Uncovering Molecular Mechanisms of Feed Efficiency in Pigs Through Multi-Omics Analysis of the Jejunum

Feed efficiency (FE) is a crucial trait in pig production that influences both economic viability and environmental sustainability. The jejunum, an essential organ for nutrient absorption, plays a significant role in determining FE by affecting how pigs process and utilize feed. To explore the genet...

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Main Authors: Saixian Zhang, Yue Xiang, Yaobang Jian, Qiulin Zhao, Jiahui Sun, Yi Huang, Jing Xu, Xiaolong Qi, Jingjin Li, Zhuqing Zheng, Liangliang Fu, Yuwen Liu, Xinyun Li
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Language:English
Published: MDPI AG 2025-01-01
Series:Animals
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Online Access:https://www.mdpi.com/2076-2615/15/2/137
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author Saixian Zhang
Yue Xiang
Yaobang Jian
Qiulin Zhao
Jiahui Sun
Yi Huang
Jing Xu
Xiaolong Qi
Jingjin Li
Zhuqing Zheng
Liangliang Fu
Yuwen Liu
Xinyun Li
author_facet Saixian Zhang
Yue Xiang
Yaobang Jian
Qiulin Zhao
Jiahui Sun
Yi Huang
Jing Xu
Xiaolong Qi
Jingjin Li
Zhuqing Zheng
Liangliang Fu
Yuwen Liu
Xinyun Li
author_sort Saixian Zhang
collection DOAJ
description Feed efficiency (FE) is a crucial trait in pig production that influences both economic viability and environmental sustainability. The jejunum, an essential organ for nutrient absorption, plays a significant role in determining FE by affecting how pigs process and utilize feed. To explore the genetic and regulatory mechanisms behind FE, we conducted an integrative multi-omics study using RNA sequencing (RNA-seq) and ATAC sequencing (ATAC-seq) on pigs with high and low FE. By comparing gene expression and chromatin accessibility profiles in the jejunum, we identified key differentially expressed genes (DEGs) and differentially accessible regions (DARs) associated with lipid metabolism and immune function, both of which are critical pathways for efficient growth. Notably, we identified transcription factors such as GATA4 and EHF and genes like <i>SCARB1</i> and <i>GRXCR1</i> that may play regulatory roles in FE. Our findings provide novel insights into the molecular mechanisms governing FE in pigs, offering potential targets for genetic selection and nutritional interventions to enhance feed efficiency and sustainability in pig production.
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institution Kabale University
issn 2076-2615
language English
publishDate 2025-01-01
publisher MDPI AG
record_format Article
series Animals
spelling doaj-art-766ef11724734bb888b11e51e37e8fb82025-01-24T13:17:42ZengMDPI AGAnimals2076-26152025-01-0115213710.3390/ani15020137Uncovering Molecular Mechanisms of Feed Efficiency in Pigs Through Multi-Omics Analysis of the JejunumSaixian Zhang0Yue Xiang1Yaobang Jian2Qiulin Zhao3Jiahui Sun4Yi Huang5Jing Xu6Xiaolong Qi7Jingjin Li8Zhuqing Zheng9Liangliang Fu10Yuwen Liu11Xinyun Li12Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, ChinaKey Laboratory 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, ChinaKey Laboratory 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, ChinaKey Laboratory 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, ChinaKey Laboratory 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, ChinaKey Laboratory 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, ChinaKey Laboratory 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, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, ChinaKey Laboratory 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, ChinaKey Laboratory 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, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, ChinaKey Laboratory 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, ChinaFeed efficiency (FE) is a crucial trait in pig production that influences both economic viability and environmental sustainability. The jejunum, an essential organ for nutrient absorption, plays a significant role in determining FE by affecting how pigs process and utilize feed. To explore the genetic and regulatory mechanisms behind FE, we conducted an integrative multi-omics study using RNA sequencing (RNA-seq) and ATAC sequencing (ATAC-seq) on pigs with high and low FE. By comparing gene expression and chromatin accessibility profiles in the jejunum, we identified key differentially expressed genes (DEGs) and differentially accessible regions (DARs) associated with lipid metabolism and immune function, both of which are critical pathways for efficient growth. Notably, we identified transcription factors such as GATA4 and EHF and genes like <i>SCARB1</i> and <i>GRXCR1</i> that may play regulatory roles in FE. Our findings provide novel insights into the molecular mechanisms governing FE in pigs, offering potential targets for genetic selection and nutritional interventions to enhance feed efficiency and sustainability in pig production.https://www.mdpi.com/2076-2615/15/2/137feed efficiencypigsjejunumRNA-seqATAC-seqlipid metabolism
spellingShingle Saixian Zhang
Yue Xiang
Yaobang Jian
Qiulin Zhao
Jiahui Sun
Yi Huang
Jing Xu
Xiaolong Qi
Jingjin Li
Zhuqing Zheng
Liangliang Fu
Yuwen Liu
Xinyun Li
Uncovering Molecular Mechanisms of Feed Efficiency in Pigs Through Multi-Omics Analysis of the Jejunum
Animals
feed efficiency
pigs
jejunum
RNA-seq
ATAC-seq
lipid metabolism
title Uncovering Molecular Mechanisms of Feed Efficiency in Pigs Through Multi-Omics Analysis of the Jejunum
title_full Uncovering Molecular Mechanisms of Feed Efficiency in Pigs Through Multi-Omics Analysis of the Jejunum
title_fullStr Uncovering Molecular Mechanisms of Feed Efficiency in Pigs Through Multi-Omics Analysis of the Jejunum
title_full_unstemmed Uncovering Molecular Mechanisms of Feed Efficiency in Pigs Through Multi-Omics Analysis of the Jejunum
title_short Uncovering Molecular Mechanisms of Feed Efficiency in Pigs Through Multi-Omics Analysis of the Jejunum
title_sort uncovering molecular mechanisms of feed efficiency in pigs through multi omics analysis of the jejunum
topic feed efficiency
pigs
jejunum
RNA-seq
ATAC-seq
lipid metabolism
url https://www.mdpi.com/2076-2615/15/2/137
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