Estudos de associação entre locos SSR e componentes da produção em arroz (Oryza sativa L.)
Autor(a) principal: | |
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Data de Publicação: | 2010 |
Tipo de documento: | Dissertação |
Idioma: | por |
Título da fonte: | Repositório Institucional da UFG |
Texto Completo: | http://repositorio.bc.ufg.br/tede/handle/tede/3340 |
Resumo: | Rice is consumed by more than half of the world population. The expectation of substantial population growth and consequently the increase of the consumption has demontrated that the present rice production will not supply the future’s demand. As a result, studies that aim at the increase of the yield must be prioritized by scientific co&unity. Aiming to identify genomic regions related to grain yield and its component traits (panicle number per meter, grain panicle number and hundred grain mass), it was carried out the associative mapping analysis. The analysis of association used two types of SSR markers: a) structural genome derived markers, and b) transcriptome derived markers, i.e. developed from transcripts from marker-anchored genomic regions previously related to yield and its components from 27 different QTL maps already published. The associative mapping methodology used included the whole genome scanning and candidate genes approaches. The molecular characterization used 186 accessions from Embrapa Rice Core Collection (ERiCC), whereas 76 accessions from lowland system of cultivation, and 113 upland system of cultivation. The experimental design was the randomized block with 4 repetitions, and included the cultivars BR Irga 409, Metica 1 and BRS Caiapó as controls. It were evaluated the following traits: Panicle number per meter (NPM), panicle (NGP), Hundred grain mass (PCG) and productivity. The 186 markers were genotyped by 29 transcript-derived SSR markers and 86 SSR markers derived from structural genome. For the irrigated accessions was verified positive correlation for panicle number per meter and productivity (0,2424; p<0,01) and by productivity and hundred grain mass (p<0,05; 0,1457) and negative correlation for panicle number per meter and grain number per panicle (-0,457; p<0,01). For the upland accessions it was observed positive correlation for grain number per panicle and productivity (0,4243; p<0,01). Negative correlations were observed for panicle number per meter and hundred grain weight (p<0,01; -0,2114). Based on 44 SSR markers developed in this work, 181 alelles were detected, an average of 5.5 alelles per locus, average PIC of 0.44 and 25 private alleles. The analysis with 115 SSR markers identified 43 significant associations for grain number per panicle considering the cultivation system upland and three associations for lowland system; 7 significant associations for panicle number per meter for lowland system, and 9 were significant for upland cultivation systems; 14 associations were significant for hundred grain mass in lowland system of cultivarion, and 43 were significant for upland system of cultivarion; 3 associations were significant for grain yield in upland system of cultivarion. The association analysis identified 61 SSR markers consistently associated to yield and its components. It were detected 33 associations statiscally significant to one or more traits, which validated the previous results obtained by QTL mapping. The markers RM125, RM152 e Q69JE3 showed the higher number of associations per trait. The association productivity and PCG, and NCP, respectively, were previously found in the literature. The markers associated to the evaluated traits permit to initiate a scientific program to identify the candidate genes and to proceed the marker assisted selection The accessions CNA0001107, CNA0005478, CNA0010533, CNA0003287, IR 36, CNA0003602, CNA0006413, CNA0006174, CNA0003289, CNA0002253, CNA0004098, CNA0001416, CNA0003490 e CNA0000994 showed the highest number of favorable alleles considering 16 the markers associated to yield and its components. The identified accessions from this work as having the higher number of favorable alleles from the evaluated traits will be recommended to be used as genitors in Brazilian rice breeding programs. The mixed approaches to the associative mapping used in the present work was interesting to permit that, even using a low marker density, in couple with the linkage disequilibrium found in rice, some previously mapped markers from QTL analyses were again associated to traits evaluated in field experiments. This strategy can be used to other traits of interest for rice, such as drought and cold tolerance, and disease resistance. |
