Transcriptomics-Based Study of Differentially Expressed Genes Related to Fat Deposition in Tibetan and Yorkshire Pigs

Gong, Xinglong; Zheng, Min; Zhang, Jian; Ye, Yourong; Duan, Mengqi; Chamba, Yangzom; Wang, Zhongbin; Shang, Peng

doi:10.3389/fvets.2022.919904

Cited by 13 publications

(9 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We focused on the 10 genes with the highest p -values in the transcriptome. Ten of these genes, including PVALB , THRSP ( 33 , 34 ), HOXA9 ( 35 ), EEPD1 ( 36 ), HOXA10 ( 37 ), and PDE4B ( 38 ) have been reported to be involved in fat deposition and meat quality. Through the PPI analysis, we found that PVALB gene was the top 1 hub gene.…”

Section: Discussionmentioning

confidence: 99%

Integration of ATAC-seq and RNA-seq analysis identifies key genes affecting intramuscular fat content in pigs

Qiao

et al. 2022

Front. Nutr.

View full text Add to dashboard Cite

Meat quality is one of the most important economic traits in pig breeding and production, and intramuscular fat (IMF) content is the major factor in improving meat quality. The IMF deposition in pigs is influenced by transcriptional regulation, which is dependent on chromatin accessibility. However, how chromatin accessibility plays a regulatory role in IMF deposition in pigs has not been reported. Xidu black is a composite pig breed with excellent meat quality, which is an ideal research object of this study. In this study, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to identify the accessible chromatin regions and key genes affecting IMF content in Xidu black pig breed with extremely high and low IMF content. First, we identified 21,960 differential accessible chromatin peaks and 297 differentially expressed genes. The motif analysis of differential peaks revealed several potential cis-regulatory elements containing binding sites for transcription factors with potential roles in fat deposition, including Mef2c, CEBP, Fra1, and AP-1. Then, by integrating the ATAC-seq and RNA-seq analysis results, we found 47 genes in the extremely high IMF (IMF_H) group compared with the extremely low IMF (IMF_L) group. For these genes, we observed a significant positive correlation between the differential gene expression and differential ATAC-seq signal (r2 = 0.42). This suggests a causative relationship between chromatin remodeling and the resulting gene expression. We identified several candidate genes (PVALB, THRSP, HOXA9, EEPD1, HOXA10, and PDE4B) that might be associated with fat deposition. Through the PPI analysis, we found that PVALB gene was the top hub gene. In addition, some pathways that might regulate fat cell differentiation and lipid metabolism, such as the PI3K-Akt signaling pathway, MAPK signaling pathway, and calcium signaling pathway, were significantly enriched in the ATAC-seq and RNA-seq analysis. To the best of our knowledge, our study is the first to use ATAC-seq and RNA-seq to examine the mechanism of IMF deposition from a new perspective. Our results provide valuable information for understanding the regulation mechanism of IMF deposition and an important foundation for improving the quality of pork.

show abstract

Section: Discussionmentioning

confidence: 99%

Integration of ATAC-seq and RNA-seq analysis identifies key genes affecting intramuscular fat content in pigs

Qiao

et al. 2022

Front. Nutr.

View full text Add to dashboard Cite

show abstract

“…It is widely distributed and is currently one of the most commonly raised pig breeds worldwide. Yorkshire pigs have excellent characteristics such as fast weight gain, high feed conversion rate, and high lean meat rate of carcasses ( Gong et al, 2022 ). At present, Tibetan pigs on the Tibetan plateau are raised mainly through stabling and half-stabling feeding, often grazing in the sports arena, and their feed, comprising grass, leaves, fruits, roots, and insects, is rich in fiber.…”

Section: Introductionmentioning

confidence: 99%

Healthy Gut Microbiome Composition Enhances Disease Resistance and Fat Deposition in Tibetan Pigs

