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Animals
Special Issues
Genetic Diversity and Population Structure of Local Pig Breeds
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Genetic Diversity and Population Structure of Local Pig Breeds

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

Deadline for manuscript submissions: closed (20 June 2023) | Viewed by 3080

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,

The role of livestock is, above all, to provide sufficient food which is protein-rich, safe, and healthy, with high nutritional and organoleptic value for humans. 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 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 in 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 microsatellites, SNPs, CNVs, and retrotransposons are used to investigate the genetic basis of traits, supplying support to phenotypic evaluation and genealogical data analysis. The collection of phenotypic data and different genomic approaches such as high-throughput genome analysis methods and single-nucleotide polymorphism genotyping can be used to investigate the genetic basis of inheritance, QTLs, new phenotypes, genomic selection, and breeding programs.

This Special Issue will focus on recent research or reviews that investigate novel approaches and/or technologies used to identify relevant new phenotypes, as well as implement all aspects of pig genetics and genomics. Research or reviews with a focus on new phenotypes, genomic selection, breeding programs, QTLs, and breed conservation are also welcome.

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
  • meat quality
  • traceability
  • typical product
  • conservation
  • biodiversity
  • food safety
  • gene annotation

Published Papers (2 papers)

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Research

15 pages, 8139 KiB  
Article
SINE Insertion in the Pig Carbonic Anhydrase 5B (CA5B) Gene Is Associated with Changes in Gene Expression and Phenotypic Variation
by Yao Zheng, Cai Chen, Mengli Wang, Ali Shoaib Moawad, Xiaoyan Wang and Chengyi Song
Animals 2023, 13(12), 1942; https://doi.org/10.3390/ani13121942 - 09 Jun 2023
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Abstract
Transposons are genetic elements that are present in mammalian genomes and occupy a large proportion of the pig genome, with retrotransposons being the most abundant. In a previous study, it was found that a SINE retrotransposon was inserted in the 1st intron [...] Read more.
Transposons are genetic elements that are present in mammalian genomes and occupy a large proportion of the pig genome, with retrotransposons being the most abundant. In a previous study, it was found that a SINE retrotransposon was inserted in the 1st intron of the CA5B gene in pigs, and the present study aimed to investigate the SINE insertion polymorphism in this gene in different pig breeds. Polymerase chain reaction (PCR) was used to confirm the polymorphism in 11 pig breeds and wild boars), and it was found that there was moderate polymorphism information content in 9 of the breeds. Further investigation in cell experiments revealed that the 330 bp SINE insertion in the RIP-CA5B site promoted expression activity in the weak promoter region of this site. Additionally, an enhancer verification vector experiment showed that the 330 bp SINE sequence acted as an enhancer on the core promoter region upstream of the CA5B gene region. The expression of CA5B in adipose tissue (back fat and leaf fat) in individuals with the (SINE+/+) genotype was significantly higher than those with (SINE+/−) and (SINE−/−) genotypes. The association analysis revealed that the (SINE+/+) genotype was significantly associated with a higher back fat thickness than the (SINE−/−) genotype. Moreover, it was observed that the insertion of SINE at the RIP-CA5B site carried ATTT repeats, and three types of (ATTT) repeats were identified among different individuals/breeds (i.e., (ATTT)4, (ATTT)6 and (ATTT)9). Overall, the study provides insights into the genetic basis of adipose tissue development in pigs and highlights the role of a SINE insertion in the CA5B gene in this process. Full article
(This article belongs to the Special Issue Genetic Diversity and Population Structure of Local Pig Breeds)
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16 pages, 2807 KiB  
Article
Characterization of Growth Secondary Hair in Min Pig Activated by Follicle Stem Cell Stimulated by Wnt and BMP Signaling Pathway
by Xinmiao He, Ziliang Qin, Ran Teng, Ming Tian, Wentao Wang, Yanzhong Feng, Heshu Chen, Haijuan He, Haifeng Zhang, Di Liu and Xinpeng Jiang
Animals 2023, 13(7), 1239; https://doi.org/10.3390/ani13071239 - 03 Apr 2023
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Abstract
In China, the national-level protected pig, the Min pig, is characterized by the development of secondary hairs and hair follicles in winter. Factors that dominate the genotype in the growth of secondary hairs are not clear through the concrete cell signaling pathways. This [...] Read more.
In China, the national-level protected pig, the Min pig, is characterized by the development of secondary hairs and hair follicles in winter. Factors that dominate the genotype in the growth of secondary hairs are not clear through the concrete cell signaling pathways. This study compared hair phenotypes based on morphological structure, transcriptomics, and potential targeting molecules in the breeds of Min, Berkshire, and Yorkshire pigs. The results indicated that Min pigs have specific characteristics for the growth of secondary hairs compared with the Berkshire and Yorkshire pigs. The transcriptome analyses and quantitative reverse transcription-polymerase chain reaction results revealed that secondary hair growth was activated by follicle stem cells. The specific inhibitors of Wnt and BMP were studied using respective signals. The density of follicles, activity of follicle stem cells, and relative gene expression results have shown that Wnt and BMP stimulate the activity of follicle stem cells, and the Wnt signaling molecule has a significantly better effect than the BMP signaling molecule on stem cells. Wnt and BMP can promote the growth of local secondary hair and gene expression. Therefore, this study was conducted to verify the development mechanisms of secondary hairs, which have potential applications in laboratory animals and comparative medicine. Full article
(This article belongs to the Special Issue Genetic Diversity and Population Structure of Local Pig Breeds)
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