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Pig Genomics and Genetics
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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 (23 December 2020) | Viewed by 68952

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Dr. Katarzyna Piórkowska

E-Mail Website
Guest Editor
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
Dr. Katarzyna Ropka-Molik

E-Mail Website
Guest Editor
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,

The pig (Sus scrofa) is the most common large mammal in the world. The Sus genus includes domestic pig and wild boar. These animals are omnivores and are biologically similar to humans; thus, they are frequently used as animal models for human medical research. In medical research, molecular biology methods are assisted by agricultural progress, for example, in pig production and breeding. Since the draft reference genome sequence of S. scrofa was assembled in 2012, the processes of identification of genes related to important phenotypic traits and of search of genetic markers for pig selection have been significantly refined. In addition, the newest wide-range high-throughput techniques, including microarrays, next-generation sequencing, and the recent PacBio sequencing platform providing ultra-long sequencing reads, allow identifying gene mutations and gene candidates throughout the whole genome, transcriptome, or epigenome and estimating quantitative traits important for breeding as well as the genetic backgrounds of inherited diseases. In this Special Issue, we will 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 and to nutritional modifications, with the aim of collecting the most recent advances. Manuscripts focusing on high-throughput methodologies, such as RNA sequencing, ATAC-seq, MACE-seq, chip-seq, and RRBS, and covering other fields of pig genetics will be appreciated.

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

Manuscript Submission Information

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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

  • Porcine genetics
  • Breeding
  • Genetic markers
  • RNA-sequencing
  • Animal genomics
  • Pig traits

Published Papers (19 papers)

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Editorial

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2 pages, 193 KiB  
Editorial
Pig Genomics and Genetics
by Katarzyna Piórkowska and Katarzyna Ropka-Molik
Genes 2021, 12(11), 1692; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12111692 - 25 Oct 2021
Viewed by 1818
Abstract
The pig (Sus scrofa) is the most popular large farm animal in the world [...] Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)

