Should we aim for genetic improvement in host resistance or tolerance to infectious disease?

Abstract

2.3.4 Step 1: Animal models to estimate the genetic relationship between resistance and performance prior to and post infection ……………………..… 31 2.3.5 Step 2: Multi-trait models to examine evidence for genetic variation in tolerance: growth associated with low versus high VL ………………………… 2.3.6 Step 3: Univariate random regression models for estimating genetic variation in tolerance …….. 2.3.7 Step 4: Random regression model using simulated performance in absence of infection for estimating genetic variance in tolerance ……...…. 34 2.4 Results ..……………………………………………... 36 2.4.1 Step 1: Relationship between resistance and performance prior to and post infection ..…...…... 36 2.4.2 Step 2: multi-trait models to examine evidence for genetic variation in tolerance ……………….. 39 2.4.3 Step 3: Estimation of genetic variance in tolerance using univariate random regression Models ………………………………………………...… 40 2.4.4 Step 4: Random regression models including simulated performance in absence of infection for estimating genetic variance in tolerance ………... 43 xii 2.5 Discussion …………………………………………... 47 2.5.1 Summary of findings …………………….… 47 2.5.2 Statistical considerations ……...…………… 49 2.5.3 Implications for genetic improvement of tolerance of pigs to PRRS and other diseases …… 52 2.5.4 Conclusions ………………………………... 55 Appendix 2.1 ………………………………….………………. 57 2.1 Simulating ADG in absence of infection …………… 57 2.1.1 Step 1: Calculate sire breeding values for growth under infection (ADG I) .…………………. 57 2.1.2 Step 2: Calculate sire breeding values for growth in the absence of infection (ADG 0) .…….. 58 2.1.3 Step 3: Calculate phenotypic values for growth without infection for progeny (half sibs) (P Prog) .... 58 Chapter 3 ……………………………………………...…………..… Harnessing longitudinal information to identify genetic variation in tolerance of pigs to Porcine Reproductive and Respiratory Syndrome virus infection ……………………… 61 xiv 3.4.2 Association of the WUR genotype with tolerance …………………………………………. 77 3.4.3 The importance of stages of infection to identify genetic variation in tolerance ……………………. 77 3.4.4 Implications for breeding programmes and conclusions ………………………………………. 79 Appendix 3.1 ……………………………………………….…. 80 3.1 Stage of infection defined by duration ……………… 80 3.2 Genetic variation in tolerance at different stages of infection ………………………………………………… 80 3.3 Genetic variation in tolerance across all stages of infection ……………………………………………….... 81 3.4 Relationship between level, slope and resistance from 21-42 dpi ………………………………………………... 82 3.5 Association of WUR genotype with tolerance slope .. 83 3.6 Relationship between level, slope and resistance across all duration stages of infection ………………………...... 83 Chapter 4 ………………………………………………………….…. 84 Genome-wide association studies for resistance and growth at different stages of infection ……………………………….