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. 2022 Apr 29;13(5):798.
doi: 10.3390/genes13050798.

Transcriptome Analysis Reveals the Differentially Expressed Genes Associated with Growth in Guangxi Partridge Chickens

Minghui Shao  1 , Kai Shi  1 , Qian Zhao  1 , Ying Duan  1 , Yangyang Shen  1 , Jinjie Tian  1 , Kun He  1 , Dongfeng Li  1 , Minli Yu  1 , Yangqing Lu  2 , Yanfei Tang  3 , Chungang Feng  1
Affiliations

Transcriptome Analysis Reveals the Differentially Expressed Genes Associated with Growth in Guangxi Partridge Chickens

Minghui Shao et al. Genes (Basel). .

Abstract

The Guangxi Partridge chicken is a well-known chicken breed in southern China with good meat quality, which has been bred as a meat breed to satisfy the increased demand of consumers. Compared with line D whose body weight is maintained at the average of the unselected group, the growth rate and weight of the selected chicken group (line S) increased significantly after breeding for four generations. Herein, transcriptome analysis was performed to identify pivotal genes and signal pathways of selective breeding that contributed to potential mechanisms of growth and development under artificial selection pressure. The average body weight of line S chickens was 1.724 kg at 90 d of age, which showed a significant increase at 90 d of age than line D chickens (1.509 kg), although only the internal organ ratios of lung and kidney changed after standardizing by body weight. The myofiber area and myofiber density of thigh muscles were affected by selection to a greater extent than that of breast muscle. We identified 51, 210, 31, 388, and 100 differentially expressed genes (DEGs) in the hypothalamus, pituitary, breast muscle, thigh muscle, and liver between the two lines, respectively. Several key genes were identified in the hypothalamus-pituitary-muscle axis, such as FST, THSB, PTPRJ, CD36, PITX1, PITX2, AMPD1, PRKAB1, PRKAB2, and related genes for muscle development, which were attached to the cytokine-cytokine receptor interaction signaling pathway, the PPAR signaling pathway, and lipid metabolism. However, signaling molecular pathways and the cell community showed that elevated activity in the liver of line S fowl was mainly involved in focal adhesion, ECM-receptor interaction, cell adhesion molecules, and signal transduction. Collectively, muscle development, lipid metabolism, and several signaling pathways played crucial roles in the improving growth performance of Guangxi Partridge chickens under artificial selection for growth rate. These results support further study of the adaptation of birds under selective pressure.

Keywords: Guangxi Partridge chicken; breeding; growth rate; hypothalamus; liver; muscle; pituitary; transcriptome.

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Conflict of interest statement

Y.T. is an employee of Guangxi Fufeng Agricultural and Animal Husbandry Group Co., Ltd. that did not provide financial support to this study. All the other authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
The organ index of six tissues between two different lines. The organ index quantified the ratio of organ weight to total body weight. Values are shown as mean ± SD (n = 10 individuals per group). * represents p < 0.05.
Figure 2
Figure 2
Comparison of muscle fiber morphology and myofiber characteristics between the two lines. Myofiber morphology observation of breast muscle (a) and thigh muscle (b) tissue section. There are two images for each chicken line of different muscle tissue. Scale bar, 100 µm. Muscle fiber area (c) and muscle fiber density (d) of breast muscle. Muscle fiber area (e) and muscle fiber density (f) of thigh muscle. Values are shown as mean ± SD (n = 3 per group). * represents p < 0.05.
Figure 3
Figure 3
The results of differential expression analysis in each tissue between line S and line D. (a) The overview of the number of differentially expressed genes (DEGs) in each tissue. The volcano plots show differentially expressed genes in the hypothalamus (b), pituitary (c), breast muscle (d), thigh muscle (e), and liver (f). Red dots indicate up-regulated genes in line S, dark blue dots indicate down-regulated genes in line S, and the light blue dots indicate no significant changes in gene expression. Significant DEGs were identified by filtering the p-value < 0.05 and |log2 (Fold Change)| > 1. Hy, Hypothalamus; Pi, Pituitary; Bm, Breast muscle; Tm, Thigh muscle; and Li, Liver.
Figure 4
Figure 4
The scatter plot of GO functional enrichment. The enriched GO terms of DEGs in the hypothalamus (a), pituitary (b), thigh muscle (c), and liver (d).
Figure 5
Figure 5
The scatter plot of KEGG pathway analysis. The enriched KEGG pathway of DEGs in the hypothalamus (a), pituitary (b), thigh muscle (c), and liver (d).
Figure 6
Figure 6
The protein-protein interaction network based on the DEGs between line S and line D. The protein-protein interaction network of DEGs in pituitary (a), breast muscle (b), thigh muscle (c), and liver (d) were analyzed and visualized by String and Cytoscape. The darker dots in the center indicate higher levels of gene interaction degree.
Figure 7
Figure 7
Validation of the RNA sequencing analysis data by quantitative real-time PCR (qRT-PCR) analysis. (a) The expression levels of differentially expressed genes were determined by qRT-PCR and RNA-Seq. Log2(FoldChange) < 0 represents down-regulated expression in line S and log2(FoldChange) > 0 represents up-regulated expression in line S. (b) The correlation analysis of gene expression between RNA-seq and qRT-PCR.
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Grants and funding

This work was funded by the National Key R&D Program of China (Grant No. 2021YFD1300100), the Guangxi Key R&D Program (No. AB21220005), and the Revitalization Program of Biological Breeding of Jiangsu Province (No. JBGS[2021]109).

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