Research

Jump to: Editorial, Review

12 pages, 2032 KiB  
Article
Phenotypic and Genomic Analysis of Cystic Hygroma in Pigs
by Anna Letko, Alexandria Marie Schauer, Martijn F. L. Derks, Llorenç Grau-Roma, Cord Drögemüller and Alexander Grahofer
Genes 2021, 12(2), 207; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12020207 - 31 Jan 2021
Cited by 2 | Viewed by 2458
Abstract
Cystic hygroma is a malformation of the lymphatic and vascular system and is recognized as a benign congenital tumor that affects humans and animals in the perinatal period. This congeni-tal disorder is rarely described in animals, and until today, cystic hygroma in pigs [...] Read more.
Cystic hygroma is a malformation of the lymphatic and vascular system and is recognized as a benign congenital tumor that affects humans and animals in the perinatal period. This congeni-tal disorder is rarely described in animals, and until today, cystic hygroma in pigs has not been described in the literature. In a purebred Piètrain litter with twelve live-born piglets, cystic hy-groma was noticed on the rump of two male pigs within the first week of life. In addition, a third case of a crossbred weaner (Large White × Landrace) was detected during a herd examina-tion. To rule out common differential diagnoses, e.g., abscess or hematoma, further clinical and pathological investigations were conducted. During clinical examination, a painless and soft mass, which was compressible, was detected on the rump of all affected animals. The ultra-sonographic examination revealed a fluid-filled and cavernous subcutaneous structure. In addi-tion, a puncture of the cyst was conducted, revealing a serosanguinous fluid with negative bacte-riological culture. In all cases, a necropsy was performed, showing that the animals had fluid-filled cysts lined by well-differentiated lymphatic endothelium. Based on the clinicopathological examination, cystic hygroma was diagnosed. Furthermore, SNP array genotyping and whole-genome sequencing was performed and provided no evidence for a chromosomal disorder. In the Piètrain family, several genome regions were homozygous in both affected piglets. None-theless, a dominant acting de novo germline variant could not be ruled out, and therefore differ-ent filtering strategies were used to find pathogenic variants. The herein presented lists of pri-vate variants after filtering against hundreds of control genomes provide no plausible candidate and no shared variants among the two sequenced cases. Therefore, further studies are needed to evaluate possible genetic etiology. In general, systematic surveillance is needed to identify ge-netic defects as early as possible and to avoid the occurrence of losses in the pig population. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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23 pages, 2354 KiB  
Article
Genes and SNPs Involved with Scrotal and Umbilical Hernia in Pigs
by Ariene Fernanda Grando Rodrigues, Adriana Mércia Guaratini Ibelli, Jane de Oliveira Peixoto, Maurício Egídio Cantão, Haniel Cedraz de Oliveira, Igor Ricardo Savoldi, Mayla Regina Souza, Marcos Antônio Zanella Mores, Luis Orlando Duitama Carreño and Mônica Corrêa Ledur
Genes 2021, 12(2), 166; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12020166 - 27 Jan 2021
Cited by 5 | Viewed by 2837
Abstract
Hernia is one of the most common defects in pigs. The most prevalent are the scrotal (SH), inguinal (IH) and umbilical (UH) hernias. We compared the inguinal ring transcriptome of normal and SH-affected pigs with the umbilical ring transcriptome of normal and UH-affected [...] Read more.
Hernia is one of the most common defects in pigs. The most prevalent are the scrotal (SH), inguinal (IH) and umbilical (UH) hernias. We compared the inguinal ring transcriptome of normal and SH-affected pigs with the umbilical ring transcriptome of normal and UH-affected pigs to discover genes and pathways involved with the development of both types of hernia. A total of 13,307 transcripts was expressed in the inguinal and 13,302 in the umbilical ring tissues with 94.91% of them present in both tissues. From those, 35 genes were differentially expressed in both groups, participating in 108 biological processes. A total of 67 polymorphisms was identified in the inguinal ring and 76 in the umbilical ring tissue, of which 11 and 14 were novel, respectively. A single nucleotide polymorphism (SNP) with deleterious function was identified in the integrin α M (ITGAM) gene. The microtubule associated protein 1 light chain 3 γ (MAP1LC3C), vitrin (VIT), aggrecan (ACAN), alkaline ceramidase 2 (ACER2), potassium calcium-activated channel subfamily M α 1 (KCNMA1) and synaptopodin 2 (SYNPO2) genes are highlighted as candidates to trigger both types of hernia. We generated the first comparative study of the pig umbilical and inguinal ring transcriptomes, contributing to the understanding of the genetic mechanism involved with these two types of hernia in pigs and probably in other mammals. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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15 pages, 2357 KiB  
Article
Weighted Single-Step GWAS Identified Candidate Genes Associated with Growth Traits in a Duroc Pig Population
by Donglin Ruan, Zhanwei Zhuang, Rongrong Ding, Yibin Qiu, Shenping Zhou, Jie Wu, Cineng Xu, Linjun Hong, Sixiu Huang, Enqin Zheng, Gengyuan Cai, Zhenfang Wu and Jie Yang
Genes 2021, 12(1), 117; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12010117 - 19 Jan 2021
Cited by 25 | Viewed by 3694
Abstract
Growth traits are important economic traits of pigs that are controlled by several major genes and multiple minor genes. To better understand the genetic architecture of growth traits, we performed a weighted single-step genome-wide association study (wssGWAS) to identify genomic regions and candidate [...] Read more.
