Advances in Pig Breeding 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 (25 August 2023) | Viewed by 18197

Special Issue Editors


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Guest Editor
College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
Interests: pig molecular genetics and breeding; genomic selection; functional genomics; meat quality, artificial intelligence linking phenotypes
Special Issues, Collections and Topics in MDPI journals
College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
Interests: pig; meat quality; reproduction traits; non-coding RNA; molecular genetics; genomic selection
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With various novel technology applications, the genetic improvement of pigs has rapidly progressed over recent decades. Nowadays, more and more economically relevant traits were expanded as breeding goals, such as litter size, birth weight, feed efficiency, lean percentage, meat quality, lifetime reproduction, robustness et al. Over the past few decades, there has been a rapid development of high-throughput genome and cell molecular biology methods, the processes of identification of genes related to important phenotypic traits and genetic markers for pig selection have been significantly discovered, leading to the development of fast, cost-effective, and more accurate methods for the implementation of breeding programs. In addition, artificial intelligence will be used to identify relevant new phenotypes and implementing tools to effectively measure traits. For this Special Issue, we call for papers covering all aspects of pig genetics and phenotypes are welcome, especially  with a focus on quantitative genetics of new phenotypes, artificial intelligence linking phenotypes, genomic selection, breeding programs, gene polymorphisms, quantitative trait loci mapping, identification of genetic regulatory mechanism and causative mutations affecting economically relevant traits, and the exploitation of native pig genetic resources.

Dr. Linyuan Shen
Dr. Mailin Gan
Guest Editors

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Keywords

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

Published Papers (13 papers)

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Research

11 pages, 1428 KiB  
Article
Comparison of Growth Performance and Plasma Metabolomics between Two Sire-Breeds of Pigs in China
by Zhongwei Xie, Mailin Gan, Junhua Du, Gao Du, Yi Luo, Bin Liu, Kangping Zhu, Wenqiang Cheng, Lei Chen, Ye Zhao, Lili Niu, Yan Wang, Jingyong Wang, Li Zhu and Linyuan Shen
Genes 2023, 14(9), 1706; https://doi.org/10.3390/genes14091706 - 27 Aug 2023
Viewed by 923
Abstract
The Yorkshire pigs, renowned for their remarkable growth rate, low feed conversion ratio (FCR), and high meat production, emerge as a novel preference for paternal breeding. In this study, we found that purebred paternal Yorkshire pigs (PY) surpass the purebred Duroc breed in [...] Read more.
The Yorkshire pigs, renowned for their remarkable growth rate, low feed conversion ratio (FCR), and high meat production, emerge as a novel preference for paternal breeding. In this study, we found that purebred paternal Yorkshire pigs (PY) surpass the purebred Duroc breed in terms of growth rate. Specifically, purebred PY attain a weight of 100 kg at an earlier age compared to purebred Duroc (Male, 145.07 vs. 162.91; Female, 145.91 vs. 167.57; p-value < 0.01). Furthermore, different hybrid combinations suggest that offspring involving purebred PY exhibit superior growth performance. Compared with purebred Duroc, the offspring of purebred PY have an earlier age in days (173.23 vs. 183.54; p-value < 0.05) at the same slaughter weight. The changes of plasma metabolites of 60-day-old purebred boars in the two sire-breeds showed that 1335 metabolites in plasma were detected. Compared with Duroc, 28 metabolites were down-regulated and 49 metabolites were up-regulated in PY. Principal component analysis (PCA) discerned notable dissimilarities in plasma metabolites between the two sire-breeds of pigs. The levels of glycerol 3-phosphate choline, cytidine, guanine, and arachidonic acid increased significantly (p-value < 0.05), exerting an impact on their growth and development. According to our results, PY could be a new paternal option as a terminal sire in three-way cross system. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics)
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15 pages, 2863 KiB  
Article
Transcriptomic Profiling of Meat Quality Traits of Skeletal Muscles of the Chinese Indigenous Huai Pig and Duroc Pig
by Xiaojin Li, Liangyue Lu, Xinwei Tong, Ruidong Li, Erhui Jin, Man Ren, Yafei Gao, Youfang Gu and Shenghe Li
Genes 2023, 14(8), 1548; https://doi.org/10.3390/genes14081548 - 28 Jul 2023
Cited by 3 | Viewed by 1072
Abstract
The Huai pig is a well-known indigenous pig breed in China. The main advantages of Huai pigs over Western commercial pig breeds include a high intramuscular fat (IMF) content and good meat quality. There are significant differences in the meat quality traits of [...] Read more.
