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Genetic Diversity, Innovative Utilization and Microbiome Profile of Local Pig...
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Genetic Diversity, Innovative Utilization and Microbiome Profile of Local Pig Breeds

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Pigs".

Deadline for manuscript submissions: 1 March 2025 | Viewed by 5609

Special Issue Editors

Dr. Enrico D’ Alessandro

E-Mail Website
Guest Editor
Department of Veterinary Science, University of Messina, 98168 Messina, Italy
Interests: pigs; swine production; genomic selection; conservation; biodiversity; food traceability; food quality; metagenomics; microbiome; mobilome
Special Issues, Collections and Topics in MDPI journals
Dr. Cai Chen

E-Mail Website
Guest Editor
College of Animal Science and Technology, Yangzhou University, Yangzhou, China
Interests: pigs; mobilome; retrotransposon insertion polymorphism; marker development; genome selection; gene regulation; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, there has been growing awareness of the importance of local breeds in terms of adaptive traits, as a reservoir of valuable genetic variation with the potential for more sustainable, added-value-oriented pork production, and because of their historical and cultural value. In the past, the development of livestock production was mainly based on the formation of local breeds that were well adapted to specific conditions and rearing practices. However, in the second half of the twentieth century, the lower economic performance of these breeds when raised under intensive production conditions resulted in a significant reduction of local pig breed populations, which were replaced by modern, highly productive pig breeds adapted to farm conditions and constraints.

The higher economic value of typical productions compared to conventional commercial products and the growing consumer preference toward quality food could support livestock biodiversity conservation plans.

Molecular DNA markers such as SNPs, CNVs, and Retrotrasposones are used to investigate the genetic basis of traits, supplying support to phenotypic evaluation and genealogical data analysis.

Furthermore, in recent times, there has been a growing interest in the study of gut microbiota, a complex and dynamic community of microbial species, which collectively modulate the health status and physiology of a variety of vertebrates, including humans and pigs. The taxonomic structure of pig microbiomes is considered pivotal for commercial breeding. Additionally, the influence of microbial taxa on host fitness and disease risk can provide relevant information to promote animal health and improve feed efficiency in the swine industry.

This Special Issue will focus on recent research or reviews that investigate novel approaches and/or technologies used to identify relevant new phenotypes and implement all aspects of pig genetics and genomics. We welcome those submissions with a focus on new phenotypes, genomic selection, breeding programs, QTLs, breeds conservation, and gut microbiome characterization. 

Dr. Enrico D’ Alessandro
Dr. Cai Chen
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • pig
  • local breeds
  • genetic improvement
  • genomics selection
  • QTL
  • pig production
  • microbiome
  • traceability
  • typical product
  • conservation
  • biodiversity
  • food safety
  • gene annotation

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Published Papers (5 papers)