Growth traits are important economic traits of pigs that are controlled by several major genes and multiple minor genes. To better understand the genetic architecture of growth traits, we performed a weighted single-step genome-wide association study (wssGWAS) to identify genomic regions and candidate genes that are associated with days to 100 kg (AGE), average daily gain (ADG), backfat thickness (BF) and lean meat percentage (LMP) in a Duroc pig population. In this study, 3945 individuals with phenotypic and genealogical information, of which 2084 pigs were genotyped with a 50 K single-nucleotide polymorphism (SNP) array, were used for association analyses. We found that the most significant regions explained 2.56–3.07% of genetic variance for four traits, and the detected significant regions (>1%) explained 17.07%, 18.59%, 23.87% and 21.94% for four traits. Finally, 21 genes that have been reported to be associated with metabolism, bone growth, and fat deposition were treated as candidate genes for growth traits in pigs. Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses implied that the identified genes took part in bone formation, the immune system, and digestion. In conclusion, such full use of phenotypic, genotypic, and genealogical information will accelerate the genetic improvement of growth traits in pigs. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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15 pages, 11808 KiB  
Article
Identification of Circular RNAs in Hypothalamus of Gilts during the Onset of Puberty
by Qingnan Li, Xiangchun Pan, Nian Li, Wentao Gong, Yaosheng Chen and Xiaolong Yuan
Genes 2021, 12(1), 84; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12010084 - 12 Jan 2021
Cited by 8 | Viewed by 2333
Abstract
The disorders of puberty have shown negative outcomes on health of mammals, and the hypothalamus is thought to be the main regulator of puberty by releasing GnRH. Many studies show that the circular RNAs (circRNAs) might be implicated in the timing of puberty [...] Read more.
The disorders of puberty have shown negative outcomes on health of mammals, and the hypothalamus is thought to be the main regulator of puberty by releasing GnRH. Many studies show that the circular RNAs (circRNAs) might be implicated in the timing of puberty in mammals. However, the circRNAs in the hypothalamus of gilts have not been explored. To profile the changes and biological functions of circRNAs in the hypothalamus during the onset of puberty, RNA-seq was utilized to establish pre-, in-, and post-pubertal hypothalamic circRNAs profiles. In this study, the functions of hypothalamic circRNAs were enriched in the signaling pathway of neurotrophin, progesterone-mediated oocyte maturation, oocyte meiosis, insulin, ErbB, and mTOR, which have been highly suggested to be involved in the timing of puberty. Furthermore, 53 circRNAs were identified to be putative hypothalamus-specific expressed circRNAs, and some of them were exclusively expressed in the one of three pubertal stages. Moreover, 22 differentially expressed circRNAs were identified and chosen to construct the circRNA-miRNA-gene network. Moreover, 10 circRNAs were found to be driven by six puberty-related genes (ESR1, NF1, APP, ENPP2, ARNT, and DICER1). Subsequently, the expression changes of several circRNAs were confirmed by RT-qPCR. Collectively, the preliminary results of hypothalamic circRNAs provided useful information for the investigation of the molecular mechanism for the timing of puberty in gilts. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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17 pages, 3904 KiB  
Article
Profiling Novel Alternative Splicing within Multiple Tissues Provides Useful Insights into Porcine Genome Annotation
by Wen Feng, Pengju Zhao, Xianrui Zheng, Zhengzheng Hu and Jianfeng Liu
Genes 2020, 11(12), 1405; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11121405 - 26 Nov 2020
Cited by 3 | Viewed by 2330
Abstract
Alternative splicing (AS) is a process during gene expression that results in a single gene coding for different protein variants. AS contributes to transcriptome and proteome diversity. In order to characterize AS in pigs, genome-wide transcripts and AS events were detected using RNA [...] Read more.
Alternative splicing (AS) is a process during gene expression that results in a single gene coding for different protein variants. AS contributes to transcriptome and proteome diversity. In order to characterize AS in pigs, genome-wide transcripts and AS events were detected using RNA sequencing of 34 different tissues in Duroc pigs. In total, 138,403 AS events and 29,270 expressed genes were identified. An alternative donor site was the most common AS form and accounted for 44% of the total AS events. The percentage of the other three AS forms (exon skipping, alternative acceptor site, and intron retention) was approximately 19%. The results showed that the most common AS events involving alternative donor sites could produce different transcripts or proteins that affect the biological processes. The expression of genes with tissue-specific AS events showed that gene functions were consistent with tissue functions. AS increased proteome diversity and resulted in novel proteins that gained or lost important functional domains. In summary, these findings extend porcine genome annotation and highlight roles that AS could play in determining tissue identity. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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16 pages, 3468 KiB  
Article
Prolonged Effect of Seminal Plasma on Global Gene Expression in Porcine Endometrium
by Marek Bogacki, Beenu Moza Jalali, Anna Wieckowska and Monika M. Kaczmarek
Genes 2020, 11(11), 1302; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11111302 - 03 Nov 2020
Cited by 2 | Viewed by 1818
Abstract
