Integrating Multi-Omics Data to Identify Key Functional Variants Affecting Feed Efficiency in Large White Boars

• Published in: Genes 2024-07, Vol.15 (8), p.980
• Main Authors: Xiang, Yue, Sun, Jiahui, Ma, Guojian, Dai, Xueting, Meng, Yuan, Fu, Chong, Zhang, Yan, Zhao, Qiulin, Li, Jingjin, Zhang, Saixian, Zheng, Zhuqing, Li, Xinyun, Fu, Liangliang, Li, Kui, Qi, Xiaolong
• Format: Article
• Language: English
• Subjects: Analysis; Animal Feed; Animal feeding and feeds; Animals; Chromatin; Chromosome 2; dietary carbohydrate; digestion; Diseases; Duodenum - metabolism; economic sustainability; Efficiency; fatty acids; feed conversion; Feed efficiency; Feeds; gene expression regulation; genes; Genetic aspects; Genetic testing; Genetic variation; Genome-wide association studies; genome-wide association study; Genome-Wide Association Study - methods; Glycolysis; Growth; Hogs; Large White; Metabolism; Methods; Multiomics; muscles; Polymorphism, Single Nucleotide; Quality control; Quantitative Trait Loci; sequence analysis; Single-nucleotide polymorphism; Small intestine; Software; Sus scrofa - genetics; swine; Swine - genetics; Swine breeds
• ISSN: 2073-4425; 2073-4425
• DOI: 10.3390/genes15080980

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 , , and . 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, 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.