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. 2018 Apr 19;13(4):e0195132.
doi: 10.1371/journal.pone.0195132. eCollection 2018.

RNA-Seq reveals differentially expressed genes affecting polyunsaturated fatty acids percentage in the Huangshan Black chicken population

Shaohua Yang  1 , Ying Wang  1 , Lulu Wang  1 , Zhaoyuan Shi  1 , Xiaoqian Ou  1 , Dan Wu  1 , Xinmiao Zhang  1 , Hao Hu  1 , Jia Yuan  1 , Wei Wang  2 , Fuhu Cao  1 , Guoqing Liu  1
Affiliations

RNA-Seq reveals differentially expressed genes affecting polyunsaturated fatty acids percentage in the Huangshan Black chicken population

Shaohua Yang et al. PLoS One. .

Abstract

Fatty acids metabolic products determine meat quality in chickens. Identifying genes associated with fatty acids composition could provide valuable information for the complex genetic networks of genes with underlying variations in fatty acids synthesis. RNA sequencing (RNA-Seq) was conducted to explore the chicken transcriptome from the thigh muscle tissue of 6 Huangshan Black Chickens with 3 extremely high and low phenotypic values for percentage of polyunsaturated fatty acids (PUFAs). In total, we obtained 41,139,108-44,901,729 uniquely mapped reads, which covered 74.15% of the current annotated transcripts including 18964 mRNA transcripts, across all the six thigh muscle tissue samples. Of these, we revealed 274 differentially expressed genes (DEGs) with a highly significant correlation with polyunsaturated fatty acids percentage between the comparison groups based on the ratio of PUFA/SFA. Gene ontology and pathway analysis indicated that the DEGs were enriched in particular biological processes affecting fatty acids metabolism, biosynthesis of unsaturated fatty acids (USFAs), and cell junction-related pathways. Integrated interpretation of differential gene expression and formerly reported quantitative trait loci (QTL) demonstrated that FADS2, DCN, FRZB, OGN, PRKAG3, LHFP, CHCHD10, CYTL1, FBLN5, and ADGRD1 are the most promising candidate genes affecting polyunsaturated fatty acids percentage.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Volcano plot displaying DEGs within two different comparison groups.
Note: the y-axis shows the mean expression value of log10(q-value), and the x-axis displays the log2fold change value. The blue dots represent the transcripts did not reach statistical significance (q > 0.05); the red dots represent whose expression levels were significantly different (q < 0.05).
Fig 2
Fig 2. Correlations of mRNA expression level of 10 randomly DEGs between high and low polyunsaturated fatty acids percentage using RNA-Seq and qRT-PCR.
Note: the x- and y-axis correspond to the log2 (ratio of FAH/FAL) measured by RNA-Seq and qRT-PCR, respectively.
See this image and copyright information in PMC

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