RNA-Seq Reveals Differentially Expressed Genes and Pathways Affecting Intramuscular Fat Metabolism in Huangshan Black Chicken Population

S H Yang,C S He,C H Li,G Q Liu

doi:10.5539/jas.v12n3p117

S H Yang, C S He + Show 2 more

Open Access

https://doi.org/10.5539/jas.v12n3p117

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Abstract

Intramuscular fat (IMF) plays an important role in meat quality due to its positive correlation with juiciness, tenderness, and flavor. However, for chickens, the molecular mechanisms underlying IMF deposition in thigh muscle have not yet been determined. Here, to identify candidate genes and signaling pathways related to IMF deposition, we deeply explored the chicken transcriptome from thigh muscles of Huangshan Black Chickens with extremely high and low phenotypic values for intramuscular fat content. A total of 128 genes differentially expressed genes (DEGs) were detected, of which 94 were up-regulated and 34 were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed these DEGs (including FABP4, G0S2, PLIN1, SCD1, LFABP, SLC1A6, SLC45A3, ACSBG1, LY86, ST8SIA5, SNAI2, HPGD, EDN2, and THRSP) were significantly enriched in lipid biosynthetic process, steroid biosynthetic and metabolic process, fatty acid metabolic process, and regulation of unsaturated fatty acid metabolic pathways. Additionally, we concluded an interaction network related to lipid metabolism, which might be contributed to the IMF deposition in chicken. Overall, we proposed some new candidate genes and interaction networks that can be associated with IMF deposition and used as biomarkers in meat quality improvement.

Highlights

During the past decades, the breeding of meat type poultry has been predominantly focused on increasing growth rate and yields of breast and thigh meat
We proposed some new candidate genes and a gene network that can be related to intramuscular fat (IMF) deposition by conducting integrated analysis
Of these, according to the value of the IMF content, the pooled RNA of sample 1-3 and sample 4-6 were selected as IMFL1 and IMFL2 while sample 7-9 and sample 10-12 as IMFH1 and IMFH2 to explore the chicken transcriptome by paired-end RNA sequencing

Summary

Introduction

The breeding of meat type poultry has been predominantly focused on increasing growth rate and yields of breast and thigh meat. The impressive progress made in these meat quality traits, there were some poor performances, such as larger fiber diameters, lower intramuscular fat, and higher proportion glycolytic fibers, which seriously decreased sensory acceptability for consumers (Du et al, 2010). It is an ongoing challenge to maintain growth rate improve meat quality. As a main determinant of meat quality, the deposition of intramuscular fat (IMF) plays an important role in flavor of meat and can dramatically promote tenderness of meat. Previous studies have discovered some important quantitative trait loci (QTL) associated with chicken IMF, which are mainly located on chromosomes 1, 2, 5, 23 (Zhao et al, 2007; Sarsenbek et al, 2013; Zhang et al, 2015). The metabolic pathways underlying IMF deposition is very complicated, the molecular mechanisms affecting IMF remains poorly understood

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