Trends and Prospects in Pig Genomics and Genetics

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

Deadline for manuscript submissions: closed (15 August 2023) | Viewed by 24868

Special Issue Editors

Department of Animal Molecular Biology, National Research Institute of Animal Production, 31-047 Cracow, Poland
Interests: pig; chicken; horse genomics; transcriptomics and epigenomics
Special Issues, Collections and Topics in MDPI journals
Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
Interests: pig and horse genomics; transcriptomics and epigenomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Pigs (Sus scrofa) are the most widespread large mammals in the world. The Sus genus includes domestic pigs and wild boar. They are omnivores and are biologically similar to humans, and thus are frequently used for human medical research and as animal models. Molecular biology methods also assist agricultural progress, including pig production and breeding. Since the draft reference genome sequence of S. scrofa was assembled in 2012, the process of the identification of genes related to important phenotypic traits and the search for genetic markers for selection has been significantly refined. In turn, the newest wide-range high-throughput techniques including microarrays, next-generation sequencing, and the recent PacBio sequencing platform providing ultra-long sequencing reads allow the identification of gene mutations and gene candidates at the whole-genome, transcriptome, or epigenome scale, and enable the estimation of quantitative traits important for breeding and the genetic background of inherited diseases.

Special Issue "Trends and Prospects in Pig Genomics and Genetics" is the second version of the successful special issue “Pig Genomics and Genetics” (https://www.mdpi.com/journal/genes/special_issues/Pig_Genomics_Genetics). In this special issue, we will continue to present the state-of-the-art in the field of pig genetics and genomics, including the identification of gene candidates linked to important pig traits as well as to nutritional modifications, assembling the most recent advances in one place. The manuscripts focusing on high-throughput methodologies, such as RNA-sequencing, ATAC-seq, MACE-seq, Chip-seq, and RRBS will be appreciated, as will manuscripts covering other fields of pig genetics.

Dr. Katarzyna Piórkowska
Dr. Katarzyna Ropka-Molik
Guest Editors

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Keywords

  • porcine
  • breeding
  • genetic marker
  • RNA-seq
  • genome
  • pig traits

Published Papers (14 papers)

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Research

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10 pages, 1214 KiB  
Article
Altered Transcript Levels of MMP13 and VIT Genes in the Muscle and Connective Tissue of Pigs with Umbilical Hernia
by Jakub Wozniak, Weronika Loba, Alicja Wysocka, Stanislaw Dzimira, Przemyslaw Przadka, Marek Switonski and Joanna Nowacka-Woszuk
Genes 2023, 14(10), 1903; https://doi.org/10.3390/genes14101903 - 01 Oct 2023
Viewed by 915
Abstract
Umbilical hernia (UH) and inguinal hernia (IH) are among the most common defects in pigs, affecting their welfare and resulting in economic losses. In this study, we aimed to verify the association of previously reported differences in transcript levels of the ACAN, [...] Read more.
Umbilical hernia (UH) and inguinal hernia (IH) are among the most common defects in pigs, affecting their welfare and resulting in economic losses. In this study, we aimed to verify the association of previously reported differences in transcript levels of the ACAN, COL6A5, MMP13, and VIT genes with the occurrence of UH and IH. We examined mRNA levels in muscle and connective tissue from 68 animals—34 affected by UH and 34 controls. In a second cohort, we examined inguinal channel samples from 46 pigs (in four groups). We determined DNA methylation levels in muscle tissue for the UH and control animals. The transcript level of MMP13 changed in the UH cases, being upregulated and downregulated in muscle and connective tissue, respectively, and the VIT gene also showed an increased muscular mRNA level. The transcript of the ACAN gene significantly decreased in old pigs with IH. We further observed an increased DNA methylation level for one CpG site within the MMP13 gene in UH individuals. We conclude that these alterations in gene mRNA levels in the UH animals depend on the tissue and can sometimes be a consequence of, not a cause of, the affected phenotype. Full article
(This article belongs to the Special Issue Trends and Prospects in Pig Genomics and Genetics)
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10 pages, 1690 KiB  
Communication
Identification of ROH Islands Conserved through Generations in Pigs Belonging to the Nero Lucano Breed
by Paola Di Gregorio, Annamaria Perna, Adriana Di Trana and Andrea Rando
Genes 2023, 14(7), 1503; https://doi.org/10.3390/genes14071503 - 23 Jul 2023
Viewed by 871
Abstract
The recovery of Nero Lucano (NL) pigs in the Basilicata region (Southern Italy) started in 2001 with the collaboration of several public authorities in order to preserve native breeds that can play a significant economic role both due to their remarkable ability to [...] Read more.