The Huai pig is a well-known indigenous pig breed in China. The main advantages of Huai pigs over Western commercial pig breeds include a high intramuscular fat (IMF) content and good meat quality. There are significant differences in the meat quality traits of the same muscle part or different muscle parts of the same variety. To investigate the potential genetic mechanism underlying the meat quality differences in different pig breeds or muscle groups, longissimus dorsi (LD), psoas major (PM), and biceps femoris (BF) muscle tissues were collected from two pig breeds (Huai and Duroc). There were significant differences in meat quality traits and amino acid content. We assessed the muscle transcriptomic profiles using high-throughput RNA sequencing. The IMF content in the LD, PM, and BF muscles of Huai pigs was significantly higher than that in Duroc pigs (p < 0.05). Similarly, the content of flavor amino acids in the three muscle groups was significantly higher in Huai pigs than that in Duroc pigs (p < 0.05). We identified 175, 110, and 86 differentially expressed genes (DEGs) between the LD, PM, and BF muscles of the Huai and Duroc pigs, respectively. The DEGs of the different pig breeds and muscle regions were significantly enriched in the biological processes and signaling pathways related to muscle fiber type, IMF deposition, lipid metabolism, PPAR signaling, cAMP signaling, amino acid metabolism, and ECM–receptor interaction. Our findings might help improve pork yield by using the obtained DEGs for marker-assisted selection and providing a theoretical reference for evaluating and improving pork quality. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics)
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13 pages, 2134 KiB  
Article
Effect of Slightly Acidic Electrolyzed Water on Growth, Diarrhea and Intestinal Bacteria of Newly Weaned Piglets
by Xiaoxia Hao, Dan Xie, Dongmei Jiang, Li Zhu, Linyuan Shen, Mailin Gan and Lin Bai
Genes 2023, 14(7), 1398; https://doi.org/10.3390/genes14071398 - 04 Jul 2023
Viewed by 1141
Abstract
As an environmentally-friendly agent, slightly acidic electrolyzed water (SAEW) was introduced in drinking water of newly weaned piglets for diarrhea prevention. In total, 72 piglets were employed and 3% SAEW was added into the normal temperature and warm (30 °C) tap water, respectively, [...] Read more.
As an environmentally-friendly agent, slightly acidic electrolyzed water (SAEW) was introduced in drinking water of newly weaned piglets for diarrhea prevention. In total, 72 piglets were employed and 3% SAEW was added into the normal temperature and warm (30 °C) tap water, respectively, for this 33-day feeding experiment. It was found that the total bacteria and coliforms in the drinking water were reduced by 70% and 100%, respectively, with the addition of 3% SAEW. After SAEW treatment, the average daily water and feed intakes of piglets were increased during the first 16 days, and the diarrhea rate was reduced by 100%, with not one case of diarrhea recorded at the end of the experiment. The microbiome results demonstrated that SAEW decreased the diversity of caecum bacteria with normal tap water supplied, and increased the richness of the caecum bacteria with warm tap water supplied. SAEW also increased the abundance of potentially beneficial genera Sutterella and Ruminococcaceae_UCG-005 and reduced the abundance of pathogenic Faecalibacterium. Moreover, twelve metabolic functions belonging to the cluster of metabolism and organismal functions, including digestion and the endocrine and excretory systems, were greatly enhanced. Correlation analysis indicated that the influence of intestinal pathogens on water and feed intakes and the diarrhea of piglets were decreased by SAEW. The results suggest that SAEW can be used as an antibiotic substitute to prevent diarrhea in newly weaned piglets. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics)
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16 pages, 2669 KiB  
Article
Characteristics of microRNAs in Skeletal Muscle of Intrauterine Growth-Restricted Pigs
by Yunhong Jing, Mailin Gan, Zhongwei Xie, Jianfeng Ma, Lei Chen, Shunhua Zhang, Ye Zhao, Lili Niu, Yan Wang, Li Zhu and Linyuan Shen
Genes 2023, 14(7), 1372; https://doi.org/10.3390/genes14071372 - 28 Jun 2023
Viewed by 1137
Abstract
microRNAs are a class of small RNAs that have been extensively studied, which are involved in many biological processes and disease occurrence. The incidence of intrauterine growth restriction is higher in mammals, especially multiparous mammals. In this study, we found that the weight [...] Read more.
