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DOI: https://doi.org/10.5713/ajas.20.0317    [Accepted] Published online October 13, 2020.
Genome-wide identification and analysis of long noncoding RNAs in longissimus muscle tissue from Kazakh cattle and Xinjiang brown cattle
Xiang-Min Yan1,2  , Zhe Zhang1,3  , Jian-Bo Liu1  , Na Li2  , Guang-Wei Yang4  , Dan Luo1  , Yang Zhang2  , Bao Yuan1  , Hao Jiang1,*  , Jia-Bao Zhang1,* 
1College of Animal Sciences, Jilin University, Changchun (130012), Jilin, China
2Institute of Animal Husbandry,Xinjiang Academy of Animal Husbandry, Urumqi (830057), Xinjiang, China
3College of Animal Science and Technology, Northwest A&F University, Yangling, (712100), Shanxi, China
4Yili State Animal Husbandry General Station, Yili (835000), Xinjiang, China
Correspondence:  Hao Jiang,Email: jhhaojiang@jlu.edu.cn
Jia-Bao Zhang, Tel: 86-431-8783-6551, Fax: 86-431-8783-6551, Email: zjb@jlu.edu.cn
Received: 9 May 2020   • Revised: 29 July 2020   • Accepted: 20 September 2020
In recent years, lncRNAs have been identified in many species, and some of them have been shown to play important roles in muscle development and myogenesis. However, the differences in lncRNAs between Kazakh cattle and Xinjiang brown cattle remain undefined; therefore, we aimed to confirm whether lncRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed lncRNAs regulate muscle differentiation.
We used RNA-seq technology to identify lncRNAs in longissimus muscles from these cattle. The expression of lncRNAs were analyzed using StringTie (1.3.1) in terms of the FPKM values of the encoding genes. The differential expression of the transcripts in the two samples were analyzed using the DESeq R software package. The resulting FDR was controlled by the Benjamini and Hochberg’s approach. KOBAS software was utilized to measure the expression of different genes in KEGG pathways. We randomly selected eight lncRNA genes and validated them by RT-qPCR.
We found that 182 lncRNA transcripts, including 102 upregulated and 80 downregulated transcripts, were differentially expressed between Kazakh cattle and Xinjiang brown cattle. The results of RT-qPCR were consistent with the sequencing results. Enrichment analysis and functional annotation of the target genes revealed that the differentially expressed lncRNAs were associated with the MAPK, Ras and PI3k/Akt signaling pathways. We also constructed a lncRNA/mRNA coexpression network for the PI3k/Akt signaling pathway.
Our study provides insights into cattle muscle-associated lncRNAs and will contribute to a more thorough understanding of the molecular mechanism underlying muscle growth and development in cattle.
Keywords: lncRNA; Longissimus Muscle; Kazakh Cattle; Xinjiang Brown Cattle
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