Joint analysis of longitudinal feed intake and single recorded production traits in pigs using a novel Horizontal model

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 r