microRNAs are a class of small RNAs that have been extensively studied, which are involved in many biological processes and disease occurrence. The incidence of intrauterine growth restriction is higher in mammals, especially multiparous mammals. In this study, we found that the weight of the longissimus dorsi of intrauterine growth-restricted pigs was significantly lower than that of normal pigs. Then, intrauterine growth-restricted pig longissimus dorsi were used to characterize miRNA expression profiles by RNA sequencing. A total of 333 miRNAs were identified, of which 26 were differentially expressed. Functional enrichment analysis showed that these differentially expressed miRNAs regulate the expression of their target genes (such as PIK3R1, CCND2, AKT3, and MAP3K7), and these target genes play an important role in the proliferation and differentiation of skeletal muscle through signaling pathways such as the PI3K-Akt, MAPK, and FoxO signaling pathways. Furthermore, miRNA-451 was significantly upregulated in IUGR pig skeletal muscle. Overexpression of miR-451 in C2C12 cells significantly promoted the expression of Mb, Myod, Myog, Myh1, and Myh7, suggesting that miR-451 may be involved in the regulation of the myoblastic differentiation of C2C12 cells. Our results reveal the role of miRNA-451 in regulating myogenic differentiation of skeletal muscle in pigs with intrauterine growth restriction. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics)
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16 pages, 3945 KiB  
Article
Fecal Microbial Structure and Metabolic Profile in Post-Weaning Diarrheic Piglets
by Xianrui Zheng, Ke Nie, Yiliang Xu, Huibin Zhang, Fan Xie, Liming Xu, Zhiyong Zhang, Yueyun Ding, Zongjun Yin and Xiaodong Zhang
Genes 2023, 14(6), 1166; https://doi.org/10.3390/genes14061166 - 26 May 2023
Cited by 2 | Viewed by 1390
Abstract
(1) Background: Piglet diarrhea is one of the most serious diseases in pigs and has brought great economic losses to the pig industry. Alteration of the gut microbiota is an important factor in the etiology of piglet diarrhea. Therefore, this study aimed to [...] Read more.
(1) Background: Piglet diarrhea is one of the most serious diseases in pigs and has brought great economic losses to the pig industry. Alteration of the gut microbiota is an important factor in the etiology of piglet diarrhea. Therefore, this study aimed to analyze the differences in the gut microbial structures and fecal metabolic profile between post-weaning diarrhea and healthy Chinese Wannan Black pigs. (2) Methods: An integrated approach of 16S rRNA gene sequencing combined with LC/MS-based metabolomics was employed in this study. (3) Results: We found an increase in the relative abundance of the bacterial genus Campylobacter and a decrease in phylum Bacteroidetes and the species Streptococcus gallolyticus subsp. macedonicus. (S. macedonicus) in piglet diarrhea. Meanwhile, obvious changes in the fecal metabolic profile of diarrheic piglets were also detected, particularly higher levels of polyamines (spermine and spermidine). Moreover, there were substantial associations between the disturbed gut microbiota and the altered fecal metabolites, especially a strong positive relationship between spermidine and Campylobacter. (4) Conclusions: These observations may provide novel insights into potential etiologies related to post-weaning diarrhea and further enhance our understanding of the role of gut microbiota in host homeostasis and in modulating gut microbial structure. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics)
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15 pages, 3433 KiB  
Article
Transcriptome Profiling of Different Developmental Stages on Longissimus Dorsi to Identify Genes Underlying Intramuscular Fat Content in Wannanhua Pigs
by Xiaojin Li, Yanan Yang, Lei Li, Man Ren, Mei Zhou and Shenghe Li
Genes 2023, 14(4), 903; https://doi.org/10.3390/genes14040903 - 12 Apr 2023
Cited by 2 | Viewed by 1339
Abstract
Intramuscular fat (IMF) is a key index to measure the tenderness and flavor of pork. Wannanhua pig, a famous indigenous pig breed in Anhui Province, is renowned for its high lipid deposition and high genetic divergence, making it an ideal model for investigating [...] Read more.
