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Advances in Pig Genetic and Genomic Breeding of 2024
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Advances in Pig Genetic and Genomic Breeding of 2024

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

Deadline for manuscript submissions: 25 March 2025 | Viewed by 11835

Special Issue Editors

Dr. Kang Xu

E-Mail Website
Guest Editor
Laboratory of Animal Nutrition Physiology and Metabolism, Institute of Subtropical Agriculture Chinese Academy of Sciences, Changsha, China
Interests: pig genetics
Special Issues, Collections and Topics in MDPI journals
Dr. Kejun Wang

E-Mail Website
Guest Editor
College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
Interests: animal pan-genome; animal genetics; gene mapping; trait dissection
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Due to its great application value, the selective breeding of pigs has been carried out since the beginning of the 20th century by identifying the genetic foundations for economic traits. The completion of multiple pig genome projects has constructed a comprehensive list of pig genes. Moreover, a large number of genes and loci have been discovered in pigs. However, years of extensive research have demonstrated that not many major genes or loci can be used for breeding. The genetic mechanisms and genomics of pigs are still the main focus.

Therefore, this Special Issue aims to focus on the genetic mechanisms of economic traits, such as reproductive performance, growth rate, intestinal digestibility (feed to meat ratio), meat-producing performance, meat quality, disease resistance, and others among different porcine varieties or strains. Moreover, we aim to analyze the genetic mechanisms and molecular regulatory networks of pig economic traits at the DNA, RNA, proteins, and chromatin levels using multiple methods, such as transcriptomics, proteomics, metabolomics, monocytomics, and multi-omics joint analysis.

In addition, mining new candidate genes and detecting genetic loci for economic traits will also be considered. Meanwhile, the role and contribution of genes and molecular makers for the formation of economic traits will be discussed.

Finally, the application of genes and loci in marker-assisted selection and the genome-wide selection of pigs will be of great concern to this Special Issue.

Dr. Kang Xu
Dr. Kejun Wang
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 genome
  • pig breeding
  • multi-omics
  • economic traits
  • molecular maker

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Published Papers (6 papers)

