Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Jun 25;13(13):2008.
doi: 10.3390/foods13132008.

RNA-Seq Reveals Pathways Responsible for Meat Quality Characteristic Differences between Two Yunnan Indigenous Chicken Breeds and Commercial Broilers

Yong Liu  1   2   3 , Xia Zhang  2   4 , Kun Wang  2 , Qihua Li  2 , Shixiong Yan  1   2 , Hongmei Shi  1   2 , Lixian Liu  2   5 , Shuangmin Liang  6 , Min Yang  2 , Zhengchang Su  7 , Changrong Ge  2 , Junjing Jia  2 , Zhiqiang Xu  6 , Tengfei Dou  2
Affiliations

RNA-Seq Reveals Pathways Responsible for Meat Quality Characteristic Differences between Two Yunnan Indigenous Chicken Breeds and Commercial Broilers

Yong Liu et al. Foods. .

Abstract

Poultry is a source of meat that is in great demand in the world. The quality of meat is an imperative point for shoppers. To explore the genes controlling meat quality characteristics, the growth and meat quality traits and muscle transcriptome of two indigenous Yunnan chicken breeds, Wuding chickens (WDs) and Daweishan mini chickens (MCs), were compared with Cobb broilers (CBs). The growth and meat quality characteristics of these two indigenous breeds were found to differ from CB. In particular, the crude fat (CF), inosine monophosphate content, amino acid (AA), and total fatty acid (TFA) content of WDs were significantly higher than those of CBs and MCs. In addition, it was found that MC pectoralis had 420 differentially expressed genes (DEGs) relative to CBs, and WDs had 217 DEGs relative to CBs. Among them, 105 DEGs were shared. The results of 10 selected genes were also confirmed by qPCR. The differentially expressed genes were six enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways including lysosomes, phagosomes, PPAR signaling pathways, cell adhesion molecules, cytokine-cytokine receptor interaction, and phagosome sphingolipid metabolism. Interestingly, four genes (LPL, GK, SCD, and FABP7) in the PPAR signal pathway related to fatty acid (FA) metabolism were elevated in WD muscles, which may account for higher CF, inosine monophosphate content, and AA and FA contents, key factors affecting meat quality. This work laid the foundation for improving the meat quality of Yunnan indigenous chickens, especially WD. In future molecular breeding, the genes in this study can be used as molecular screening markers and applied to the molecular breeding of chicken quality characteristics.

Keywords: RNA-Seq; chicken; differentially expressed genes; fat metabolism; meat quality characteristics.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Growth performance of three chicken breeds. (A) Body weight. (B) Daily body weight gain. (C) Feed intake. (D) Feed/Body weight gain (feed conversion efficiency, FCE). Statistically significant differences in different breeds at the same age are indicated by * (*: p < 0.05; **: p < 0.01). Statistically significant different ages within a breed are indicated with letters (lower case letter: p < 0.05; upper case letters: p < 0.01).
Figure 2
Figure 2
Development in skeletal muscle of three chicken breeds. (A) Comparison of breast muscle weight. (B) Comparison of breast muscle rate. (C) Comparison of leg muscle weight. (D) Comparison of leg muscle rate. *: p < 0.05; **: p < 0.01.
Figure 3
Figure 3
Histological stain of breast muscle fibers of the three chicken breeds. (A) Histology of breast muscle fibers at 84 d; H&E stain (10 × 20). (B) Comparison of histological characteristics of breast muscle fiber. **: p < 0.01.
Figure 4
Figure 4
Histological stain of leg muscle fibers of the three chicken breeds. (A) Histology of leg muscle fibers in 84 d; H&E stain (10 × 20). (B) Comparison of histological characteristics of leg muscle fiber. **: p < 0.01.
Figure 5
Figure 5
Analysis of DEGs. (A) Venn plot of DEGs in MC vs. CB and WD vs. CB groups. Green indicates MC vs. CB. Red indicates WD vs. CB. (B) KEGG analysis bubble chart. The x-axis represents rich factor (rich factor = number of DEGs enriched in the pathway/number of all genes in the background gene set). The y-axis represents the enriched pathway. Color represents enrichment significance, and the size of the bubble represents the number of DEGs enriched in the pathway. (C) Heat-map cluster of DEGs in MC vs. CB and WD vs. CB.
Figure 6
Figure 6
PPI network related to growth performance and meat quality.
Figure 7
Figure 7
Relative expression levels of 10 genes in three breeds of chicken. *: p < 0.05. (A) Relative expression of GH. (B) Relative expression of PAX5. (C) Relative expression of CDH2. (D) Relative expression of ANGPTL4. (E) Relative expression of IGLL1. (F) Relative expression of PLIN1. (G) Relative expression of LPL. (H) Relative expression of GK. (I) Relative expression of SCD. (J) Relative expression of FABP7.
Figure 8
Figure 8
The potential regulatory network of lipid metabolism according to the DEGs enriched in the KEGG pathways.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Wang T., Zhang Y., Guo Y., Zhang X., Yang H., Tian X., Zhu M., Guo Z., Zeng S., Luo K., et al. RNA-sequence reveals differentially expressed genes affecting the crested trait of Wumeng crested chicken. Poult. Sci. 2021;100:101357. doi: 10.1016/j.psj.2021.101357. - DOI - PMC - PubMed
    1. Piórkowska K., Żukowski K., Nowak J., Połtowicz K., Ropka-Molik K., Gurgul A. Genome-wide RNA-Seq analysis of breast muscles of two broiler chicken groups differing in shear force. Anim. Genet. 2016;47:68–80. doi: 10.1111/age.12388. - DOI - PubMed
    1. Dou T., Li Z., Wang K., Liu L., Rong H., Xu Z., Huang Y., Gu D., Chen X., Hu W., et al. Regulation of myostatin expression is associated with growth and muscle development in commercial broiler and DMC muscle. Mol. Biol. Rep. 2018;45:511–522. - PMC - PubMed
    1. Dou T., Zhao S., Rong H., Gu D., Li Q., Huang Y., Xu Z., Chu X., Tao L., Liu L., et al. Biological mechanisms discriminating growth rate and adult body weight phenotypes in two Chinese indigenous chicken breeds. BMC Genom. 2017;18:469 - PMC - PubMed
    1. Ozsolak F., Milos P.M. RNA sequencing: Advances, challenges and opportunities. Nat. Rev. Genet. 2011;12:87–98. doi: 10.1038/nrg2934. - DOI - PMC - PubMed

LinkOut - more resources