Heterochromatic knobs gene-like effects on flowering time, and the seed aging epigenetic-genetic program in maize
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Tipo de documento: | Tese |
Idioma: | eng |
Título da fonte: | Biblioteca Digital de Teses e Dissertações da USP |
Texto Completo: | https://doi.org/10.11606/T.11.2020.tde-14012021-140924 |
Resumo: | Maize (Zea mays spp. mays) is a cultivated species known for its wide genetic variability. A large part of the diversity observed in the genome size is due to the presence of repetitive sequences, which can compose up to 90% of DNA in a species. In particular, knobs are regions of constitutive heterochromatin present in the maize genome and due to their repetitive nature, no specific function has been assigned until this moment. Because it is a cytological region visibly observed under a microscope, knobs give the maize genome a unique karyotype variability. Despite no assigned role, there is evidence of a possible influence of the knobs on maize phenotypic traits. Seed aging is an equally relevant area, as it can subsidize seed storage practices, which are essential for the conservation of genetic resources, including the maize crop. There is a relationship between seed aging and the impact on crop yield and this has been demonstrated through cytogenetic and physiological studies. However, a deeper understanding of the consequences of aging on the plants epigenome remains unclear. In this context, the two chapters of this thesis are structured, which have very different objectives, but which are complementary with regard to the scientific contribution to the areas of genetics and maize breeding. The first chapter discussed the hypotheses of the heterochromatic knobs contribution to the genome size and maize flowering time. In this study, maize inbred line families (JD 1-3, JD 2-1 and JD 4-4) and the hybrids obtained between them were used. They were mapped to the knobs in specific positions on chromosomes 3, 5, 7 and 9. All of this material was characterized in terms of male and female flowering time and genome size. The data were analysed using an adaptation of the Genome-Wide Association Study (GWAS), where knobs were used in place of molecular markers of single nucleotide polymorphism (SNPs). These analyses showed a significant association between the knob on the short arm of chromosome 9 and the flowering time, in which the knob presence in homozygosity or heterozygosis on chromosome 9 can lead to a reduction in the maize flowering time, making it earlier. The second chapter aimed to evaluate the effects of natural seed aging and its impacts on germination, behaviour of chromosomes and maize chromatin. In this study, genotypes of the JD 4-1 inbred line family were used, which were kept stored for 24 years in a cold chamber. Aged and non-aged seeds were analysed comparatively for the parameters of mitotic index, chromosomal changes, germination percentage, meiotic analysis and DNA methylation. There were significant differences between treatments for all parameters analysed. The most expressive result was observed in the methylation level, in which the aged seeds presented higher DNA methylation values than the non-aged seeds. Among the aged seeds, there were also differences in methylation, showing that there is a genotype-specific response to aging. The combined action between the genetic background and epigenetic indexing contributed to maintaining the aged seeds viability after long years of storage. |
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info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/doctoralThesis Heterochromatic knobs gene-like effects on flowering time, and the seed aging epigenetic-genetic program in maize Efeitos gene-like dos knobs heterocromáticos no tempo de florescimento e o programa epigenético-genético de envelhecimento de semente em milho 2020-12-02Mateus MondinMargarida Lopes Rodrigues de Aguiar PerecinMaria Helena de Souza GoldmanLudmila Cristina OliveiraRenata Flávia de CarvalhoUniversidade de São PauloAgronomia (Genética e Melhoramento de Plantas)USPBR Zea mays Zea mays Aging tolerance Alterações cromossômicas Chromosomal changes Envelhecimento de sementes Epigenética Epigenetics Flowering time Genome size Heterochromatic knobs Knobs heterocromáticos Seed aging Tamanho do genoma Tempo de florescimento Tolerância ao envelhecimento Maize (Zea mays spp. mays) is a cultivated species known for its wide