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Brondani, Claudiohttp://lattes.cnpq.br/4775600104554147Vianello, Rosana P.Borba, Tereza Cristina de OliveiraCoelho, Alexandre Siqueira GuedesBrondani, Cláudiohttp://lattes.cnpq.br/8410045564570544Bueno, Clistiane dos Anjos Mendes2014-10-13T21:16:57Z2010-08-16BUENO, Clistiane dos Anjos Mendes. Estudos de associação entre locos SSR e componentes da produção em arroz (Oryza sativa L.). 2010. 139 f. Dissertação (Mestrado em Agronomia) - Universidade Federal de Goiás, Goiânia, 2010.http://repositorio.bc.ufg.br/tede/handle/tede/3340Rice is consumed by more than half of the world population. The expectation of substantial population growth and consequently the increase of the consumption has demontrated that the present rice production will not supply the future’s demand. As a result, studies that aim at the increase of the yield must be prioritized by scientific co&unity. Aiming to identify genomic regions related to grain yield and its component traits (panicle number per meter, grain panicle number and hundred grain mass), it was carried out the associative mapping analysis. The analysis of association used two types of SSR markers: a) structural genome derived markers, and b) transcriptome derived markers, i.e. developed from transcripts from marker-anchored genomic regions previously related to yield and its components from 27 different QTL maps already published. The associative mapping methodology used included the whole genome scanning and candidate genes approaches. The molecular characterization used 186 accessions from Embrapa Rice Core Collection (ERiCC), whereas 76 accessions from lowland system of cultivation, and 113 upland system of cultivation. The experimental design was the randomized block with 4 repetitions, and included the cultivars BR Irga 409, Metica 1 and BRS Caiapó as controls. It were evaluated the following traits: Panicle number per meter (NPM), panicle (NGP), Hundred grain mass (PCG) and productivity. The 186 markers were genotyped by 29 transcript-derived SSR markers and 86 SSR markers derived from structural genome. For the irrigated accessions was verified positive correlation for panicle number per meter and productivity (0,2424; p<0,01) and by productivity and hundred grain mass (p<0,05; 0,1457) and negative correlation for panicle number per meter and grain number per panicle (-0,457; p<0,01). For the upland accessions it was observed positive correlation for grain number per panicle and productivity (0,4243; p<0,01). Negative correlations were observed for panicle number per meter and hundred grain weight (p<0,01; -0,2114). Based on 44 SSR markers developed in this work, 181 alelles were detected, an average of 5.5 alelles per locus, average PIC of 0.44 and 25 private alleles. The analysis with 115 SSR markers identified 43 significant associations for grain number per panicle considering the cultivation system upland and three associations for lowland system; 7 significant associations for panicle number per meter for lowland system, and 9 were significant for upland cultivation systems; 14 associations were significant for hundred grain mass in lowland system of cultivarion, and 43 were significant for upland system of cultivarion; 3 associations were significant for grain yield in upland system of cultivarion. The association analysis identified 61 SSR markers consistently associated to yield and its components. It were detected 33 associations statiscally significant to one or more traits, which validated the previous results obtained by QTL mapping. The markers RM125, RM152 e Q69JE3 showed the higher number of associations per trait. The association productivity and PCG, and NCP, respectively, were previously found in the literature. The markers associated to the evaluated traits permit to initiate a scientific program to identify the candidate genes and to proceed the marker assisted selection The accessions CNA0001107, CNA0005478, CNA0010533, CNA0003287, IR 36, CNA0003602, CNA0006413, CNA0006174, CNA0003289, CNA0002253, CNA0004098, CNA0001416, CNA0003490 e CNA0000994 showed the highest number of favorable alleles considering 16 the markers associated to yield and its components. The identified accessions from this work as having the higher number of favorable alleles from the evaluated traits will be recommended to be used as genitors in Brazilian rice breeding programs. The mixed approaches to the associative mapping used in the present work was interesting to permit that, even using a low marker density, in couple with the linkage disequilibrium found in rice, some previously mapped markers from QTL analyses were again associated to traits evaluated in field experiments. This strategy can be used to other traits of interest for rice, such as drought and cold tolerance, and disease resistance.O arroz é consumido por mais da metade da população mundial. As expectativas de aumento substancial da população, e consequentemente aumento do consumo, têm demonstrado que a produção atual da cultura não