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Advances in Pig Genetics and Breeding
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Advances in Pig Genetics and Breeding

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (25 December 2024) | Viewed by 3795

Special Issue Editors

Dr. Linyuan Shen

E-Mail Website
Guest Editor
College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
Interests: pig molecular genetics and breeding; genomic selection; functional genomics; meat quality; artificial intelligence linking phenotypes
Special Issues, Collections and Topics in MDPI journals
Dr. Mailin Gan

E-Mail Website
Guest Editor
College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
Interests: pig; meat quality; reproduction traits; non-coding RNA; molecular genetics; genomic selection
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Owing to various novel technological applications, the genetic improvement of pigs has rapidly progressed in recent decades. Nowadays, more and more economically relevant traits are being expanded as breeding objectives, such as litter size, birth weight, feed efficiency, lean percentage, meat quality, lifetime reproduction, and robustness. In addition, there have been rapid developments in high-throughput genome and cell molecular biology methods, and the processes involved in the identification of genes related to important phenotypic traits and genetic markers for pig selection have been significantly enhanced, leading to the development of fast, cost-effective, and more accurate methods for use in the implementation of breeding programs. In addition, artificial intelligence is now being employed to identify relevant new phenotypes and to implement tools to effectively measure traits. For this Special Issue, articles addressing all aspects of pig genetics and phenotypes are welcome, especially with a focus on the quantitative genetics of new phenotypes, the use of artificial intelligence to link phenotypes, genomic selection, breeding programs, gene polymorphisms, quantitative trait locus mapping, the identification of the genetic regulatory mechanisms and causative mutations affecting economically relevant traits, and the exploitation of native pig genetic resources.

Dr. Linyuan Shen
Dr. Mailin Gan
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. Genes is an international peer-reviewed open access monthly 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 2600 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

  • pigs
  • transcriptomics
  • epigenomics
  • genetic mechanisms
  • genetic parameters
  • genomic selection
  • artificial intelligence linking phenotypes

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Published Papers (2 papers)