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Research

12 pages, 1248 KiB  
Article
Polymorphism Identification in the Coding Sequences (ORFs) of the Porcine Pregnancy-Associated Glycoprotein 2-like Gene Subfamily in Pigs
by Martyna Bieniek-Kobuszewska and Grzegorz Panasiewicz
Genes 2024, 15(9), 1149; https://doi.org/10.3390/genes15091149 - 31 Aug 2024
Viewed by 544
Abstract
Pregnancy-associated glycoproteins (PAGs) are a polygenic family with many scattered genes and pseudogenes resulting from the duplication or fusion of a pseudogene with expression beginning in the trophoblast during the peri-implantation period and continuing in the trophectoderm. In this study, single-nucleotide polymorphism (SNP) [...] Read more.
Pregnancy-associated glycoproteins (PAGs) are a polygenic family with many scattered genes and pseudogenes resulting from the duplication or fusion of a pseudogene with expression beginning in the trophoblast during the peri-implantation period and continuing in the trophectoderm. In this study, single-nucleotide polymorphism (SNP) and insertion/deletion (InDels) in the open reading frame (nine exons) of crossbreed pigs are reported for the first time. Novel SNPs/InDels were researched using genomic DNA templates isolated from the leukocytes of crossbreed pigs (N = 25), which were amplified, gel-out-purified, and sequenced. Sixteen SNPs and one InDel (g.6961_6966 Ins TGCCAA) were identified in the crossbreed pigs. In silico analysis revealed that among 16 SNPs, only 10 SNPs cause amino acid (aa) substitutions, and InDel codes asparagine (N298) and alanine (A299). The results provide a novel broad-based database (main pattern) that will be critical for future research into the possible correlations between the SNP genotypes of the pPAG2-L subfamily in pigs of various breeds whose reproductive traits are known. Full article
(This article belongs to the Special Issue Advances in Pig Genetic and Genomic Breeding of 2024)
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15 pages, 18790 KiB  
Article
Whole-Transcriptome Analysis Sheds Light on the Biological Contexts of Intramuscular Fat Deposition in Ningxiang Pigs
by Zhao Jin, Hu Gao, Yawei Fu, Ruimin Ren, Xiaoxiao Deng, Yue Chen, Xiaohong Hou, Qian Wang, Gang Song, Ningyu Fan, Haiming Ma, Yulong Yin and Kang Xu
Genes 2024, 15(5), 642; https://doi.org/10.3390/genes15050642 - 19 May 2024
Cited by 1 | Viewed by 1289
Abstract
The quality of pork is significantly impacted by intramuscular fat (IMF). However, the regulatory mechanism of IMF depositions remains unclear. We performed whole-transcriptome sequencing of the longissimus dorsi muscle (IMF) from the high (5.1 ± 0.08) and low (2.9 ± 0.51) IMF groups [...] Read more.
The quality of pork is significantly impacted by intramuscular fat (IMF). However, the regulatory mechanism of IMF depositions remains unclear. We performed whole-transcriptome sequencing of the longissimus dorsi muscle (IMF) from the high (5.1 ± 0.08) and low (2.9 ± 0.51) IMF groups (%) to elucidate potential mechanisms. In summary, 285 differentially expressed genes (DEGs), 14 differentially expressed miRNAs (DEMIs), 83 differentially expressed lncRNAs (DELs), and 79 differentially expressed circRNAs (DECs) were identified. DEGs were widely associated with IMF deposition and liposome differentiation. Furthermore, competing endogenous RNA (ceRNA) regulatory networks were constructed through co-differential expression analyses, which included circRNA-miRNA-mRNA (containing 6 DEMIs, 6 DEGs, 47 DECs) and lncRNA-miRNA-mRNA (containing 6 DEMIs, 6 DEGs, 36 DELs) regulatory networks. The circRNAs sus-TRPM7_0005, sus-MTUS1_0004, the lncRNAs SMSTRG.4269.1, and MSTRG.7983.2 regulate the expression of six lipid metabolism-related target genes, including PLCB1, BAD, and GADD45G, through the binding sites of 2-4068, miR-7134-3p, and miR-190a. For instance, MSTRG.4269.1 regulates its targets PLCB1 and BAD via miRNA 2_4068. Meanwhile, sus-TRPM7_0005 controls its target LRP5 through ssc-miR-7134-3P. These findings indicate molecular regulatory networks that could potentially be applied for the marker-assisted selection of IMF to enhance pork quality. Full article
(This article belongs to the Special Issue Advances in Pig Genetic and Genomic Breeding of 2024)
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19 pages, 5558 KiB  
Article
Mechanism of Apoptosis in Porcine Ovarian Granulosa Cells Triggered by T-2 Toxin
by Yige Chen, Xianrui Zheng, Ren Zhou, Huibin Zhang, Yangguang Liu, Xiaojing Hu and Zongjun Yin
Genes 2024, 15(5), 579; https://doi.org/10.3390/genes15050579 - 1 May 2024
Viewed by 3653
Abstract
T-2 toxin (T-2), an A-type mono mycotoxin produced by various Fusarium species, disrupts DNA/RNA and protein synthesis upon entering the body, resulting in pathological conditions in various tissues/organs and posing a significant threat to human and animal health. However, the mechanisms underlying its [...] Read more.
T-2 toxin (T-2), an A-type mono mycotoxin produced by various Fusarium species, disrupts DNA/RNA and protein synthesis upon entering the body, resulting in pathological conditions in various tissues/organs and posing a significant threat to human and animal health. However, the mechanisms underlying its toxicity remain unclear. With the goal of learning how T-2 affects reproduction in animals, we utilized primary porcine ovarian granulosa cells (pGCs) as a carrier in vitro and constructed concentration models for analyzing cell morphology and RNA-sequencing (RNA-seq). Our findings showed that T-2 could influence pGCs morphology, induce cell cycle arrest, and promote apoptosis in a dose-dependent manner. The results of RNA-seq analyses indicated that a total of 8216 genes exhibited significant differential expression (DEG) following T-2 treatment, of which 4812 were observed to be down-regulated and 3404 were up-regulated. The DEGs following T-2 toxin treatment of pGCs had a notable impact on many metabolic pathways such as PI3K-Akt, Ras, MAPK, and apoptosis, which in turn altered important physiological processes. Gene set enrichment analysis (GSEA) indicated that the differences in the harmful effects of T-2 might be caused by the varying control of cellular processes and the pathway responsible for steroid metabolism. These results present further insights regarding the mechanism of T-2 action on sow reproductive toxicity, enhance our understanding of T-2 reproductive toxicological effects, and lay a theoretical foundation for the judicious prevention of T-2-induced reproductive toxicity. Full article