Intramuscular fat (IMF) is a key index to measure the tenderness and flavor of pork. Wannanhua pig, a famous indigenous pig breed in Anhui Province, is renowned for its high lipid deposition and high genetic divergence, making it an ideal model for investigating the lipid position trait mechanisms in pigs. However, the regulatory mechanisms of lipid deposition and development in pigs remain unclear. Furthermore, the temporal differences in gene regulation are based on muscle growth and IMF deposition. The purpose of this study was to study the expression changes of longissimus dorsi (LD) at different growth stages of WH pigs at the molecular level, to screen the candidate genes and signaling pathways related to IMF during development by transcriptome sequencing technology, and to explore the transcriptional regulation mechanism of IMF deposition-related genes at different development stages. In total, 616, 485, and 1487 genes were differentially expressed between LD60 and LD120, LD120 and LD240, and LD60 and LD240, respectively. Numerous differentially expressed genes (DEGs) associated with lipid metabolism and muscle development were identified, and most of them were involved in IMF deposition and were significantly up-regulated in LD120 and LD240 compared to LD60. STEM (Short Time-series Expression Miner) analysis indicated significant variations in the mRNA expression across distinct muscle development stages. The differential expression of 12 selected DEGs was confirmed by RT-qPCR. The results of this study contribute to our understanding of the molecular mechanism of IMF deposition and provide a new way to accelerate the genetic improvement of pork quality. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics)
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15 pages, 1845 KiB  
Article
Molecular Design-Based Breeding: A Kinship Index-Based Selection Method for Complex Traits in Small Livestock Populations
by Jiamin Gu, Jianwei Guo, Zhenyang Zhang, Yuejin Xu, Qamar Raza Qadri, Zhe Zhang, Zhen Wang, Qishan Wang and Yuchun Pan
Genes 2023, 14(4), 807; https://doi.org/10.3390/genes14040807 - 27 Mar 2023
Viewed by 1940
Abstract
Genomic selection (GS) techniques have improved animal breeding by enhancing the prediction accuracy of breeding values, particularly for traits that are difficult to measure and have low heritability, as well as reducing generation intervals. However, the requirement to establish genetic reference populations can [...] Read more.
Genomic selection (GS) techniques have improved animal breeding by enhancing the prediction accuracy of breeding values, particularly for traits that are difficult to measure and have low heritability, as well as reducing generation intervals. However, the requirement to establish genetic reference populations can limit the application of GS in pig breeds with small populations, especially when small populations make up most of the pig breeds worldwide. We aimed to propose a kinship index based selection (KIS) method, which defines an ideal individual with information on the beneficial genotypes for the target trait. Herein, the metric for assessing selection decisions is a beneficial genotypic similarity between the candidate and the ideal individual; thus, the KIS method can overcome the need for establishing genetic reference groups and continuous phenotype determination. We also performed a robustness test to make the method more aligned with reality. Simulation results revealed that compared to conventional genomic selection methods, the KIS method is feasible, particularly, when the population size is relatively small. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics)
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16 pages, 8402 KiB  
Article
tsRNA Landscape and Potential Function Network in Subcutaneous and Visceral Pig Adipose Tissue
by Linghui Wang, Hao Gu, Tianci Liao, Yuhang Lei, Yanhao Qiu, Qiuyang Chen, Lei Chen, Shunhua Zhang, Jinyong Wang, Xiaoxia Hao, Dongmei Jiang, Ye Zhao, Lili Niu, Xuewei Li, Linyuan Shen, Mailin Gan and Li Zhu
Genes 2023, 14(4), 782; https://doi.org/10.3390/genes14040782 - 23 Mar 2023
Cited by 3 | Viewed by 1248
Abstract
Noncoding RNAs (ncRNAs) called tsRNAs (tRNA-derived short RNAs) have the ability to regulate gene expression. The information on tsRNAs in fat tissue is, however, limited. By sequencing, identifying, and analyzing tsRNAs using pigs as animal models, this research reports for the first time [...] Read more.