genetic variability. A large part of the diversity observed in the genome size is due to the presence of repetitive sequences, which can compose up to 90% of DNA in a species. In particular, knobs are regions of constitutive heterochromatin present in the maize genome and due to their repetitive nature, no specific function has been assigned until this moment. Because it is a cytological region visibly observed under a microscope, knobs give the maize genome a unique karyotype variability. Despite no assigned role, there is evidence of a possible influence of the knobs on maize phenotypic traits. Seed aging is an equally relevant area, as it can subsidize seed storage practices, which are essential for the conservation of genetic resources, including the maize crop. There is a relationship between seed aging and the impact on crop yield and this has been demonstrated through cytogenetic and physiological studies. However, a deeper understanding of the consequences of aging on the plants epigenome remains unclear. In this context, the two chapters of this thesis are structured, which have very different objectives, but which are complementary with regard to the scientific contribution to the areas of genetics and maize breeding. The first chapter discussed the hypotheses of the heterochromatic knobs contribution to the genome size and maize flowering time. In this study, maize inbred line families (JD 1-3, JD 2-1 and JD 4-4) and the hybrids obtained between them were used. They were mapped to the knobs in specific positions on chromosomes 3, 5, 7 and 9. All of this material was characterized in terms of male and female flowering time and genome size. The data were analysed using an adaptation of the Genome-Wide Association Study (GWAS), where knobs were used in place of molecular markers of single nucleotide polymorphism (SNPs). These analyses showed a significant association between the knob on the short arm of chromosome 9 and the flowering time, in which the knob presence in homozygosity or heterozygosis on chromosome 9 can lead to a reduction in the maize flowering time, making it earlier. The second chapter aimed to evaluate the effects of natural seed aging and its impacts on germination, behaviour of chromosomes and maize chromatin. In this study, genotypes of the JD 4-1 inbred line family were used, which were kept stored for 24 years in a cold chamber. Aged and non-aged seeds were analysed comparatively for the parameters of mitotic index, chromosomal changes, germination percentage, meiotic analysis and DNA methylation. There were significant differences between treatments for all parameters analysed. The most expressive result was observed in the methylation level, in which the aged seeds presented higher DNA methylation values than the non-aged seeds. Among the aged seeds, there were also differences in methylation, showing that there is a genotype-specific response to aging. The combined action between the genetic background and epigenetic indexing contributed to maintaining the aged seeds viability after long years of storage. O milho (Zea mays spp. mays) é uma espécie cultivada conhecida por sua ampla variabilidade genética. Grande parte da diversidade observada no tamanho dos genomas é devido a presença de sequências repetitivas, as quais podem compor até 90% de DNA em uma espécie. De modo especial, knobs são regiões de heterocromatina constitutiva presentes no genoma do milho e devido à sua natureza repetitiva, nenhuma função específica foi atribuída até o momento. Por ser uma região citológica visivelmente observada ao microscópio, os knobs dão ao genoma do milho uma variabilidade cariotípica única. Apesar de nenhuma função atribuída, há evidências de uma possível influência dos knobs sobre características fenotípicas do milho. O envelhecimento de sementes é uma área igualmente relevante, pois pode subsidiar práticas de armazenamento de sementes, as quais são primordiais para a conservação de recursos genéticos, incluindo a cultura do milho. Existe uma relação entre o envelhecimento de sementes e o impacto sobre rendimento das culturas e isto tem sido demonstrado por meio de estudos citogenéticos e fisiológicos. No entanto, um entendimento mais aprofundado sobre as consequências do envelhecimento sobre o epigenoma das plantas ainda permanece obscuro. Nesse contexto, estrutura-se os dois capítulos desta tese, os quais apresentam objetivos bem distintos, mas que são complementares no que diz