Seminal plasma (SP) deposited in the porcine uterine tract at the time of mating is known to elicit an initial response that is beneficial for pregnancy outcome. However, whether SP has any long-term effect on alterations in endometrial molecular and cellular processes is [...] Read more.
Seminal plasma (SP) deposited in the porcine uterine tract at the time of mating is known to elicit an initial response that is beneficial for pregnancy outcome. However, whether SP has any long-term effect on alterations in endometrial molecular and cellular processes is not known. In this study, using microarray analyses, differential changes in endometrial transcriptome were evaluated after Day 6 of SP-infusion (6DPI) or Day 6 of pregnancy as compared to corresponding day of estrous cycle. Both, pregnancy and SP induced significant changes in the endometrial transcriptome and most of these changes were specific for a particular group. Functional analysis of differentially expressed genes (DEGs) using Ingenuity Pathway Analysis revealed that inhibition in immune response was affected by both pregnancy and SP infusion. Long-term effects of SP included differential expression of genes involved in inhibition of apoptosis, production of reactive oxygen species and steroid biosynthesis, and activation of processes such as proliferation of connective tissue cells and microvascular endothelial cells. Moreover, interleukin-2 and interferon-γ was identified to be responsible for regulating expression of many DEGs identified on 6DPI. The present study provides evidence for the long-term effects of SP on porcine endometrium that can be beneficial for pregnancy success. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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11 pages, 2228 KiB  
Article
Expression Profile of Porcine TRIM26 and Its Inhibitory Effect on Interferon-β Production and Antiviral Response
by Hui Huang, Mona Sharma, Yanbing Zhang, Chenxi Li, Ke Liu, Jianchao Wei, Donghua Shao, Beibei Li, Zhiyong Ma, Ruibing Cao and Yafeng Qiu
Genes 2020, 11(10), 1226; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11101226 - 19 Oct 2020
Cited by 4 | Viewed by 2442
Abstract
TRIM26, a member of the tripartite motif (TRIM) family has been shown to be involved in modulation of innate antiviral response. However, the functional characteristics of porcine TRIM26 (porTRIM26) are unclear. In this study, we used a synthesized antigen peptide to generate a [...] Read more.
TRIM26, a member of the tripartite motif (TRIM) family has been shown to be involved in modulation of innate antiviral response. However, the functional characteristics of porcine TRIM26 (porTRIM26) are unclear. In this study, we used a synthesized antigen peptide to generate a polyclonal antibody against porTRIM26 with which to study the expression and function of porTRIM26. We demonstrated that polyinosinic:polycytidylic acid (poly (I:C)) stimulation and viral infection (vesicular stomatitis (VSV) or porcine reproductive and respiratory syndrome virus (PRRSV)) induce expression of porTRIM26, whereas knock-down expression of porTRIM26 promotes interferon (IFN)-β production after poly (I:C) stimulation and virus infection (VSV or PRRSV). The importance of the porTRIM26-mediated modulation of the antiviral response was also shown in VSV- or PRRSV-infected cells. In summary, these findings show that porTRIM26 has an inhibitory role in IFN-β expression and the antiviral response. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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22 pages, 3841 KiB  
Article
3′quant mRNA-Seq of Porcine Liver Reveals Alterations in UPR, Acute Phase Response, and Cholesterol and Bile Acid Metabolism in Response to Different Dietary Fats
by Maria Oczkowicz, Tomasz Szmatoła, Małgorzata Świątkiewicz, Anna Koseniuk, Grzegorz Smołucha, Wojciech Witarski and Alicja Wierzbicka
Genes 2020, 11(9), 1087; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11091087 - 18 Sep 2020
Cited by 3 | Viewed by 3048
Abstract
Animal fats are considered to be unhealthy, in contrast to vegetable fats, which are rich in unsaturated fatty acids. However, the use of some fats, such as coconut oil, is still controversial. In our experiment, we divided experimental animals (domestic pigs) into three [...] Read more.
Animal fats are considered to be unhealthy, in contrast to vegetable fats, which are rich in unsaturated fatty acids. However, the use of some fats, such as coconut oil, is still controversial. In our experiment, we divided experimental animals (domestic pigs) into three groups differing only in the type of fat used in the diet: group R: rapeseed oil (n = 5); group B: beef tallow (n = 5); group C: coconut oil (n = 6). After transcriptomic analysis of liver samples, we identified 188, 93, and 53 DEGs (differentially expressed genes) in R vs. B, R vs. C, and B vs. C comparisons, respectively. Next, we performed a functional analysis of identified DEGs with String and IPA software. We observed the enrichment of genes engaged in the unfolded protein response (UPR) and the acute phase response among genes upregulated in B compared to R. In contrast, cholesterol biosynthesis and cholesterol efflux enrichments were observed among genes downregulated in B when compared to R. Moreover, activation of the UPR and inhibition of the sirtuin signaling pathway were noted in C when compared to R. The most striking difference in liver transcriptomic response between C and B was the activation of the acute phase response and inhibition of bile acid synthesis in the latest group. Our results suggest that excessive consumption of animal fats leads to the activation of a cascade of mutually propelling processes harmful to the liver: inflammation, UPR, and imbalances in the biosynthesis of cholesterol and bile acids via altered organelle membrane composition. Nevertheless, these studies should be extended with analysis at the level of proteins and their function. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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13 pages, 2841 KiB  