Noncoding RNAs (ncRNAs) called tsRNAs (tRNA-derived short RNAs) have the ability to regulate gene expression. The information on tsRNAs in fat tissue is, however, limited. By sequencing, identifying, and analyzing tsRNAs using pigs as animal models, this research reports for the first time the characteristics of tsRNAs in subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT). A total of 474 tsRNAs, 20 and 21 of which were particularly expressed in VAT and SAT, respectively, were found in WAT. According to the analysis of the tsRNA/miRNA/mRNA co-expression network, the tsRNAs with differential expression were primarily engaged in the endocrine and immune systems, which fall under the classification of organic systems, as well as the global and overview maps and lipid metropolis, which fall under the category of metabolism. This research also discovered a connection between the activity of the host tRNA engaged in translation and the production of tsRNAs. This research also discovered that tRF-Gly-GCC-037/tRF-Gly-GCC-042/tRF-Gly-CCC-016 and miR-218a/miR281b may be involved in the regulation of fatty acid metabolism in adipose tissue through SCD based on the tsRNA/miRNA/mRNA/fatty acid network. In conclusion, our findings enrich the understanding of ncRNAs in WAT metabolism and health regulation, as well as reveal the differences between SAT and VAT at the level of tsRNAs. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics)
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12 pages, 9485 KiB  
Article
Evaluating the Effects of Cryopreservation on the Viability and Gene Expression of Porcine-Ear-Skin Fibroblasts
by Jiacheng Cao, Yingyu Xie, Jing Wang, Yongjie Huang, Xiaohan Zhang, Tianfang Xiao and Shaoming Fang
Genes 2023, 14(3), 751; https://doi.org/10.3390/genes14030751 - 20 Mar 2023
Viewed by 1747
Abstract
Owing to the inherent heterogeneity and plasticity of fibroblasts, they are considered as the conventional biological resources for basic and clinical medical research. Thus, it is essential to generate knowledge about the establishment of fibroblast cultures and the effects of cryopreservation processes on [...] Read more.
Owing to the inherent heterogeneity and plasticity of fibroblasts, they are considered as the conventional biological resources for basic and clinical medical research. Thus, it is essential to generate knowledge about the establishment of fibroblast cultures and the effects of cryopreservation processes on their biological characteristics. Since the pig (Sus scrofa) possesses numerous genetic, physiological, and anatomical similarities with humans, porcine fibroblasts are naturally regarded as useful analogues of human fibroblasts. Nonetheless, less attention has been given to the alterations in viability and gene expression of cryopreserved porcine fibroblasts. In this study, we aimed to obtain fibroblasts from porcine ear skin and evaluate the effects of cryopreservation on the cell survival, proliferation, and gene expression profiles of the fibroblasts by trypan-blue-staining assay, Cell Counting kit-8 (CCK-8) assay, and RNA-sequencing analysis, respectively. Our results suggested that morphologically stable fibroblast cultures can be constructed from pig-ear skin. The post-thaw survival rate of the cryopreserved fibroblasts at 0 h and 24 h was over 90%. The proliferative activity of the cryopreserved fibroblasts was similar to that of the non-cryopreserved fibroblasts after 7 days of in vitro culture, which suggested that cryopreservation did not influence the viability. The RNA-sequencing analysis indicated that this should be attributed to the 867 differentially expressed genes (DGEs) identified, which are involved in molecular process related to cell recovery and survival after cryo-stimulation. In addition, eight important DEGs BMP2, GDF15, EREG, AREG, HBEGF, LIF, IL-6, and HOX-7 could potentially be applied to improve the efficiency of fibroblast cryopreservation, but comprehensive and systematic studies on understanding the underlying mechanisms responsible for their modulatory roles are urgently needed. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics)
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12 pages, 3023 KiB  
Article
Association Analysis of PRKAA2 and MSMB Polymorphisms and Growth Traits of Xiangsu Hybrid Pigs
by Jiali Xu, Yong Ruan, Jinkui Sun, Pengfei Shi, Jiajin Huang, Lingang Dai, Meimei Xiao and Houqiang Xu
Genes 2023, 14(1), 113; https://doi.org/10.3390/genes14010113 - 30 Dec 2022
Cited by 5 | Viewed by 1184
Abstract
In this study, Xiangsu hybrid pig growth traits were evaluated via PRKAA2 and MSMB as candidate genes. Sanger sequencing revealed three mutation sites in PRKAA2, namely, g.42101G>T, g.60146A>T, and g.61455G>A, and all these sites were intronic mutations. Moreover, six mutation sites were [...] Read more.