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16 pages, 4739 KiB  
Article
Genome-Wide Association Studies of Hair Whorl in Pigs
by Wenyu Jiang, Xidi Yang, Liangyu Zhu, Yiting Yang, Chengming Liu, Yong Du, Yan Wang, Lili Niu, Ye Zhao, Yihui Liu, Mailin Gan, Linyuan Shen and Li Zhu
Genes 2024, 15(10), 1249; https://doi.org/10.3390/genes15101249 - 25 Sep 2024
Viewed by 1521
Abstract
Background: In pigs, a hair whorl refers to hairs that form a ring of growth around the direction of the hair follicle at the dorsal hip. In China, a hair whorl is considered a negative trait that affects marketing, and no studies have [...] Read more.
Background: In pigs, a hair whorl refers to hairs that form a ring of growth around the direction of the hair follicle at the dorsal hip. In China, a hair whorl is considered a negative trait that affects marketing, and no studies have been conducted to demonstrate whether hair whorl affects pig performance and provide an explanation for its genetic basis. Methods: Performance-measured traits and slaughter-measured traits of hair whorl and non-hair whorl pigs were differentially analyzed, followed by genome-wide association analysis (GWAS) and copy number variation (CNV) methods to investigate the genetic basis of hair whorl in pigs. Results: Differential analysis of 2625 pigs (171 hair whorl and 2454 non-hair whorl) for performance measures showed that hair whorl and non-hair whorl pigs differed significantly (p < 0.05) in traits such as live births, total litter size, and healthy litter size (p < 0.05), while differential analysis of carcass and meat quality traits showed a significant difference only in the 45 min pH (p = 0.0265). GWAS identified 4 SNP loci significantly associated with the hair whorl trait, 2 of which reached genome-significant levels, and 23 candidate genes were obtained by annotation with the Ensembl database. KEGG and GO enrichment analyses showed that these genes were mainly enriched in the ErbB signaling, endothelial apoptosis regulation, and cell proliferation pathways. In addition, CNV analysis identified 652 differential genes between hair whorl and non-hair whorl pigs, which were mainly involved in the signal transduction, transcription factor activity, and nuclear and cytoplasmic-related pathways. Conclusions: The candidate genes and copy number variation differences identified in this study provide a new theoretical basis for pig breeding efforts. Full article
(This article belongs to the Special Issue Advances in Pig Genetics and Breeding)
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14 pages, 5773 KiB  
Article
Integrated Metagenomic and Metabolomics Profiling Reveals Key Gut Microbiota and Metabolites Associated with Weaning Stress in Piglets
by Xianrui Zheng, Liming Xu, Qingqing Tang, Kunpeng Shi, Ziyang Wang, Lisha Shi, Yueyun Ding, Zongjun Yin and Xiaodong Zhang
Genes 2024, 15(8), 970; https://doi.org/10.3390/genes15080970 - 23 Jul 2024
Cited by 1 | Viewed by 1817
Abstract
(1) Background: Weaning is a challenging and stressful event in the pig’s life, which disrupts physiological balance and induces oxidative stress. Microbiota play a significant role during the weaning process in piglets. Therefore, this study aimed to investigate key gut microbiota and metabolites [...] Read more.
(1) Background: Weaning is a challenging and stressful event in the pig’s life, which disrupts physiological balance and induces oxidative stress. Microbiota play a significant role during the weaning process in piglets. Therefore, this study aimed to investigate key gut microbiota and metabolites associated with weaning stress in piglets. (2) Methods: A total of ten newborn piglet littermates were randomly assigned to two groups: S (suckling normally) and W (weaned at 21 d; all euthanized at 23 d). Specimens of the cecum were dehydrated with ethanol, cleared with xylene, embedded in paraffin, and cut into 4 mm thick serial sections. After deparaffinization, the sections were stained with hematoxylin and eosin (H&E) for morphometric analysis. Cecal metagenomic and liver LC-MS-based metabolomics were employed in this study. Statistical comparisons were performed by a two-tailed Student’s t-test, and p < 0.05 indicated statistical significance. (3) Results: The results showed that weaning led to intestinal morphological damage in piglets. The intestinal villi of suckling piglets were intact, closely arranged in an orderly manner, and finger-shaped, with clear contours of columnar epithelial cells. In contrast, the intestines of weaned piglets showed villous atrophy and shedding, as well as mucosal bleeding. Metagenomics and metabolomics analyses showed significant differences in composition and function between suckling and weaned piglets. The W piglets showed a decrease and increase in the relative abundance of Bacteroidetes and Proteobacteria (p < 0.05), respectively. The core cecal flora in W piglets were Campylobacter and Clostridium, while those in S piglets were Prevotella and Lactobacillus. At the phylum level, the relative abundance of Bacteroidetes significantly decreased (p < 0.05) in weaned piglets, while Proteobacteria significantly increased (p < 0.05). Significant inter-group differences were observed in pathways and glycoside hydrolases in databases, such as the KEGG and CAZymes, including fructose and mannose metabolism, salmonella infection, antifolate resistance, GH135, GH16, GH32, and GH84. We identified 757 differential metabolites between the groups through metabolomic analyses—350 upregulated and 407 downregulated (screened in positive ion mode). In negative ion mode, 541 differential metabolites were identified, with 270 upregulated and 271 downregulated. Major differential metabolites included glycerophospholipids, histidine, nitrogen metabolism, glycine, serine, threonine, β-alanine, and primary bile acid biosynthesis. The significant differences in glycine, serine, and threonine metabolites may be potentially related to dysbiosis caused by weaning stress. Taken together, the identification of microbiome and metabolome signatures of suckling and weaned piglets has paved the way for developing health-promoting nutritional strategies, focusing on enhancing bacterial metabolite production in early life stages. Full article
(This article belongs to the Special Issue Advances in Pig Genetics and Breeding)
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