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https://doi.org/10.5713/ab.21.0308    [Accepted] Published online October 29, 2021.
Identifying long non-coding RNAs and characterizing their functional roles in swine mammary gland from colostrogenesis to lactogenesis
Lijun Shi1  , Longchao Zhang1  , Ligang Wang1  , Xin Liu1  , Hongmei Gao1  , Xinhua Hou1  , Fuping Zhao1  , Hua Yan1  , Wentao Cai1,*  , Lixian Wang1,* 
Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Correspondence:  Wentao Cai, Tel: +18600565640, Fax: +010-62816065, Email: wtaocai@gmail.com
Lixian Wang,Email: iaswlx@263.net
Received: 6 July 2021   • Revised: 13 August 2021   • Accepted: 11 September 2021
Abstract
Objective
This study was conducted to identify the functional long non-coding RNAs (lncRNAs) for swine lactation by RNA-seq data of mammary gland.
Methods
According to the RNA-seq data of swine mammary gland, we screened lncRNAs, performed differential expression analysis, and confirmed the functional lncRNAs for swine lactation by validation of GWAS (Genome wide association study) signals, functional annotation and weighted gene co-expression network analysis (WGCNA).
Results
We totally identified 286 differentially expressed (DE) lncRNAs in mammary gland at different stages from 14 days prior to (-) parturition to day 1 after (+) parturition, and the expressions of most of lncRNAs were strongly changed from Day -2 to Day +1. Further, the genome wide association study (GWAS) signals of sow milk ability trait were significantly enriched in DE lncRNAs. Functional annotation revealed that these DE lncRNAs were mainly involved in mammary gland and lactation developing, milk composition metabolism and colostrum function. By performing weighted gene co-expression network analysis (WGCNA), we identified 7 out of 12 lncRNA-mRNA modules that were highly associated with the mammary gland at day -14, day -2 and day +1, in which, 35 lncRNAs and 319 mRNAs were involved.

Conclusion

This study suggested that 18 lncRNAs and their 20 target genes were promising candidates for swine parturition and colostrum occurrence processes. Our research provided new insights into lncRNA profiles and their regulating mechanisms from colostrogenesis to lactogenesis in swine.
Keywords: Colostrum; LncRNA; Mammary Gland; Pig; WGCNA
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