biostudies-literatureRen LChina Agriculture Research System of MOF and MARAHigh-Level Talent Agglomeration Program of Hunan111 ProjectNatural Science Foundation of Hunan Province GrantsHunan Provincial Natural Science and Technology Major ProjectNational Natural Science Foundation of ChinaHuxiang Young Talent ProjectLaboratory of Lingnan Modern Agriculture Project19https://www.ebi.ac.uk/biostudies/studies/S-EPMC9123727biostudies-literatureUnknown15(1)<h4>Background</h4>Heterosis of growth traits in allotriploid fish has benefited the production of aquaculture for many years, yet its genetic and molecular basis has remained obscure. Now, an allotriploid complex, including two triploids and their diploid inbred parents, has provided an excellent model for investigating the potential regulatory mechanisms of heterosis.<h4>Results</h4>Here, we performed a series of analyses on DNA methylation modification and miRNA expression in combination with gene expression in the allotriploid complex. We first established a model of cis- and trans-regulation related to DNA methylation and miRNA in allotriploids. Then, comparative analyses showed that DNA methylation contributed to the emergence of a dosage compensation effect, which reduced gene expression levels in the triploid to the diploid state. We detected 31 genes regulated by DNA methylation in the subgenomes of the allotriploids. Finally, the patterns of coevolution between small RNAs and their homoeologous targets were classified and used to predict the regulation of miRNA expression in the allotriploids.<h4>Conclusions</h4>Our results uncovered the regulatory network between DNA methylation and miRNAs in allotriploids, which not only helps us understand the regulatory mechanisms of heterosis of growth traits but also benefits the study and application of epigenetics in aquaculture.Epigenetics & chromatinHeterosis of growth trait regulated by DNA methylation and miRNA in allotriploid fish.PMC91237272017NK1031NT202100831730098D20007CARS-452019RS1044317023342021RC30932020JJ5355Ren LLuo MZhang HCui JZhang XGao XLiu SfalseHeterosis of growth trait regulated by DNA methylation and miRNA in allotriploid fish.<h4>Background</h4>Heterosis of growth traits in allotriploid fish has benefited the production of aquaculture for many years, yet its genetic and molecular basis has remained obscure. Now, an allotriploid complex, including two triploids and their diploid inbred parents, has provided an excellent model for investigating the potential regulatory mechanisms of heterosis.<h4>Results</h4>Here, we performed a series of analyses on DNA methylation modification and miRNA expression in combination with gene expression in the allotriploid complex. We first established a model of cis- and trans-regulation related to DNA methylation and miRNA in allotriploids. Then, comparative analyses showed that DNA methylation contributed to the emergence of a dosage compensation effect, which reduced gene expression levels in the triploid to the diploid state. We detected 31 genes regulated by DNA methylation in the subgenomes of the allotriploids. Finally, the patterns of coevolution between small RNAs and their homoeologous targets were classified and used to predict the regulation of miRNA expression in the allotriploids.<h4>Conclusions</h4>Our results uncovered the regulatory network between DNA methylation and miRNAs in allotriploids, which not only helps us understand the regulatory mechanisms of heterosis of growth traits but also benefits the study and application of epigenetics in aquaculture.2022-01-01T00:00:00Z2022 May2025-04-22T13:08:14.349Z2025-02-19T04:56:40.673ZS-EPMC91237273559796610.1186/s13072-022-00455-6