Analysis of Different Ploidy and Parent–Offspring Genomic DNA Methylation in the Loach Misgurnus anguillicaudatus

He, Zhou; Ma, Tianyu; Zhang, Rui; Xu, Qi-Zheng; Fu, Shoukuan; Qin, Yanjie; Wen, Xiaopeng; Wang, Yuan; Li, Yajuan

doi:10.3390/ijms17081299

Cited by 11 publications

(6 citation statements)

References 24 publications

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“…In Pacific oysters, the role of epigenetics in mediating the effects of temperature on oyster physiology has been investigated ( Fellous, Favrel & Riviere, 2015 ). Recent efforts have also aimed at understanding the role epigenetics may play in other important phenomena in aquaculture, including sex control via ploidy manipulation ( Covelo-Soto et al, 2015 ; Jiang et al, 2016 ; Zhou et al, 2016 ), the effects of inbreeding ( Venney, Johansson & Heath, 2016 ) and adaptation to captivity ( Le Luyer et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Epigenetic considerations in aquaculture

Gavery

Roberts

2017

PeerJ

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Epigenetics has attracted considerable attention with respect to its potential value in many areas of agricultural production, particularly under conditions where the environment can be manipulated or natural variation exists. Here we introduce key concepts and definitions of epigenetic mechanisms, including DNA methylation, histone modifications and non-coding RNA, review the current understanding of epigenetics in both fish and shellfish, and propose key areas of aquaculture where epigenetics could be applied. The first key area is environmental manipulation, where the intention is to induce an ‘epigenetic memory’ either within or between generations to produce a desired phenotype. The second key area is epigenetic selection, which, alone or combined with genetic selection, may increase the reliability of producing animals with desired phenotypes. Based on aspects of life history and husbandry practices in aquaculture species, the application of epigenetic knowledge could significantly affect the productivity and sustainability of aquaculture practices. Conversely, clarifying the role of epigenetic mechanisms in aquaculture species may upend traditional assumptions about selection practices. Ultimately, there are still many unanswered questions regarding how epigenetic mechanisms might be leveraged in aquaculture.

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Section: Introductionmentioning

confidence: 99%

Epigenetic considerations in aquaculture

Gavery

Roberts

2017

PeerJ

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“…Therefore, we have previously studied the chromosome numbers, DNA content, meiosis and reproductive characteristics of triploid loaches [ 15 , 16 ] with fertility as the endpoint. From the viewpoint of epigenetics, differences in DNA methylation levels and the control of key genes in hybrid triploid loaches and their parents have been analyzed [ 17 ]. However, the molecular mechanisms controlling the fertility of these fish remain unclear.…”

Section: Introductionmentioning

confidence: 99%

Gonadal transcriptome analysis of hybrid triploid loaches (Misgurnus anguillicaudatus) and their diploid and tetraploid parents

Zhang

et al. 2018

PLoS ONE

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Hybrid triploid loaches (Misgurnus anguillicaudatus) were generated from natural tetraploid and diploid loaches. We studied the gonads of parents and offspring from direct and reciprocal crosses through histological and transcriptome analyses. The triploid offspring had inferior ability to form sperm and egg cells compared with diploid forms. After sequencing the transcriptomes, 655,109,158 clean reads were obtained, and 62,821 unigenes and 178,962 transcripts were assembled. Of these unigenes, 23,189 were annotated in the GO database, 18,525 in the KEGG database and 24,661 in the KOG database. 36 fertility-related genes were found to be differentially expressed between the direct cross (2n × 4n) progenies and their parents, while 53 fertility-related genes between the reciprocal cross (4n × 2n) progenies and their parents. Following protein-protein interaction network analyses, 54 differentially expressed genes, including PLCB4, cyp17a1 and Pla2g4d, were mined, yielding candidate genes involved in the poor fertility of hybrid triploid loaches. This is the first report of transcriptomes of gonads of hybrid triploid loaches and their parents, offering a substantial contribution to sequence resources for this species and providing a deep insight into the molecular mechanism controlling the fertility of hybrid triploid fish.

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“…2013 ). Only 12 loci (2.94%) displayed significant methylation difference between diploid and synthesized triploid brown trout ( Salmo trutta L.) (Covelo-Soto and Leunda 2015), while 73.05% and 68.17% of methylation patterns changed in naturally occurring triploid and tetraploid loach Misgurnus anguillicaudatus compared with diploid loach ( Zhou et al. 2016 ).…”

Section: Discussionmentioning

confidence: 99%

Whole Genome Incorporation and Epigenetic Stability in a Newly Synthetic Allopolyploid of Gynogenetic Gibel Carp

Shao

Wang

et al. 2018

Genome Biology and Evolution

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Allopolyploidization plays an important role in speciation, and some natural or synthetic allopolyploid fishes have been extensively applied to aquaculture. Although genetic and epigenetic inheritance and variation associated with plant allopolyploids have been well documented, the relative research in allopolyploid animals is scarce. In this study, the genome constitution and DNA methylation inheritance in a newly synthetic allopolyploid of gynogenetic gibel carp were analyzed. The incorporation of a whole genome of paternal common carp sperm in the allopolyploid was confirmed by genomic in situ hybridization, chromosome localization of 45S rDNAs, and sequence comparison. Pooled sample-based methylation sensitive amplified polymorphism (MSAP) revealed that an overwhelming majority (98.82%) of cytosine methylation patterns in the allopolyploid were inherited from its parents of hexaploid gibel carp clone D and common carp. Compared to its parents, 11 DNA fragments in the allopolyploid were proved to be caused by interindividual variation, recombination, deletion, and mutation through individual sample-based MSAP and sequencing. Contrast to the rapid and remarkable epigenetic changes in most of analyzed neopolyploids, no cytosine methylation variation was detected in the gynogenetic allopolyploid. Therefore, the newly synthetic allopolyploid of gynogenetic gibel carp combined genomes from its parents and maintained genetic and epigenetic stability after its formation and subsequently seven successive gynogenetic generations. Our current results provide a paradigm for recurrent polyploidy consequences in the gynogenetic allopolyploid animals.

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Analysis of Different Ploidy and Parent–Offspring Genomic DNA Methylation in the Loach Misgurnus anguillicaudatus

Cited by 11 publications

References 24 publications

Epigenetic considerations in aquaculture

Epigenetic considerations in aquaculture

Gonadal transcriptome analysis of hybrid triploid loaches (Misgurnus anguillicaudatus) and their diploid and tetraploid parents

Whole Genome Incorporation and Epigenetic Stability in a Newly Synthetic Allopolyploid of Gynogenetic Gibel Carp

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