Evaluation of body growth and immunity-related differentially expressed genes through deep RNA sequencing in the piglets of Jeju native pig and Berkshire

Ghosh, Mrinmoy; Sodhi, Simrinder Singh; Song, Ki Duk; Kim, J. H.; Mongre, Raj Kumar; Sharma, Neelesh; Singh, Nirbhay Kumar; Kim, S. W.; Lee, H. K.; Jeong, Dong Kee

doi:10.1111/age.12281

Cited by 21 publications

(15 citation statements)

References 27 publications

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“…Next-generation sequencing (NGS) is a term that includes several high-throughput sequencing technologies including but not limited to: Illumina, Roche 454 and SOLiD sequencing and RNA-Seq (van Dijk et al, 2014). RNA-Seq for example, has been used to investigate differentially expressed genes in the transcriptome of different breeds of pig (Ghosh et al, 2015), which showed that genes involved in body growth and the immune system were more highly expressed in Berkshire pigs compared to Jeju native pigs. RNA-seq has also been used to identify genes and inhibitory, non-coding microRNA (miRNAs) that are differentially expressed between pigs with different feed efficiencies (Jing et al, 2015;Brameld and Parr, 2016).…”

Section: Next Generation Sequencingmentioning

confidence: 99%

Molecular approaches to the diagnosis and monitoring of production diseases in pigs

Giles

Belkhiri

Barrow

et al. 2017

Research in Veterinary Science

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Production disease in pigs is caused by a variety of different pathogens, mainly enteric and respiratory and can result in significant economic loss. Other factors such as stress, poor husbandry and nutrition can also contribute to an animal's susceptibility to disease. Molecular biomarkers of production disease could be of immense value by improving diagnosis and risk analysis to determine best practice with an impact on increased economic output and animal welfare. In addition to the use of multiplex PCR or microarrays to detect individual or mixed pathogens during infection, these technologies can also be used to monitor the host response to infection via gene expression. The patterns of gene expression associated with cellular damage or initiation of the early immune response may indicate the type of pathology and, by extension the types of pathogen involved. Molecular methods can therefore be used to monitor both the presence of a pathogen and the host response to it during production disease. The field of biomarker discovery and implementation is expanding as technologies such as microarrays and next generation sequencing become more common. Whilst a large number of studies have been carried out in human medicine, further work is needed to identify molecular biomarkers in veterinary medicine and in particular those associated with production disease in the pig industry. The pig transcriptome is highly complex and still not fully understood. Further gene expression studies are needed to identify molecular biomarkers which may have predictive value in identifying the environmental, nutritional and other risk factors which are associated with production diseases in pigs.

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Section: Next Generation Sequencingmentioning

confidence: 99%

Molecular approaches to the diagnosis and monitoring of production diseases in pigs

Giles

Belkhiri

Barrow

et al. 2017

Research in Veterinary Science

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“…RNA-seq using NGS technology has become widely used for high-throughput researches of gene expression. Such technology has been successfully used to identify genes associated with economically important quantitative traits, such as body growth, immune, disease resistance, and meat quality (Mu et al, 2014; Sodhi et al, 2014; Ghosh et al, 2015; Xiao et al, 2015). In this study, we compared the gene expression difference in the whole blood samples of DPL and Landrace pigs 6 h after stimulation with class C CpG ODN 2429 (a TLR9 agonist) in vivo using RNA-seq technology.…”

Section: Introductionmentioning

confidence: 99%

CpG Oligodeoxynucleotides Induce Differential Cytokine and Chemokine Gene Expression Profiles in Dapulian and Landrace Pigs

Yang

Wang

et al. 2016

Front. Microbiol.

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Oligodeoxynucleotides containing unmethylated CpG motifs (CpG ODN) mimic the immunostimulatory activity of microbial DNA by interacting with Toll-like receptor 9 (TLR9) to activate both the innate and adaptive immune responses in different species. However, few studies have been published to compare the effects of CpG ODN on different pig breeds. Therefore, in this study, whole blood gene expression profiles of DPL and Landrace pigs treated with CpG ODN were studied using RNA-seq technology. Five Hundred differentially expressed genes (DEGs) were identified between the two breeds. DPL pigs had significantly higher number of immune-relevant DEGs than the Landrace pigs after CpG ODN treatment. Pathway analysis showed that cytokine-cytokine receptor interaction and chemokine signaling pathway were the major enriched pathways of the immune-relevant DEGs. Further in vitro experiments showed that PBMCs of the DPL pigs had significantly higher levels of TLR9 mRNA than those of the Landrace pigs, both before and after CpG ODN stimulation. Cytokine and chemokine induction in the PBMCs of both breeds were also measured after CpG ODN stimulation. Our data showed that mRNA levels of cytokines (IFNα, IL8, IL12 p40) and chemokines (CXCL9, CXCL13) were significantly higher in the PBMCs of the DPL pigs than those of the Landrace pigs. Taken together, our data provide new information regarding the pig breed difference in response to CpG ODN stimulation and that higher levels of TLR9 mRNA in DPL pigs may be a major contributor for disease resistance.

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“…The JNP has black skin, erect, unfolded ears and is well-known for its tender and juicy meat. Consumers prefer JNP meat because of its superior taste, tenderness and marbling quality compared to the meat from western breeds [2]. JNP meat can be regarded as one of the best pork in Korea.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide scans for detecting the selection signature of the Jeju-island native pig in Korea

Lee

Won

Kim³

et al. 2020

Asian-Australas J Anim Sci

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Objective: The Jeju native pig (JNP) found on the Jeju Island of Korea is a unique black pig known for high-quality meat. To investigate the genetic uniqueness of JNP, we analyzed the selection signature of the JNP in comparison to commercial pigs such as Berkshire and Yorkshire pigs.Methods: We surveyed the genetic diversity to identify the genetic stability of the JNP, using the linkage disequilibrium method. A selective sweep of the JNP was performed to identify the selection signatures. To do so, the population differentiation measure, Weir-Cockerham’s F<sub>st</sub> was utilized. This statistic directly measures the population differentiation at the variant level. Additionally, we investigated the gene ontologies (GOs) and genetic features.Results: Compared to the Berkshire and Yorkshire pigs, the JNP had lower genetic diversity in terms of linkage disequilibrium decays. We summarized the selection signatures of the JNP as GO. In the JNP and Berkshire pigs, the most enriched GO terms were epithelium development and neuron-related. Considering the JNP and Yorkshire pigs, cellular response to oxygen-containing compound and generation of neurons were the most enriched GO.Conclusion: The selection signatures of the JNP were identified through the population differentiation statistic. The genes with possible selection signatures are expected to play a role in JNP’s unique pork quality.

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Evaluation of body growth and immunity-related differentially expressed genes through deep RNA sequencing in the piglets of Jeju native pig and Berkshire

Cited by 21 publications

References 27 publications

Molecular approaches to the diagnosis and monitoring of production diseases in pigs

Molecular approaches to the diagnosis and monitoring of production diseases in pigs

CpG Oligodeoxynucleotides Induce Differential Cytokine and Chemokine Gene Expression Profiles in Dapulian and Landrace Pigs

Genome-wide scans for detecting the selection signature of the Jeju-island native pig in Korea

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