suprirá a demanda. A produção de grãos do arroz é uma característica complexa determinada pelos seus três componentes: número de panículas, número de grãos por panícula e peso de grãos, os quais são típicos caracteres quantitativos. A evolução no mapeamento do genoma, o sequenciamento e as pesquisas em genômica funcional têm fornecido ferramentas poderosas para estudar as bases genética e molecular desses caracteres quantitativos. Buscando identificar regiões genômicas responsáveis pela produtividade e componentes de produção (número de panículas por metro, número de grãos por panícula e peso de 100 grãos), foi realizada a análise de mapeamento associativo. O mapeamento associativo foi realizado com dois tipos de marcadores SSR: a) marcadores fluorescentes, e b) marcadores desenvolvidos a partir de transcritos de regiões genômicas ancoradas por marcadores previamente relacionados à produção e seus componentes por 27 análises de QTLs publicadas na literatura. Dessa forma, nesse trabalho foi utilizada uma metodologia híbrida de mapeamento associativo incluindo as técnicas de whole genome scanning e de genes candidatos. A caracterização molecular foi realizada em 186 acessos da coleção nuclear de arroz da embrapa (CNAE), sendo 76 acessos do sistema de cultivo irrigado e 113 do sistema de cultivo de sequeiro, selecionados por não apresentarem vínculo genético. Destes três acessos foram utilizados como testemunha em ambos experimentos, sendo BR Irga 409, Metica 1 e BRS Caiapó. Os acessos foram avaliados em dois experimentos de campo, um para os genótipos do sistema de cultivo irrigado, e outro para os do sistema de cultivo de sequeiro, no delineamento de blocos casualizados com 4 repetições. Foram avaliados os seguintes caracteres: Número de panículas por metro (NPM), Número de grãos por panícula (NGP), Peso de 100 grãos (PCG) e Produtividade em kg.ha-1 (Prod). Para a análise de associação foram utilizados 29 marcadores SSR derivados de transcritos e 86 marcadores SSR derivados de sequências do DNA estrutural. Em relação as análises fenotípicas, os coeficientes de variação obtidos foram consistentes de acordo com o sistema de cultivo. Para os acessos de arroz irrigado foi verificada correlação positiva para NPM e Prod (0,2424; p<0,01) e Prod e PCG (0,1457; p<0,05) e correlação negativa para NPM e NGP (-0,457; p<0,01). Para os acessos do sistema de cultivo de sequeiro foi observada correlação positiva para NGP e Prod (0,4243; p<0,01). Correlação negativa foi observada para NPM e PCG (-0,2114; p<0,01). Em relação aos dados moleculares, para este trabalho foram desenvolvidos 44 marcadores SSR baseados em 27 mapas de QTLs. Destes, foram obtidos 181 alelos e uma média de 5,5 alelos por loco. Resultante da análise dos 44 marcadores SSR foram obtidos 29 marcadores que apresentaram padrão de bandas polimórfico, destes foram obtidas um PIC médio de 0,44 e 25 alelos privados. Para a análise de associação foram usados 29 marcadores polimórficos juntamente aos 86 marcadores fluorescentes (previamente avaliados por Borba et al. 2009), foram identificadas 43 associações significativas para NGP nos acessos de sequeiro e três associações significativas nos acessos de irrigado; 7 associações significativas para NPM nos acessos de irrigado e 9 associações significativas nos acessos de sequeiro; 14 associações foram significativas para PCG nos acessos de irrigado e 43 associações foram significativas nos acessos de sequeiro; 14 3 associações significativas para Prod foram encontradas nos acessos de sequeiro. A análise de associação identificou 61 marcadores SSR associados de forma consistente à produção e aos seus componentes. Foram detectadas 33 associações estatisticamente significativas a um ou mais caracteres, as quais validaram os resultados encontrados por meio das análises de mapeamento de QTLs realizadas em trabalhos anteriores. Os marcadores RM125, RM152 e Q69JE3 apresentaram maior número de associações por caracteres, sendo que algumas associações já foram previamente descritas na literatura. Os marcadores associados aos caracteres avaliados podem ser usados em programa de melhoramento visando a identificação de genes candidatos e seleção assistida. Os acessos CNA0001107, CNA0005478, CNA0010533, CNA0003287, IR 36, CNA0003602, CNA0006413, CNA0006174, CNA0003289, CNA0002253, CNA0004098, CNA0001416, CNA0003490 e CNA0000994 foram os que apresentaram o maior número de alelos favoráveis nos locos marcadores associados aos caracteres produção e seus componentes. Os acessos identificados por este trabalho como tendo o maior número de alelos favoráveis para os caracteres avaliadas serão recomendados para uso como genitores em programas de melhoramento de arroz do Brasil. A metodologia híbrida de mapeamento associativo utilizado por este trabalho foi interessante por permitir que, mesmo utilizando baixa resolução, juntamente