Evidence map›Paper›PMID 40394505›Full record

ArticleBMC genomics2025

DNA methylation regulates growth traits by influencing metabolic pathways in Pacific white shrimp (Litopenaeus vannamei).

Xin Zhang, Chaoqun Hu, Ting Chen, Pengying Li, Yehui Tan, Chunhua Ren, Yanhong Wang, Xiao Jiang, Bo Ma, Jiayue Yin and 4 more

Abstract read
PubMed Full text at PMC Publisher
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Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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2 · The registry

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

14 authors.

Xin ZhangKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (KLBBSA), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
Chaoqun HuKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (KLBBSA), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
Ting ChenKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (KLBBSA), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
Pengying LiShanghai Ocean University, Shanghai, China.
Yehui TanKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (KLBBSA), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
Chunhua RenKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (KLBBSA), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
Yanhong WangKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (KLBBSA), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
Xiao JiangKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (KLBBSA), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
Bo MaKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (KLBBSA), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
Jiayue YinKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (KLBBSA), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
Yunyi HuangKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (KLBBSA), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
Liyan LiuYuehai Feed Group Co., Ltd, Zhanjiang, China.
Huo LiGuangdong Jinyang Biotechnology Co., Ltd, Maoming, China.
Peng LuoKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (KLBBSA), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China. luopeng@scsio.ac.cn.

Funding

Molecular Mechanism of Rapid Growth and Stress Resistance Traits in Penaeus vannamei E4DQ2B01National Key Research and Development Program of China 2023YFD2401701Research on Breeding Technology of Candidate Species for Guangdong Modern Marine Ranching 2024-MRB-00-001Seed Industry Revitalization Project of Provincial Rural Revitalization Strategy Special Funds 2022-SPY-00-001Strategic Priority Research Program of the Chinese Academy of Sciences XDB07302004
6 · The paper itself

Abstract

backgroundDNA methylation is a critical epigenetic modification that dynamically regulates gene expression associated with economic traits. Pacific white shrimp (Litopenaeus vannamei) is one of the most important aquatic species for culturing, and growth trait is one of the most important economic traits for its production. However, research on DNA methylation regulation of growth traits is still at an early stage. This study explored DNA methylome dynamics and their associations with the regulatory mechanism behind growth traits using full-subfamily individuals with discrepant growth performance.

resultsThe DNA methylation-related genes in L. vannamei were identified, and the expression of DNA methylation genes showed significantly higher levels in the slow growth (SG) group compared to the fast-growing (FG) individuals. The Whole Genome Bisulfite Sequencing (WGBS) analysis revealed that the methylation levels in the muscles of shrimp were notably decreased in SG individuals compared to FG individuals. A total of 532 differentially methylated promoters and 2,067 differentially methylated regions were identified. Through integrative analysis of DNA methylation and transcriptomic data from SG and FG group shrimp, a total of 47 genes were screened out with differential methylation levels (DMGs) and expression levels (DEGs). Functional enrichment analysis revealed that the overlapping DEGs/DMGs were enriched mainly in metabolic pathways, starch and sucrose metabolism, linoleic acid metabolism, ascorbate and aldarate metabolism, pentose and glucuronate interconversions.

conclusionsDNA methylation plays a role in the regulation of growth traits in L. vannamei. The level of DNA methylation was found to be negatively correlated with growth traits. Through comprehensive analysis, it was discovered that DNA methylation predominantly affects growth performance by up-regulating the expression of genes involved in metabolic pathways, such as glucose metabolism and amino acid metabolism in L. vannamei. This suggests a higher metabolism activity in SG individuals derived DNA methylation to cope with some unknown internal stress or environmental stress rather than being allocated for growth.

Indexed as

DNA MethylationMetabolic Networks and PathwaysPenaeidaeAnimalsEpigenesis, GeneticGene Expression ProfilingPromoter Regions, GeneticDNA methylationGene expressionGrowth traitLitopenaeus vannamei

Identifiers

PMID40394505
PMCPMC12093746

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