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

PLOS ONE, Nov 2019

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

April RNA-Seq reveals differentially expressed genes affecting polyunsaturated fatty acids percentage in the Huangshan Black chicken population Shaohua Yang 0 2 3 4 Ying Wang 0 2 3 4 Lulu Wang 0 2 3 4 Zhaoyuan Shi 0 2 3 4 Xiaoqian Ou 0 2 3 4 Dan Wu 0 2 3 4 Xinmiao Zhang 0 2 3 4 Hao Hu 0 2 3 4 Jia Yuan 0 2 3 4 Wei Wang 0 1 2 4 Fuhu Cao 0 2 3 4 Guoqing Liu 0 2 3 4 0 demonstrated that FADS2 , DCN, FRZB, OGN, PRKAG3, LHFP, CHCHD10, CYTL1 1 Agricultural Products Quality and Safety Supervision and Management Bureau , Xuancheng, Anhui , P. R. China 2 University-Research in Hefei University of Technology XC2016JZBZ03 Dr Shaohua Yang; Fundamental Research Funds for the Central Universities JZ2017HGTA0228 Dr Shaohua Yang; the innovation Project for College Students 3 College of Food Science and Engineering, Hefei University of Technology , Hefei, Anhui , P. R. China 4 Editor: Marinus F.W. te Pas, Wageningen UR Livestock Research , NETHERLANDS 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) FBLN5, and ADGRD1 are the most promising candidate genes affecting polyunsaturated fatty acids percentage. Introduction During recent decades, the breeding of meat type poultry focused on increasing growth performance and improving breast and thigh meat yields. Although the impressive progress made in these meat quality traits, there were some poor performances, such as excessive deposition of abdominal fat, deterioration of taste quality, and decreased sensory acceptability for 2017CXCYS235 Dr Shaohua Yang; Wanjiang Institute of Poultry Technology XC2015AKKG002 Dr Shaohua Yang; the Science and Technology Bureau of AnHui XC2015XKKJ02, XC2015AKKG003 Dr Shaohua Yang. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. consumers. As an indigenous breed in China, the Huangshan Black Chicken has a distinct appearance and quality in meat and egg products. Compared with the Arbor Acres (AA) broiler, the Huangshan Black Chicken is highly popular in China because of its polyunsaturated fatty acids concentration. Therefore, the elucidation of the precise molecular mechanisms underlying fatty acids traits in Huangshan Black chickens will have both economic and biological consequences. In the past several decades, candidate gene analysis, quantitative trait locus (QTL) mapping, and genome-wide association studies (GWASs) have been the main approaches to identify genes or causal mutations for meat quality traits in chickens. A large number of promising genetic associations and genomic regions have been successfully identified. As of December 21, 2017, 8,363 QTLs for 383different traits have been reported in 277 papers in chickens (http://www.animalgenome.org/cgi-bin/QTLdb/GG/index). Of these, 339 QTLs for abdominal fat traits and 144 for breast muscle traits have been detected in the chicken chromosomal regions. Moreover, GWASs can be used to identify the genes and variants underlying important traits more precisely [1±2]. In chickens, GWASs have already been performed for egg production and quality [ 3 ], growth [4±5], meat quality [6±7] and disease resistance traits [8±9]. Although these techniques have contributed significantly to our better understanding of mechanisms underlying meat quality traits [ 6,7 ], several potential limitations still exist. One major limitation is the fine mapping required to identify causative variants. Additionally, some novel genes or biological pathways associated with the target trait may be excluded unintentionally. In recent years, next generation sequencing (NGS) technologies are increasingly being used for identifying differential expression as well as opportunities to explore novel transcripts [ 10 ]. Of these, RNA-Seq has been widely utilized t (...truncated)


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Shaohua Yang, Ying Wang, Lulu Wang, Zhaoyuan Shi, Xiaoqian Ou, Dan Wu, Xinmiao Zhang, Hao Hu, Jia Yuan, Wei Wang, Fuhu Cao, Guoqing Liu. RNA-Seq reveals differentially expressed genes affecting polyunsaturated fatty acids percentage in the Huangshan Black chicken population, PLOS ONE, 2018, Volume 13, Issue 4, DOI: 10.1371/journal.pone.0195132