The recovery of Nero Lucano (NL) pigs in the Basilicata region (Southern Italy) started in 2001 with the collaboration of several public authorities in order to preserve native breeds that can play a significant economic role both due to their remarkable ability to adapt to difficult environments and the value of typical products from their area of origin. In this study, by using the Illumina Porcine SNP60 BeadChip, we compared the genetic structures of NL pigs reared in a single farm in two different periods separated by a time interval corresponding to at least three generations. The results showed an increase in the percentage of polymorphic loci, a decrease in the inbreeding coefficient calculated according to ROH genome coverage (FROH), a reduction in the number of ROH longer than 16 Mb and an increase in ROH with a length between 2 and 4 Mb, highlighting a picture of improved genetic variability. In addition, ROH island analysis in the two groups allowed us to identify five conserved regions, located on chromosomes 1, 4, 8, 14 and 15, containing genes involved in biological processes affecting immune response, reproduction and production traits. Only the conserved ROH island on chromosome 14 contains markers which, according to the literature, are associated with QTLs affecting thoracic vertebra number, teat number, gestation length, age at puberty and mean platelet volume. Full article
(This article belongs to the Special Issue Trends and Prospects in Pig Genomics and Genetics)
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23 pages, 6005 KiB  
Article
Transcriptomic Characterization of Genes Regulating the Stemness in Porcine Atrial Cardiomyocytes during Primary In Vitro Culture
by Rut Bryl, Mariusz J. Nawrocki, Karol Jopek, Mariusz Kaczmarek, Dorota Bukowska, Paweł Antosik, Paul Mozdziak, Maciej Zabel, Piotr Dzięgiel and Bartosz Kempisty
Genes 2023, 14(6), 1223; https://doi.org/10.3390/genes14061223 - 04 Jun 2023
Viewed by 1472
Abstract
Heart failure remains a major cause of death worldwide. There is a need to establish new management options as current treatment is frequently suboptimal. Clinical approaches based on autologous stem cell transplant is potentially a good alternative. The heart was long considered an [...] Read more.
Heart failure remains a major cause of death worldwide. There is a need to establish new management options as current treatment is frequently suboptimal. Clinical approaches based on autologous stem cell transplant is potentially a good alternative. The heart was long considered an organ unable to regenerate and renew. However, several reports imply that it may possess modest intrinsic regenerative potential. To allow for detailed characterization of cell cultures, whole transcriptome profiling was performed after 0, 7, 15, and 30 days of in vitro cell cultures (IVC) from the right atrial appendage and right atrial wall utilizing microarray technology. In total, 4239 differentially expressed genes (DEGs) with ratio > abs |2| and adjusted p-value ≤ 0.05 for the right atrial wall and 4662 DEGs for the right atrial appendage were identified. It was shown that a subset of DEGs, which have demonstrated some regulation of expression levels with the duration of the cell culture, were enriched in the following GO BP (Gene Ontology Biological Process) terms: “stem cell population maintenance” and “stem cell proliferation”. The results were validated by RT-qPCR. The establishment and detailed characterization of in vitro culture of myocardial cells may be important for future applications of these cells in heart regeneration processes. Full article
(This article belongs to the Special Issue Trends and Prospects in Pig Genomics and Genetics)
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13 pages, 2152 KiB  
Communication
Droplet Digital PCR Quantification of Selected Intracellular and Extracellular microRNAs Reveals Changes in Their Expression Pattern during Porcine In Vitro Adipogenesis
by Adrianna Bilinska, Marcin Pszczola, Monika Stachowiak, Joanna Stachecka, Franciszek Garbacz, Mehmet Onur Aksoy and Izabela Szczerbal
Genes 2023, 14(3), 683; https://doi.org/10.3390/genes14030683 - 09 Mar 2023
Cited by 2 | Viewed by 1759
Abstract
Extracellular miRNAs have attracted considerable interest because of their role in intercellular communication, as well as because of their potential use as diagnostic and prognostic biomarkers for many diseases. It has been shown that miRNAs secreted by adipose tissue can contribute to the [...] Read more.
