Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio

Abstract We developed novel miRNA-based markers based on salt responsive miRNA sequences to detect polymorphisms in miRNA sequences and locations. The validation of 76 combined miRNA + miRNA and miRNA + ISSR markers in the three extreme pistachio populations led to the identification of three select...

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Autores principales:	Masoomeh Jannesar, Seyed Mahdi Seyedi, Christopher Botanga
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ca962321bb8747b2b748b4c83b110ff8
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spelling	oai:doaj.org-article:ca962321bb8747b2b748b4c83b110ff82021-12-02T19:16:14ZTargeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio10.1038/s41598-021-98402-02045-2322https://doaj.org/article/ca962321bb8747b2b748b4c83b110ff82021-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-98402-0https://doaj.org/toc/2045-2322Abstract We developed novel miRNA-based markers based on salt responsive miRNA sequences to detect polymorphisms in miRNA sequences and locations. The validation of 76 combined miRNA + miRNA and miRNA + ISSR markers in the three extreme pistachio populations led to the identification of three selected markers that could link salt tolerance phenotype to genotype and divided pistachio genotypes and Pistacia species into three clusters. This novel functional marker system, in addition to more efficient performance, has higher polymorphisms than previous miRNA-based marker systems. The functional importance of the target gene of five miRNAs in the structure of the three selected markers in regulation of different genes such as ECA2, ALA10, PFK, PHT1;4, PTR3, KUP2, GRAS, TCP, bHLH, PHD finger, PLATZ and genes involved in developmental, signaling and biosynthetic processes shows that the polymorphism associated with these selected miRNAs can make a significant phenotypic difference between salt sensitive and tolerant pistachio genotypes. The sequencing results of selected bands showed the presence of conserved miRNAs in the structure of the mitochondrial genome. Further notable findings of this study are that the sequences of PCR products of two selected markers were annotated as Gypsy and Copia retrotransposable elements. The transposition of retrotransposons with related miRNAs by increasing the number of miRNA copies and changing their location between nuclear and organellar genomes can affect the regulatory activity of these molecules. These findings show the crucial role of retrotransposon-derived miRNAs as mobile epigenetic regulators between intracellular genomes in regulating salt stress responses as well as creating new and tolerant phenotypes for adaptation to environmental conditions.Masoomeh JannesarSeyed Mahdi SeyediChristopher BotangaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-21 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Masoomeh Jannesar Seyed Mahdi Seyedi Christopher Botanga Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio
description	Abstract We developed novel miRNA-based markers based on salt responsive miRNA sequences to detect polymorphisms in miRNA sequences and locations. The validation of 76 combined miRNA + miRNA and miRNA + ISSR markers in the three extreme pistachio populations led to the identification of three selected markers that could link salt tolerance phenotype to genotype and divided pistachio genotypes and Pistacia species into three clusters. This novel functional marker system, in addition to more efficient performance, has higher polymorphisms than previous miRNA-based marker systems. The functional importance of the target gene of five miRNAs in the structure of the three selected markers in regulation of different genes such as ECA2, ALA10, PFK, PHT1;4, PTR3, KUP2, GRAS, TCP, bHLH, PHD finger, PLATZ and genes involved in developmental, signaling and biosynthetic processes shows that the polymorphism associated with these selected miRNAs can make a significant phenotypic difference between salt sensitive and tolerant pistachio genotypes. The sequencing results of selected bands showed the presence of conserved miRNAs in the structure of the mitochondrial genome. Further notable findings of this study are that the sequences of PCR products of two selected markers were annotated as Gypsy and Copia retrotransposable elements. The transposition of retrotransposons with related miRNAs by increasing the number of miRNA copies and changing their location between nuclear and organellar genomes can affect the regulatory activity of these molecules. These findings show the crucial role of retrotransposon-derived miRNAs as mobile epigenetic regulators between intracellular genomes in regulating salt stress responses as well as creating new and tolerant phenotypes for adaptation to environmental conditions.
format	article
author	Masoomeh Jannesar Seyed Mahdi Seyedi Christopher Botanga
author_facet	Masoomeh Jannesar Seyed Mahdi Seyedi Christopher Botanga
author_sort	Masoomeh Jannesar
title	Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio
title_short	Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio
title_full	Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio
title_fullStr	Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio
title_full_unstemmed	Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio
title_sort	targeted designing functional markers revealed the role of retrotransposon derived mirnas as mobile epigenetic regulators in adaptation responses of pistachio
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/ca962321bb8747b2b748b4c83b110ff8
work_keys_str_mv	AT masoomehjannesar targeteddesigningfunctionalmarkersrevealedtheroleofretrotransposonderivedmirnasasmobileepigeneticregulatorsinadaptationresponsesofpistachio AT seyedmahdiseyedi targeteddesigningfunctionalmarkersrevealedtheroleofretrotransposonderivedmirnasasmobileepigeneticregulatorsinadaptationresponsesofpistachio AT christopherbotanga targeteddesigningfunctionalmarkersrevealedtheroleofretrotransposonderivedmirnasasmobileepigeneticregulatorsinadaptationresponsesofpistachio
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Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio

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