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
. 2022 Nov 15;11(22):3654.
doi: 10.3390/foods11223654.

Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig

Xin Liu  1 , Weilong Tian  1   2 , Ligang Wang  1 , Longchao Zhang  1 , Jing Liang  2 , Lixian Wang  1
Affiliations

Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig

Xin Liu et al. Foods. .

Abstract

Pigs' backfat quality has an important impact on the quality of pork and pork products and has a strong relationship with nutrition and sensory characteristics. This study aimed to identify the related candidate genes of backfat quality and to preliminary clarify the molecular regulatory mechanism underlying pig backfat quality phenotypes. Expression assessments of long non-coding RNA (lncRNA) and mRNA profiling in backfat from high-quality (firm and white) and low-quality (soft and yellow) Beijing Black pigs were performed by RNA sequencing. Significantly different expressions were observed in 610 protein-coding genes and 290 lncRNAs between the two groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway annotation showed that some candidate differentially expressed genes that participate in lipid-related pathways and pigmentation terms may play a role in backfat quality in pigs. The cis-target and trans-target genes were predicted to explore the regulatory function of lncRNAs, and integrative analyses of different expression lncRNAs targets and different expression genes were performed. The results showed the regulatory networks of lncRNA-mRNA related to backfat quality, and our study obtained strong candidate genes for backfat quality: ELOVL5, SCD, DGAT2, SLC24A5, and TYRP1, which were involved in fat metabolism, adipogenesis regulation, and pigmentation. To our knowledge, this study is the first to demonstrate the molecular genetic mechanisms of backfat quality in pigs, and these findings improve the current understanding of backfat quality mechanisms and provide a foundation for further studies.

Keywords: backfat quality; candidate genes; lncRNAs; mRNAs; pigs.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Genomic characteristics of mRNAs and lncRNAs in pig backfat (A) Length distribution of annotated mRNAs, annotated lncRNAs, novel mRNAs, and novel lncRNAs; (B) FPKM value of mRNAs and lncRNAs; (C) Exon number distribution of annotated mRNAs, annotated lncRNAs, novel mRNAs and novel lncRNAs; (D) ORF length distribution of annotated mRNAs, annotated lncRNAs, novel mRNAs and novel lncRNAs.
Figure 2
Figure 2
Expression profiles of distinct RNAs in backfat. (A) Volcano plots of DEGs; (B) Volcano plots of DELs; (C) Heatmap of DEGs; (D) Heatmap of DELs.
Figure 3
Figure 3
Functional enrichment analyses of DEGs: (A) GO enrichment annotation of DEGs; (B) Significant GO-BP terms related to pigmentation; (C) KEGG enrichment annotation of DEGs; (D) The interaction network between lipid-related mRNAs-pathway.
Figure 4
Figure 4
Functional enrichment analyses of DELs: (A) KEGG pathways enrichment annotation of CTGs; (B) KEGG pathways enrichment annotation of GTGs; (C) Significant GO-BP terms related to pigmentation; (D) The interaction network between DELs-CTGs-pathway; (E) The interaction network between DELs-TTGs-pathway.
Figure 5
Figure 5
Expression regulation network constructed by differentially expressed mRNA-lnRNA.
Figure 6
Figure 6
Validation of differentially expressed genes and lncRNAs using qPCR.
See this image and copyright information in PMC

References

    1. Kucha C.T., Liu L., Ngadi M.O. Non-Destructive Spectroscopic Techniques and Multivariate Analysis for Assessment of Fat Quality in Pork and Pork Products: A Review. Sensors. 2018;18:377. doi: 10.3390/s18020377. - DOI - PMC - PubMed
    1. Hugo A., Roodt E. Significance of porcine fat quality in meat technology: A review. Food Rev. Int. 2007;23(2):175–198. doi: 10.1080/87559120701225037. - DOI
    1. Hallenstvedt E., Kjos N.P., Overland M., Thomassen M. Changes in texture, colour and fatty acid composition of male and female pig shoulder fat due to different dietary fat sources. Meat Sci. 2012;90:519–527. doi: 10.1016/j.meatsci.2011.08.009. - DOI - PubMed
    1. Wood J.D. Fat Deposition and the Quality of Fat Tissue in Meat Animals. In: Wiseman J., editor. Fats in Animal Nutrition. Butterworths; London, UK: 1984. pp. 407–435.
    1. Seman D.L., Barron W.N.G., Matzinger M. Evaluating the ability to measure pork fat quality for the production of commercial bacon. Meat Sci. 2013;94:262–266. doi: 10.1016/j.meatsci.2013.01.009. - DOI - PubMed

LinkOut - more resources