respeito à contribuição científica para as áreas de genética e melhoramento do milho. O primeiro capítulo discutiu as hipóteses da contribuição dos knobs heterocromáticos para o tamanho do genoma e o tempo de florescimento em milho. Neste estudo foram utilizadas famílias de linhagens isogênicas de milho (JD 1-3, JD 2-1 e JD 4-4) e os híbridos obtidos entre elas, mapeadas para os knobs em posições específicas nos cromossomos 3, 5, 7 e 9. Todo este material foi caracterizado quanto ao tempo de florescimento masculino e feminino e o tamanho do genoma. Os dados foram analisados por meio de uma adaptação do Genome-Wide Association Study (GWAS), onde os knobs foram utilizados em lugar dos marcadores moleculares de polimorfismo de nucleotídeo único (SNPs). Estas análises mostraram uma associação significativa entre o knob no braço curto do cromossomo 9 e o tempo de florescimento, no qual a presença do knob em homozigose ou heterozigose pode levar a uma redução no tempo de florescimento do milho, tornando-o mais precoce. O segundo capítulo teve como objetivo avaliar os efeitos do envelhecimento natural de sementes e seus impactos na germinação, comportamento dos cromossomos e da cromatina do milho. Foram utilizados neste estudo genótipos da família de linhagens JD 4-1, os quais foram mantidos armazenados por 24 anos em câmara fria. Sementes envelhecidas e não-envelhecidas foram analisadas comparativamente quanto aos parâmetros de índice mitótico, alterações cromossômicas, porcentagem de germinação, análises meióticas e metilação do DNA. Houve diferenças significativas entre os tratamentos para todos os parâmetros analisados. O resultado mais expressivo foi observado no nível de metilação, no qual as sementes envelhecidas apresentaram valores médios de metilação do DNA maiores do que as sementes não envelhecidas. Entre as sementes envelhecidas também houve diferenças quanto a metilação, mostrando que há uma resposta genótipo-específico ao envelhecimento. A ação combinada entre o componente genético e a indexação epigenética contribuíram para manutenção da viabilidade das sementes envelhecidas após longos anos de armazenamento. https://doi.org/10.11606/T.11.2020.tde-14012021-140924info:eu-repo/semantics/openAccessengreponame:Biblioteca Digital de Teses e Dissertações da USPinstname:Universidade de São Paulo (USP)instacron:USP2023-12-21T18:55:04Zoai:teses.usp.br:tde-14012021-140924Biblioteca Digital de Teses e Dissertaçõeshttp://www.teses.usp.br/PUBhttp://www.teses.usp.br/cgi-bin/mtd2br.plvirginia@if.usp.br|| atendimento@aguia.usp.br||virginia@if.usp.bropendoar:27212023-12-22T12:38:02.514020Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP)false |
dc.title.en.fl_str_mv |
Heterochromatic knobs gene-like effects on flowering time, and the seed aging epigenetic-genetic program in maize |
dc.title.alternative.pt.fl_str_mv |
Efeitos gene-like dos knobs heterocromáticos no tempo de florescimento e o programa epigenético-genético de envelhecimento de semente em milho |
title |
Heterochromatic knobs gene-like effects on flowering time, and the seed aging epigenetic-genetic program in maize |
spellingShingle |
Heterochromatic knobs gene-like effects on flowering time, and the seed aging epigenetic-genetic program in maize Renata Flávia de Carvalho |
title_short |
Heterochromatic knobs gene-like effects on flowering time, and the seed aging epigenetic-genetic program in maize |
title_full |
Heterochromatic knobs gene-like effects on flowering time, and the seed aging epigenetic-genetic program in maize |
title_fullStr |
Heterochromatic knobs gene-like effects on flowering time, and the seed aging epigenetic-genetic program in maize |
title_full_unstemmed |
Heterochromatic knobs gene-like effects on flowering time, and the seed aging epigenetic-genetic program in maize |
title_sort |
Heterochromatic knobs gene-like effects on flowering time, and the seed aging epigenetic-genetic program in maize |
author |
Renata Flávia de Carvalho |
author_facet |
Renata Flávia de Carvalho |
author_role |
author |
dc.contributor.advisor1.fl_str_mv |
Mateus Mondin |
dc.contributor.advisor-co1.fl_str_mv |
Margarida Lopes Rodrigues de Aguiar Perecin |
dc.contributor.referee1.fl_str_mv |
Maria Helena de Souza Goldman |
dc.contributor.referee2.fl_str_mv |
Ludmila Cristina Oliveira |
dc.contributor.author.fl_str_mv |
Renata Flávia de Carvalho |
contributor_str_mv |
Mateus Mondin Margarida Lopes Rodrigues de Aguiar Perecin Maria Helena de Souza Goldman Ludmila Cristina Oliveira |