Article
Identification of DNMT3B2 as the Predominant Isoform of DNMT3B in Porcine Alveolar Macrophages and Its Involvement in LPS-Stimulated TNF-α Expression
by Yanbing Zhang, Hui Li, Xiao Xiang, Yan Lu, Mona Sharma, Zongjie Li, Ke Liu, Jianchao Wei, Donghua Shao, Beibei Li, Zhiyong Ma and Yafeng Qiu
Genes 2020, 11(9), 1065; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11091065 - 10 Sep 2020
Cited by 3 | Viewed by 2331
Abstract
DNA methyltransferase 3B (DNMT3B) as one member of the DNMT family functions as a de novo methyltransferase, characterized as more than 30 splice variants in humans and mice. However, the expression patterns of DNMT3B in pig as well as the biological function of [...] Read more.
DNA methyltransferase 3B (DNMT3B) as one member of the DNMT family functions as a de novo methyltransferase, characterized as more than 30 splice variants in humans and mice. However, the expression patterns of DNMT3B in pig as well as the biological function of porcine DNMT3B remain to be determined. In this study, we first examined the expression patterns of DNMT3B in porcine alveolar macrophages (PAM). We demonstrated that only DNMT3B2 and DNMT3B3 were the detectable isoforms in PAM. Furthermore, we revealed that DNTM3B2 was the predominant isoform in PAM. Next, in the model of LPS (lipopolysaccharide)-activated PAM, we showed that in comparison to the unstimulated PAM, (1) expression of DNTM3B is reduced; (2) the methylation level of TNF-α gene promoter is decreased. We further establish that DNMT3B2-mediated methylation of TNF-α gene promoter restricts induction of TNF-α in the LPS-stimulated PAM. In summary, these findings reveal that DNMT3B2 is the predominant isoform in PAM and its downregulation contributes to expression of TNF-α via hypomethylation of TNF-α gene promoter in the LPS-stimulated PAM. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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14 pages, 2426 KiB  
Article
Generation of Marker-Free pbd-2 Knock-in Pigs Using the CRISPR/Cas9 and Cre/loxP Systems
by Jing Huang, Antian Wang, Chao Huang, Yufan Sun, Bingxiao Song, Rui Zhou and Lu Li
Genes 2020, 11(8), 951; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11080951 - 18 Aug 2020
Cited by 18 | Viewed by 5836
Abstract
Porcine β-defensin 2 (PBD-2), expressed by different tissues of pigs, is a multifunctional cationic peptide with antimicrobial, immunomodulatory and growth-promoting abilities. As the latest generation of genome-editing tool, CRISPR/Cas9 system makes it possible to enhance the expression of PBD-2 in pigs by site-specific [...] Read more.
Porcine β-defensin 2 (PBD-2), expressed by different tissues of pigs, is a multifunctional cationic peptide with antimicrobial, immunomodulatory and growth-promoting abilities. As the latest generation of genome-editing tool, CRISPR/Cas9 system makes it possible to enhance the expression of PBD-2 in pigs by site-specific knock-in of pbd-2 gene into the pig genome. In this study, we aimed to generate marker-free pbd-2 knock-in pigs using the CRISPR/Cas9 and Cre/loxP systems. Two copies of pbd-2 gene linked by a T2A sequence were inserted into the porcine Rosa26 locus through CRISPR/Cas9-mediated homology-directed repair. The floxed selectable marker gene neoR, used for G418 screening of positive cell clones, was removed by cell-penetrating Cre recombinase with a recombination efficiency of 48.3%. Cloned piglets were produced via somatic cell nuclear transfer and correct insertion of pbd-2 genes was confirmed by PCR and Southern blot. Immunohistochemistry and immunofluorescence analyses indicated that expression levels of PBD-2 in different tissues of transgenic (TG) piglets were significantly higher than those of their wild-type (WT) littermates. Bactericidal assays demonstrated that there was a significant increase in the antimicrobial properties of the cell culture supernatants of porcine ear fibroblasts from the TG pigs in comparison to those from the WT pigs. Altogether, our study improved the protein expression level of PBD-2 in pigs by site-specific integration of pbd-2 into the pig genome, which not only provided an effective pig model to study the anti-infection mechanisms of PBD-2 but also a promising genetic material for the breeding of disease-resistant pigs. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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16 pages, 3821 KiB  
Article
Exploring the lncRNAs Related to Skeletal Muscle Fiber Types and Meat Quality Traits in Pigs
by Rongyang Li, Bojiang Li, Aiwen Jiang, Yan Cao, Liming Hou, Zengkai Zhang, Xiying Zhang, Honglin Liu, Kee-Hong Kim and Wangjun Wu
Genes 2020, 11(8), 883; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11080883 - 04 Aug 2020
Cited by 26 | Viewed by 4600
Abstract
The alteration in skeletal muscle fiber is a critical factor affecting livestock meat quality traits and human metabolic diseases. Long non-coding RNAs (lncRNAs) are a diverse class of non-coding RNAs with a length of more than 200 nucleotides. However, the mechanisms underlying the [...] Read more.
