Molecular Mechanisms Affecting Important Traits of Pigs

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 10442

Special Issue Editors

National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Interests: QTL mapping; systems genetics; genetic and genomic prediction; phenotype refinement

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Guest Editor
Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
Interests: multi-omics study; breeding and genetics; meat quality traits

Special Issue Information

Dear Colleagues,

The importance of the pig is unquestionable due to its global significance as a food source, as well as its relevance as a biomedical model organism. Despite some progress in the traditional genetic improvement of economically important traits, inadequacies and challenges remain to be overcome to elucidate the biological mechanisms of pigs. The aim of this Special Issue is to publish original research papers or reviews concerning the molecular mechanisms affecting economically important traits of pigs, or the provision of a framework to pinpoint causal variation associated with important phenotypes (e.g., disease resistance, pork quality, feeding behavior, feed efficiency, carcass composition) in pigs.

In future research, the use of multi-omics data will provide new insights into the genetic analysis of important economic traits in pigs. A major bottleneck that now needs to be overcome is the development of analysis methods and tools for translating these methods into practical applications for genetic improvements. Hence, we are pleased to invite you to share work relating to using omics technologies to promote a more integrative understanding of complex systems in phenotype variation through the application of genomics, transcriptomics, and proteomics technologies combined with, but not limited to, bioinformatics.

We invite you to share your recent findings through this Special Issue.

Dr. Jie Yang
Dr. Xueyan Zhao
Guest Editors

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Keywords

  • pigs
  • quantitative traits
  • GWAS
  • multi-omics
  • candidate gene

Published Papers (9 papers)

