Differential DNA methylation analysis reveals key genes in Chinese Qingyu and Landrace pigs
Abstract
The Chinese Qingyu pig is a typical domestic fatty pig breed and an invaluable indigenous genetic resource in China. Compared with the Landrace pig, the Qingyu pig has unique meat characteristics, including muscle development, intramuscular fat, and other meat quality traits. At present, few studies have explored epigenetic differences due to DNA methylation between the Qingyu pig and the Landrace pig. In this study, 30 Qingyu pigs and 31 Landrace pigs were subjected to reduced representation bisulfite sequencing (RRBS). Genome-wide differential DNA methylation analysis was conducted. Six genomic regions, including regions on Sus scrofa chromosome (SSC) 1: 266.09–274.23 Mb, SSC5: 0.88–10.68 Mb, SSC8: 41.23–48.51 Mb, SSC12: 45.43–54.38 Mb, SSC13: 202.15–207.95 Mb, and SSC14: 126.43–139.85 Mb, were regarded as key regions that may be associated with phenotypic differences between the Qingyu pig and the Landrace pig. Furthermore, according to further analysis, five differentially methylated genes (ADCY1, FUBP3, GRIN2B, KIT, and PIK3R6) were identified as key candidate genes that might be associated with meat characteristics. Our findings provide new insights into the differences in DNA methylation between the Qingyu pig and the Landrace pig. These results enrich the epigenetic research of the Chinese Qingyu pig.
Résumé
La race porcine chinoise Qingyu est une race domestique typique à forte teneur en gras et constitue une précieuse ressource génétique indigène en Chine. Comparé au porc Landrace, le Qingyu présente des caractéristiques uniques au niveau de sa viande, dont le développement du muscle, le gras intramusculaire et d’autres aspects de la qualité de la viande. À ce jour, peu d’études ont exploré les différences épigénétiques due à la méthylation de l’ADN entre les races Qingyu et Landrace. Dans ce travail, 30 porcs Qingyu et 31 porcs Landrace ont été examinés au moyen de séquençage au bisulfite d’une représentation réduite du génome (RRBS). Une analyse pangénomique de la méthylation différentielle a été réalisée. Six régions du génome du Sus scrofa (SSC1 : 266.09–274.23 Mb, SSC5 : 0.88–10.68 Mb, SSC8 : 41.23–48.51 Mb, SSC12 : 45.43–54.38 Mb, SSC13 : 202.15–207.95 Mb et SSC14 : 126.43–139.85 Mb) ont été trouvées comme étant des régions clés possiblement associées aux différences phénotypiques entre les races Qingyu et Landrace. De plus, sur la base d’analyses plus approfondies, cinq gènes affichant une méthylation différentielle (ADCY1, FUBP3, GRIN2B, KIT, PIK3R6) sont présentés comme étant des gènes clés associés aux caractéristiques de la viande. Ces résultats apportent un nouvel éclairage sur les différences de méthylation de l’ADN entre les races Qingyu et Landrace. Ces travaux viennent alimenter la recherche épigénétique sur les porcs chinois Qingyu. [Traduit par la Rédaction]
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Genome
Volume 65 • Number 1 • January 2022
Pages: 19 - 26
History
Received: 21 January 2021
Accepted: 30 June 2021
Accepted manuscript online: 9 July 2021
Version of record online: 9 July 2021
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© 2021.
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This study was supported by grants from the Sichuan Science and Technology Program (2020YFN0024, 2021YFYZ0030), the China Agriculture Research System of MOF and MARA (CARS-35-01A), the National Key R&D Program of China (2018YFD0501204), the National Natural Science Foundation of China (C170102), and the Sichuan Innovation Team of Pig (sccxtd-2021-08).
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Kai Wang, Pingxian Wu, Shujie Wang, Xiang Ji, Dong Chen, Weihang Xiao, Yiren Gu, Yangshuang Zeng, Xu Xu, and Guoqing Tang. 2022. Differential DNA methylation analysis reveals key genes in Chinese Qingyu and Landrace pigs. Genome.
65(1): 19-26. https://doi.org/10.1139/gen-2021-0006
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