The alteration in skeletal muscle fiber is a critical factor affecting livestock meat quality traits and human metabolic diseases. Long non-coding RNAs (lncRNAs) are a diverse class of non-coding RNAs with a length of more than 200 nucleotides. However, the mechanisms underlying the regulation of lncRNAs in skeletal muscle fibers remain elusive. To understand the genetic basis of lncRNA-regulated skeletal muscle fiber development, we performed a transcriptome analysis to identify the key lncRNAs affecting skeletal muscle fiber and meat quality traits on a pig model. We generated the lncRNA expression profiles of fast-twitch Biceps femoris (Bf) and slow-twitch Soleus (Sol) muscles and identified the differentially expressed (DE) lncRNAs using RNA-seq and performed bioinformatics analyses. This allowed us to identify 4581 lncRNA genes among six RNA libraries and 92 DE lncRNAs between Bf and Sol which are the key candidates for the conversion of skeletal muscle fiber types. Moreover, we detected the expression patterns of lncRNA MSTRG.42019 in different tissues and skeletal muscles of various development stages. In addition, we performed a correlation analyses between the expression of DE lncRNA MSTRG.42019 and meat quality traits. Notably, we found that DE lncRNA MSTRG.42019 was highly expressed in skeletal muscle and its expression was significantly higher in Sol than in Bf, with a positive correlation with the expression of Myosin heavy chain 7 (MYH7) (r = 0.6597, p = 0.0016) and a negative correlation with meat quality traits glycolytic potential (r = −0.5447, p = 0.0130), as well as drip loss (r = −0.5085, p = 0.0221). Moreover, we constructed the lncRNA MSTRG.42019–mRNAs regulatory network for a better understanding of a possible mechanism regulating skeletal muscle fiber formation. Our data provide the groundwork for studying the lncRNA regulatory mechanisms of skeletal muscle fiber conversion, and given the importance of skeletal muscle fiber types in muscle-related diseases, our data may provide insight into the treatment of muscular diseases in humans. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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15 pages, 1410 KiB  
Article
Evaluation of the CRISPR/Cas9 Genetic Constructs in Efficient Disruption of Porcine Genes for Xenotransplantation Purposes Along with an Assessment of the Off-Target Mutation Formation
by Natalia Ryczek, Magdalena Hryhorowicz, Daniel Lipiński, Joanna Zeyland and Ryszard Słomski
Genes 2020, 11(6), 713; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11060713 - 26 Jun 2020
Cited by 7 | Viewed by 3310
Abstract
The increasing life expectancy of humans has led to an increase in the number of patients with chronic diseases and organ failure. However, the imbalance between the supply and the demand for human organs is a serious problem in modern transplantology. One of [...] Read more.
The increasing life expectancy of humans has led to an increase in the number of patients with chronic diseases and organ failure. However, the imbalance between the supply and the demand for human organs is a serious problem in modern transplantology. One of many solutions to overcome this problem is the use of xenotransplantation. The domestic pig (Sus scrofa domestica) is currently considered as the most suitable for human organ procurement. However, there are discrepancies between pigs and humans that lead to the creation of immunological barriers preventing the direct xenograft. The introduction of appropriate modifications to the pig genome to prevent xenograft rejection is crucial in xenotransplantation studies. In this study, porcine GGTA1, CMAH, β4GalNT2, vWF, ASGR1 genes were selected to introduce genetic modifications. The evaluation of three selected gRNAs within each gene was obtained, which enabled the selection of the best site for efficient introduction of changes. Modifications were examined after nucleofection of porcine primary kidney fibroblasts with CRISPR/Cas9 system genetic constructs, followed by the tracking of indels by decomposition (TIDE) analysis. In addition, off-target analysis was carried out for selected best gRNAs using the TIDE tool, which is new in the research conducted so far and shows the utility of this tool in these studies. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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20 pages, 2277 KiB  
Article
Identification of Molecular Mechanisms Related to Pig Fatness at the Transcriptome and miRNAome Levels
by Katarzyna Ropka-Molik, Klaudia Pawlina-Tyszko, Kacper Żukowski, Mirosław Tyra, Natalia Derebecka, Joanna Wesoły, Tomasz Szmatoła and Katarzyna Piórkowska
Genes 2020, 11(6), 600; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11060600 - 29 May 2020
Cited by 9 | Viewed by 3328
Abstract
Fat deposition and growth rate are closely related to pork quality and fattening efficiency. The next-generation sequencing (NGS) approach for transcriptome and miRNAome massive parallel sequencing of adipocyte tissue was applied to search for a molecular network related to fat deposition in pigs. [...] Read more.
Fat deposition and growth rate are closely related to pork quality and fattening efficiency. The next-generation sequencing (NGS) approach for transcriptome and miRNAome massive parallel sequencing of adipocyte tissue was applied to search for a molecular network related to fat deposition in pigs. Pigs were represented by three breeds (Large White, Pietrain, and Hampshire) that varied in fat content within each breed. The obtained results allowed for the detection of significant enrichment of Gene Ontology (GO) terms and pathways associated directly and indirectly with fat deposition via regulation of fatty acid metabolism, fat cell differentiation, inflammatory response, and extracellular matrix (ECM) organization and disassembly. Moreover, the results showed that adipocyte tissue content strongly affected the expression of leptin and other genes related to a response to excessive feed intake. The findings indicated that modification of genes and miRNAs involved in ECM rearrangements can be essential during fat tissue growth and development in pigs. The identified molecular network within genes and miRNAs that were deregulated depending on the subcutaneous fat level are proposed as candidate factors determining adipogenesis, fatness, and selected fattening characteristics in pigs. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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19 pages, 3303 KiB  
Article