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Research

13 pages, 3909 KiB  
Article
Identification of Selection Signatures and Candidate Genes Related to Environmental Adaptation and Economic Traits in Tibetan Pigs
by Pengliang Liu, Yan Liang, Li Li, Xuebin Lv, Zhiping He and Yiren Gu
Animals 2024, 14(4), 654; https://doi.org/10.3390/ani14040654 - 19 Feb 2024
Viewed by 771
Abstract
Tibetan pigs are indigenous to the Qinghai–Tibet Plateau and have been the subject of extensive genomic research primarily focused on their adaptation to high altitudes. However, genetic modifications associated with their response to low-altitude acclimation have not been thoroughly explored. To investigate the [...] Read more.
Tibetan pigs are indigenous to the Qinghai–Tibet Plateau and have been the subject of extensive genomic research primarily focused on their adaptation to high altitudes. However, genetic modifications associated with their response to low-altitude acclimation have not been thoroughly explored. To investigate the genetic basis underlying the low-altitude acclimation of Tibetan pigs, we generated and analyzed genotyping data of Tibetan pigs that inhabit high-altitude regions (average altitude 4000 m) and Tibetan pigs that have inhabited nearby low-altitude regions (average altitude 500 m) for approximately 20 generations. We found that the highland and lowland Tibetan pigs have distinguishable genotype and phenotype variations. We identified 46 and 126 potentially selected SNPs associated with 29 and 56 candidate genes in highland and lowland Tibetan pigs, respectively. Candidate genes in the highland Tibetan pigs were involved in immune response (NFYC and STAT1) and radiation (NABP1), whereas candidate genes in the lowland Tibetan pigs were related to reproduction (ESR2, DMRTA1, and ZNF366), growth and development (NTRK3, FGF18, and MAP1B), and blood pressure regulation (CARTPT). These findings will help to understand the mechanisms of environmental adaptation in Tibetan pigs and offer valuable information into the genetic improvement of Tibetan pigs pertaining to low-altitude acclimation and economic traits. Full article
(This article belongs to the Special Issue Molecular Mechanisms Affecting Important Traits of Pigs)
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14 pages, 8091 KiB  
Article
Integrated Microbiome and Serum Metabolome Analysis Reveals Molecular Regulatory Mechanisms of the Average Daily Weight Gain of Yorkshire Pigs
by Shan Jiang, Jinglei Si, Jiayuan Mo, Shuai Zhang, Kuirong Chen, Jiuyu Gao, Di Xu, Lijing Bai, Ganqiu Lan and Jing Liang
Animals 2024, 14(2), 278; https://doi.org/10.3390/ani14020278 - 16 Jan 2024
Viewed by 909
Abstract
The average daily weight gain (ADG) is considered a crucial indicator for assessing growth rates in the swine industry. Therefore, investigating the gastrointestinal microbiota and serum metabolites influencing the ADG in pigs is pivotal for swine breed selection. This study involved the inclusion [...] Read more.
The average daily weight gain (ADG) is considered a crucial indicator for assessing growth rates in the swine industry. Therefore, investigating the gastrointestinal microbiota and serum metabolites influencing the ADG in pigs is pivotal for swine breed selection. This study involved the inclusion of 350 purebred Yorkshire pigs (age: 90 ± 2 days; body weight: 41.20 ± 4.60 kg). Concurrently, serum and fecal samples were collected during initial measurements of blood and serum indices. The pigs were categorized based on their ADG, with 27 male pigs divided into high-ADG (HADG) and low-ADG (LADG) groups based on their phenotype values. There were 12 pigs in LADG and 15 pigs in HADG. Feces and serum samples were collected on the 90th day. Microbiome and non-targeted metabolomics analyses were conducted using 16S rRNA sequencing and liquid chromatography-mass spectrometry (LC-MS). Pearson correlation, with Benjamini–Hochberg (BH) adjustment, was employed to assess the associations between these variables. The abundance of Lactobacillus and Prevotella in LADG was significantly higher than in HADG, while Erysipelothrix, Streptomyces, Dubosiella, Parolsenella, and Adlercreutzia in LADG were significantly lower than in HADG. The concentration of glutamine, etiocholanolone glucuronide, and retinoyl beta-glucuronide in LADG was significantly higher than in HADG, while arachidonic acid, allocholic acid, oleic acid, phenylalanine, and methyltestosterone in LADG were significantly lower than in HADG. The LactobacillusStreptomyces networks (Lactobacillus, Streptomyces, methyltestosterone, phenylalanine, oleic acid, arachidonic acid, glutamine, 3-ketosphingosine, L-octanoylcarnitine, camylofin, 4-guanidinobutyrate 3-methylcyclopentadecanone) were identified as the most influential at regulating swine weight gain. These findings suggest that the gastrointestinal tract regulates the daily weight gain of pigs through the network of Lactobacillus and Streptomyces. However, this study was limited to fecal and serum samples from growing and fattening boars. A comprehensive consideration of factors affecting the daily weight gain in pig production, including gender, parity, season, and breed, is warranted. Full article
(This article belongs to the Special Issue Molecular Mechanisms Affecting Important Traits of Pigs)
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16 pages, 3740 KiB  
