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. 2022 Oct 31;17(10):e0276004.
doi: 10.1371/journal.pone.0276004. eCollection 2022.

Integrated analysis of lncRNA and gene expression in longissimus dorsi muscle at two developmental stages of Hainan black goats

Lihong Gu  1   2 , Qijie He  3 , Wanliang Xia  1 , Guang Rong  1 , Dingfa Wang  1 , Mao Li  1 , Fengjie Ji  1 , Weiping Sun  1 , Ting Cao  1 , Hanlin Zhou  1 , Tieshan Xu  1
Affiliations

Integrated analysis of lncRNA and gene expression in longissimus dorsi muscle at two developmental stages of Hainan black goats

Lihong Gu et al. PLoS One. .

Abstract

It is deemed that meat quality of kids' is better than that of adults' for Hainan black goat. Generally, meat quality is affected by many indicators, such as intramuscular fat (IMF) content, muscle fiber diameter and shear force. It is indicated that long non-coding RNAs (lncRNAs) play essential roles in meat quality of goats. However, it is unclear whether and how lncRNAs and genes play their roles in meat quality of Hainan Black goats. Here, we firstly compared the meat quality between two-month-old kids (kids) and adult goats (adults). Then, the lncRNA-seq and RNA-seq data were integrated and analyzed to explore the potential functions of lncRNAs and genes. The results showed that adults' IMF content and muscle fiber diameter were extremely significantly higher than that of kids (P<0.01). For the sequenced data, average 84,970,398, and 83,691,250 clean reads were obtained respectively for Kids and adults, among which ~96% were mapped to the reference genome of goats. Through analyzing, 18,242 goat annotated genes, 1,429 goat annotated lncRNAs and 2,967 novel lncRNAs were obtained. Analysis of differential expression genes (DEGs) and lncRNAs (DELs) showed that 328 DEGs and 98 DELs existed between kids and adults. Furthermore, functional enrichment analysis revealed that a number of DEGs and DELs were mainly associated with IMF. Primarily, DGAT2 expressed higher in adults than that in kids and CPT1A expressed higher in kids than that in adults. Both of them were overlapped by DEGs and targets of DELs, suggesting the two DEGs and the DELs targeted by the two DEGs might be the potential regulators of goat IMF deposition. Taken together, our results provide basic support for further understanding the function and mechanism of lncRNAs and genes in meat quality of Hainan black goats.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Identification and characterization of lncRNAs in longissimus dorsi (LD) muscle of Hainan black goats at two developmental stages.
(A) Length comparison of goat annotated lncRNAs and mRNAs. (B) Exon number comparison of goat annotated lncRNAs and mRNAs. (C) Filtration of the candidate novel lncRNAs indicated by Venn diagrams based on coding potential analysis. (D) Novel lncRNAs exon number distribution. (E) Novel lncRNAs length distribution.
Fig 2
Fig 2. Analysis of differentially expressed (DE) lncRNAs and mRNAs.
(A) DE mRNA count. (B) DE lncRNAs count. (C) Expression levels (FPKM distribution) of DE transcripts (including mRNAs and lncRNAs).
Fig 3
Fig 3. Functional enrichment analysis of targets of differentially expressed lncRNAs (DELs).
(A), (B), and (C) represent GO (Gene Ontology) categories enrichment analysis of target genes for biology process, cellular components, and molecular function, respectively. (D) KEGG pathways of genes targeted by DELs.
Fig 4
Fig 4. Functional enrichment analysis of differentially expressed genes (DEGs).
(A), (B), and (C) represent GO (Gene Ontology) categories enrichment analysis of DEGs for biology process, cellular components, and molecular function, respectively.
Fig 5
Fig 5. Expression profile analysis of DELs related to adipogenesis.
(A) Expression levels of five DELs detected using qRT- PCR. (B) Expression levels of five DELs calculated using FPKM method.
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