Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
Genes (Basel). 2024 Jul 25;15(8):980. 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.
通过饲料转化率（FCR）优化饲料效率对于经济可行性和可持续性至关重要。在这项研究中，我们整合了 RNA-seq、ATAC-seq 和全基因组关联研究（GWAS）数据，以研究与猪饲料效率相关的关键功能变异。在低 FCR 和高 FCR 猪的十二指肠和肌肉组织中差异表达基因的鉴定表明，与膳食碳水化合物消化相关的途径是个体间饲料效率差异的原因。通过 ATAC-seq 鉴定的差异开放染色质区域与参与糖酵解和脂肪酸代谢过程的基因有关。GWAS 鉴定出 211 个与饲料效率性状相关的显著单核苷酸多态性，候选基因包括、和。十二指肠 ATAC-seq 数据和 GWAS 数据的整合确定了六个关键功能变异，特别是在染色体 2 上的 1500985-1509676 区域。在这些区域中，发现在饲料转化率高的猪的十二指肠组织中高度表达，表明其作为潜在靶基因的作用。总的来说，多组学数据的整合提供了对饲料效率遗传基础的深入了解，为培育更高效的猪品种提供了有价值的信息。
