different parities using a MTM ranged from 0.12 to 0.18 and were higher than the heritability based on the RM (0.08). Posterior means of the genetic correlations between litter sizes of different parities were positive and ranged from 0.24 to 0.71. Data sets were simulated based on the same pedigree structure and genetic parameters of the Mule ewe population obtained from both models. The simulation showed that the relative loss in accuracy and increase in mean squared error (MSE) was substantially higher when using the RM, given that the parameters estimated from the observed data using the opposite model are the true parameters. In contrast, Bayesian information criterion (BIC) selected the RM as most appropriate model given the data because of substantial penalty for the higher number of parameters to be estimated in the MTM model. In conclusion, when the relative change in accuracy and MSE is of main interest for estimation of breeding values of litter size of different parities, the MTM is recommended for the given population. When reduction in risk of using the wrong model is the main aim, the BIC suggest that the RM is the most appropriate model.

Genetic parameters of piglet survival and birth weight from a two-generation crossbreeding experiment under outdoor conditions designed to disentangle direct and maternal effects.

Multivariate Bayesian linear-threshold models were used to estimate genetic parameters of peri- and postnatal piglet survival and individual birth weight of piglets reared under outdoor conditions. Data of 21,835 individual piglet observations were available from a 2-generation crossbreeding experiment selected for direct and maternal genetic effects of postnatal piglet survival on piglet and dam levels, respectively. In the first generation, approximately one-half of the Landrace sires used were selected for large or average breeding values of maternal genetic effects on postnatal piglet survival, whereas in the second generation the Large White sires used were selected for direct genetic effects of the same trait. Estimates of direct and maternal heritability were 0.21 and 0.15, 0.24 and 0.14, and 0.36 and 0.28 for piglet survival at birth and during the nursing period, and individual birth weight, respectively. In particular, direct heritabilities are substantially larger than those from the literature estimated for indoor-reared piglets, suggesting that genetic effects of these traits are substantially greater under outdoor conditions. Direct or maternal genetic correlations between survival traits or with birth weight were small (ranging from 0.06 to 0.17), indicating that peri- and postnatal survival are genetically under rather different control, and survival was only slightly positively influenced by birth weight. There were significant (P < 0.05) negative genetic correlations between direct and maternal genetic effects within each of the analyzed traits ranging from -0.36 to -0.45, which have to be considered when selecting for piglet survival. Adjustment of traits for litter size or inclusion of genetic groups showed insignificant effects on the magnitude of the estimated genetic parameters. The magnitude of genetic parameters suggested that there is substantial potential for genetic improvement of survival traits and birth weight in direct and maternal genetic effects, especially when piglets are kept under outdoor conditions.

Genetic relationship between longevity and objectively or subjectively assessed performance traits in sheep using linear censored models.

Genetic parameters of longevity in crossbred Mule ewes, and genetic relationships among longevity, growth, body composition, and subjectively assessed traits on Mule lambs and ewes have been estimated using Bayesian linear censored models. Additionally, the genetic associations between longevity and culling reasons were examined. Data comprised 1,797 observations of Mule ewes for longevity, culling reasons, growth, body composition, mouth scores, and type traits. Longevity was defined as the time (in years) from 2 yr of age (the age at first lambing of most ewes) to culling or death. Censored data (i.e., observations for which only the lower bound of the true longevity is known, such as when the animals are still alive) comprised 24% of all observations for longevity. Bivariate analyses were used to analyze the longevity of the ewe with each performance trait by fitting linear Bayesian models considering censored observations. Longevity was split into 3 different sub-traits: age at culling due to teeth/mouth conditions, age at culling due to udder conditions, and age at culling due to other culling reasons. These sub-traits and their aggregation into the overall trait of longevity were analyzed in a multiple-trait model. The heritability of longevity was moderate at 0.27, whereas heritabilities of the growth and body composition traits ranged from 0.11 for average of shoulder, loin, and gigot conformation to 0.36 for ewe BW at first premating. Mouth scores and type traits had heritabilities ranging from 0.13 for jaw position to 0.39 for fleece quality. All analyzed traits showed low genetic correlations with longevity, ranging from -0.20 for average conformation scores in live animals to 0.18 for tooth angle. Teeth/mouth conditions resulted in the greatest heritability (0.15) among the sub-traits based on the separate culling reasons. Genetic correlations between separate culling reasons were low to high (0.12 to 0.63 for teeth/mouth conditions with udder conditions and other culling reasons, respectively). Longevity may be preferred as a selection criterion because of (i) its moderate heritability compared with its component sub-traits based on specific culling reasons, and (ii) its moderate to high genetic correlation with these component sub-traits. The moderate heritability for longevity reflects the potential of this trait for genetic improvement, especially when longevity is based on clearly defined culling reasons.