In this study, Xiangsu hybrid pig growth traits were evaluated via PRKAA2 and MSMB as candidate genes. Sanger sequencing revealed three mutation sites in PRKAA2, namely, g.42101G>T, g.60146A>T, and g.61455G>A, and all these sites were intronic mutations. Moreover, six mutation sites were identified in MSMB: intronic g.4374G>T, exonic g.4564T>C, exonic g.6378G>A, exonic g.6386C>T, intronic g.8643G>A, and intronic g.8857A>G. Association analysis revealed that g.42101G>T, g.60146A>T, g.61455G>A, g.4374G>T, g.4564T>C, g.6378G>A, g.6386C>T, g.8643G>A, and g.8857A>G showed different relationship patterns among body weight, body length, body height, chest circumference, abdominal circumference, tube circumference, and chest depth. Real-time polymerase chain reaction results revealed that the expression of PRKAA2 was highest in the longissimus dorsi muscle, followed by that in the heart, kidney, liver, lung, and spleen. The expression of MSMB was highest in the spleen, followed by that in the liver, kidney, lung, heart, and longissimus dorsi muscle. These results suggest that PRKAA2 and MSMB can be used in marker-assisted selection to improve growth related traits in Xiangsu hybrid pigs, providing new candidate genes for Pig molecular breeding. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics)
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14 pages, 5853 KiB  
Article
Distinct Gut Microbiome Induced by Different Feeding Regimes in Weaned Piglets
by Jie Zhang, Xi Long, Qinfeng Liao, Jie Chai, Tinghuan Zhang, Li Chen, Hang He, Yancong Yuan, Kun Wan, Jinyong Wang and Anfang Liu
Genes 2023, 14(1), 49; https://doi.org/10.3390/genes14010049 - 23 Dec 2022
Cited by 1 | Viewed by 1376
Abstract
It is well accepted that the gut microbiota of breast-fed (BF) and formula-fed (FF) infants are significantly different. However, there is still a limited number of studies comparing the gut microbiota of BF and FF piglets, despite increasing numbers of FF piglets in [...] Read more.
It is well accepted that the gut microbiota of breast-fed (BF) and formula-fed (FF) infants are significantly different. However, there is still a limited number of studies comparing the gut microbiota of BF and FF piglets, despite increasing numbers of FF piglets in the modern pig industry. The present study identified the differences in gut microbiota composition between BF- and FF-weaned Rongchang piglets at 30 days old, using pair-end sequencing on the Illumina HiSeq 2500 platform. The BF piglets had lower microbiota diversities than FF piglets (p < 0.05), and the community structures were well clustered as a result of each feeding pattern. Firmicutes and Bacteroidetes represented the most dominant phyla, and Ruminococcus, Prevotella, and Gemmiger were prominent genera in all piglets. Ruminococcus, Prevotella, Oscillospira, Eubacterium, Gemmiger, Dorea, and Lactobacillus populations were significantly higher, while Treponema and Coprococcus were significantly lower in BF piglets compared to FF piglets (p < 0.05). The metabolism pathways in the BF piglets were significantly different from FF piglets, which included carbohydrate and amino acid metabolism (p < 0.05). In addition, the top 10 abundance of microbiota were more or less significantly associated with the two phenotypes (p < 0.05). Collectively, these findings provide probable explanations for the importance of BF in neonates and support a theoretical basis for feeding regimes in indigenous Chinese piglets. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics)
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12 pages, 2542 KiB  
Article
Pituitary-Gland-Based Genes Participates in Intrauterine Growth Restriction in Piglets
by Xiang Ji, Qi Shen, Pingxian Wu, Hongyue Chen, Shujie Wang, Dong Chen, Yang Yu, Zongyi Guo, Jinyong Wang and Guoqing Tang
Genes 2022, 13(11), 2141; https://doi.org/10.3390/genes13112141 - 17 Nov 2022
Cited by 1 | Viewed by 1499
Abstract
Intrauterine growth restriction (IUGR) is a major problem associated with piglet growth performance. The incidence of IUGR is widespread in Rongchang pigs. The pituitary gland is important for regulating growth and metabolism, and research has identified genes associated with growth and development. The [...] Read more.
