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

文献类型： 外文期刊

第一作者： Xiang, Yue

作者： Xiang, Yue;Meng, Yuan;Li, Jingjin;Zhang, Saixian;Li, Kui;Qi, Xiaolong;Xiang, Yue;Sun, Jiahui;Ma, Guojian;Dai, Xueting;Fu, Chong;Zhang, Yan;Zhao, Qiulin;Zheng, Zhuqing;Li, Xinyun;Fu, Liangliang;Xiang, Yue;Sun, Jiahui;Ma, Guojian;Dai, Xueting;Fu, Chong;Zhang, Yan;Zhao, Qiulin;Zheng, Zhuqing;Li, Xinyun;Fu, Liangliang

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关键词： pigs; feed efficiency; ATAC-seq; GWAS; duodenum; muscle

期刊名称：GENES （ 影响因子：2.8； 五年影响因子：3.2 ）

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年卷期： 2024 年 15 卷 8 期

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收录情况： SCI

摘要： 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.

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