The influence of host genotype and gut microbial interactions on feed efficiency traits in pigs

Feed efficiency and growth performance are economically important traits in pigs. Precious studies have been revealed that both genetics and gut microbes could influence host phenotypes, however, the mechanisms by which they affect pig growth and feed efficiency remain poorly understood. In this study, 361 crossbred Duroc × (Landrace × Yorkshire) commercial pigs were genotyped using GeneSeek Porcine SNP50K BeadChip, and the microbiotas from fecal samples were acquired using microbial 16S rRNA gene sequencing technology to investigate the impact of host genetics and gut microorganisms on growth and feed efficiency. The results showed that the heritability and enterobacterial force ranged from 0.27 to 0.46 and 0 to 0.03, respectively. Genome-wide association studies (GWAS) identified seven significant SNPs to be associated with growth and feed efficiency, and several genes, including <i>AIF1L</i>, <i>ASS1</i>, and <i>QRFP</i> were highlighted as candidates for the analyzed traits. Additionally, microbiome-genome-wide association studies GWAS revealed potential links between <i>CCAR2</i>, <i>EGR3</i>, <i>GSTM3</i>, and <i>GPR61</i> genes and the abundance of microorganisms, such as <i>Trueperella</i>, <i>Victivallis</i>, and <i>Erysipelatoclostridium</i>. In addition, six microbial genera linked to growth and feed efficiency were identified as follows <i>Lachnospiraceae_UCG-005</i>, <i>Prevotellaceae_UCG-003</i>, <i>Prevotellaceae_NK3B31_group</i>, <i>Prevotella_1</i>, <i>Prevotella_9</i>, and <i>Veillonella</i>. Our findings provide novel insights into the factors influencing host phenotypic complexity and identify potential microbial targets for enhancing pig feed efficiency through selective breeding. This could aid in the development of strategies to manipulate the gut microbiota to optimize growth rates and feed efficiency in pig breeding.