Comparative Analyses between Skeletal Muscle miRNAomes from Large White and Min Pigs Revealed MicroRNAs Associated with Postnatal Muscle Hypertrophy

<div><p>The molecular mechanism regulated by microRNAs (miRNAs) that underlies postnatal hypertrophy of skeletal muscle is complex and remains unclear. Here, the miRNAomes of <i>longissimus dorsi</i> muscle collected at five postnatal stages (60, 120, 150, 180, and 210 days after birth) from Large White (commercial breed) and Min pigs (indigenous breed of China) were analyzed by Illumina sequencing. We identified 734 miRNAs comprising 308 annotated miRNAs and 426 novel miRNAs, of which 307 could be considered pig-specific. Comparative analysis between two breeds suggested that 60 and 120 days after birth were important stages for skeletal muscle hypertrophy and intramuscular fat accumulation. A total of 263 miRNAs were significantly differentially expressed between two breeds at one or more developmental stages. In addition, the differentially expressed miRNAs between every two adjacent developmental stages in each breed were determined. Notably, ssc-miR-204 was significantly more highly expressed in Min pig skeletal muscle at all postnatal stages compared with its expression in Large White pig skeletal muscle. Based on gene ontology and KEGG pathway analyses of its predicted target genes, we concluded that ssc-miR-204 may exert an impact on postnatal hypertrophy of skeletal muscle by regulating myoblast proliferation. The results of this study will help in elucidating the mechanism underlying postnatal hypertrophy of skeletal muscle modulated by miRNAs, which could provide valuable information for improvement of pork quality and human myopathy.</p></div

dataset

 Data were collected from two Large White populations with different genetic backgrounds in one Chinese commercial pig company, which were introduced from Canadian and French lines, respectively.  </p

Additional file 1 of Genetic gain and inbreeding from simulation of different genomic mating schemes for pig improvement

Additional file 1: Fig. S1. SNP effects cross the whole genome at the heritability of 0.1. Fig. S2. SNP effects cross the whole genome at the heritability of 0.3. Fig. S3. SNPeffects cross the whole genome at the heritability of 0.5

Pairwise comparisons of differentially expressed (DE) miRNAs in skeletal muscle at different developmental stages.

<p>The comparisons were made for Large White and Min pigs. The numbers marked in the overlapping areas indicate the common DE miRNAs.</p

Expression levels of miR-204 at five postnatal development stages between Large White and Min pigs.

<p>Expression levels of miR-204 at five postnatal development stages between Large White and Min pigs.</p

Cluster analysis of miRNA libraries from skeletal muscle of Large White and Min pigs.

<p>The skeletal muscle was collected at different developmental stages. LW, Large White pig; M, Min pig.</p

Additional file 1: of Genome shuffling of the nonconventional yeast Pichia anomala for improved sugar alcohol production

Fig. S1. The colorimetric assay of sugar alcohols. a The flow chart of the colorimetric method for sugar alcohol screening. b The correlation of the two sugar alcohol-detection methods by linear regression. H and C represent the HPLC and colorimetric methods, respectively. Fig. S2. Comparison of the DNA content among the parent and shuffled strains, as determined by flow cytometry. The DNA content is shown for a haploid control strain S. cerevisiae BY4741, haploid parent strain P. anomala HP, diploid strain P. anomala TIB-x229 and shuffled strains GS2-1, GS2-2 and GS2-3

Differentially expressed miRNAs between every two adjacent developmental stages in Large White and Min pigs.

<p>Differentially expressed miRNAs between every two adjacent developmental stages in Large White and Min pigs.</p

Number of known miRNAs, homologous novel miRNAs, and nonhomologous miRNAs.

<p>Number of known miRNAs, homologous novel miRNAs, and nonhomologous miRNAs.</p

Length distribution of the small RNA sequences.

<p>LW, Large White pig; M, Min pig.</p