Genome-Wide Transcriptome and Metabolome Analyses Provide Novel Insights and Suggest a Sex-Specific Response to Heat Stress in Pigs
by Krishnamoorthy Srikanth, Jong-Eun Park, Sang Yun Ji, Ki Hyun Kim, Yoo Kyung Lee, Himansu Kumar, Minji Kim, Youl Chang Baek, Hana Kim, Gul-Won Jang, Bong-Hwan Choi and Sung Dae Lee
Genes 2020, 11(5), 540; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11050540 - 11 May 2020
Cited by 10 | Viewed by 3592
Abstract
Heat stress (HS) negatively impacts pig production and swine health. Therefore, to understand the genetic and metabolic responses of pigs to HS, we used RNA-Seq and high resolution magic angle spinning (HR-MAS) NMR analyses to compare the transcriptomes and metabolomes of Duroc pigs [...] Read more.
Heat stress (HS) negatively impacts pig production and swine health. Therefore, to understand the genetic and metabolic responses of pigs to HS, we used RNA-Seq and high resolution magic angle spinning (HR-MAS) NMR analyses to compare the transcriptomes and metabolomes of Duroc pigs (n = 6, 3 barrows and 3 gilts) exposed to heat stress (33 °C and 60% RH) with a control group (25 °C and 60% RH). HS resulted in the differential expression of 552 (236 up, 316 down) and 879 (540 up, 339 down) genes and significant enrichment of 30 and 31 plasma metabolites in female and male pigs, respectively. Apoptosis, response to heat, Toll-like receptor signaling and oxidative stress were enriched among the up-regulated genes, while negative regulation of the immune response, ATP synthesis and the ribosomal pathway were enriched among down-regulated genes. Twelve and ten metabolic pathways were found to be enriched (among them, four metabolic pathways, including arginine and proline metabolism, and three metabolic pathways, including pantothenate and CoA biosynthesis), overlapping between the transcriptome and metabolome analyses in the female and male group respectively. The limited overlap between pathways enriched with differentially expressed genes and enriched plasma metabolites between the sexes suggests a sex-specific response to HS in pigs. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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11 pages, 8256 KiB  
Article
AQP3 Facilitates Proliferation and Adipogenic Differentiation of Porcine Intramuscular Adipocytes
by Xiaoyu Wang, Jing Yang, Ying Yao, Xin’E Shi, Gongshe Yang and Xiao Li
Genes 2020, 11(4), 453; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11040453 - 22 Apr 2020
Cited by 6 | Viewed by 2630
Abstract
The meat quality of animal products is closely related to the intramuscular fat content. Aquaglyceroporin (AQP) defines a class of water/glycerol channels that primarily facilitate the passive transport of glycerol and water across biological membranes. In this study, the AQP3 protein of the [...] Read more.
The meat quality of animal products is closely related to the intramuscular fat content. Aquaglyceroporin (AQP) defines a class of water/glycerol channels that primarily facilitate the passive transport of glycerol and water across biological membranes. In this study, the AQP3 protein of the AQP family was mainly studied in the adipogenic function of intramuscular adipocytes in pigs. Here, we found that AQP3 was increased at both mRNA and protein levels upon adipogenic stimuli in porcine intramuscular adipocytes in vitro. Western blot results showed knockdown of AQP3 by siRNA significantly suppressed the expression of adipogenic genes (PPARγ, aP2, etc.), repressed Akt phosphorylation, as well as reducing lipid accumulation. Furthermore, deletion of AQP3 by siRNA significantly downregulated expression of cell cycle genes (cyclin D, E), and decreased the number of EdU-positive cells as well as cell viability. Collectively, our data indicate that AQP3 is of great importance in both adipogenic differentiation and proliferation in intramuscular adipocytes, providing a potential target for modulating fat infiltration in skeletal muscles. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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13 pages, 2681 KiB  
Article
Transcriptional Regulation of HMOX1 Gene in Hezuo Tibetan Pigs: Roles of WT1, Sp1, and C/EBPα
by Wei Wang, Qiaoli Yang, Kaihui Xie, Pengfei Wang, Ruirui Luo, Zunqiang Yan, Xiaoli Gao, Bo Zhang, Xiaoyu Huang and Shuangbao Gun
Genes 2020, 11(4), 352; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11040352 - 26 Mar 2020
Cited by 8 | Viewed by 2643
Abstract
Heme oxygenase 1 (HMOX1) is a stress-inducing enzyme with multiple cardiovascular protective functions, especially in hypoxia stress. However, transcriptional regulation of swine HMOX1 gene remains unclear. In the present study, we first detected tissue expression profiles of HMOX1 gene in adult [...] Read more.
Heme oxygenase 1 (HMOX1) is a stress-inducing enzyme with multiple cardiovascular protective functions, especially in hypoxia stress. However, transcriptional regulation of swine HMOX1 gene remains unclear. In the present study, we first detected tissue expression profiles of HMOX1 gene in adult Hezuo Tibetan pig and analyzed the gene structure. We found that the expression level of HMOX1 gene was highest in the spleen of the Hezuo Tibetan pig, followed by liver, lung, and kidney. A series of 5’ deletion promoter plasmids in pGL3-basic vector were used to identify the core promoter region and confirmed that the minimum core promoter region of swine HMOX1 gene was located at −387 bp to −158 bp region. Then we used bioinformatics analysis to predict transcription factors in this region. Combined with site-directed mutagenesis and RNA interference assays, it was demonstrated that the three transcription factors WT1, Sp1 and C/EBPα were important transcription regulators of HMOX1 gene. In summary, our study may lay the groundwork for further functional study of HMOX1 gene. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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Review