(This article belongs to the Special Issue Advances in Pig Genetic and Genomic Breeding of 2024)
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11 pages, 1273 KiB  
Article
Detection and Analysis of Genes Affecting the Number of Thoracic Vertebrae in Licha Black Pigs
by Yuan Wang, Min Wang, Xiaojin He, Ruilan Dong, Hongjiang Liu and Guanghui Yu
Genes 2024, 15(4), 477; https://doi.org/10.3390/genes15040477 - 10 Apr 2024
Viewed by 1090
Abstract
The number of thoracic vertebrae (NTV) in pigs is an important economic trait that significantly influences pork production. While the Licha black pig is a well-known Chinese pig breed with multiple thoracic vertebrae, the genetic mechanism is still unknown. Here, we performed a [...] Read more.
The number of thoracic vertebrae (NTV) in pigs is an important economic trait that significantly influences pork production. While the Licha black pig is a well-known Chinese pig breed with multiple thoracic vertebrae, the genetic mechanism is still unknown. Here, we performed a selective signal analysis on the genome of Licha black pigs, comparing individuals with 15 NTV versus those with 16 NTV to better understand functional genes associated with NTV. A total of 2265 selection signal regions were detected across the genome, including 527 genes and 1073 QTL that overlapped with the selection signal regions. Functional enrichment analysis revealed that LRP5 and SP5 genes were involved in biological processes such as bone morphogenesis and Wnt protein binding. Furthermore, three genes, LRP8, DEF6, and SCUBE3, associated with osteoblast differentiation and bone formation, were located within or close to the QTL related to bone development and vertebrae number. These five genes were hypothesized to be potential candidates for regulating the NTV trait in Licha black pigs. Our findings revealed several candidate genes that play crucial roles in NTV regulation and provide a theoretical foundation to understand the genetic mechanism of the NTV trait in pig breeding. Full article
(This article belongs to the Special Issue Advances in Pig Genetic and Genomic Breeding of 2024)
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13 pages, 4630 KiB  
Article
Genome-Wide Association Studies and Runs of Homozygosity to Identify Reproduction-Related Genes in Yorkshire Pig Population
by Lige Zhang, Songyuan Zhang, Meng Yuan, Fengting Zhan, Mingkun Song, Peng Shang, Feng Yang, Xiuling Li, Ruimin Qiao, Xuelei Han, Xinjian Li, Meiying Fang and Kejun Wang
Genes 2023, 14(12), 2133; https://doi.org/10.3390/genes14122133 - 27 Nov 2023
Cited by 4 | Viewed by 1777
Abstract
Reproductive traits hold considerable economic importance in pig breeding and production. However, candidate genes underpinning the reproductive traits are still poorly identified. In the present study, we executed a genome-wide association study (GWAS) and runs of homozygosity (ROH) analysis using the PorcineSNP50 BeadChip [...] Read more.
Reproductive traits hold considerable economic importance in pig breeding and production. However, candidate genes underpinning the reproductive traits are still poorly identified. In the present study, we executed a genome-wide association study (GWAS) and runs of homozygosity (ROH) analysis using the PorcineSNP50 BeadChip array for 585 Yorkshire pigs. Results from the GWAS identified two genome-wide significant and eighteen suggestive significant single nucleotide polymorphisms (SNPs) associated with seven reproductive traits. Furthermore, we identified candidate genes, including ELMO1, AOAH, INSIG2, NUP205, LYPLAL1, RPL34, LIPH, RNF7, GRK7, ETV5, FYN, and SLC30A5, which were chosen due to adjoining significant SNPs and their functions in immunity, fertilization, embryonic development, and sperm quality. Several genes were found in ROH islands associated with spermatozoa, development of the fetus, mature eggs, and litter size, including INSL6, TAF4B, E2F7, RTL1, CDKN1C, and GDF9. This study will provide insight into the genetic basis for pig reproductive traits, facilitating reproduction improvement using the marker-based selection methods. Full article
(This article belongs to the Special Issue Advances in Pig Genetic and Genomic Breeding of 2024)
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16 pages, 4258 KiB  
Article
Identification and Functional Prediction of Long Non-Coding RNA in Longissimus Dorsi Muscle of Queshan Black and Large White Pigs
by Yaqing Dou, Kunlong Qi, Yingke Liu, Chenlei Li, Chenglei Song, Yilin Wei, Zhe Zhang, Xinjian Li, Kejun Wang, Xiuling Li, Ruimin Qiao, Feng Yang and Xuelei Han
Genes 2023, 14(1), 197; https://doi.org/10.3390/genes14010197 - 12 Jan 2023
Cited by 5 | Viewed by 2730
Abstract
Long non-coding RNA (lncRNA) participates in the regulation of various biological processes, but its function and characteristics in intramuscular fat (IMF) deposition in different breeds of pigs have not been fully understood. IMF content is one of the important factors affecting pork quality. [...] Read more.
Long non-coding RNA (lncRNA) participates in the regulation of various biological processes, but its function and characteristics in intramuscular fat (IMF) deposition in different breeds of pigs have not been fully understood. IMF content is one of the important factors affecting pork quality. In the present study, the differentially expressed lncRNAs (DE lncRNAs) and their target genes were screened by comparing Queshan Black (QS) and Large White (LW) pigs based on RNA-seq. The results displayed 55 DE lncRNAs between QS and LW, 29 upregulated and 26 downregulated, with 172 co-located target genes, and 6203 co-expressed target genes. The results of GO and KEGG analysis showed that the target genes of DE lncRNAs were involved in multiple pathways related to lipogenesis and lipid metabolism, such as the lipid biosynthetic process, protein phosphorylation, activation of MAPK activity, and the Jak-STAT signaling pathway. By constructing regulatory networks, lincRNA-ZFP42-ACTC1, lincRNA-AMY2-STAT1, and/or lincRNA-AMY2/miR-204/STAT1 were sieved, and the results indicate that lncRNA could participate in IMF deposition through direct regulation or ceRNA. These findings provide a basis for analyzing the molecular mechanism of IMF deposition in pigs and lay a foundation for developing and utilizing high-quality resources of local pig breeds. Full article
(This article belongs to the Special Issue Advances in Pig Genetic and Genomic Breeding of 2024)
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