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Lenoir G, Flatres-Grall L, Muñoz-Tamayo R, David I, Friggens NC. Disentangling the dynamics of energy allocation to develop a proxy for robustness of fattening pigs. Genet Sel Evol 2023; 55:77. [PMID: 37936078 PMCID: PMC10629156 DOI: 10.1186/s12711-023-00851-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND There is a growing need to improve robustness of fattening pigs, but this trait is difficult to phenotype. Our first objective was to develop a proxy for robustness of fattening pigs by modelling the longitudinal energy allocation coefficient to growth, with the resulting environmental variance of this allocation coefficient considered as a proxy for robustness. The second objective was to estimate its genetic parameters and correlations with traits under selection and with phenotypes that are routinely collected. In total, 5848 pigs from a Pietrain NN paternal line were tested at the AXIOM boar testing station (Azay-sur-Indre, France) from 2015 to 2022. This farm is equipped with an automatic feeding system that records individual weight and feed intake at each visit. We used a dynamic linear regression model to characterize the evolution of the allocation coefficient between the available cumulative net energy, which was estimated from feed intake, and cumulative weight gain during the fattening period. Longitudinal energy allocation coefficients were analysed using a two-step approach to estimate both the genetic variance of the coefficients and the genetic variance in their residual variance, which will be referred to as the log-transformed squared residual (LSR). RESULTS The LSR trait, which could be interpreted as an indicator of the response of the animal to perturbations/stress, showed a low heritability (0.05 ± 0.01), a high favourable genetic correlation with average daily growth (- 0.71 ± 0.06), and unfavourable genetic correlations with feed conversion ratio (- 0.76 ± 0.06) and residual feed intake (- 0.83 ± 0.06). Segmentation of the population in four classes using estimated breeding values for LSR showed that animals with the lowest estimated breeding values were those with the worst values for phenotypic proxies of robustness, which were assessed using records routinely collected on farm. CONCLUSIONS Results of this study show that selection for robustness, based on estimated breeding values for environmental variance of the allocation coefficients to growth, can be considered in breeding programs for fattening pigs.
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Affiliation(s)
- Guillaume Lenoir
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120, Palaiseau, France.
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31320, Castanet Tolosan, France.
- AXIOM, 37310, Azay-Sur-Indre, France.
| | | | - Rafael Muñoz-Tamayo
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120, Palaiseau, France
| | - Ingrid David
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31320, Castanet Tolosan, France
| | - Nicolas C Friggens
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120, Palaiseau, France
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David I, Ricard A, Huynh-Tran VH, Dekkers JCM, Gilbert H. Quality of breeding value predictions from longitudinal analyses, with application to residual feed intake in pigs. Genet Sel Evol 2022; 54:32. [PMID: 35562648 PMCID: PMC9103455 DOI: 10.1186/s12711-022-00722-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/20/2022] [Indexed: 11/10/2022] Open
Abstract
Background An important goal in animal breeding is to improve longitudinal traits. The objective of this study was to explore for longitudinal residual feed intake (RFI) data, which estimated breeding value (EBV), or combination of EBV, to use in a breeding program. Linear combinations of EBV (summarized breeding values, SBV) or phenotypes (summarized phenotypes) derived from the eigenvectors of the genetic covariance matrix over time were considered, and the linear regression method (LR method) was used to facilitate the evaluation of their prediction accuracy. Results Weekly feed intake, average daily gain, metabolic body weight, and backfat thickness measured on 2435 growing French Large White pigs over a 10-week period were analysed using a random regression model. In this population, the 544 dams of the phenotyped animals were genotyped. These dams did not have own phenotypes. The quality of the predictions of SBV and breeding values from summarized phenotypes of these females was evaluated. On average, predictions of SBV at the time of selection were unbiased, slightly over-dispersed and less accurate than those obtained with additional phenotypic information. The use of genomic information did not improve the quality of predictions. The use of summarized instead of longitudinal phenotypes resulted in predictions of breeding values of similar quality. Conclusions For practical selection on longitudinal data, the results obtained with this specific design suggest that the use of summarized phenotypes could facilitate routine genetic evaluation of longitudinal traits. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00722-w.