Extracellular miRNAs have attracted considerable interest because of their role in intercellular communication, as well as because of their potential use as diagnostic and prognostic biomarkers for many diseases. It has been shown that miRNAs secreted by adipose tissue can contribute to the pathophysiology of obesity. Detailed knowledge of the expression of intracellular and extracellular microRNAs in adipocytes is thus urgently required. The system of in vitro differentiation of mesenchymal stem cells (MSCs) into adipocytes offers a good model for such an analysis. The aim of this study was to quantify eight intracellular and extracellular miRNAs (miR-21a, miR-26b, miR-30a, miR-92a, miR-146a, miR-148a, miR-199, and miR-383a) during porcine in vitro adipogenesis using droplet digital PCR (ddPCR), a highly sensitive method. It was found that only some miRNAs associated with the inflammatory process (miR-21a, miR-92a) were highly expressed in differentiated adipocytes and were also secreted by cells. All miRNAs associated with adipocyte differentiation were highly abundant in both the studied cells and in the cell culture medium. Those miRNAs showed a characteristic expression profile with upregulation during differentiation. Full article
(This article belongs to the Special Issue Trends and Prospects in Pig Genomics and Genetics)
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9 pages, 1437 KiB  
Communication
Genetic Diversity and Population Structure of the Native Pulawska and Three Commercial Pig Breeds Based on Microsatellite Markers
by Anna Radko, Anna Koseniuk and Grzegorz Smołucha
Genes 2023, 14(2), 276; https://doi.org/10.3390/genes14020276 - 20 Jan 2023
Cited by 2 | Viewed by 1357
Abstract
Swine DNA profiling is highly important for animal identification and parentage verification and also increasingly important for meat traceability. This work aimed to analyze the genetic structure and genetic diversity in selected Polish pig breeds. The study used a set of 14 microsatellite [...] Read more.
Swine DNA profiling is highly important for animal identification and parentage verification and also increasingly important for meat traceability. This work aimed to analyze the genetic structure and genetic diversity in selected Polish pig breeds. The study used a set of 14 microsatellite (STR) markers recommended by ISAG for parentage verification in the native Puławska pig (PUL, n = 85) and three commercial pig breeds: Polish Large White (PLW, n = 74), Polish Landrace (PL, n = 85) and foreign breed Duroc (DUR, n = 84). Genetic differentiation among breeds accounted for 18% of the total genetic variability (AMOVA). Bayesian structure analysis (STRUCTURE) indicated that the four distinct genetic clusters obtained corresponded to the four breeds studied. The genetic Reynolds distances (Ɵw) showed a close relationship between PL and PLW breeds and the most distant for DUR and PUL pigs. The genetic differentiation values (FST) were lower between PL and PLW and higher between PUL and DUR. The principal coordinate analysis (PCoA) supported the classification of the populations into four clusters. Full article
(This article belongs to the Special Issue Trends and Prospects in Pig Genomics and Genetics)
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13 pages, 1721 KiB  
Article
LncPLAAT3-AS Regulates PLAAT3-Mediated Adipocyte Differentiation and Lipogenesis in Pigs through miR-503-5p
by Zhiming Wang, Jin Chai, Yuhao Wang, Yiren Gu, Keren Long, Mingzhou Li and Long Jin
Genes 2023, 14(1), 161; https://doi.org/10.3390/genes14010161 - 06 Jan 2023
Cited by 4 | Viewed by 1264
Abstract
Animal fat deposition has a significant impact on meat flavor and texture. However, the molecular mechanisms of fat deposition are not well understood. LncPLAAT3-AS is a naturally occurring transcript that is abundant in porcine adipose tissue. Here, we focus on the [...] Read more.