Article
An Analysis of a Transposable Element Expression Atlas during 27 Developmental Stages in Porcine Skeletal Muscle: Unveiling Molecular Insights into Pork Production Traits
by Chao Wang, Bowen Lei and Yuwen Liu
Animals 2023, 13(22), 3581; https://doi.org/10.3390/ani13223581 - 20 Nov 2023
Viewed by 1030
Abstract
The development and growth of porcine skeletal muscle determine pork quality and yield. While genetic regulation of porcine skeletal muscle development has been extensively studied using various omics data, the role of transposable elements (TEs) in this context has been less explored. To [...] Read more.
The development and growth of porcine skeletal muscle determine pork quality and yield. While genetic regulation of porcine skeletal muscle development has been extensively studied using various omics data, the role of transposable elements (TEs) in this context has been less explored. To bridge this gap, we constructed a comprehensive atlas of TE expression throughout the developmental stages of porcine skeletal muscle. This was achieved by integrating porcine TE genomic coordinates with whole-transcriptome RNA-Seq data from 27 developmental stages. We discovered that in pig skeletal muscle, active Tes are closely associated with active epigenomic marks, including low levels of DNA methylation, high levels of chromatin accessibility, and active histone modifications. Moreover, these TEs include 6074 self-expressed TEs that are significantly enriched in terms of muscle cell development and myofibril assembly. Using the TE expression data, we conducted a weighted gene co-expression network analysis (WGCNA) and identified a module that is significantly associated with muscle tissue development as well as genome-wide association studies (GWAS) of the signals of pig meat and carcass traits. Within this module, we constructed a TE-mediated gene regulatory network by adopting a unique multi-omics integration approach. This network highlighted several established candidate genes associated with muscle-relevant traits, including HES6, CHRNG, ACTC1, CHRND, MAMSTR, and PER2, as well as novel genes like ENSSSCG00000005518, ENSSSCG00000033601, and PIEZO2. These novel genes hold promise for regulating muscle-related traits in pigs. In summary, our research not only enhances the TE-centered dissection of the genetic basis underlying pork production traits, but also offers a general approach for constructing TE-mediated regulatory networks to study complex traits or diseases. Full article
(This article belongs to the Special Issue Molecular Mechanisms Affecting Important Traits of Pigs)
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20 pages, 7612 KiB  
Article
Integrative Analysis of Transcriptomic and Lipidomic Profiles Reveals a Differential Subcutaneous Adipose Tissue Mechanism among Ningxiang Pig and Berkshires, and Their Offspring
by Xiaoxiao Deng, Yuebo Zhang, Gang Song, Yawei Fu, Yue Chen, Hu Gao, Qian Wang, Zhao Jin, Yulong Yin and Kang Xu
Animals 2023, 13(21), 3321; https://doi.org/10.3390/ani13213321 - 25 Oct 2023
Viewed by 1145
Abstract
Adipose tissue composition contributes greatly to the quality and nutritional value of meat. Transcriptomic and lipidomic techniques were used to investigate the molecular mechanisms of the differences in fat deposition in Ningxiang pigs, Berkshires and F1 offspring. Transcriptomic analysis identified 680, 592, [...] Read more.
Adipose tissue composition contributes greatly to the quality and nutritional value of meat. Transcriptomic and lipidomic techniques were used to investigate the molecular mechanisms of the differences in fat deposition in Ningxiang pigs, Berkshires and F1 offspring. Transcriptomic analysis identified 680, 592, and 380 DEGs in comparisons of Ningxiang pigs vs. Berkshires, Berkshires vs. F1 offspring, and Ningxiang pigs vs. F1 offspring. The lipidomic analysis screened 423, 252, and 50 SCLs in comparisons of Ningxiang pigs vs. Berkshires, Berkshires vs. F1 offspring, and Ningxiang pigs vs. F1 offspring. Lycine, serine, and the threonine metabolism pathway, fatty acid biosynthesis and metabolism-related pathways were significantly enriched in comparisons of Berkshires vs. Ningxiang pigs and Berkshires vs. F1 offspring. The DEGs (PHGDH, LOC110256000) and the SCLs (phosphatidylserines) may have a great impact on the glycine, serine, and the threonine metabolism pathway. Moreover, the DEGs (FASN, ACACA, CBR4, SCD, ELOV6, HACD2, CYP3A46, CYP2B22, GPX1, and GPX3) and the SCLs (palmitoleic acid, linoleic acid, arachidonic acid, and icosadienoic acid) play important roles in the fatty acid biosynthesis and metabolism of fatty acids. Thus, the difference in fat deposition among Ningxiang pig, Berkshires, and F1 offspring may be caused by differences in the expression patterns of key genes in multiple enriched KEGG pathways. This research revealed multiple lipids that are potentially available biological indicators and screened key genes that are potential targets for molecular design breeding. The research also explored the molecular mechanisms of the difference in fat deposition among Ningxiang pig, Berkshires, and F1 pigs, and provided an insight into selection for backfat thickness and the fat composition of adipose tissue for future breeding strategies. Full article
(This article belongs to the Special Issue Molecular Mechanisms Affecting Important Traits of Pigs)