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Affiliation(s)
- Ingrid David
- GenPhySE, INRAE, Université de Toulouse, INPT, 31326, Castanet Tolosan, France.
| | - Anne Ricard
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78352, Jouy-en-Josas, France.,Département Recherche et Innovation, Institut Français du Cheval et de l'Equitation, 61310, Exmes, France
| | - Van-Hung Huynh-Tran
- GenPhySE, INRAE, Université de Toulouse, INPT, 31326, Castanet Tolosan, France
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Hélène Gilbert
- GenPhySE, INRAE, Université de Toulouse, INPT, 31326, Castanet Tolosan, France
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David I, Huynh Tran VH, Gilbert H. New residual feed intake criterion for longitudinal data. Genet Sel Evol 2021; 53:53. [PMID: 34171995 PMCID: PMC8235855 DOI: 10.1186/s12711-021-00641-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 05/26/2021] [Indexed: 11/28/2022] Open
Abstract
Background Residual feed intake (RFI) is one measure of feed efficiency, which is usually obtained by multiple regression of feed intake (FI) on measures of production, body weight gain and tissue composition. If phenotypic regression is used, the resulting RFI is generally not genetically independent of production traits, whereas if RFI is computed using genetic regression coefficients, RFI and production traits are independent at the genetic level. The corresponding regression coefficients can be easily derived from the result of a multiple trait model that includes FI and production traits. However, this approach is difficult to apply in the case of multiple repeated measurements of FI and production traits. To overcome this difficulty, we used a structured antedependence approach to account for the longitudinality of the data with a phenotypic regression model or with different genetic and environmental regression coefficients [multi- structured antedependence model (SAD) regression model]. Results After demonstrating the properties of RFI obtained by the multi-SAD regression model, we applied the two models to FI and production traits that were recorded for 2435 French Large White pigs over a 10-week period. Heritability estimates were moderate with both models. With the multi-SAD regression model, heritability estimates were quite stable over time, ranging from 0.14 ± 0.04 to 0.16 ± 0.05, while heritability estimates showed a U-shaped profile with the phenotypic regression model (ranging from 0.19 ± 0.06 to 0.28 ± 0.06). Estimates of genetic correlations between RFI at different time points followed the same pattern for the two models but higher estimates were obtained with the phenotypic regression model. Estimates of breeding values that can be used for selection were obtained by eigen-decomposition of the genetic covariance matrix. Correlations between these estimated breeding values obtained with the two models ranged from 0.66 to 0.83. Conclusions The multi-SAD model is preferred for the genetic analysis of longitudinal RFI because, compared to the phenotypic regression model, it provides RFI that are genetically independent of production traits at all time points. Furthermore, it can be applied even when production records are missing at certain time points. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00641-2.
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Affiliation(s)
- Ingrid David
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France.
| | | | - Hélène Gilbert
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
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Marie-Etancelin C, Francois D, Weisbecker JL, Marcon D, Moreno-Romieux C, Bouvier F, Tortereau F. Detailed genetic analysis of feeding behaviour in Romane lambs and links with residual feed intake. J Anim Breed Genet 2019; 136:174-182. [PMID: 30945778 DOI: 10.1111/jbg.12392] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 11/28/2022]
Abstract
Breeding strategies based on feed efficiency are now implemented in most animal species using residual feed intake (RFI) criteria. Although relevant, the correlated responses of feeding behaviour traits resulting from such selection on RFI are poorly documented. We report the estimated feeding behaviour at three time levels (visit, meal and day) and genetic parameters between the feeding behaviour traits and their links with RFI and its components. Feed intake, feeding duration at three time levels (per visit, meal and day), feeding rate, number of visits and time-between-visits were estimated for 951 Romane lambs fed via automatic concentrate feeders. Heritability estimates of feeding behaviour traits ranged from 0.19 to 0.54 with higher estimates for the day level than the visit level. Daily feed intake was not genetically linked to feed intake at the visit level, whereas feeding duration between visit and day levels was moderately correlated (Rg = +0.41 ± 0.12). RFI was not significantly correlated with feeding rate, but was positively linked to feed intake and feeding duration at the day level (+0.73 ± 0.09 and +0.41 ± 0.13, respectively) and negatively at the visit level (-0.33 ± 0.14 and -0.22 ± 0.17, respectively). Selecting animals with lower RFI values might modify their feeding behaviour by increasing feed intake and feeding duration at the visit level but decrease the number of visits per day (+0.51 ± 0.14).
