Longitudinal analysis of direct and indirect effects on average daily gain in rabbits using a structured antedependence model

Abstract

BackgroundIndirect 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.ResultsThe 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.ConclusionsIndirect 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.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0395-9) contains supplementary material, which is available to authorized users.

New residual feed intake criterion for longitudinal data

“…The RR approach has also been used to model RFI when FI is recorded longitudinally but only single records are available for production traits [ 35 ]. However, applying the RR approach to multiple traits requires estimation of more parameters than with the SAD approach and can lead to convergence problems [ 27 ]. The SAD approach has also other advantages over the RR approach, including providing a better fit to the data in many situations [ 17 , 18 , 24 , 25 ], suffering less from the drawbacks reported for the RR model such as border effects [ 36 ], and from the challenge to properly estimate correlations that decrease over time [ 18 ].…”

“…The multi-SAD regression model is derived from a multiple trait SAD model [ 24 , 27 ]. A detailed description of the general form of the multiple trait SAD model is given in David et al [ 24 ].…”

Dynamic distribution of gut microbiota in meat rabbits at different growth stages and relationship with average daily gain (ADG)

“…ADG is a complex quantitative trait [74], therefore, a total of 105 Ira rabbits (53 males and 52 females) were used in the present study derived from Laidewang Animal Husbandry Co., Ltd., Sanming, China. Six to eight pup rabbits per cage were raised with their dam under natural light and room temperature in the same commercial farm.…”