com o desequilíbrio de ligação encontrado em arroz, determinados locos previamente mapeados em análises de QTLs foram novamente associados aos caracteres avaliados nos ensaios de campo. Esta estratégia pode ser repetida para outros caracteres de interesse em arroz, como tolerância à seca e frio e resistência a doenças.Submitted by Erika Demachki (erikademachki@gmail.com) on 2014-10-13T20:47:06Z No. of bitstreams: 2 Dissertacão - Clistiane dos Anjos Mendes - 2010.pdf: 3556172 bytes, checksum: 0afdcb2cfe1cae06f8e21fb23ad19fba (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5)Approved for entry into archive by Jaqueline Silva (jtas29@gmail.com) on 2014-10-13T21:16:57Z (GMT) No. of bitstreams: 2 Dissertacão - Clistiane dos Anjos Mendes - 2010.pdf: 3556172 bytes, checksum: 0afdcb2cfe1cae06f8e21fb23ad19fba (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5)Made available in DSpace on 2014-10-13T21:16:57Z (GMT). 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dc.title.por.fl_str_mv |
Estudos de associação entre locos SSR e componentes da produção em arroz (Oryza sativa L.) |
dc.title.alternative.eng.fl_str_mv |
Studies of association between SSR loci and yield componests in rice (Oryza sativa L.) |
title |
Estudos de associação entre locos SSR e componentes da produção em arroz (Oryza sativa L.) |
spellingShingle |
Estudos de associação entre locos SSR e componentes da produção em arroz (Oryza sativa L.) Bueno, Clistiane dos Anjos Mendes Oryza sativa L. Coleção nuclear Mapeamento associativo Core collection Association mapping AGRONOMIA::CIENCIA DO SOLO |
title_short |
Estudos de associação entre locos SSR e componentes da produção em arroz (Oryza sativa L.) |
title_full |
Estudos de associação entre locos SSR e componentes da produção em arroz (Oryza sativa L.) |
title_fullStr |
Estudos de associação entre locos SSR e componentes da produção em arroz (Oryza sativa L.) |
title_full_unstemmed |
Estudos de associação entre locos SSR e componentes da produção em arroz (Oryza sativa L.) |
title_sort |
Estudos de associação entre locos SSR e componentes da produção em arroz (Oryza sativa L.) |
author |
Bueno, Clistiane dos Anjos Mendes |
author_facet |
Bueno, Clistiane dos Anjos Mendes |
author_role |
author |
dc.contributor.advisor1.fl_str_mv |
Brondani, Claudio |
dc.contributor.advisor1Lattes.fl_str_mv |
http://lattes.cnpq.br/4775600104554147 |
dc.contributor.advisor-co1.fl_str_mv |
Vianello, Rosana P. |
dc.contributor.referee1.fl_str_mv |
Borba, Tereza Cristina de Oliveira |
dc.contributor.referee2.fl_str_mv |
Coelho, Alexandre Siqueira Guedes |
dc.contributor.referee3.fl_str_mv |
Brondani, Cláudio |
dc.contributor.authorLattes.fl_str_mv |
http://lattes.cnpq.br/8410045564570544 |
dc.contributor.author.fl_str_mv |
Bueno, Clistiane dos Anjos Mendes |
contributor_str_mv |
Brondani, Claudio Vianello, Rosana P. Borba, Tereza Cristina de Oliveira Coelho, Alexandre Siqueira Guedes Brondani, Cláudio |
dc.subject.por.fl_str_mv |
Oryza sativa L. Coleção nuclear Mapeamento associativo |
topic |
Oryza sativa L. Coleção nuclear Mapeamento associativo Core collection Association mapping AGRONOMIA::CIENCIA DO SOLO |
dc.subject.eng.fl_str_mv |
Core collection Association mapping |
dc.subject.cnpq.fl_str_mv |
AGRONOMIA::CIENCIA DO SOLO |
description |
Rice is consumed by more than half of the world population. The expectation of substantial population growth and consequently the increase of the consumption has demontrated that the present rice production will not supply the future’s demand. As a result, studies that aim at the increase of the yield must be prioritized by scientific co&unity. Aiming to identify genomic regions related to grain yield and its component traits (panicle number per meter, grain panicle number and hundred grain mass), it was carried out the associative mapping analysis. The analysis of association used two types of SSR markers: a) structural genome derived markers, and b) transcriptome derived markers, i.e. developed from transcripts from marker-anchored genomic regions previously related to yield and its components from 27 different QTL maps already published. The associative mapping methodology used included the whole genome scanning and candidate genes approaches. The molecular characterization used 186 accessions from Embrapa Rice Core Collection (ERiCC), whereas 76 accessions from lowland system of cultivation, and 113 upland system of cultivation. The experimental design was the randomized block with 4 repetitions, and included the cultivars BR Irga 409, Metica 1 and BRS Caiapó as controls. It were evaluated the following traits: Panicle number per meter (NPM), panicle (NGP), Hundred grain mass (PCG) and productivity. The 186 markers were genotyped by 29 transcript-derived SSR markers and 86 SSR markers derived from structural genome. For the irrigated