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Affiliation(s)
| | - Dominique Francois
- GenPhySE, INRA, INPT, INP-ENVT, Université de Toulouse, Castanet Tolosan, France
| | | | - Didier Marcon
- Unité Expérimentale La Sapinière, INRA, Osmoy, France
| | | | | | - Flavie Tortereau
- GenPhySE, INRA, INPT, INP-ENVT, Université de Toulouse, Castanet Tolosan, France
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Huynh-Tran VH, Gilbert H, David I. Genetic structured antedependence and random regression models applied to the longitudinal feed conversion ratio in growing Large White pigs. J Anim Sci 2018; 95:4752-4763. [PMID: 29293706 DOI: 10.2527/jas2017.1864] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The objective of the present study was to compare a random regression model, usually used in genetic analyses of longitudinal data, with the structured antedependence (SAD) model to study the longitudinal feed conversion ratio (FCR) in growing Large White pigs and to propose criteria for animal selection when used for genetic evaluation. The study was based on data from 11,790 weekly FCR measures collected on 1,186 Large White male growing pigs. Random regression (RR) using orthogonal polynomial Legendre and SAD models was used to estimate genetic parameters and predict FCR-based EBV for each of the 10 wk of the test. The results demonstrated that the best SAD model (1 order of antedependence of degree 2 and a polynomial of degree 2 for the innovation variance for the genetic and permanent environmental effects, i.e., 12 parameters) provided a better fit for the data than RR with a quadratic function for the genetic and permanent environmental effects (13 parameters), with Bayesian information criteria values of -10,060 and -9,838, respectively. Heritabilities with the SAD model were higher than those of RR over the first 7 wk of the test. Genetic correlations between weeks were higher than 0.68 for short intervals between weeks and decreased to 0.08 for the SAD model and -0.39 for RR for the longest intervals. These differences in genetic parameters showed that, contrary to the RR approach, the SAD model does not suffer from border effect problems and can handle genetic correlations that tend to 0. Summarized breeding values were proposed for each approach as linear combinations of the individual weekly EBV weighted by the coefficients of the first or second eigenvector computed from the genetic covariance matrix of the additive genetic effects. These summarized breeding values isolated EBV trajectories over time, capturing either the average general value or the slope of the trajectory. Finally, applying the SAD model over a reduced period of time suggested that similar selection choices would result from the use of the records from the first 8 wk of the test. To conclude, the SAD model performed well for the genetic evaluation of longitudinal phenotypes.
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David I, Sánchez JP, Piles M. Longitudinal analysis of direct and indirect effects on average daily gain in rabbits using a structured antedependence model. Genet Sel Evol 2018; 50:25. [PMID: 29747574 PMCID: PMC5946580 DOI: 10.1186/s12711-018-0395-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 04/24/2018] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Indirect genetic effects (IGE) are important components of various traits in several species. Although the intensity of social interactions between partners likely vary over time, very few genetic studies have investigated how IGE vary over time for traits under selection in livestock species. To overcome this issue, our aim was: (1) to analyze longitudinal records of average daily gain (ADG) in rabbits subjected to a 5-week period of feed restriction using a structured antedependence (SAD) model that includes IGE and (2) to evaluate, by simulation, the response to selection when IGE are present and genetic evaluation is based on a SAD model that includes IGE or not. RESULTS The direct genetic variance for ADG (g/d) increased from week 1 to 3 [from 8.03 to 13.47 (g/d)2] and then decreased [6.20 (g/d)2 at week 5], while the indirect genetic variance decreased from week 1 to 4 [from 0.43 to 0.22 (g/d)2]. The correlation between the direct genetic effects of different weeks was moderate to high (ranging from 0.46 to 0.86) and tended to decrease with time interval between measurements. The same trend was observed for IGE for weeks 2 to 5 (correlations ranging from 0.62 to 0.91). Estimates of the correlation between IGE of week 1 and IGE of the other weeks did not follow the same pattern and correlations were lower. Estimates of correlations between direct and indirect effects were negative at all times. After seven generations of simulated selection, the increase in ADG from selection on EBV from a SAD model that included IGE was higher (~ 30%) than when those effects were omitted. CONCLUSIONS Indirect genetic effects are larger just after mixing animals at weaning than later in the fattening period, probably because of the establishment of social hierarchy that is generally observed at that time. Accounting for IGE in the selection criterion maximizes genetic progress.
