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URL: https://dx.doi.org/DOI:10.17504/protocols.io.mpkc5kw

Authors: Yu Xi, Huijing Liu, Yuqiang Zhao, Ji Li, Wenchao Li, Guorong Liu, Jiayong Lin, Wanghong Liu, Jinlong Zhang, Minggang Lei, Debin Ni

Summary: Tongcheng pigs (TC) and Yorkshire (YK) are two pig breeds with distinguished morphologies in muscle. A comprehensive study of porcine microRNAome (miRNAome) in longissimus muscle during 5 developmental stages (40, 55, 63, 70 and 90 dpc (days post coitum)) using Solexa sequencing technology, was carried out in order to compare miRNA expression involved in the differentiated regulation of skeletal muscle development between the TC and YK breeds. Known miRNAs and novel miRNAs were identified by alignment and annotation. MiRNA expression profiles were normalized by transcript per million (TPM). Principal component analysis (PCA) and hierarchical cluster analysis (HCA) were used to cluster the samples based on the expression values of miRNAs. The short time-series expression miner (STEM) was conducted in order to further explore the temporal expression characteristics of miRNAs in the TC and YK breeds. Then the analysis of differentially expressed (DE) miRNAs was performed. Functional annotation of the predicted miRNA targets was performed based on Gene Ontology slim database (GO-Slim) and Kyoto Encyclopedia of Genes and Genomes database (KEGG). Ssc-miR-499-5p is the only multipoint (no less than 4 time points)-DE miRNA with considerable expression level during the time periods investigated. Combining the target prediction and dual luciferase reporter assay, we validated DSTN was the target gene of ssc-miR-499-5p. The results are expected to facilitate the understanding of the differences of miRNAs in myogenesis between the TC and YK breed and provide implications for the improvement of meat quality in animal production.

Associated Publications: Xi Y, Liu H, Zhao Y, Li J, Li W, Liu G, Lin J, Liu W, Zhang J, Lei M, Ni D (2018) Comparative analyses of longissimus muscle miRNAomes reveal microRNAs associated with differential regulation of muscle fiber development between Tongcheng and Yorkshire pigs. PLoS ONE 13(7): e0200445. doi: 10.1371/journal.pone.0200445

Affiliations: Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education and Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China., Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education and Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China., Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education and Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China., Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education and Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China., Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education and Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China., Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education and Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China., Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education and Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China., Swine breeding quality supervision and inspection center of the Ministry of Agriculture (Wuhan), Huazhong Agricultural University, Wuhan, P.R. China., Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education and Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China., 1.Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education and Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China. 2. Swine breeding quality supervision and inspection center of the Ministry of Agriculture (Wuhan), Huazhong Agricultural University, Wuhan, P.R. China. 3. National Engineering Research Center For Livestock, Huazhong Agricultural University, Wuhan, P.R. China., Swine breeding quality supervision and inspection center of the Ministry of Agriculture (Wuhan), Huazhong Agricultural University, Wuhan, P.R. China.

External URL: https://doi.org/10.1371/journal.pone.0200445

Version: 1

Publication Date: 2018

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