Joint contributions of host genetics and heritable gut microbiota to semen quality variation in Duroc boars

Host genetics and gut microbiota jointly influence host phenotypes. To investigate the genetic and microbial factors affecting boar semen quality, we analyzed whole-genome resequencing and fecal 16S rRNA sequencing data from 1128 Duroc boars. Gut microbiota profiling showed that Firmicutes, Bacteroidetes, and Proteobacteria were dominant phyla, while farm type, herd type, strain, and age significantly affected microbial composition. Genome-wide association analysis identified 32 significant SNPs associated with semen traits, and microbiome-wide association analysis detected 251 genus-level associations. Variance component analysis indicated that host genetics, gut microbiota, and their interactions contributed substantially to semen quality variation. Heritability analysis identified 73 heritable genera, and microbial GWAS further detected 242 SNPs associated with 18 heritable genera. Mendelian randomization analysis further supported a significant association between the heritable genus Intestinibacter and sperm motility. Notably, overlapping genomic regions on chromosome 10 were associated with both Intestinibacter abundance and sperm motility, suggesting that host genetic variation may influence semen quality directly or indirectly through modulation of heritable gut microbiota. These findings provide new insights into host genetics-microbiota interactions underlying boar semen quality.