Integrating multi-omics data to identify key functional variants affecting feed efficiency in pigs

Optimizing feed efficiency through the feed conversion ratio (FCR) is paramount for economic viability and sustainability. In this study, we integrated RNA-seq, ATAC-seq, and genome-wide association study (GWAS) data to investigate key functional variants associated with feed efficiency in pigs. Identification of differentially expressed genes in the duodenal and muscle tissues of low- and high-FCR pigs revealed that pathways related to digestion of dietary carbohydrate are responsible for differences in feed efficiency between individuals. Differential open chromatin regions identified by ATAC-seq were linked to genes involved in glycolytic and fatty acid processes. GWAS identified 211 significant single nucleotide polymorphisms associated with feed efficiency traits, with candidate genes PPP1R14C, TH, and CTSD. Integration of duodenal ATAC-seq data and GWAS data identified six key functional variants, particularly in the 1500985–1509676 region on chromosome 2. In those regions, CTSD was found to be highly expressed in the duodenal tissues of pigs with a high feed conversion ratio, suggesting its role as a potential target gene. Overall, the integration of multi-omics data provided insights into the genetic basis of feed efficiency, offering valuable information for breeding more efficient pig breeds. In this study, we utilized six Large White pigs, three with extremely high FCR values and three with extremely low FCR values. These pigs were raised on the same commercial farm under similar conditions and fed the same diet. All pigs were euthanized at 180 days of age after an overnight fasting period. Muscle and duodenal samples were collected and stored at -80°C for subsequent experiments. The sampling procedures received approval from the Ethics Committee of Huazhong Agricultural University. RNA-seq analysis was conducted on samples from three pigs with the highest FCR levels and three with the lowest FCR levels. In addition, ATAC-seq analysis was performed on samples from two pigs with extremely high FCR levels and two with extremely low FCR levels