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Affiliation(s)
- Ingrid David
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326, Castanet Tolosan, France.
| | - Juan-Pablo Sánchez
- Institute for Food and Agriculture Research and Technology, Torre Marimon s/n, 08140, Caldes de Montbui, Barcelona, Spain
| | - Miriam Piles
- Institute for Food and Agriculture Research and Technology, Torre Marimon s/n, 08140, Caldes de Montbui, Barcelona, Spain
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Wang W. Checking identifiability of covariance parameters in linear mixed effects models. J Appl Stat 2017. [DOI: 10.1080/02664763.2016.1238050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Wei Wang
- Department of Surgical Outcomes and Analysis, Kaiser Permanente, San Diego, CA, USA
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Shirali M, Strathe AB, Mark T, Nielsen B, Jensen J. Joint analysis of longitudinal feed intake and single recorded production traits in pigs using a novel Horizontal model. J Anim Sci 2017; 95:1050-1062. [PMID: 28380533 DOI: 10.2527/jas.2016.0606] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A novel Horizontal model is presented for multitrait analysis of longitudinal traits through random regression analysis combined with single recorded traits. Weekly ADFI on test for Danish Duroc, Landrace, and Yorkshire boars were available from the national test station and were collected from 30 to 100 kg BW. Single recorded production traits of ADG from birth to 30 kg BW (ADG30), ADG from 30 to 100 kg BW (ADG100), and lean meat percentage (LMP) were available from breeding herds or the national test station. The Horizontal model combined random regression analysis of feed intake (FI) with single recorded traits of ADG100, LMP, and ADG30. In the Horizontal model, the FI data were horizontally structured with FI on each week as a "trait." The additive genetic and litter effects were modeled to be common across different FI records by reducing the rank of the covariance matrices using second- and first-order Legendre polynomials of age on test, respectively. The fixed effect and random residual variance were estimated for each weekly FI trait. Residual feed intake (RFI) was derived from the conditional distribution of FI given the breeding values of ADG100 and LMP. The heritability of FI varied by week on test in Duroc (0.12 to 0.19), Landrace (0.13 to 0.22), and Yorkshire (0.21 to 0.23). The heritability of RFI was lowest and highest in wk 6 (0.03) and 10 (0.10), respectively, in Duroc and wk 7 (0.04 and 0.02) and 1 (0.09 and 0.20), respectively, in Landrace and Yorkshire. The proportion of FI genetic variance explained by RFI ranged from 20 to 75% in Duroc, from 19 to 75% in Landrace, and from 11 to 91% in Yorkshire. Average daily gain from 30 to 100 kg BW and ADG30 heritabilities were moderate in Duroc (0.24 and 0.22, respectively), Landrace (0.34 and 0.25, respectively), and Yorkshire (0.34 and 0.22, respectively). Lean meat percentage heritability was moderate in Duroc (0.37) and large in Landrace (0.62) and Yorkshire (0.60). The genetic correlation of FI with ADG100 increased by week on test followed by a 32% decrease from wk 7 in Duroc and a 7% decrease in dam line breeds. Defining RFI as genetically independent of production traits leads to consistent and easy interpretable breeding values. The genetic parameters of traits in the feed efficiency complex and their dynamics over the test period showed breed differences that could be related to the fatness and growth potential of the breeds. The Horizontal model can be used to simultaneously analyze repeated and single recorded traits through proper modeling of the environmental variances and covariances.
