Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon

Arora, D. K.; Srikanth, Krishnamoorthy; Lee, Jongin; Lee, Daehwan; Park, Nayoung; Wy, Suyeon; Kim, Hyeonji; Park, Jong-Eun; Chai, Han-Ha; Lim, Dajeong; Cho, In-Cheol; Kim, Jaebum; Park, Woncheoul

doi:10.1038/s41598-021-86683-4

Cited by 11 publications

(14 citation statements)

References 83 publications

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“…3 Reference pig is taken from Fig. 1 of Arora et al, [ 6 ] (A) Volcano plot of fold change expression level (y-axis) against –Log 10 P (x-axis). Each point represents a transcript; those with significant differential expression (FDR ≤ 0.05) are indicated in red.…”

Section: Resultsmentioning

confidence: 99%

“…gDNA from Nanchukmacdon pig backfat and liver was subjected to bisulfite conversion using the fragment size (250 bp±25 bp), and the sequencing libraries were constructed as previously described [ 6 ]. Similarly, RNA-seq data were generated for Nanchukmacdon pig ( N =5) after RNA isolation of backfat and liver tissues using the TRIzol method following the prescribed protocol and previously described [ 33 ].…”

Section: Methodsmentioning

confidence: 99%

“…Due to the enhanced taste but low reproduction of JNP, a threat of extinction has loomed over the JNP breed [ 5 ]. To address this issue, an breeding program was conducted to develop a pig breed with a high reproduction rate and sustain the superior taste characteristics [ 6 ]. In the course of the intensive breeding program and continued close monitoring using modern biological methods, a pig breed referred to as ‘Nanchukmacdon’ was developed.…”

Section: Introductionmentioning

confidence: 99%

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Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig

et al. 2021

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Background DNA methylation and demethylation at CpG islands is one of the main regulatory factors that allow cells to respond to different stimuli. These regulatory mechanisms help in developing tissue without affecting the genomic composition or undergoing selection. Liver and backfat play important roles in regulating lipid metabolism and control various pathways involved in reproductive performance, meat quality, and immunity. Genes inside these tissue store a plethora of information and an understanding of these genes is required to enhance tissue characteristics in the future generation. Results A total of 16 CpG islands were identified, and they were involved in differentially methylation regions (DMRs) as well as differentially expressed genes (DEGs) of liver and backfat tissue samples. The genes C7orf50, ACTB and MLC1 in backfat and TNNT3, SIX2, SDK1, CLSTN3, LTBP4, CFAP74, SLC22A23, FOXC1, GMDS, GSC, GATA4, SEMA5A and HOXA5 in the liver, were categorized as differentially-methylated. Subsequently, Motif analysis for DMRs was performed to understand the role of the methylated motif for tissue-specific differentiation. Gene ontology studies revealed association with collagen fibril organization, the Bone Morphogenetic Proteins (BMP) signaling pathway in backfat and cholesterol biosynthesis, bile acid and bile salt transport, and immunity-related pathways in methylated genes expressed in the liver. Conclusions In this study, to understand the role of genes in the differentiation process, we have performed whole-genome bisulfite sequencing (WGBS) and RNA-seq analysis of Nanchukmacdon pigs. Methylation and motif analysis reveals the critical role of CpG islands and transcriptional factors binding site (TFBS) in guiding the differential patterns. Our findings could help in understanding how methylation of certain genes plays an important role and can be used as biomarkers to study tissue specific characteristics.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig

et al. 2021

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“…Using the existing WGS knowledge and understanding of molecular architecture, we oversaw the development of a breed with an enhanced trait value [ 18 , 19 ]. These approaches already helped in the identification of different genomic regions with selection signals, suggesting the contribution of the region in influencing different traits related to phenotypic or genotypic composition [ 20 , 21 ]. Similarly, with a better understanding of the genetic architecture and using advanced molecular breeding approaches these pitfalls can be overcome and a more stable ET breed can be developed with an L type immunogenicity response.…”

Section: Introductionmentioning

confidence: 99%

Multi-omics approaches for comprehensive analysis and understanding of the immune response in the miniature pig breed

et al. 2022

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The porcine immune system has an important role in pre-clinical studies together with understanding the biological response mechanisms before entering into clinical trials. The size distribution of the Korean minipig is an important feature that make this breed ideal for biomedical research and safe practice in post clinical studies. The extremely tiny (ET) minipig serves as an excellent model for various biomedical research studies, but the comparatively frail and vulnerable immune response to the environment over its Large (L) size minipig breed leads to additional after born care. To overcome this pitfall, comparative analysis of the genomic regions under selection in the L type breed could provide a better understanding at the molecular level and lead to the development of an enhanced variety of ET type minipig. In this study, we utilized whole genome sequencing (WGS) to identify traces of artificial selection and integrated them with transcriptome data generated from blood samples to find strongly selected and differentially expressed genes of interest. We identified a total of 35 common genes among which 7 were differentially expressed and showed selective sweep in the L type over the ET type minipig breed. The stabilization of these genes were further confirmed using nucleotide diversity analysis, and these genes could serve as potential biomarkers for the development of a better variety of ET type pig breed.

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“…In the previous study, selective sweeps between pig breeds were explored using XP-CLR and XP-EHH (Jeong et al 2015 ; Arora et al 2021 ). They found the variants and the genes showing the selective sweeps.…”

Section: Introductionmentioning

confidence: 99%

Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea

Lee

Son

Heo

et al. 2021

Animal Cells and Systems

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Although there have been many genome-wide association studies (GWAS) and selective sweep analyses to understand pig genomic regions related to growth performance, these methods considered only the gene effect and selection signal, respectively. In this study, we suggest the cross-population phenotype associated variant (XP-PAV) analysis as a novel method to determine the genomic variants with different effects between the two populations. XP-PAV analysis could reveal the differential genetic variants between the two populations by considering the gene effect and selection signal simultaneously. In this study, we used daily weight gain (DWG) and back fat thickness (BF) as phenotypes and the Landrace and Yorkshire populations were used for XP-PAV analysis. The main aim was to reveal the differential selection by considering the gene effect between Landrace and Yorkshire pigs. In the gene ontology analysis of XP-PAV results, differential selective genes in DWG analysis were involved in the regulation of interleukin-2 production and cell cycle G2/M transition. The protein modification and glycerophospholipid biosynthetic processes were the most enriched terms in the BF analysis. Therefore, we could identify genetic differences for immune and several metabolic pathways between Landrace and Yorkshire breeds using the XP-PAV analysis. In this study, we expect that XP-PAV analysis will play a role in determining useful selective variants with gene effects and provide a new interpretation of the genetic differences between the two populations.

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Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon

Cited by 11 publications

References 83 publications

Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig

Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig

Multi-omics approaches for comprehensive analysis and understanding of the immune response in the miniature pig breed

Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea

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