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Advances in Pig Breeding and Genetics (Volume II)
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Advances in Pig Breeding and Genetics (Volume II)

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

Deadline for manuscript submissions: closed (10 April 2024) | Viewed by 2957

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, among others. In addition, there has been a rapid development of 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 the implementation of breeding programs. In addition, artificial intelligence is now employed to identify relevant new phenotypes and 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 loci 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

  • pig
  • transcriptomics
  • epigenomics
  • genetic mechanism
  • genetic parameter
  • genomic selection
  • artificial intelligence linking phenotypes

Published Papers (3 papers)

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Research

13 pages, 796 KiB  
Article
Genome-Wide Association Analysis of Semen Characteristics in Piétrain Boars
by Henry Reyer, Ibrahim Abou-Soliman, Martin Schulze, Hubert Henne, Norbert Reinsch, Jennifer Schoen and Klaus Wimmers
Genes 2024, 15(3), 382; https://doi.org/10.3390/genes15030382 - 20 Mar 2024
Viewed by 763
Abstract
Since artificial insemination is common practice in pig breeding, the quality and persistence of the semen are decisive for the usability of individual boars. In the current study, genome-wide association analyses were performed to investigate the genetic variability underlying phenotypic variations in semen [...] Read more.
Since artificial insemination is common practice in pig breeding, the quality and persistence of the semen are decisive for the usability of individual boars. In the current study, genome-wide association analyses were performed to investigate the genetic variability underlying phenotypic variations in semen characteristics. These traits comprise sperm morphology and sperm motility under different temporal and thermal storage conditions, in addition to standard semen quality parameters. Two consecutive samples of the fourth and fifth ejaculates from the same boar were comprehensively analyzed in a genotyped Piétrain boar population. A total of 13 genomic regions on different chromosomes were identified that contain single-nucleotide polymorphisms significantly associated with these traits. Subsequent analysis of the genomic regions revealed candidate genes described to be involved in spermatogenesis, such as FOXL3, GPER1, PDGFA, PRKAR1B, SNRK, SUN1, and TSPO, and sperm motility, including ARRDC4, CEP78, DNAAF5, and GPER1. Some of these genes were also associated with male fertility or infertility in mammals (e.g., CEP78, GPER1). The analyses based on these laboriously determined and valuable phenotypes contribute to a better understanding of the genetic background of male fertility traits in pigs and could prospectively contribute to the improvement of sperm quality through breeding approaches. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics (Volume II))
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11 pages, 2791 KiB  
Communication
Genomic Scanning of Inbreeding Depression for Litter Size in Two Varieties of Iberian Pigs
by Carlos Hervás-Rivero, Houssemeddine Srihi, David López-Carbonell, Joaquim Casellas, Noelia Ibáñez-Escriche, Sara Negro and Luis Varona
Genes 2023, 14(10), 1941; https://doi.org/10.3390/genes14101941 - 15 Oct 2023
Viewed by 1083
Abstract
Inbreeding depression is expected to be more pronounced in fitness-related traits, such as pig litter size. Recent studies have suggested that the genetic determinism of inbreeding depression may be heterogeneous across the genome. Therefore, the objective of this study was to conduct a [...] Read more.
Inbreeding depression is expected to be more pronounced in fitness-related traits, such as pig litter size. Recent studies have suggested that the genetic determinism of inbreeding depression may be heterogeneous across the genome. Therefore, the objective of this study was to conduct a genomic scan of the whole pig autosomal genome to detect the genomic regions that control inbreeding depression for litter size in two varieties of Iberian pigs (Entrepelado and Retinto). The datasets consisted of 2069 (338 sows) and 2028 (327 sows) records of litter size (Total Number Born and Number Born Alive) for the Entrepelado and Retinto varieties. All sows were genotyped using the Geneseek GGP PorcineHD 70 K chip. We employed the Unfavorable Haplotype Finder software to extract runs of homozygosity (ROHs) and conducted a mixed-model analysis to identify highly significant differences between homozygous and heterozygous sows for each specific ROH. A total of eight genomic regions located on SSC2, SSC5, SSC7, SSC8, and SSC13 were significantly associated with inbreeding depression, housing some relevant genes such as FSHR, LHCGR, CORIN, AQP6, and CEP120. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics (Volume II))
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11 pages, 3027 KiB  
Article
A Comparative Study on the Growth Performance and Gut Microbial Composition of Duroc and Yorkshire Boars
by Junhua Du, Mailin Gan, Zhongwei Xie, Gao Du, Yi Luo, Bin Liu, Kangping Zhu, Lei Chen, Ye Zhao, Lili Niu, Yan Wang, Jingyong Wang, Li Zhu and Linyuan Shen
Genes 2023, 14(9), 1726; https://doi.org/10.3390/genes14091726 - 29 Aug 2023
Viewed by 821
Abstract
The intestinal microbiota is required for maintaining the development and health of the host. However, the gut microbiota contributing to the regulation of the growth performance and health of Duroc and Yorkshire boars remains largely unknown. In this study, we first evaluated the [...] Read more.
The intestinal microbiota is required for maintaining the development and health of the host. However, the gut microbiota contributing to the regulation of the growth performance and health of Duroc and Yorkshire boars remains largely unknown. In this study, we first evaluated the difference in the growth performance between Duroc and Yorkshire boars when their body weight reached 100 kg. Relative to Duroc boars, Yorkshire boars weighed 100 kg at a younger age and exhibited a significantly lower backfat thickness and eye muscle area. Microbial analysis of the fecal samples revealed a marked difference in gut microbiota composition between the two pig models and remarkably increased α-diversity in Yorkshire boars compared to Duroc boars. Further analysis indicated that Bacteroidota, Prevotellaceae, and Ruminococcaceae might be associated with the growth performance and lean meat rate of Yorkshire boars. Taken together, these results highlight that Yorkshire boars exhibit a faster growth rate and higher lean meat rate compared to Duroc boars, and these differences may be attributed to the influence of the gut microbiota, thereby providing valuable insight into optimizing pig breeding systems and selecting terminal paternal sires to enhance overall productivity and quality. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics (Volume II))
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