RNA-Seq Analysis Reveals Hub Genes Involved in Chicken Intramuscular Fat and Abdominal Fat Deposition During Development

Xing, Siyuan; Liu, Ranran; Zhao, Guiping; Liu, Lu; Groenen, M.A.M.; Madsen, Ole; Zheng, Maiqing; Yang, Xinting; Crooijmans, R.P.M.A.; Wen, Jie

doi:10.3389/fgene.2020.01009

Cited by 31 publications

(29 citation statements)

References 45 publications

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“…A study comparing the transcriptomes of the intestine and muscle, between divergent feed-efficient broilers, showed that ACSBG2 influences the muscular lipid utilization and was among the highest expressed genes in muscle (Reyer et al, 2018). We, however, did not find high expression of ACSBG2 in breast muscle at the nine different developmental stages of the same 27 slow-growing chicken used in this study (Xing et al, 2020). This difference between the studies may be caused by using different chicken breeds that differ in their growth rate.…”

Section: Discussioncontrasting

confidence: 71%

Time Course Transcriptomic Study Reveals the Gene Regulation During Liver Development and the Correlation With Abdominal Fat Weight in Chicken

et al. 2021

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Background: The liver is the central metabolic organ of animals. In chicken, knowledge on the relationship between gene expression in the liver and fat deposition during development is still limited. A time-course transcriptomic study from the embryonic (day 12) to the egg-producing period (day 180 after hatch) was performed to profile slow-growing meat type chicken liver gene expression and to investigate its correlation with abdominal fat deposition.Results: The transcriptome profiles showed a separation of the different developmental stages. In total, 13,096 genes were ubiquitously expressed at all the tested developmental stages. The analysis of differentially expressed genes between adjacent developmental stages showed that biosynthesis of unsaturated fatty acids pathway was enriched from day 21 to day 140 after hatch. The correlation between liver gene expression and the trait abdominal fat weight (AFW) was analyzed by weighted gene co-expression network analysis. The genes MFGE8, HHLA1, CKAP2, and ACSBG2 were identified as hub genes in AFW positively correlated modules, which suggested important roles of these genes in the lipid metabolism in chicken liver.Conclusion: Our results provided a resource of developmental transcriptome profiles in chicken liver and suggested that the gene ACSBG2 among other detected genes can be used as a candidate gene for selecting low AFW chickens.

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Section: Discussioncontrasting

confidence: 71%

Time Course Transcriptomic Study Reveals the Gene Regulation During Liver Development and the Correlation With Abdominal Fat Weight in Chicken

et al. 2021

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“…RNA-seq is effective for identifying differentially expressed (DE) genes as well as quantifying transcriptomes ( 22 , 23 ). This technique has been frequently used in the functional analysis of lncRNAs/mRNAs in adipose tissue in cattle ( 24 – 27 ), sheep ( 28 ), pigs ( 29 ), and chickens ( 30 ). Jiang et al ( 25 ) isolated 3,716 candidate lncRNAs from fat samples from calves and adult cattle and confirmed their crucial role in cattle of various ages.…”

Section: Introductionmentioning

confidence: 99%

Interference With ACSL1 Gene in Bovine Adipocytes: Transcriptome Profiling of mRNA and lncRNA Related to Unsaturated Fatty Acid Synthesis

Bai

Chen

et al. 2021

Front. Vet. Sci.

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The enzyme long-chain acyl-CoA synthetase 1 (ACSL1) is essential for lipid metabolism. The ACSL1 gene controls unsaturated fatty acid (UFA) synthesis as well as the formation of lipid droplets in bovine adipocytes. Here, we used RNA-Seq to determine lncRNA and mRNA that regulate UFA synthesis in bovine adipocytes using RNA interference and non-interference with ACSL1. The corresponding target genes of differentially expressed (DE) lncRNAs and the DE mRNAs were found to be enriched in lipid and FA metabolism-related pathways, according to GO and KEGG analyses. The differentially expressed lncRNA- differentially expressed mRNA (DEL-DEM) interaction network indicated that some DELs, such as TCONS_00069661, TCONS_00040771, TCONS_ 00035606, TCONS_00048301, TCONS_001309018, and TCONS_00122946, were critical for UFA synthesis. These findings assist our understanding of the regulation of UFA synthesis by lncRNAs and mRNAs in bovine adipocytes.

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“…However, similar to GWAS for quantitative traits that are performed with SNPs, association analyses based on gene expression levels and phenotypic records can be carried out to detect candidate genes for traits of interest. In addition to association studies, weighted gene co-expression network analysis (WGCNA) is widely used in gene expression analyses to explore the correlation patterns among expression levels of genes and to associate gene co-expression network modules to traits [ 20 ], including breast muscle IMF [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

Large-scale transcriptome sequencing in broiler chickens to identify candidate genes for breast muscle weight and intramuscular fat content

et al. 2021

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Background In broiler production, breast muscle weight and intramuscular fat (IMF) content are important economic traits. Understanding the genetic mechanisms that underlie these traits is essential to implement effective genetic improvement programs. To date, genome-wide association studies (GWAS) and gene expression analyses have been performed to identify candidate genes for these traits. However, GWAS mainly detect associations at the DNA level, while differential expression analyses usually have low power because they are typically based on small sample sizes. To detect candidate genes for breast muscle weight and IMF contents (intramuscular fat percentage and relative content of triglycerides, cholesterol, and phospholipids), we performed association analyses based on breast muscle transcriptomic data on approximately 400 Tiannong partridge chickens at slaughter age. Results First, by performing an extensive simulation study, we evaluated the statistical properties of association analyses of gene expression levels and traits based on the linear mixed model (LMM) and three regularized linear regression models, i.e., least absolute shrinkage and selection operator (LASSO), ridge regression (RR), and elastic net (EN). The results show that LMM, LASSO and EN with tuning parameters that are determined based on the one standard error rule exhibited the lowest type I error rates. Using results from all three models, we detected 43 candidate genes with expression levels that were associated with breast muscle weight. In addition, candidate genes were detected for intramuscular fat percentage (1), triglyceride content (2), cholesterol content (1), and phospholipid content (1). Many of the identified genes have been demonstrated to play roles in the development and metabolism of skeletal muscle or adipocyte. Moreover, weighted gene co-expression network analyses revealed that many candidate genes were harbored by gene co-expression modules, which were also significantly correlated with the traits of interest. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that these modules are involved in muscle development and contraction, and in lipid metabolism. Conclusions Our study provides valuable insight into the transcriptomic bases of breast muscle weight and IMF contents in Chinese indigenous yellow broilers. Our findings could be useful for the genetic improvement of these traits in broiler chickens.

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RNA-Seq Analysis Reveals Hub Genes Involved in Chicken Intramuscular Fat and Abdominal Fat Deposition During Development

Cited by 31 publications

References 45 publications

Time Course Transcriptomic Study Reveals the Gene Regulation During Liver Development and the Correlation With Abdominal Fat Weight in Chicken

Time Course Transcriptomic Study Reveals the Gene Regulation During Liver Development and the Correlation With Abdominal Fat Weight in Chicken

Interference With ACSL1 Gene in Bovine Adipocytes: Transcriptome Profiling of mRNA and lncRNA Related to Unsaturated Fatty Acid Synthesis

Large-scale transcriptome sequencing in broiler chickens to identify candidate genes for breast muscle weight and intramuscular fat content

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