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Tran VHH, Gilbert H, David I. How to improve breeding value prediction for feed conversion ratio in the case of incomplete longitudinal body weights. J Anim Sci 2017; 95:39-48. [PMID: 28177346 DOI: 10.2527/jas.2016.0980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
With the development of automatic self-feeders, repeated measurements of feed intake are becoming easier in an increasing number of species. However, the corresponding BW are not always recorded, and these missing values complicate the longitudinal analysis of the feed conversion ratio (FCR). Our aim was to evaluate the impact of missing BW data on estimations of the genetic parameters of FCR and ways to improve the estimations. On the basis of the missing BW profile in French Large White pigs (male pigs weighed weekly, females and castrated males weighed monthly), we compared 2 different ways of predicting missing BW, 1 using a Gompertz model and 1 using a linear interpolation. For the first part of the study, we used 17,398 weekly records of BW and feed intake recorded over 16 consecutive weeks in 1,222 growing male pigs. We performed a simulation study on this data set to mimic missing BW values according to the pattern of weekly proportions of incomplete BW data in females and castrated males. The FCR was then computed for each week using observed data (obser_FCR), data with missing BW (miss_FCR), data with BW predicted using a Gompertz model (Gomp_FCR), and data with BW predicted by linear interpolation (interp_FCR). Heritability (h) was estimated, and the EBV was predicted for each repeated FCR using a random regression model. In the second part of the study, the full data set (males with their complete BW records, castrated males and females with missing BW) was analyzed using the same methods (miss_FCR, Gomp_FCR, and interp_FCR). Results of the simulation study showed that h were overestimated in the case of missing BW and that predicting BW using a linear interpolation provided a more accurate estimation of h and of EBV than a Gompertz model. Over 100 simulations, the correlation between obser_EBV and interp_EBV, Gomp_EBV, and miss_EBV was 0.93 ± 0.02, 0.91 ± 0.01, and 0.79 ± 0.04, respectively. The heritabilities obtained with the full data set were quite similar for miss_FCR, Gomp_FCR, and interp_FCR. In conclusion, when the proportion of missing BW is high, genetic parameters of FCR are not well estimated. In French Large White pigs, in the growing period extending from d 65 to 168, prediction of missing BW using a Gompertz growth model slightly improved the estimations, but the linear interpolation improved the estimation to a greater extent. This result is due to the linear rather than sigmoidal increase in BW over the study period.
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David I, Garreau H, Balmisse E, Billon Y, Canario L. Multiple-trait structured antedependence model to study the relationship between litter size and birth weight in pigs and rabbits. Genet Sel Evol 2017; 49:11. [PMID: 28107818 PMCID: PMC5439150 DOI: 10.1186/s12711-017-0288-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Some genetic studies need to take into account correlations between traits that are repeatedly measured over time. Multiple-trait random regression models are commonly used to analyze repeated traits but suffer from several major drawbacks. In the present study, we developed a multiple-trait extension of the structured antedependence model (SAD) to overcome this issue and validated its usefulness by modeling the association between litter size (LS) and average birth weight (ABW) over parities in pigs and rabbits. METHODS The single-trait SAD model assumes that a random effect at time [Formula: see text] can be explained by the previous values of the random effect (i.e. at previous times). The proposed multiple-trait extension of the SAD model consists in adding a cross-antedependence parameter to the single-trait SAD model. This model can be easily fitted using ASReml and the OWN Fortran program that we have developed. In comparison with the random regression model, we used our multiple-trait SAD model to analyze the LS and ABW of 4345 litters from 1817 Large White sows and 8706 litters from 2286 L-1777 does over a maximum of five successive parities. RESULTS For both species, the multiple-trait SAD fitted the data better than the random regression model. The difference between AIC of the two models (AIC_random regression-AIC_SAD) were equal to 7 and 227 for pigs and rabbits, respectively. A similar pattern of heritability and correlation estimates was obtained for both species. Heritabilities were lower for LS (ranging from 0.09 to 0.29) than for ABW (ranging from 0.23 to 0.39). The general trend was a decrease of the genetic correlation for a given trait between more distant parities. Estimates of genetic correlations between LS and ABW were negative and ranged from -0.03 to -0.52 across parities. No correlation was observed between the permanent environmental effects, except between the permanent environmental effects of LS and ABW of the same parity, for which the estimate of the correlation was strongly negative (ranging from -0.57 to -0.67). CONCLUSIONS We demonstrated that application of our multiple-trait SAD model is feasible for studying several traits with repeated measurements and showed that it provided a better fit to the data than the random regression model.
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Affiliation(s)
- Ingrid David
- GenPhySE, INRA, INPT, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France.
| | - Hervé Garreau
- GenPhySE, INRA, INPT, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | | | | | - Laurianne Canario
- GenPhySE, INRA, INPT, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
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