Epigenetic diversity of Saccharum spp. accessions assessed by methylation-sensitive amplification polymorphism (MSAP)
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1007/s13205-020-02257-7 http://hdl.handle.net/11449/195397 |
Resumo: | The epigenetic diversity of six genotype groups (commercial cultivars, S. officinarum, S. spontaneum, S. robustum, S. barberi, and Erianthus sp.) was assessed through methylation-sensitive amplification polymorphism (MSAP). A total of 1341 MSAP loci were analyzed, of which 1117 (83.29%) were susceptible to cytosine methylation and responsible for a higher proportion of overall diversity among genotypes. The MSAP selective primer combinations captured different proportions of internal and external cytosine methylation loci across genotype groups, while the average external cytosine frequency was higher for all genotype groups. The genotypes were divided into two subpopulations with a high differentiation index (phi st = 0.086) based on epigenetic loci. The genotypes were clustered in three subgroups for both methylated and unmethylated loci, considering dissimilarity values. Four methylated fragments (MFs) were randomly selected and subsequently sequenced and compared with sugarcane public databases using BLASTN. MF alignments suggest that cytosine methylation occurs in sugarcane near CpG islands and tandem repeats within transcribed regions and putative cis-regulatory sequences, which assigned functions are associated with stress adaptation. These results provide the first insights about the distribution of this epigenetic mark in sugarcane genome, and suggest a biological relevance of methylated loci. |
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Epigenetic diversity of Saccharum spp. accessions assessed by methylation-sensitive amplification polymorphism (MSAP)Saccharum sppWild accessionsCytosine methylationEpigenome diversityThe epigenetic diversity of six genotype groups (commercial cultivars, S. officinarum, S. spontaneum, S. robustum, S. barberi, and Erianthus sp.) was assessed through methylation-sensitive amplification polymorphism (MSAP). A total of 1341 MSAP loci were analyzed, of which 1117 (83.29%) were susceptible to cytosine methylation and responsible for a higher proportion of overall diversity among genotypes. The MSAP selective primer combinations captured different proportions of internal and external cytosine methylation loci across genotype groups, while the average external cytosine frequency was higher for all genotype groups. The genotypes were divided into two subpopulations with a high differentiation index (phi st = 0.086) based on epigenetic loci. The genotypes were clustered in three subgroups for both methylated and unmethylated loci, considering dissimilarity values. Four methylated fragments (MFs) were randomly selected and subsequently sequenced and compared with sugarcane public databases using BLASTN. MF alignments suggest that cytosine methylation occurs in sugarcane near CpG islands and tandem repeats within transcribed regions and putative cis-regulatory sequences, which assigned functions are associated with stress adaptation. These results provide the first insights about the distribution of this epigenetic mark in sugarcane genome, and suggest a biological relevance of methylated loci.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Univ Estadual Paulista, BR-14884900 Jaboticabal, SP, BrazilCtr Cana, Inst Agron, CP 206, BR-14001970 Ribeirao Preto, SP, BrazilUniv Estadual Paulista, BR-14884900 Jaboticabal, SP, BrazilFAPESP: 2013/22500-5SpringerUniversidade Estadual Paulista (Unesp)Ctr CanaMartins, Alessandra Alves [UNESP]Silva, Marcel F. daPinto, Luciana Rossini2020-12-10T17:33:19Z2020-12-10T17:33:19Z2020-05-24info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article14http://dx.doi.org/10.1007/s13205-020-02257-73 Biotech. Heidelberg: Springer Heidelberg, v. 10, n. 6, 14 p., 2020.2190-572Xhttp://hdl.handle.net/11449/19539710.1007/s13205-020-02257-7WOS:000535133400001Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPeng3 Biotechinfo:eu-repo/semantics/openAccess2021-10-22T20:36:17Zoai:repositorio.unesp.br:11449/195397Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T20:48:55.300071Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Epigenetic diversity of Saccharum spp. accessions assessed by methylation-sensitive amplification polymorphism (MSAP) |
