Comparative Transcriptomic and Metabolomic Profiling of Ovaries from Two Pig Breeds with Contrasting Reproductive Phenotype

Although numerous quantitative trait loci (QTLs) and candidate genes have been implicated in litter size in certain pig breeds, the genetic basis underlying the pronounced differences in reproductive capacity among breeds remains incompletely understood. To elucidate the underlying mechanisms responsible for the heterogeneity in reproductive capacity, we performed integrated transcriptomic and metabolomic analyses on ovarian tissues from two pig breeds with contrasting litter sizes: Diannan Small-ear (DSE) pigs and Yorkshire (YK) pigs. YK pigs exhibited significantly higher total born piglets. Transcriptome analysis revealed that upregulated DEGs in YK ovaries were enriched in ovarian steroidogenesis, retinol metabolism, vitamin digestion/absorption, and folate biosynthesis. In contrast, DSE pigs showed enrichment in inflammatory and immune-related pathways. Furthermore, integrative transcriptomic and metabolomic analysis revealed that upregulated DEGs in YK pigs, such as STAR and COL3A1, and concurrently elevated metabolites (e.g., L-threonine, L-asparagine, L-proline, L-methionine, arachidonic acid, and progesterone) were jointly enriched in three key pathways: protein digestion and absorption, mineral absorption, and aldosterone synthesis and secretion. These genes and metabolites are implicated in granulosa cell and oocyte proliferation, maturation, and protection against oxidative damage. Our findings provide a theoretical foundation for future strategies aimed at improving reproductive performance through targeted modulation of key genes and metabolites.