Research Article: Integrative analysis of long noncoding RNA and mRNA reveals candidate lncRNAs responsible for meat quality at different physiological stages in Gushi chicken

Date Published: April 9, 2019

Publisher: Public Library of Science

Author(s): Donghua Li, Fang Li, Keren Jiang, Meng Zhang, Ruili Han, Ruirui Jiang, Zhuanjian Li, Yadong Tian, Fengbin Yan, Xiangtao Kang, Guirong Sun, Juan J. Loor.

http://doi.org/10.1371/journal.pone.0215006

Abstract

Long noncoding RNAs (lncRNAs) play important roles in transcriptional and posttranscriptional regulation. However, the effects of lncRNAs on the meat quality of chicken hasn’t been elucidated clearly yet. Gushi chickens are popular in China because of their superior meat quality, particularly the tender flesh, and unique flavor. Gushi chickens are popular in China because of their superior meat quality, delicate flesh, and unique flavor. We performed RNA-Seq analysis of breast muscle from Gushi chicken at two physiological stages, including juvenile (G20W) and laying (G55W). In total, 186 lncRNAs and 881 mRNAs were differentially expressed between G20W and G55W (fold change ≥ 2.0, P < 0.05). Among them, 131 lncRNAs presented upregulated and 55 were downregulated. We identified the cis and trans target genes of the differentially expressed lncRNAs, and constructed lncRNA-mRNA interaction networks. The results showed that differentially expressed mRNAs and lncRNAs were mainly involved in ECM-receptor interaction, glycerophospholipid metabolism, ubiquitin-mediated proteolysis, and the biosynthesis of amino acids. In summary, our study utilized RNA-seq analysis to predict the functions of lncRNA on chicken meat quality. Furthermore, comprehensive analysis identified lncRNAs and their target genes, which may contribute to a better understanding of the molecular mechanisms underlying in poultry meat quality and provide a theoretical basis for further research.

Partial Text

Along with the improvement in life quality in modern society, more and more consumers paid attention to the food safety and food quality, such as the meat quality, which includes color, flavor, juiciness, fat content and tenderness. The market demands guided the direction of breeding program in poultry industry, which has made a conversion to balance the growth rate and meat quality to some extent. Meat quality is significantly affected by a series of complex factors, including breed, age, genetics, nutrition and feeding environment [1–5]. The Gushi chicken was an eminent representative with high meat quality of indigenous chicken breeds, which origins from the Gushi county of Henan province in China. The high meat quality performs in many facets. For example, high intramuscular fat (IMF) content, low shear force (SF), low drip loss, low pH decreasing, nice color and flavor. In our previous study, the laying-stage Gushi hens (55 weeks, G55W) exhibited higher serum lipid levels, IMF deposition capacity, water holding capacity (WHC), SF, intermuscular fat width (IFW) and unsaturated fatty acid (UFA) levels than the juvenile Gushi hens (20 weeks, G20W) showed, while G20W showed higher drip losses and muscle tenderness. Global DNA methylation profiles indicated that G55W exhibited higher global DNA methylation levels than G20W [2]. But phenotypic characteristics of meat quality are not only controlled by coding genes but also by noncoding genes at transcriptional regulatory level. Although many studies have investigated meat quality differences among different breeds at the mRNA level [6–8], little has been demonstrated between the different physiological stages from the same breed.

Meat quality traits are comprehensive economic characteristics controlled by polygenic traits, which are easily affected by many factors, such as castration, gender, age, and species. Species, as a major genetic factor, plays the leading role in defining the characteristics of meat quality. IMF is one of the important factors influencing meat quality and is mainly distributed in muscle and muscle fibers. IMF contains many phospholipids, and phospholipids containing large amounts of polyunsaturated fatty acids can be produced via lipid degradation reactions. IMF deposition can loosen muscle fibers, fat and connective tissue in the overlapping structure, thereby decreasing physical strength and promoting the separation of muscle fiber bundles, which especially improves the tenderness of meat [41, 42].

In conclusion, we first generated the expression profiles of lncRNAs in breast tissue from two developmental stages of Gushi chicken (G20W and G55W) based on RNA-Seq. Our results suggest that those lncRNAs might play important roles in meat quality. Overall, this study takes the first step toward understanding the molecular mechanisms underlying variations in poultry meat quality and helps to provide a theoretical basis for further research. However, the regulatory mechanisms of lncRNAs require further verification.

 

Source:

http://doi.org/10.1371/journal.pone.0215006

 

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