216 Contribution of host gut microbiome in prediction of meat quality and carcass composition traits in swine

Abstract

Abstract The objective of this study was to assess the improvement in predictive ability (PA) for meat quality and carcass composition traits by including the effect of host gut microbiome. Data were collected from Duroc sired three-way crossbred individuals (n = 1,123) genotyped from 60k SNP chips. Fecal 16S microbial sequences for all individuals were obtained at three different stages: weaning (WEAN: 18.64±1.09 days); week 15 (W_15: 118.2±1.18 days); and off test (OT: 196.4±7.80 days). A 4-fold cross validation was used, with animals grouped based on sire relatedness. Analysis was conducted in “BGLR” package in R. The first model included the fixed effect of dam line, contemporary group, and sex, as well as random pen and additive genetic effect (with genomic relationship matrix). The second model included same fixed and random effects with the addition of the microbiome effect (with microbiome relationship matrix). With the inclusion of microbiome, the PA increased for majority of traits. For carcass traits, the increase in PA was greatest for belly weight which changed from 0.22±0.06 to 0.32±0.06 at OT and lowest for loin depth and ham weight which changed from 0.14±0.06 to 0.15 ±0.06 and 0.12±0.02 to 0.13 ±0.03 at WEAN respectively. For meat quality traits, the increase in PA was greatest for subjective firmness score which changed from 0.16±0.04 to 0.19±0.04 at OT and lowest for marbling score and intramuscular fat which changed from 0.27±0.09 to 0.28±0.08 and 0.39±0.05 to 0.40±0.05 at WEAN respectively. Higher predictive ability was observed at OT rather than at WEAN and W_15 microbiome information. The results may lead to a newer approach to the genetic evaluation program of swine.