Animal fat deposition has a significant impact on meat flavor and texture. However, the molecular mechanisms of fat deposition are not well understood. LncPLAAT3-AS is a naturally occurring transcript that is abundant in porcine adipose tissue. Here, we focus on the regulatory role of lncPLAAT3-AS in promoting preadipocyte proliferation and adipocyte differentiation. By overexpressing or repressing lncPLAAT3 expression, we found that lncPLAAT3-AS promoted the transcription of its host gene PLAAT3, a regulator of adipocyte differentiation. In addition, we predicted the region of lncPLAAT3-AS that binds to miR-503-5p and showed by dual luciferase assay that lncPLAAT3-AS acts as a sponge to absorb miR-503-5p. Interestingly, miR-503-5p also targets and represses PLAAT3 expression and helps regulate porcine preadipocyte proliferation and differentiation. Taken together, these results show that lncPLAAT3-AS upregulates PLAAT3 expression by absorbing miR-503-5p, suggesting a potential regulatory mechanism based on competing endogenous RNAs. Finally, we explored lncPLAAT3-AS and PLAAT3 expression in adipose tissue and found that both molecules were expressed at significantly higher levels in fatty pig breeds compared to lean pig breeds. In summary, we identified the mechanism by which lncPLAAT3-AS regulates porcine preadipocyte proliferation and differentiation, contributing to our understanding of the molecular mechanisms of lipid deposition in pigs. Full article
(This article belongs to the Special Issue Trends and Prospects in Pig Genomics and Genetics)
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20 pages, 11437 KiB  
Article
Meta-Analysis of SNPs Determining Litter Traits in Pigs
by Ewa Sell-Kubiak, Jan Dobrzanski, Martijn F. L. Derks, Marcos S. Lopes and Tomasz Szwaczkowski
Genes 2022, 13(10), 1730; https://doi.org/10.3390/genes13101730 - 26 Sep 2022
Cited by 4 | Viewed by 1928
Abstract
Nearly 2000 SNPs associated with pig litter size traits have been reported based on genome-wide association studies (GWASs). The aims of this study were to gather and integrate previously reported associations between SNPs and five litter traits: total number born (TNB), number born [...] Read more.
Nearly 2000 SNPs associated with pig litter size traits have been reported based on genome-wide association studies (GWASs). The aims of this study were to gather and integrate previously reported associations between SNPs and five litter traits: total number born (TNB), number born alive (NBA), number of stillborn (SB), litter birth weight (LWT), and corpus luteum number (CLN), in order to evaluate their common genetic background and to perform a meta-analysis (MA) of GWASs for total number born (TNB) recorded for animals from five pig populations. In this study, the genes with the largest number of associations with evaluated litter traits were GABRG3, RBP7, PRKD1, and STXBP6. Only 21 genes out of 233 associated with the evaluated litter traits were reported in more than one population or for more than one trait. Based on this evaluation, the most interesting candidate gene is PRKD1, which has an association with SB and TNB traits. Based on GO term analysis, PRKD1 was shown to be involved in angiogenesis as well. As a result of the MA, two new genomic regions, which have not been previously reported, were found to be associated with the TNB trait. One SNP was located on Sus scrofa chromosome (SSC) 14 in the intron of the FAM13C gene. The second SNP was located on SSC9 within the intron of the AGMO gene. Functional analysis revealed a strong candidate causal gene underlying the QTL on SSC9. The third best hit and the most promising candidate gene for litter size was found within the SOSTDC1 gene, associated with lower male fertility in rats. We showed that litter traits studied across pig populations have only a few genomic regions in common based on candidate gene comparison. PRKD1 could be an interesting candidate gene with a wider association with fertility. The MA identified new genomic regions on SSC9 and SSC14 associated with TNB. Further functional analysis indicated the most promising gene was SOSTDC1, which was confirmed to affect male fertility in other mammals. This is an important finding, as litter traits are by default linked with females rather than males. Full article
(This article belongs to the Special Issue Trends and Prospects in Pig Genomics and Genetics)
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15 pages, 1380 KiB  
Article
Variations in Fibrinogen-like 1 (FGL1) Gene Locus as a Genetic Marker Related to Fat Deposition Based on Pig Model and Liver RNA-Seq Data
by Katarzyna Piórkowska, Kacper Żukowski, Katarzyna Ropka-Molik and Mirosław Tyra
Genes 2022, 13(8), 1419; https://doi.org/10.3390/genes13081419 - 09 Aug 2022
Cited by 1 | Viewed by 1757
Abstract
The goal of this study was to evaluate the effects of mutations in the FGL1 gene associated with pig productive traits to enrich the genetic marker pool for further selection and to support the studies on FGL1 in the context of the fat [...] Read more.
