Linoleic acid is an essential polyunsaturated fatty acid that cannot be synthesized by humans or animals themselves and can only be obtained externally.  The amount of linoleic acid present has an impact on the quality and flavour of meat and indirectly affects consumer preference.  However, the molecular mechanisms influencing the deposition of linoleic acid in organisms are not clear.  As the molecular mechanisms of linoleic acid deposition are not well understood, to investigate the main effector genes affecting the linoleic acid content, this study aimed to screen for hub genes in slow-type yellow-feathered chickens by transcriptome sequencing (RNA-Seq) and weighted gene coexpression network analysis (WGCNA).  We screened for candidate genes associated with the linoleic acid content in slow-type yellow-feathered broilers.  A total of 399 Tiannong partridge chickens were slaughtered at 126 days of age, fatty acid levels were measured in pectoral muscle, and pectoral muscle tissue was collected for transcriptome sequencing.  Transcriptome sequencing results were combined with phenotypes for WGCNA to screen for candidate genes.  KEGG enrichment analysis was also performed on the genes that were significantly enriched in the modules with the highest correlation.  A total of 13 310 genes were identified after quality control of transcriptomic data from 399 pectoral muscle tissues.  WGCNA was performed, and a total of 26 modules were obtained, eight of which were highly correlated with the linoleic acid content.  Four key genes, namely, MDH2, ATP5B, RPL7A and PDGFRA, were screened according to the criteria |GS|>0.2 and |MM|>0.8.  The functional enrichment results showed that the genes within the target modules were mainly enriched in metabolic pathways.  In this study, a large-sample-size transcriptome analysis revealed that metabolic pathways play an important role in the regulation of the linoleic acid content in Tiannong partridge chickens, and MDH2, ATP5B, RPL7A and PDGFRA were screened as important candidate genes affecting the linoleic acid content.  The results of this study provide a theoretical basis for selecting molecular markers and comprehensively understanding the molecular mechanism affecting the linoleic acid content in muscle, providing an important reference for the breeding of slow-type yellow-feathered broiler chickens.

Indigenous chicken products are increasingly favored by consumers due to their unique meat and egg quality.  However, the relatively poor egg-laying performance largely impacts the economic benefits and hinders sustainable development of the local chicken industry.  Thus, excavating key genes and effective molecular markers associated with egg-laying performance is necessary to improve egg production via genetic selection in indigenous breeds.  In the present study, comparative hypothalamic transcriptome between pre-laying (15 weeks old) and peak-laying (30 weeks old) Lushi blue-shelled-egg (LBS) chicken was performed.  A total of 518 differentially expressed genes (DEGs) were identified.  Among the DEGs, 64 genes were enriched in 10 Gene Ontology (GO) terms associated with reproductive regulation via GO analysis and considered as potential candidate genes regulating egg-laying performance.  Of the 64 genes, 16 showed high connectivity (degree≥12) by protein–protein interaction (PPI) network analysis and were considered as potential core candidate genes (PCCGs).  To further look for key candidate genes from the PCCGs, firstly, the expression patterns of the 16 genes were examined in the hypothalamus of two indigenous breeds (LBS and Gushi (GS) chickens) between the pre-laying and peak-laying stages using quantitative real-time PCR (qRT-PCR).  Eleven out of the 16 genes showed significantly differential expression (P<0.05) with the same changing trends in the two breeds.  Then, correlations between the expression levels of the above 11 genes and egg numbers and reproductive hormone concentrations in serum were investigated in high-yielding and low-yielding GS chickens.  Of the 11 genes, eight showed significant correlations (P<0.05) between their expression levels and egg numbers, and between expression levels and reproductive hormone concentration in serum.  Furthermore, an association study on single nucleotide polymorphisms (SNPs) identified in these eight genes and egg production traits was carried out in 640 GS hens, and a significant association (P<0.05) between the SNPs and egg numbers was confirmed.  In conclusion, the eight genes, including CNR1, AP2M1, NRXN1, ANXA5, PENK, SLC1A2, SNAP25 and TRH, were demonstrated as key genes regulating egg production in indigenous chickens, and the SNPs sites within the genes might be served as markers to provide a guide for indigenous chicken breeding.  These findings provide a novel insight for further understanding the regulatory mechanisms of egg-laying performance and developing molecular markers to improve egg production of indigenous breeds.