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13 pages, 2833 KiB  
Article
Identification of Candidate Genes for Economically Important Carcass Cutting in Commercial Pigs through GWAS
by Fuchen Zhou, Jianping Quan, Donglin Ruan, Yibin Qiu, Rongrong Ding, Cineng Xu, Yong Ye, Gengyuan Cai, Langqing Liu, Zebin Zhang, Jie Yang, Zhenfang Wu and Enqin Zheng
Animals 2023, 13(20), 3243; https://doi.org/10.3390/ani13203243 - 18 Oct 2023
Cited by 1 | Viewed by 994
Abstract
During the process of pork production, the carcasses of pigs are divided and sold, which provides better economic benefits and market competitiveness for pork production than selling the carcass as a whole. Due to the significant cost of post-slaughter phenotypic measurement, the genetic [...] Read more.
During the process of pork production, the carcasses of pigs are divided and sold, which provides better economic benefits and market competitiveness for pork production than selling the carcass as a whole. Due to the significant cost of post-slaughter phenotypic measurement, the genetic architecture of tenderloin weight (TLNW) and rib weight (RIBW)—important components of pig carcass economic value—remain unknown. In this study, we conducted genome-wide association studies (GWAS) for TLNW and RIBW traits in a population of 431 Duroc × Landrace × Yorkshire (DLY) pigs. In our study, the most significant single nucleotide polymorphism (SNP) associated with TLNW was identified as ASGA0085853 (3.28 Mb) on Sus scrofa chromosome 12 (SSC12), while for RIBW, it was Affx-1115046258 (172.45 Mb) on SSC13. Through haplotype block analysis, we discovered a novel quantitative trait locus (QTL) associated with TLNW, spanning a 5 kb region on SSC12, and a novel RIBW-associated QTL spanning 1.42 Mb on SSC13. Furthermore, we hypothesized that three candidate genes, TIMP2 and EML1, and SMN1, are associated with TLNW and RIBW, respectively. Our research not only addresses the knowledge gap regarding TLNW, but also serves as a valuable reference for studying RIBW. The identified SNP loci strongly associated with TLNW and RIBW may prove useful for marker-assisted selection in pig breeding programs. Full article
(This article belongs to the Special Issue Molecular Mechanisms Affecting Important Traits of Pigs)
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18 pages, 3241 KiB  
Article
PorcineAI-Enhancer: Prediction of Pig Enhancer Sequences Using Convolutional Neural Networks
by Ji Wang, Han Zhang, Nanzhu Chen, Tong Zeng, Xiaohua Ai and Keliang Wu
Animals 2023, 13(18), 2935; https://doi.org/10.3390/ani13182935 - 15 Sep 2023
Viewed by 980
Abstract
Understanding the mechanisms of gene expression regulation is crucial in animal breeding. Cis-regulatory DNA sequences, such as enhancers, play a key role in regulating gene expression. Identifying enhancers is challenging, despite the use of experimental techniques and computational methods. Enhancer prediction in the [...] Read more.
Understanding the mechanisms of gene expression regulation is crucial in animal breeding. Cis-regulatory DNA sequences, such as enhancers, play a key role in regulating gene expression. Identifying enhancers is challenging, despite the use of experimental techniques and computational methods. Enhancer prediction in the pig genome is particularly significant due to the costliness of high-throughput experimental techniques. The study constructed a high-quality database of pig enhancers by integrating information from multiple sources. A deep learning prediction framework called PorcineAI-enhancer was developed for the prediction of pig enhancers. This framework employs convolutional neural networks for feature extraction and classification. PorcineAI-enhancer showed excellent performance in predicting pig enhancers, validated on an independent test dataset. The model demonstrated reliable prediction capability for unknown enhancer sequences and performed remarkably well on tissue-specific enhancer sequences.The study developed a deep learning prediction framework, PorcineAI-enhancer, for predicting pig enhancers. The model demonstrated significant predictive performance and potential for tissue-specific enhancers. This research provides valuable resources for future studies on gene expression regulation in pigs. Full article
(This article belongs to the Special Issue Molecular Mechanisms Affecting Important Traits of Pigs)
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13 pages, 1117 KiB  
Article
Copy Number Variation Regions Differing in Segregation Patterns Span Different Sets of Genes
by Katherine D. Arias, Juan Pablo Gutiérrez, Iván Fernández, Isabel Álvarez and Félix Goyache
Animals 2023, 13(14), 2351; https://doi.org/10.3390/ani13142351 - 19 Jul 2023
Cited by 1 | Viewed by 1050
Abstract
Copy number variations regions (CNVRs) can be classified either as segregating, when found in both parents, and offspring, or non-segregating. A total of 65 segregating and 31 non-segregating CNVRs identified in at least 10 individuals within a dense pedigree of the Gochu Asturcelta [...] Read more.