The goal of this study was to evaluate the effects of mutations in the FGL1 gene associated with pig productive traits to enrich the genetic marker pool for further selection and to support the studies on FGL1 in the context of the fat deposition (FD) process. The variant calling and χ2 analyses of liver RNA-seq data were used to indicate genetic markers. FGL1 mutations were genotyped in the Złotnicka White (n = 72), Polish Large White (n = 208), Duroc (n = 72), Polish Landrace (PL) (n = 292), and Puławska (n = 178) pig breeds. An association study was performed using a general linear model (GLM) implemented in SAS® software. More than 50 crucial mutations were identified in the FGL1 gene. The association study showed a significant effect of the FGL1 on intramuscular fat (IMF), loin eye area, backfat thickness at the lumbar, ham mass (p = 0.0374), meat percentage (p = 0.0205), and loin fat (p = 0.0003). Alternate homozygotes and heterozygotes were found in the PL and Duroc, confirming the selective potential for these populations. Our study supports the theory that liver FGL1 is involved in the FD process. Moreover, since fat is the major determinant of flavor development in meat, the FGL1 rs340465447_A allele can be used as a target in pig selection focused on elevated fat levels. Full article
(This article belongs to the Special Issue Trends and Prospects in Pig Genomics and Genetics)
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14 pages, 3047 KiB  
Article
Alternative Splicing Isoforms of Porcine CREB Are Differentially Involved in Transcriptional Transactivation
by Dongjie Zhang, Qian Zhang, Liang Wang, Jiaxin Li, Wanjun Hao, Yuanlu Sun, Di Liu and Xiuqin Yang
Genes 2022, 13(8), 1304; https://doi.org/10.3390/genes13081304 - 22 Jul 2022
Cited by 1 | Viewed by 1366
Abstract
The cAMP response element-binding protein (CREB), a basic leucine zipper transcription factor, is involved in the activation of numerous genes in a variety of cell types. The CREB gene is rich in alternative splicing (AS) events. However, studies on the AS of CREB [...] Read more.
The cAMP response element-binding protein (CREB), a basic leucine zipper transcription factor, is involved in the activation of numerous genes in a variety of cell types. The CREB gene is rich in alternative splicing (AS) events. However, studies on the AS of CREB genes in pigs are limited, and few reports have compared the roles of isoforms in activating gene expression. Here, five AS transcripts, V1–5, were characterized by RT-PCR and two, V3 and V5, were new identifications. Both V1 and V2 have all the functional domains of the CREB protein, with similar tissue expression profiles and mRNA stability, suggesting that they have similar roles. The transcriptional transactivation activities of four isoforms encoding complete polypeptides were analyzed on the expression of the B-cell CLL/lymphoma 2-like protein 2 and the poly (A)-binding protein, nuclear 1 genes with a dual-luciferase reporter system, and differential activities were observed. Both V1 and V2 have promoting effects, but their roles are gene-specific. V3 has no effect on the promoter of the two genes, while V4 functions as a repressor. The mechanisms underlying the differential roles of V1 and V2 were analyzed with RNA-seq, and the genes specifically regulated by V1 and V2 were identified. These results will contribute to further revealing the role of CREB and to analyzing the significance of AS in genes. Full article
(This article belongs to the Special Issue Trends and Prospects in Pig Genomics and Genetics)
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19 pages, 6724 KiB  
Article
Transcriptomic Profile of Genes Regulating the Structural Organization of Porcine Atrial Cardiomyocytes during Primary In Vitro Culture
by Mariusz J. Nawrocki, Karol Jopek, Mariusz Kaczmarek, Maciej Zdun, Paul Mozdziak, Marek Jemielity, Bartłomiej Perek, Dorota Bukowska and Bartosz Kempisty
Genes 2022, 13(7), 1205; https://doi.org/10.3390/genes13071205 - 05 Jul 2022
Cited by 1 | Viewed by 1718
Abstract
Numerous cardiovascular diseases (CVD) eventually lead to severe myocardial dysfunction, which is the most common cause of death worldwide. A better understanding of underlying molecular mechanisms of cardiovascular pathologies seems to be crucial to develop effective therapeutic options. Therefore, a worthwhile endeavor is [...] Read more.