Intrauterine growth restriction (IUGR) is a major problem associated with piglet growth performance. The incidence of IUGR is widespread in Rongchang pigs. The pituitary gland is important for regulating growth and metabolism, and research has identified genes associated with growth and development. The pituitary gland of newborn piglets with normal birth weight (NBW group, n = 3) and (IUGR group, n = 3) was collected for transcriptome analysis. A total of 323 differentially expression genes (DEGs) were identified (|log2(fold-change)| > 1 and q value < 0.05), of which 223 were upregulated and 100 were downregulated. Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed that the DEGs were mainly related to the extracellular matrix, regulation of the multicellular organismal process, tissue development and angiogenesis, which participate in the growth and immune response in IUGR piglets. Moreover, 7 DEGs including IGF2, THBS1, ITGA1, ITGA8, EPSTI1, FOSB, and UCP2 were associated with growth and immune response. Furthermore, based on the interaction network analysis of the DEGs, two genes, IGF2 and THBS1, participated in cell proliferation, embryonic development and angiogenesis. IGF2 and THBS1 were also the main genes participating in the IUGR. This study identified the core genes involved in IUGR in piglets and provided a reference for exploring the effect of the pituitary gland on piglet growth. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics)
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14 pages, 1807 KiB  
Article
Identification of circRNAs Associated with Adipogenesis Based on RNA-Seq Data in Pigs
by Qiaowei Li, Liyuan Wang, Kai Xing, Yalan Yang, Adeyinka Abiola Adetula, Yuwen Liu, Guoqiang Yi, Hongfu Zhang, Torres Sweeney and Zhonglin Tang
Genes 2022, 13(11), 2062; https://doi.org/10.3390/genes13112062 - 07 Nov 2022
Cited by 1 | Viewed by 1479
Abstract
Adipocytes or fat cells play a vital role in the storage and release of energy in pigs, and many circular RNAs (circRNAs) have emerged as important regulators in various tissues and cell types in pigs. However, the spatio-temporal expression pattern of circRNAs between [...] Read more.
Adipocytes or fat cells play a vital role in the storage and release of energy in pigs, and many circular RNAs (circRNAs) have emerged as important regulators in various tissues and cell types in pigs. However, the spatio-temporal expression pattern of circRNAs between different adipose deposition breeds remains elusive. In this study, RNA sequencing (RNA-seq) produced transcriptome profiles of Western Landrace (lean-type) and Chinese Songliao black pigs (obese-type) with different thicknesses of subcutaneous fat tissues and were used to identify circRNAs involved in the regulation of adipogenesis. Gene expression analysis revealed 883 circRNAs, among which 26 and 11 circRNAs were differentially expressed between Landrace vs. Songliao pigs and high- vs. low-thickness groups, respectively. We also analyzed the interaction between circRNAs and microRNAs (miRNAs) and constructed their interaction network in adipogenesis; gene ontology classification and pathway analysis revealed two vital circRNAs, with the majority of their target genes enriched in biological functions such as fatty acids biosynthesis, fatty acid metabolism, and Wnt/TGF-β signaling pathways. These candidate circRNAs can be taken as potential targets for further experimental studies. Our results show that circRNAs are dynamically expressed and provide a valuable basis for understanding the molecular mechanism of circRNAs in pig adipose biology. Full article
(This article belongs to the Special Issue Advances in Pig Breeding and Genetics)
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