Integrated Analysis of Methylome, Transcriptome and miRNAome of Three Pig Breeds

Abstract

Aim: Integrated analysis of methylome and transcriptome may help understand the molecular basis of the different breeds with different traits of commercial interest. Materials & methods: We obtained the first genome-wide methylome with single-base resolution, miRNAome and transcriptome from three swine breeds. Results: We displayed the landscape of the three omics in the whole-genome level. Integrated outcomes of methylome with genetic selection, miRNAome and transcriptome are also provided. Finally, we identified 11 candidate differentially methylated genes associated with phenotype variance in pigs. Conclusion: DNA methylation not only suppresses transcriptome but also miRNAome. The different -omics data have complicated interaction in directly or indirectly and exhibited close relations with the distinct phenotypic traits of growth, disease resistance and energy metabolism.

Keywords::

• important economic trait
• methylome
• transcriptome

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at:

www.tandfonline.com/doi/full/10.2217/epi-2017-0087

Authors’ contributions

CC Li contributed in conceptualization. YH Fu, C Zou, LY Shen and MZ Li contributed in methodology. YH Fu looked after software. JX Li, QZ Tang and YH Fu looked after validation. YH Fu and QZ Tang looked after formal analysis. JX Li, CC Li, LJ and YH Fu looked after investigation. CC Li, YH Fu and JX Li looked after resources. YH Fu and CC Li looked after data curation. Writing – original draft preparation was done by YH Fu. YH Fu and CC Li looked after writing review & editing. YH Fu looked after visualization. CC Li, MZ Li and SH Zhao looked after supervision. CC Li and SH Zhao looked after project administration. CC Li looked after funding acquisition.

Financial & competing interests disclosure

The work was supported by National Natural Science Foundation of China (NSFC, 31472076, 31402046), the National Basic Research Program of China (973 Program, 2013CB835205), the Science Fund for Distinguished Young Scholars of Hubei Province of China (2014CFA024), the Research Project of Chinese Ministry of Education (113048A) and the Fundamental Research Funds for the Central Universities (2662017PY030). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

Animals care and all the experimentation in this study were carried out in accordance with the preapproved guidelines from Regulation Proclamation No.5 of the Standing Committee of Hubei People’s Congress, and all experimental procedures and sample collection methods were approved by the Institutional Animal Care and Use Committee of Huazhong Agricultural University, Wuhan, China (permit HZAUSW2015-0003).

Accessions codes

The genome sequencing reads have been deposited into the NCBI the Gene Expression Omnibus (GEO) under the accession GSE90901 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90901), GSE92433 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92433) and GSE92417 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92417).

Additional information

Funding

The work was supported by National Natural Science Foundation of China (NSFC, 31472076, 31402046), the National Basic Research Program of China (973 Program, 2013CB835205), the Science Fund for Distinguished Young Scholars of Hubei Province of China (2014CFA024), the Research Project of Chinese Ministry of Education (113048A) and the Fundamental Research Funds for the Central Universities (2662017PY030). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.