Numerous cardiovascular diseases (CVD) eventually lead to severe myocardial dysfunction, which is the most common cause of death worldwide. A better understanding of underlying molecular mechanisms of cardiovascular pathologies seems to be crucial to develop effective therapeutic options. Therefore, a worthwhile endeavor is a detailed molecular characterization of cells extracted from the myocardium. A transcriptomic profile of atrial cardiomyocytes during long-term primary cell culture revealed the expression patterns depending on the duration of the culture and the heart segment of origin (right atrial appendage and right atrium). Differentially expressed genes (DEGs) were classified as involved in ontological groups such as: “cellular component assembly”, “cellular component organization”, “cellular component biogenesis”, and “cytoskeleton organization”. Transcriptomic profiling allowed us to indicate the increased expression of COL5A2, COL8A1, and COL12A1, encoding different collagen subunits, pivotal in cardiac extracellular matrix (ECM) structure. Conversely, genes important for cellular architecture, such as ABLIM1, TMOD1, XIRP1, and PHACTR1, were downregulated during in vitro culture. The culture conditions may create a favorable environment for reconstruction of the ECM structures, whereas they may be suboptimal for expression of some pivotal transcripts responsible for the formation of intracellular structures. Full article
(This article belongs to the Special Issue Trends and Prospects in Pig Genomics and Genetics)
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16 pages, 6214 KiB  
Article
Characterization of a Read-through Fusion Transcript, BCL2L2-PABPN1, Involved in Porcine Adipogenesis
by Jiyuan Zhu, Zewei Yang, Wanjun Hao, Jiaxin Li, Liang Wang, Jiqiao Xia, Dongjie Zhang, Di Liu and Xiuqin Yang
Genes 2022, 13(3), 445; https://doi.org/10.3390/genes13030445 - 28 Feb 2022
Cited by 3 | Viewed by 2150
Abstract
cis-Splicing of adjacent genes (cis-SAGe) has been involved in multiple physiological and pathological processes in humans. However, to the best of our knowledge, there is no report of cis-SAGe in adipogenic regulation. In this study, a cis-SAGe product, [...] Read more.
cis-Splicing of adjacent genes (cis-SAGe) has been involved in multiple physiological and pathological processes in humans. However, to the best of our knowledge, there is no report of cis-SAGe in adipogenic regulation. In this study, a cis-SAGe product, BCL2L2–PABPN1 (BP), was characterized in fat tissue of pigs with RT-PCR and RACE method. BP is an in-frame fusion product composed of 333 aa and all the functional domains of both parents. BP is highly conserved among species and rich in splicing variants. BP was found to promote proliferation and inhibit differentiation of primary porcine preadipocytes. A total of 3074/44 differentially expressed mRNAs (DEmRs)/known miRNAs (DEmiRs) were identified in porcine preadipocytes overexpressing BP through RNA-Seq analysis. Both DEmRs and target genes of DEmiRs were involved in various fat-related pathways with MAPK and PI3K-Akt being the top enriched. PPP2CB, EGFR, Wnt5A and EHHADH were hub genes among the fat-related pathways identified. Moreover, ssc-miR-339-3p was found to be critical for BP regulating adipogenesis through integrated analysis of mRNA and miRNA data. The results highlight the role of cis-SAGe in adipogenesis and contribute to further revealing the mechanisms underlying fat deposition, which will be conductive to human obesity control. Full article
(This article belongs to the Special Issue Trends and Prospects in Pig Genomics and Genetics)
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10 pages, 472 KiB  
Article
Additive and Dominance Genomic Analysis for Litter Size in Purebred and Crossbred Iberian Pigs
by Houssemeddine Srihi, José Luis Noguera, Victoria Topayan, Melani Martín de Hijas, Noelia Ibañez-Escriche, Joaquim Casellas, Marta Vázquez-Gómez, María Martínez-Castillero, Juan Pablo Rosas and Luis Varona
Genes 2022, 13(1), 12; https://doi.org/10.3390/genes13010012 - 22 Dec 2021
Cited by 5 | Viewed by 2597
Abstract
INGA FOOD S. A., as a Spanish company that produces and commercializes fattened pigs, has produced a hybrid Iberian sow called CASTÚA by crossing the Retinto and Entrepelado varieties. The selection of the parental populations is based on selection criteria calculated from purebred [...] Read more.