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Research

13 pages, 7485 KiB  
Article
A Comparative Metabolomics Study of the Potential Marker Compounds in Feces from Different Hybrid Offspring of Huainan Pigs
by Yufu Li, Mingyang Jia, Junfeng Chen, Fujiu Liu, Qiaoling Ren, Xiangzhou Yan, Baosong Xing, Chuanying Pan and Jing Wang
Animals 2024, 14(22), 3282; https://doi.org/10.3390/ani14223282 - 14 Nov 2024
Viewed by 294
Abstract
As a notable native Chinese genetic population, the Huainan pig has an exceptional meat quality but a low percentage of lean meat and subpar genetic performance. To better exploit the superior genetic traits of the Huainan pig and address knowledge gaps regarding the [...] Read more.
As a notable native Chinese genetic population, the Huainan pig has an exceptional meat quality but a low percentage of lean meat and subpar genetic performance. To better exploit the superior genetic traits of the Huainan pig and address knowledge gaps regarding the optimization of its hybrid offspring, this study used Huainan pigs as the maternal line and bred them with Yorkshire, Landrace, and Berkshire sires. This approach produced three hybrid combinations: Yorkshire × Huainan (YH), Landrace × Huainan (LH), and Berkshire × Huainan (BH). The body size, fat ratio, and average backfat thickness of these hybrid progeny were evaluated under the same feeding management and nutritional circumstances. The results revealed that the average backfat thickness of YH was significantly lower than that of LH and BH. In order to better understand the causes of these variations, fecal samples were taken from three pigs in each group for metabolomic analysis. A total of 2291 metabolites were identified, including benzene derivatives (16.6%), amino acids and their metabolites (14.5%), and organic acids (13.4%), with pyruvaldehyde and norethindrone acetate elevated in YH compared to LH and BH. In addition, the three hybrid pig groups commonly exhibited differences in the “glycerophospholipid metabolism” pathway. This variation may also contribute to differences in their fat ratio and backfat thickness. Our findings provide a novel perspective on the role of hybrid vigor in advancing the genetic population of Huainan pigs, while also revealing the unique metabolic characteristics of the YH with regard to fat deposition. This study is expected to enhance the conservation and effective utilization of genetic resources within the Huainan pig population. Full article
(This article belongs to the Special Issue Genetic Diversity, Innovative Utilization and Microbiome Profile of Local Pig Breeds)
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12 pages, 4125 KiB  
Article
Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study
by Wei Zhang, Yao Jiang, Zelan Ni, Mei Zhou, Linqing Liu, Xiaoyu Li, Shiguang Su and Chonglong Wang
Animals 2024, 14(10), 1419; https://doi.org/10.3390/ani14101419 - 9 May 2024
Viewed by 1022
Abstract
Copy number variation (CNV) is an important structural variation used to elucidate complex economic traits. In this study, we sequenced 25 Wannan spotted pigs (WSPs) to detect their CNVs and identify their selection signatures compared with those of 10 Asian wild boars. A [...] Read more.
Copy number variation (CNV) is an important structural variation used to elucidate complex economic traits. In this study, we sequenced 25 Wannan spotted pigs (WSPs) to detect their CNVs and identify their selection signatures compared with those of 10 Asian wild boars. A total of 14,161 CNVs were detected in the WSPs, accounting for 0.72% of the porcine genome. The fixation index (Fst) was used to identify the selection signatures, and 195 CNVs with the top 1% of the Fst value were selected. Eighty genes were identified in the selected CNV regions. Functional GO and KEGG analyses revealed that the genes within these selected CNVs are associated with key traits such as reproduction (GAL3ST1 and SETD2), fatty acid composition (PRKG1, ACACA, ACSL3, UGT8), immune system (LYZ), ear size (WIF1), and feed efficiency (VIPR2). The findings of this study contribute novel insights into the genetic CNVs underlying WSP characteristics and provide essential information for the protection and utilization of WSP populations. Full article
(This article belongs to the Special Issue Genetic Diversity, Innovative Utilization and Microbiome Profile of Local Pig Breeds)
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14 pages, 2144 KiB  
Article
Exploration of Genome-Wide Recombination Rate Variation Patterns at Different Scales in Pigs
by Zuoquan Chen, Meng Zhou, Yingchun Sun, Xi Tang, Zhiyan Zhang and Lusheng Huang
Animals 2024, 14(9), 1345; https://doi.org/10.3390/ani14091345 - 29 Apr 2024
Viewed by 1129
Abstract
Meiotic recombination is a prevalent process in eukaryotic sexual reproduction organisms that plays key roles in genetic diversity, breed selection, and species evolution. However, the recombination events differ across breeds and even within breeds. In this study, we initially computed large-scale population recombination [...] Read more.
Meiotic recombination is a prevalent process in eukaryotic sexual reproduction organisms that plays key roles in genetic diversity, breed selection, and species evolution. However, the recombination events differ across breeds and even within breeds. In this study, we initially computed large-scale population recombination rates of both sexes using approximately 52 K SNP genotypes in a total of 3279 pigs from four different Chinese and Western breeds. We then constructed a high-resolution historical recombination map using approximately 16 million SNPs from a sample of unrelated individuals. Comparative analysis of porcine recombination events from different breeds and at different resolutions revealed the following observations: Firstly, the 1Mb-scale pig recombination maps of the same sex are moderately conserved among different breeds, with the similarity of recombination events between Western pigs and Chinese indigenous pigs being lower than within their respective groups. Secondly, we identified 3861 recombination hotspots in the genome and observed medium- to high-level correlation between historical recombination rates (0.542~0.683) and estimates of meiotic recombination rates. Third, we observed that recombination hotspots are significantly far from the transcription start sites of pig genes, and the silico–predicted PRDM9 zinc finger domain DNA recognition motif is significantly enriched in the regions of recombination hotspots compared to recombination coldspots, highlighting the potential role of PRDM9 in regulating recombination hotspots in pigs. Our study analyzed the variation patterns of the pig recombination map at broad and fine scales, providing a valuable reference for genomic selection breeding and laying a crucial foundation for further understanding the molecular mechanisms of pig genome recombination. Full article