Jump to: Editorial, Research

22 pages, 820 KiB  
Review
Application of Genetically Engineered Pigs in Biomedical Research
by Magdalena Hryhorowicz, Daniel Lipiński, Szymon Hryhorowicz, Agnieszka Nowak-Terpiłowska, Natalia Ryczek and Joanna Zeyland
Genes 2020, 11(6), 670; https://doi.org/10.3390/genes11060670 - 19 Jun 2020
Cited by 30 | Viewed by 11703
Abstract
Progress in genetic engineering over the past few decades has made it possible to develop methods that have led to the production of transgenic animals. The development of transgenesis has created new directions in research and possibilities for its practical application. Generating transgenic [...] Read more.
Progress in genetic engineering over the past few decades has made it possible to develop methods that have led to the production of transgenic animals. The development of transgenesis has created new directions in research and possibilities for its practical application. Generating transgenic animal species is not only aimed towards accelerating traditional breeding programs and improving animal health and the quality of animal products for consumption but can also be used in biomedicine. Animal studies are conducted to develop models used in gene function and regulation research and the genetic determinants of certain human diseases. Another direction of research, described in this review, focuses on the use of transgenic animals as a source of high-quality biopharmaceuticals, such as recombinant proteins. The further aspect discussed is the use of genetically modified animals as a source of cells, tissues, and organs for transplantation into human recipients, i.e., xenotransplantation. Numerous studies have shown that the pig (Sus scrofa domestica) is the most suitable species both as a research model for human diseases and as an optimal organ donor for xenotransplantation. Short pregnancy, short generation interval, and high litter size make the production of transgenic pigs less time-consuming in comparison with other livestock species This review describes genetically modified pigs used for biomedical research and the future challenges and perspectives for the use of the swine animal models. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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24 pages, 599 KiB  
Review
Survey of SNPs Associated with Total Number Born and Total Number Born Alive in Pig
by Siroj Bakoev, Lyubov Getmantseva, Faridun Bakoev, Maria Kolosova, Valeria Gabova, Anatoly Kolosov and Olga Kostyunina
Genes 2020, 11(5), 491; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11050491 - 30 Apr 2020
Cited by 17 | Viewed by 4106
Abstract
Reproductive productivity depend on a complex set of characteristics. The number of piglets at birth (Total number born, Litter size, TNB) and the number of alive piglets at birth (Total number born alive, NBA) are the main indicators of the reproductive productivity of [...] Read more.
Reproductive productivity depend on a complex set of characteristics. The number of piglets at birth (Total number born, Litter size, TNB) and the number of alive piglets at birth (Total number born alive, NBA) are the main indicators of the reproductive productivity of sows in pig breeding. Great hopes are pinned on GWAS (Genome-Wide Association Studies) to solve the problems associated with studying the genetic architecture of reproductive traits of pigs. This paper provides an overview of international studies on SNP (Single nucleotide polymorphism) associated with TNB and NBA in pigs presented in PigQTLdb as “Genome map association”. Currently on the base of Genome map association results 306 SNPs associated with TNB (218 SNPs) and NBA (88 SNPs) have been identified and presented in the Pig QTLdb database. The results are based on research of pigs such as Large White, Yorkshire, Landrace, Berkshire, Duroc and Erhualian. The presented review shows that most SNPs found in chromosome areas where candidate genes or QTLs (Quantitative trait locus) have been identified. Further research in the given direction will allow to obtain new data that will become an impulse for creating breakthrough breeding technologies and increase the production efficiency in pig farming. Full article
(This article belongs to the Special Issue Pig Genomics and Genetics)
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