Copy number variations regions (CNVRs) can be classified either as segregating, when found in both parents, and offspring, or non-segregating. A total of 65 segregating and 31 non-segregating CNVRs identified in at least 10 individuals within a dense pedigree of the Gochu Asturcelta pig breed was subjected to enrichment and functional annotation analyses to ascertain their functional independence and importance. Enrichment analyses allowed us to annotate 1018 and 351 candidate genes within the bounds of the segregating and non-segregating CNVRs, respectively. The information retrieved suggested that the candidate genes spanned by segregating and non-segregating CNVRs were functionally independent. Functional annotation analyses allowed us to identify nine different significantly enriched functional annotation clusters (ACs) in segregating CNVR candidate genes mainly involved in immunity and regulation of the cell cycle. Up to five significantly enriched ACs, mainly involved in reproduction and meat quality, were identified in non-segregating CNVRs. The current analysis fits with previous reports suggesting that segregating CNVRs would explain performance at the population level, whereas non-segregating CNVRs could explain between-individuals differences in performance. Full article
(This article belongs to the Special Issue Molecular Mechanisms Affecting Important Traits of Pigs)
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10 pages, 784 KiB  
Article
Genome-Wide Association Study Identifies the Crucial Candidate Genes for Teat Number in Crossbred Commercial Pigs
by Lijuan Yang, Xuehua Li, Zhanwei Zhuang, Shenping Zhou, Jie Wu, Cineng Xu, Donglin Ruan, Yibin Qiu, Hua Zhao, Enqin Zheng, Gengyuan Cai, Zhenfang Wu and Jie Yang
Animals 2023, 13(11), 1880; https://doi.org/10.3390/ani13111880 - 5 Jun 2023
Cited by 1 | Viewed by 1262
Abstract
The number of teats is a crucial reproductive trait with significant economic implications on maternal capacity and litter size. Consequently, improving this trait is essential to facilitate genetic selection for increased litter size. In this study, we performed a genome-wide association study (GWAS) [...] Read more.
The number of teats is a crucial reproductive trait with significant economic implications on maternal capacity and litter size. Consequently, improving this trait is essential to facilitate genetic selection for increased litter size. In this study, we performed a genome-wide association study (GWAS) of the number of teats in a three-way crossbred commercial Duroc × (Landrace × Yorkshire) (DLY) pig population comprising 1518 animals genotyped with the 50K BeadChip. Our analysis identified crucial quantitative trait loci (QTL) for the number of teats, containing the ABCD4 and VRTN genes on porcine chromosome 7. Our results establish SNP variants of ABCD4 and VRTN as new molecular markers for improving the number of teats in DLY pigs. Furthermore, the most significant noteworthy single nucleotide polymorphism (SNP) (7_97568284) was identified within the ABCD4 gene, exhibiting a significant association with the total teat number traits. This SNP accounted for a substantial proportion of the genetic variance, explaining 6.64% of the observed variation. These findings reveal a novel gene on SSC7 for the number of teats and provide a deeper understanding of the genetic mechanisms underlying reproductive traits. Full article
(This article belongs to the Special Issue Molecular Mechanisms Affecting Important Traits of Pigs)
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11 pages, 3578 KiB  
Article
Genome-Wide Association Analysis Identifies Genomic Regions and Candidate Genes for Growth and Fatness Traits in Diannan Small-Ear (DSE) Pigs
by Mei Liu, Qun Lan, Long Yang, Qiuchun Deng, Taiyun Wei, Heng Zhao, Peiya Peng, Xiaoding Lin, Yuhan Chen, Haiming Ma, Hongjiang Wei and Yulong Yin
Animals 2023, 13(9), 1571; https://doi.org/10.3390/ani13091571 - 8 May 2023
Cited by 2 | Viewed by 1568
Abstract
In the livestock industry, the growth and fatness traits are directly related to production efficiency and economic profits. As for Diannan small-ear (DSE) pigs, a unique indigenous breed, the genetic architecture of growth and fatness traits is still elusive. The aim of this [...] Read more.
In the livestock industry, the growth and fatness traits are directly related to production efficiency and economic profits. As for Diannan small-ear (DSE) pigs, a unique indigenous breed, the genetic architecture of growth and fatness traits is still elusive. The aim of this study was to search the genetic loci and candidate genes associated with phenotypic traits in DSE pigs using GWAS based on the Geneseek Porcine 50K SNP Chip data. A total of 22,146 single nucleotide polymorphisms (SNPs) were detected in 265 DSE pigs and used for Genome-wide association studies (GWAS) analysis. Seven SNPs were found to be associated with back height, chest circumference, cannon bone circumference, and backfat thickness at the suggestive significance level. Based on gene annotation results, these seven SNPs were, respectively, mapped to the following candidate genes, VIPR2, SLC10A2, NUCKS1, MCT1, CHCHD3, SMOX, and GPR1, which are mainly involved with adipocyte differentiation, lipid metabolism, skeletal muscle development, and average daily weight gain. Our work offers novel insights into the genetic architecture of economically important traits in swine and may play an important role in breeding using molecular markers in the DSE breed. Full article
(This article belongs to the Special Issue Molecular Mechanisms Affecting Important Traits of Pigs)
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