INGA FOOD S. A., as a Spanish company that produces and commercializes fattened pigs, has produced a hybrid Iberian sow called CASTÚA by crossing the Retinto and Entrepelado varieties. The selection of the parental populations is based on selection criteria calculated from purebred information, under the assumption that the genetic correlation between purebred and crossbred performance is high; however, these correlations can be less than one because of a GxE interaction or the presence of non-additive genetic effects. This study estimated the additive and dominance variances of the purebred and crossbred populations for litter size, and calculated the additive genetic correlations between the purebred and crossbred performances. The dataset consisted of 2030 litters from the Entrepelado population, 1977 litters from the Retinto population, and 1958 litters from the crossbred population. The individuals were genotyped with a GeneSeek® GGP Porcine70K HDchip. The model of analysis was a ‘biological’ multivariate mixed model that included additive and dominance SNP effects. The estimates of the additive genotypic variance for the total number born (TNB) were 0.248, 0.282 and 0.546 for the Entrepelado, Retinto and Crossbred populations, respectively. The estimates of the dominance genotypic variances were 0.177, 0.172 and 0.262 for the Entrepelado, Retinto and Crossbred populations. The results for the number born alive (NBA) were similar. The genetic correlations between the purebred and crossbred performance for TNB and NBA—between the brackets—were 0.663 in the Entrepelado and 0.881 in Retinto poplulations. After backsolving to obtain estimates of the SNP effects, the additive genetic variance associated with genomic regions containing 30 SNPs was estimated, and we identified four genomic regions that each explained > 2% of the additive genetic variance in chromosomes (SSC) 6, 8 and 12: one region in SSC6, two regions in SSC8, and one region in SSC12. Full article
(This article belongs to the Special Issue Trends and Prospects in Pig Genomics and Genetics)
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15 pages, 5250 KiB  
Article
SESN3 Inhibited SMAD3 to Relieve Its Suppression for MiR-124, Thus Regulating Pre-Adipocyte Adipogenesis
by Weimin Lin, Jindi Zhao, Mengting Yan, Xuexin Li, Kai Yang, Wei Wei, Lifan Zhang and Jie Chen
Genes 2021, 12(12), 1852; https://doi.org/10.3390/genes12121852 - 23 Nov 2021
Cited by 4 | Viewed by 1732
Abstract
Sestrin-3, together with the other two members Sestrin-1 and Sestrin-2, belongs to the Sestrin family. The Sestrin protein family has been demonstrated to be involved in antioxidative, metabolic homeostasis, and even the development of nonalcoholic steatohepatitis (NASH). However, the adipogenic regulatory role of [...] Read more.
Sestrin-3, together with the other two members Sestrin-1 and Sestrin-2, belongs to the Sestrin family. The Sestrin protein family has been demonstrated to be involved in antioxidative, metabolic homeostasis, and even the development of nonalcoholic steatohepatitis (NASH). However, the adipogenic regulatory role of SESN3 in adipogenesis still needs to be further explored. In this study, we demonstrated SESN3 inhibited porcine pre-adipocyte proliferation, thus suppressing its adipogenesis. Meanwhile, SESN3 has been demonstrated to inhibit Smad3 thus protecting against NASH. Further, for our previous study, we found mmu-miR-124 involved in 3T3-L1 cell adipogenesis regulation. In this study, we also identified that ssc-miR-124 inhibited porcine pre-adipocyte proliferation, thus suppressing its adipogenesis, and the SMAD3 was an inhibitor of ssc-miR-124 by binding to its promoter. Furthermore, the ssc-miR-124 targeted porcine C/EBPα and GR and thus inhibited pre-adipocyte adipogenesis. In conclusion, SESN3 inhibited SMAD3, thus improving ssc-miR124, and then suppressed C/EBPα and GR to regulate pre-adipocytes adipogenesis. Full article
(This article belongs to the Special Issue Trends and Prospects in Pig Genomics and Genetics)
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Review

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13 pages, 676 KiB  
Review
Current Analytical Methods and Research Trends Are Used to Identify Domestic Pig and Wild Boar DNA in Meat and Meat Products
by Małgorzata Natonek-Wiśniewska, Agata Piestrzynska-Kajtoch, Anna Koseniuk and Piotr Krzyścin
Genes 2022, 13(10), 1825; https://doi.org/10.3390/genes13101825 - 09 Oct 2022
Cited by 1 | Viewed by 2098
Abstract
The pig, one of the most important livestock species, is a meaningful source of global meat production. It is necessary, however, to prove whether a food product that a discerning customer selects in a store is actually made from pork or venison, or [...] Read more.
The pig, one of the most important livestock species, is a meaningful source of global meat production. It is necessary, however, to prove whether a food product that a discerning customer selects in a store is actually made from pork or venison, or does not contain it at all. The problem of food authenticity is widespread worldwide, and cases of meat adulteration have accelerated the development of food and the identification methods of feed species. It is worth noting that several different molecular biology techniques can identify a porcine component. However, the precise differentiation between wild boar and a domestic pig in meat products is still challenging. This paper presents the current state of knowledge concerning the species identification of the domestic pig and wild boar DNA in meat and its products. Full article
(This article belongs to the Special Issue Trends and Prospects in Pig Genomics and Genetics)
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