Special Issue "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: 20 November 2023 | Viewed by 2619

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
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

Manuscript Submission Information

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Keywords

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

Published Papers (4 papers)

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Research

Article
PorcineAI-Enhancer: Prediction of Pig Enhancer Sequences Using Convolutional Neural Networks
Animals 2023, 13(18), 2935; https://doi.org/10.3390/ani13182935 - 15 Sep 2023
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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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Article
Copy Number Variation Regions Differing in Segregation Patterns Span Different Sets of Genes
Animals 2023, 13(14), 2351; https://doi.org/10.3390/ani13142351 - 19 Jul 2023
Viewed by 562
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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Article
Genome-Wide Association Study Identifies the Crucial Candidate Genes for Teat Number in Crossbred Commercial Pigs
Animals 2023, 13(11), 1880; https://doi.org/10.3390/ani13111880 - 05 Jun 2023
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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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Article
Genome-Wide Association Analysis Identifies Genomic Regions and Candidate Genes for Growth and Fatness Traits in Diannan Small-Ear (DSE) Pigs
Animals 2023, 13(9), 1571; https://doi.org/10.3390/ani13091571 - 08 May 2023
Viewed by 896
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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