ImmuneDEX: a strategy for the genetic improvement of immune competence in Australian Angus cattle

Abstract

In animal breeding and genetics, the ability to cope with disease, here defined as immune competence (IC), with minimal detriment to growth and fertility is a desired objective which addresses both animal production and welfare considerations. However, defining and objectively measuring IC phenotypes using testing methods which are practical to apply on-farm has been challenging. Based on previously described protocols, we measured both cell-mediated immune response (Cell-IR) and antibody-mediated immune response (Ab-IR) and combined these measures to determine an animal’s IC. Using a population of 2,853 Australian Angus steers and heifers, we compared 2 alternative methods to combine both metrics into a single phenotype to be used as a tool for the genetic improvement of IC. The first method, named ZMEAN, is obtained by taking the average of the individual metrics after subjecting each to a Z-score standardization. The second, ImmuneDEX (IDEX), is a weighted average that considers the correlation between Cell-IR and Ab-IR, as well as the difference in ranking of individuals by each metric, and uses these as weights in the averaging. Both simulation and real data were used to understand the behavior of ZMEAN and IDEX. To further ascertain the relationship between IDEX and other traits of economic importance, we evaluated a range of traits related to growth, feedlot performance, and carcass characteristics. We report estimates of heritability of 0.31 ± 0.06 for Cell-IR, 0.42 ± 0.06 for Ab-IR, 0.42 ± 0.06 for ZMEAN and 0.370 ± 0.06 for IDEX, as well as a unity genetic correlation (rg) between ZMEAN and IDEX. While a moderately positive rg was estimated between Cell-IR and Ab-IR (rg = 0.33 ± 0.12), strongly positive estimates were obtained between IDEX and Cell-IR (rg = 0.80 ± 0.05) and between IDEX and Ab-IR (rg = 0.85 ± 0.04). We obtained a moderately negative rg between IC traits and growth including an rg = −0.38 ± 0.14 between IDEX and weaning weight, and negligible with carcass fat measurements, including an rg = −0.03 ± 0.12 between IDEX and marbling. Given that breeding with a sole focus on production might inadvertently increase susceptibility to disease and associated antibiotic use, our analyses suggest that ImmuneDEX will provide a basis to breed animals that are both highly productive and with an enhanced ability to resist disease.

ImmuneDEX: updated genomic estimates of genetic parameters and breeding values for Australian Angus cattle

“…Further research is needed to (re)evaluate the relationship between the immune competence phenotypes analysed here and productivity-based phenotypes related to growth, feedlot performance and carcass characteristics. In particular, it would be of interest to recapitulate the negative genetic correlation between the immune competence traits and the growth traits, such as -0.38 AE 0.14 between IDEX and the weaning weight estimated by Reverter et al (2021). Such finding would agree with previous reports showing that selection for productivity, with no emphasis on health and fitness traits, has increased susceptibility to disease in many species of food-producing animals (Rauw et al 1998).…”

“…for Cell-IR, Ab-IR and IDEX were 17.093 (AE2.852), 153.646 (AE31.236) and 0.260 (AE0.047) respectively. The estimated r g between Cell-IR and Ab-IR was 0.138 AE 0.095, closer to zero and more precisely estimated because of the larger sample size than the 0.33 AE 0.12 (Reverter et al 2021), 0.48 AE 0.19 (Hine et al 2019) or the 0.40 AE 0.22 from Dominik et al (2019) values reported previously. However, strongly positive estimates of genetic correlation were obtained between IDEX and Cell-IR (r g = 0.740 AE 0.044) and between IDEX and Ab-IR (r g = 0.741 AE 0.036).…”

“…However, strongly positive estimates of genetic correlation were obtained between IDEX and Cell-IR (r g = 0.740 AE 0.044) and between IDEX and Ab-IR (r g = 0.741 AE 0.036). These high genetic correlation estimates between component traits and the composite trait are comparatively less extreme, but within two s.e., of the ones reported by Reverter et al (2021) of 0.80 AE 0.05 (for IDEX and Cell-IR) and 0.85 AE 0.04 (for IDEX and Ab-IR). Taken together, these values anticipate the suitability of IDEX as a single phenotype to aid in the genetic improvement of immune competence and potentially general disease resistance in the current population.…”

“…Table 1 provides summary statistics for all phenotypes and covariates used in analyses. To approximate normality, the immune competence phenotypes for Cell-IR and Ab-IR were log-and square root-transformed respectively, and were consistent with the values reported by Reverter et al (2021), using a subset of 2853 animals. Across all 3715 animals from the current study, and using raw unadjusted measurements, the correlation between Cell-IR and Ab-IR was moderately positive at 0.195 AE 0.016 and slightly higher for steers (0.206 AE 0.020) than for heifers (0.138 AE 0.027).…”

“…More recently, Reverter et al (2021) expanded that earlier work by using a population of 2853 Australian Angus steers and heifers to estimate pedigree-based genetic parameters for immune response metrics. The authors also introduced ImmuneDEX (IDEX) as a single phenotype that describes immune competence by combining Cell-IR and Ab-IR into a single measure and reported its relationship with commonly measured traits related to growth, feedlot performance and carcass characteristics.…”