accessions was verified positive correlation for panicle number per meter and productivity (0,2424; p<0,01) and by productivity and hundred grain mass (p<0,05; 0,1457) and negative correlation for panicle number per meter and grain number per panicle (-0,457; p<0,01). For the upland accessions it was observed positive correlation for grain number per panicle and productivity (0,4243; p<0,01). Negative correlations were observed for panicle number per meter and hundred grain weight (p<0,01; -0,2114). Based on 44 SSR markers developed in this work, 181 alelles were detected, an average of 5.5 alelles per locus, average PIC of 0.44 and 25 private alleles. The analysis with 115 SSR markers identified 43 significant associations for grain number per panicle considering the cultivation system upland and three associations for lowland system; 7 significant associations for panicle number per meter for lowland system, and 9 were significant for upland cultivation systems; 14 associations were significant for hundred grain mass in lowland system of cultivarion, and 43 were significant for upland system of cultivarion; 3 associations were significant for grain yield in upland system of cultivarion. The association analysis identified 61 SSR markers consistently associated to yield and its components. It were detected 33 associations statiscally significant to one or more traits, which validated the previous results obtained by QTL mapping. The markers RM125, RM152 e Q69JE3 showed the higher number of associations per trait. The association productivity and PCG, and NCP, respectively, were previously found in the literature. The markers associated to the evaluated traits permit to initiate a scientific program to identify the candidate genes and to proceed the marker assisted selection The accessions CNA0001107, CNA0005478, CNA0010533, CNA0003287, IR 36, CNA0003602, CNA0006413, CNA0006174, CNA0003289, CNA0002253, CNA0004098, CNA0001416, CNA0003490 e CNA0000994 showed the highest number of favorable alleles considering 16 the markers associated to yield and its components. The identified accessions from this work as having the higher number of favorable alleles from the evaluated traits will be recommended to be used as genitors in Brazilian rice breeding programs. The mixed approaches to the associative mapping used in the present work was interesting to permit that, even using a low marker density, in couple with the linkage disequilibrium found in rice, some previously mapped markers from QTL analyses were again associated to traits evaluated in field experiments. This strategy can be used to other traits of interest for rice, such as drought and cold tolerance, and disease resistance. |
publishDate |
2010 |
dc.date.issued.fl_str_mv |
2010-08-16 |
dc.date.accessioned.fl_str_mv |
2014-10-13T21:16:57Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/masterThesis |
format |
masterThesis |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
BUENO, Clistiane dos Anjos Mendes. Estudos de associação entre locos SSR e componentes da produção em arroz (Oryza sativa L.). 2010. 139 f. Dissertação (Mestrado em Agronomia) - Universidade Federal de Goiás, Goiânia, 2010. |
dc.identifier.uri.fl_str_mv |
http://repositorio.bc.ufg.br/tede/handle/tede/3340 |
identifier_str_mv |
BUENO, Clistiane dos Anjos Mendes. Estudos de associação entre locos SSR e componentes da produção em arroz (Oryza sativa L.). 2010. 139 f. Dissertação (Mestrado em Agronomia) - Universidade Federal de Goiás, Goiânia, 2010. |
url |
http://repositorio.bc.ufg.br/tede/handle/tede/3340 |
dc.language.iso.fl_str_mv |
por |
language |
por |
dc.relation.program.fl_str_mv |
842119561133988381 |
dc.relation.confidence.fl_str_mv |
600 600 600 600 |
dc.relation.department.fl_str_mv |
4500684695727928426 |
dc.relation.cnpq.fl_str_mv |
-5919840527232375671 |
dc.relation.sponsorship.fl_str_mv |
-2555911436985713659 |
dc.rights.driver.fl_str_mv |
http://creativecommons.org/licenses/by-nc-nd/4.0/ info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
http://creativecommons.org/licenses/by-nc-nd/4.0/ |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Universidade Federal de Goiás |
dc.publisher.program.fl_str_mv |
Programa de Pós-graduação em Agronomia (EAEA) |
dc.publisher.initials.fl_str_mv |
UFG |
dc.publisher.country.fl_str_mv |
Brasil |
dc.publisher.department.fl_str_mv |
Escola de Agronomia e Engenharia de Alimentos - EAEA (RG) |
publisher.none.fl_str_mv |
Universidade Federal de Goiás |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da UFG instname:Universidade Federal de Goiás (UFG) instacron:UFG |
instname_str |
Universidade Federal de Goiás (UFG) |
instacron_str |
UFG |
institution |
UFG |
reponame_str |
Repositório Institucional da UFG |
collection |
Repositório Institucional da UFG |
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