Abstract
BackgroundThe Chinese Chenghua pig (CHP) is a typical Chinese domestic fatty pig breed with superior meat quality characteristics, while the Yorkshire pig (YP) has the characteristics of fast growth and a high rate of lean meat. Long term natural selection and artificial selection resulted in great phenotypic differences between the two breeds, including growth, development, production performance, meat quality, and coat color. However, genome-wide DNA methylation differences between CHP and YP remain unclear.ResultsDNA methylation data were generated for muscle tissues of CHP and YP using reduced representation bisulfite sequencing (RRBS). In this study, a total of 2,416,211 CpG sites were identified. Besides, the genome-wide DNA methylation analysis revealed 722 differentially methylated regions (DMRs) and 466 differentially methylated genes (DMGs) in pairwise CHP vs. YP comparison. Six key genomic regions (Sus scrofa chromosome (SSC)1:253.47–274.23 Mb, SSC6:148.71–169.49 Mb, SSC7:0.25–9.86 Mb, SSC12:43.06–61.49 Mb, SSC14:126.43–140.95 Mb, and SSC18:49.17–54.54 Mb) containing multiple DMRs were identified, and differences of methylation patterns in these regions may be related to phenotypic differences between CHP and YP. Based on the functional analysis of DMGs, 8 DMGs (ADCY1, AGBL4, EXOC2, FUBP3, PAPPA2, PIK3R1, MGMT and MYH8) were considered as important candidate genes associated with muscle development and meat quality traits in pigs.ConclusionsThis study explored the difference in meat quality between CHP and YP from the epigenetic point of view, which has important reference significance for the local pork industry and pork food processing.
Highlights
The Chinese Chenghua pig (CHP) is a typical Chinese domestic fatty pig breed with superior meat quality characteristics, while the Yorkshire pig (YP) has the characteristics of fast growth and a high rate of lean meat
We identified the differentially methylation regions (DMRs) and differentially methylation genes (DMGs) of CHP and YP to determine some of the important genomic regions and key genes associated with these phenotypic differences and providing new insights into the epigenetic mechanisms underlying the differences between the two pig breeds
According to the functions of differentially methylated genes (DMGs), we identified 8 DMGs (ADCY1, AGBL4, EXOC2, FUBP3, pregnancyassociated plasma protein A2 (PAPPA2), PIK3R1, MGMT, and MYH8) which were possibly related to the difference in appearance, meat quality, disease resistance, reproductive capacity, and adaptability between CHP and YP (Table 5)
Summary
The Chinese Chenghua pig (CHP) is a typical Chinese domestic fatty pig breed with superior meat quality characteristics, while the Yorkshire pig (YP) has the characteristics of fast growth and a high rate of lean meat. Long term natural selection and artificial selection resulted in great phenotypic differences between the two breeds, including growth, development, production performance, meat quality, and coat color. Genomewide DNA methylation differences between CHP and YP remain unclear. Epigenetic modifications of the genome can have both short-term and long-term effects on gene expression in different environments [1]. DNA methylation was the first discovered epigenetic modification and one of the most thoroughly studied [2]. DNA methylation is critical for mammalian growth and development [4]. DNA methylation is traditionally regarded as a heritable and stable silence marker, which is essential for X-inactivation [5], silencing of genomic elements such as transposons [6], and genetic imprinting [7]. The role of DNA methylation dynamics on skeletal muscle development and disease has been reported [8]
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