et al. 2022

View full text Add to dashboard Cite

The gut microbiota is involved in a range of physiological processes in animals, and modulating the microbiome composition is considered a novel target for identifying animal traits. Tibetan pigs show better fat deposition and disease resistance compared to Yorkshire pigs. However, studies investigating the correlation between favorable characteristics in Tibetan pigs and the gut microbial community remain scarce. In the current study, 1,249,822 high-quality sequences were obtained by amplicon sequencing of the colon contents of Tibetan and Yorkshire pigs. We found that at the boundary level, the abundance and relative abundance of colon bacterial community in Tibetan pigs were higher than that in Yorkshire pigs (P > 0.05). Phylum level, Firmicutes were the dominant colonic microflora of Tibetan and Yorkshire pigs, and the ratio of Firmicutes to Bacteroides in Tibetan pigs was slightly higher than in Yorkshire pigs. Actinobacteria and Spirobacteria were significantly higher in Tibetan pigs than in Yorkshire pigs (P < 0.05). At the genus level, the relative abundance of Bifidobacterium, Lactobacillus, and Bacteriologist, which are related to disease resistance, was significantly higher than that in Yorkshire pigs in Yorkshire pigs. In conclusion, the composition and abundance of colonic intestinal microflora in Tibetan pigs were closely related to their superior traits. Bifidobacteria, Ruminococcaceae, and Family-XIII-AD3011-Group are conducive to improving disease resistance in Tibetan pigs. Lactobacillus and Solobacterium were observed to be the main bacterial communities involved in fat deposition in Tibetan pigs. This study will provide a new reference for the development and utilization of Tibetan pigs in future.

show abstract

“…DEGs were identified between different comparison groups (WDL vs WGH, RSQ vs CRQ) using the DESeq2 package in R (version 4.2.1) based on negative binomial distribution. Considering previous studies [ 31 , 32 ] and our specific experimental situation, adjusted P -values ( P -adjust) < 0.05 and |log2FoldChange|> 0 were established as the thresholds for significance. Adjusted P -values were calculated using the Benjamini–Hochberg method.…”

Section: Methodsmentioning

confidence: 99%

Transcriptome analysis of the Bactrian camel (Camelus bactrianus) reveals candidate genes affecting milk production traits

Yao,

Dou,

Zhao

et al. 2023

BMC Genomics

View full text Add to dashboard Cite

Background Milk production traits are complex traits with vital economic importance in the camel industry. However, the genetic mechanisms regulating milk production traits in camels remain poorly understood. Therefore, we aimed to identify candidate genes and metabolic pathways that affect milk production traits in Bactrian camels. Methods We classified camels (fourth parity) as low- or high-yield, examined pregnant camels using B-mode ultrasonography, observed the microscopic changes in the mammary gland using hematoxylin and eosin (HE) staining, and used RNA sequencing to identify differentially expressed genes (DEGs) and pathways. Results The average standard milk yield over the 300 days during parity was recorded as 470.18 ± 9.75 and 978.34 ± 3.80 kg in low- and high-performance camels, respectively. Nine female Junggar Bactrian camels were subjected to transcriptome sequencing, and 609 and 393 DEGs were identified in the low-yield vs. high-yield (WDL vs. WGH) and pregnancy versus colostrum period (RSQ vs. CRQ) comparison groups, respectively. The DEGs were compared with genes associated with milk production traits in the Animal Quantitative Trait Loci database and in Alashan Bactrian camels, and 65 and 46 overlapping candidate genes were obtained, respectively. Functional enrichment and protein–protein interaction network analyses of the DEGs and candidate genes were conducted. After comparing our results with those of other livestock studies, we identified 16 signaling pathways and 27 core candidate genes associated with maternal parturition, estrogen regulation, initiation of lactation, and milk production traits. The pathways suggest that emerged milk production involves the regulation of multiple complex metabolic and cellular developmental processes in camels. Finally, the RNA sequencing results were validated using quantitative real-time PCR; the 15 selected genes exhibited consistent expression changes. Conclusions This study identified DEGs and metabolic pathways affecting maternal parturition and milk production traits. The results provides a theoretical foundation for further research on the molecular mechanism of genes related to milk production traits in camels. Furthermore, these findings will help improve breeding strategies to achieve the desired milk yield in camels. Graphical Abstract

show abstract

Transcriptomics-Based Study of Differentially Expressed Genes Related to Fat Deposition in Tibetan and Yorkshire Pigs

Cited by 13 publications

References 32 publications

Integration of ATAC-seq and RNA-seq analysis identifies key genes affecting intramuscular fat content in pigs

Integration of ATAC-seq and RNA-seq analysis identifies key genes affecting intramuscular fat content in pigs

Healthy Gut Microbiome Composition Enhances Disease Resistance and Fat Deposition in Tibetan Pigs

Transcriptome analysis of the Bactrian camel (Camelus bactrianus) reveals candidate genes affecting milk production traits

Contact Info

Product

Resources

About