title |
Epigenetic diversity of Saccharum spp. accessions assessed by methylation-sensitive amplification polymorphism (MSAP) |
spellingShingle |
Epigenetic diversity of Saccharum spp. accessions assessed by methylation-sensitive amplification polymorphism (MSAP) Martins, Alessandra Alves [UNESP] Saccharum spp Wild accessions Cytosine methylation Epigenome diversity |
title_short |
Epigenetic diversity of Saccharum spp. accessions assessed by methylation-sensitive amplification polymorphism (MSAP) |
title_full |
Epigenetic diversity of Saccharum spp. accessions assessed by methylation-sensitive amplification polymorphism (MSAP) |
title_fullStr |
Epigenetic diversity of Saccharum spp. accessions assessed by methylation-sensitive amplification polymorphism (MSAP) |
title_full_unstemmed |
Epigenetic diversity of Saccharum spp. accessions assessed by methylation-sensitive amplification polymorphism (MSAP) |
title_sort |
Epigenetic diversity of Saccharum spp. accessions assessed by methylation-sensitive amplification polymorphism (MSAP) |
author |
Martins, Alessandra Alves [UNESP] |
author_facet |
Martins, Alessandra Alves [UNESP] Silva, Marcel F. da Pinto, Luciana Rossini |
author_role |
author |
author2 |
Silva, Marcel F. da Pinto, Luciana Rossini |
author2_role |
author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Ctr Cana |
dc.contributor.author.fl_str_mv |
Martins, Alessandra Alves [UNESP] Silva, Marcel F. da Pinto, Luciana Rossini |
dc.subject.por.fl_str_mv |
Saccharum spp Wild accessions Cytosine methylation Epigenome diversity |
topic |
Saccharum spp Wild accessions Cytosine methylation Epigenome diversity |
description |
The epigenetic diversity of six genotype groups (commercial cultivars, S. officinarum, S. spontaneum, S. robustum, S. barberi, and Erianthus sp.) was assessed through methylation-sensitive amplification polymorphism (MSAP). A total of 1341 MSAP loci were analyzed, of which 1117 (83.29%) were susceptible to cytosine methylation and responsible for a higher proportion of overall diversity among genotypes. The MSAP selective primer combinations captured different proportions of internal and external cytosine methylation loci across genotype groups, while the average external cytosine frequency was higher for all genotype groups. The genotypes were divided into two subpopulations with a high differentiation index (phi st = 0.086) based on epigenetic loci. The genotypes were clustered in three subgroups for both methylated and unmethylated loci, considering dissimilarity values. Four methylated fragments (MFs) were randomly selected and subsequently sequenced and compared with sugarcane public databases using BLASTN. MF alignments suggest that cytosine methylation occurs in sugarcane near CpG islands and tandem repeats within transcribed regions and putative cis-regulatory sequences, which assigned functions are associated with stress adaptation. These results provide the first insights about the distribution of this epigenetic mark in sugarcane genome, and suggest a biological relevance of methylated loci. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-12-10T17:33:19Z 2020-12-10T17:33:19Z 2020-05-24 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1007/s13205-020-02257-7 3 Biotech. Heidelberg: Springer Heidelberg, v. 10, n. 6, 14 p., 2020. 2190-572X http://hdl.handle.net/11449/195397 10.1007/s13205-020-02257-7 WOS:000535133400001 |
url |
http://dx.doi.org/10.1007/s13205-020-02257-7 http://hdl.handle.net/11449/195397 |
identifier_str_mv |
3 Biotech. Heidelberg: Springer Heidelberg, v. 10, n. 6, 14 p., 2020. 2190-572X 10.1007/s13205-020-02257-7 WOS:000535133400001 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
3 Biotech |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
14 |
dc.publisher.none.fl_str_mv |
Springer |
publisher.none.fl_str_mv |
Springer |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808129251267837952 |