description |
Maize (Zea mays spp. mays) is a cultivated species known for its wide genetic variability. A large part of the diversity observed in the genome size is due to the presence of repetitive sequences, which can compose up to 90% of DNA in a species. In particular, knobs are regions of constitutive heterochromatin present in the maize genome and due to their repetitive nature, no specific function has been assigned until this moment. Because it is a cytological region visibly observed under a microscope, knobs give the maize genome a unique karyotype variability. Despite no assigned role, there is evidence of a possible influence of the knobs on maize phenotypic traits. Seed aging is an equally relevant area, as it can subsidize seed storage practices, which are essential for the conservation of genetic resources, including the maize crop. There is a relationship between seed aging and the impact on crop yield and this has been demonstrated through cytogenetic and physiological studies. However, a deeper understanding of the consequences of aging on the plants epigenome remains unclear. In this context, the two chapters of this thesis are structured, which have very different objectives, but which are complementary with regard to the scientific contribution to the areas of genetics and maize breeding. The first chapter discussed the hypotheses of the heterochromatic knobs contribution to the genome size and maize flowering time. In this study, maize inbred line families (JD 1-3, JD 2-1 and JD 4-4) and the hybrids obtained between them were used. They were mapped to the knobs in specific positions on chromosomes 3, 5, 7 and 9. All of this material was characterized in terms of male and female flowering time and genome size. The data were analysed using an adaptation of the Genome-Wide Association Study (GWAS), where knobs were used in place of molecular markers of single nucleotide polymorphism (SNPs). These analyses showed a significant association between the knob on the short arm of chromosome 9 and the flowering time, in which the knob presence in homozygosity or heterozygosis on chromosome 9 can lead to a reduction in the maize flowering time, making it earlier. The second chapter aimed to evaluate the effects of natural seed aging and its impacts on germination, behaviour of chromosomes and maize chromatin. In this study, genotypes of the JD 4-1 inbred line family were used, which were kept stored for 24 years in a cold chamber. Aged and non-aged seeds were analysed comparatively for the parameters of mitotic index, chromosomal changes, germination percentage, meiotic analysis and DNA methylation. There were significant differences between treatments for all parameters analysed. The most expressive result was observed in the methylation level, in which the aged seeds presented higher DNA methylation values than the non-aged seeds. Among the aged seeds, there were also differences in methylation, showing that there is a genotype-specific response to aging. The combined action between the genetic background and epigenetic indexing contributed to maintaining the aged seeds viability after long years of storage. |
publishDate |
2020 |
dc.date.issued.fl_str_mv |
2020-12-02 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/doctoralThesis |
format |
doctoralThesis |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://doi.org/10.11606/T.11.2020.tde-14012021-140924 |
url |
https://doi.org/10.11606/T.11.2020.tde-14012021-140924 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
Universidade de São Paulo |
dc.publisher.program.fl_str_mv |
Agronomia (Genética e Melhoramento de Plantas) |
dc.publisher.initials.fl_str_mv |
USP |
dc.publisher.country.fl_str_mv |
BR |
publisher.none.fl_str_mv |
Universidade de São Paulo |
dc.source.none.fl_str_mv |
reponame:Biblioteca Digital de Teses e Dissertações da USP instname:Universidade de São Paulo (USP) instacron:USP |
instname_str |
Universidade de São Paulo (USP) |
instacron_str |
USP |
institution |
USP |
reponame_str |
Biblioteca Digital de Teses e Dissertações da USP |
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Biblioteca Digital de Teses e Dissertações da USP |
repository.name.fl_str_mv |
Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP) |
repository.mail.fl_str_mv |
virginia@if.usp.br|| atendimento@aguia.usp.br||virginia@if.usp.br |
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1794502723229450240 |