Bayesian analysis of genetic associations of skin lesions and behavioural traits to identify genetic components of individual aggressiveness in pigs.

There is increasing interest in genetic selection against behavioural traits that impact negatively on welfare and productivity in commercial livestock production. Post-mixing aggressiveness in pigs shows wide phenotypic variation, affects health, welfare and growth performance and is a routine feature of production. A Bayesian approach was used to estimate the heritability of three traits associated with aggressiveness in pigs during the 24 h post-mixing; duration in reciprocal aggression, and in receipt of, or delivery of non-reciprocal aggression (NRA). For the purposes of genetic selection, recording aggressive behaviour is excessively labour intensive. The genetic correlations were quantified between the behavioural traits and an easily measurable indicator trait; the number of skin lesions following mixing (lesion score, LS). The heritabilities for the three behavioural traits ranged from 0.17 to 0.46 (receipt of NRA and reciprocal aggression respectively). The duration in reciprocal aggression and in delivery of NRA showed a strong genetic correlation (r g = 0.79 with 95% Bayesian credibility interval of 0.62-0.94). The genetic correlation between LS and these two behaviours indicated that selection on breeding values of LS could be used to reduce aggressiveness. The duration in receipt of NRA appeared to be regulated by different genes or genomic effects compared with the other behavioural traits and LS. Although duration in receipt of NRA was not genetically associated with LS, it was lowly but significantly environmentally associated with the residuals of central and caudal LS (r e = 0.28-0.32), indicating that pigs that received NRA also received bites on the central and caudal third of the body. The pen that the animals were mixed into was found to be a very important factor for the analysed traits, in particular those representing behavioural characteristics. Based on the estimated genetic parameters, it is concluded that selection on breeding values for reduced LS (especially central LS) is expected to reduce reciprocal aggression and the delivery of NRA but will not change the receipt of NRA directly.

A Bayesian approach to the effect of selection for growth rate on sensory meat quality of rabbit.

The effect of selection for growth rate on the sensory characteristics of rabbit meat was assessed by comparing a selected and a control population of rabbits. Embryos belonging to generation 7th were frozen, thawed and implanted in does in order to produce the control group. The control group was formed from the offspring of the embryos belonging to the 7th generation. Selected animals belonging to 21st generation (S) were compared with animals of the control group (C), both were contemporary. Forty animals per group were slaughtered at 9-weeks-old. The sensory analysis was carried out on samples of the Longissimus dorsi muscle. The parameters evaluated were: intensity of rabbit flavour (IRF), aniseed odour (AO), aniseed flavour (AF), liver flavour (LF), tenderness (T), juiciness (J), fibrousness (F). A Bayesian analysis was performed. The ratio of the selection and control effects was analysed. There was a difference between the selected and control groups for IRF, AO, AF and LF. Conversely, no differences were found in T, J and F between groups. Selected group had 3% and 23% higher values of IRF and LF, respectively, than the control group. A relevant effect of selection on AO and AF appeared (probability of relevance P(r)=1), with lower values for selected animals. There was a difference between male and female groups for IRF, but this was not relevant. No differences between sexes were found for the rest of the characteristics evaluated. Selection for growth rate did not affect the main sensory characteristics of meat, like T and J but, it had a negative effect on some flavour characteristics.