(This article belongs to the Special Issue Genetic Diversity, Innovative Utilization and Microbiome Profile of Local Pig Breeds)
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20 pages, 4950 KiB  
Article
Comprehensive Multi-Omic Evaluation of the Microbiota and Metabolites in the Colons of Diverse Swine Breeds
by Yanbin Zhu, Guangming Sun, Yangji Cidan, Bin Shi, Zhankun Tan, Jian Zhang and Wangdui Basang
Animals 2024, 14(8), 1221; https://doi.org/10.3390/ani14081221 - 18 Apr 2024
Viewed by 1044
Abstract
Pigs stand as a vital cornerstone in the realm of human sustenance, and the intricate composition of their intestinal microbiota wields a commanding influence over their nutritional and metabolic pathways. We employed multi-omic evaluations to identify microbial evidence associated with differential growth performance [...] Read more.
Pigs stand as a vital cornerstone in the realm of human sustenance, and the intricate composition of their intestinal microbiota wields a commanding influence over their nutritional and metabolic pathways. We employed multi-omic evaluations to identify microbial evidence associated with differential growth performance and metabolites, thereby offering theoretical support for the implementation of efficient farming practices for Tibetan pigs and establishing a robust foundation for enhancing pig growth and health. In this work, six Duroc × landrace × yorkshi (DLY) pigs and six Tibetan pigs were used for the experiment. Following humane euthanasia, a comprehensive analysis was undertaken to detect the presence of short-chain fatty acids (SCFAs), microbial populations, and metabolites within the colonic environment. Additionally, metabolites present within the plasma were also assessed. The outcomes of our analysis unveiled the key variables affecting the microbe changes causing the observed differences in production performance between these two distinct pig breeds. Specifically, noteworthy discrepancies were observed in the microbial compositions of DLY pigs, characterized by markedly higher levels of Alloprevotella and Prevotellaceae_UCG-003 (p < 0.05). These disparities, in turn, resulted in significant variations in the concentrations of acetic acid, propionic acid, and the cumulative SCFAs (p < 0.05). Consequently, the DLY pigs exhibited enhanced growth performance and overall well-being, which could be ascribed to the distinct metabolite profiles they harbored. Conversely, Tibetan pigs exhibited a significantly elevated relative abundance of the NK4A214_group, which consequently led to a pronounced increase in the concentration of L-cysteine. This elevation in L-cysteine content had cascading effects, further manifesting higher levels of taurine within the colon and plasma. It is noteworthy that taurine has the potential to exert multifaceted impacts encompassing microbiota dynamics, protein and lipid metabolism, as well as bile acid metabolism, all of which collectively benefit the pigs. In light of this, Tibetan pigs showcased enhanced capabilities in bile acid metabolism. In summation, our findings suggest that DLY pigs excel in their proficiency in short-chain fatty acid metabolism, whereas Tibetan pigs exhibit a more pronounced competence in the realm of bile acid metabolism. These insights underscore the potential for future studies to leverage these breed-specific differences, thereby contributing to the amelioration of production performance within these two distinct pig breeds. Full article
(This article belongs to the Special Issue Genetic Diversity, Innovative Utilization and Microbiome Profile of Local Pig Breeds)
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16 pages, 3117 KiB  
Article
Comparative Analysis of Intestinal Inflammation and Microbiota Dysbiosis of LPS-Challenged Piglets between Different Breeds
by Chao Li, Yanping Wang, Xueyan Zhao, Jingxuan Li, Huaizhong Wang, Yifan Ren, Houwei Sun, Xiaodong Zhu, Qinye Song and Jiying Wang
Animals 2024, 14(5), 665; https://doi.org/10.3390/ani14050665 - 20 Feb 2024
Cited by 1 | Viewed by 1471
Abstract
Post-weaning diarrhea is common in piglets, causing huge economic losses worldwide. Associations between LPS challenge, intestinal inflammation, and microbiota have been reported in Duroc × Landrace × Yorkshire (DLY) crossbred pigs. However, the effects of LPS challenge in other breeds remain unclear. In [...] Read more.
Post-weaning diarrhea is common in piglets, causing huge economic losses worldwide. Associations between LPS challenge, intestinal inflammation, and microbiota have been reported in Duroc × Landrace × Yorkshire (DLY) crossbred pigs. However, the effects of LPS challenge in other breeds remain unclear. In the current study, we performed a comprehensive comparative analysis of the effects of LPS challenge on jejunal mucosal morphology, jejunal microbial composition, and serum indexes in two pig breeds: DLY and Heigai, an indigenous Chinese breed. The results showed that LPS caused considerable damage to the mucosal morphology, enhanced serum levels of inflammatory cytokines and the intestinal permeability index, and lowered the antioxidant capacity index. LPS challenge also changed the microbial composition and structure of the jejunum, significantly increased the abundances of Escherichia-Shigella in DLY pigs, and decreased those of Gemella and Saccharimonadales in Heigai pigs. Furthermore, LPS challenge triggered functional changes in energy metabolism and activities related to the stress response in the jejunal bacterial community, alleviating the inflammatory response in Heigai pigs. This study also revealed that Heigai pigs had a weaker immune response to LPS challenge than DLY pigs, and identified several genera related to the breed-specific phenotypes of Heigai pigs, including Gemella, Saccharimonadales, Clostridia_UCG_014, Terrisporobacter, and Dielma. Our collective findings uncovered differences between Heigai and DLY pigs in intestinal inflammation and microbiota dysbiosis induced by LPS challenge, providing a theoretical basis for unraveling the mechanism of intestinal inflammation in swine and proposing microbial candidates involved in the resistance to diarrhea in piglets. Full article
(This article belongs to the Special Issue Genetic Diversity, Innovative Utilization and Microbiome Profile of Local Pig Breeds)
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