SNP markers found in non-coding regions can distinguish among low-variant genotypes of arabica and other coffee species.
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
Texto Completo: | http://www.alice.cnptia.embrapa.br/alice/handle/doc/1150820 https://doi.org/10.1007/s10722-022-01498-0 |
Resumo: | Development of efficient and scalable methods for molecular identification of Coffea spp. are necessary to accelerate studies related to the characterization of germplasm for both conservation or breeding purposes, and the validation of coffee germplasm. The low genetic diversity of coffee hinders the establishment of protocols that facilitate the molecular characterization of a given genotype. In this study, nucleotide variability was analyzed at 22 loci in the genome of 19 coffee accessions using de novo primer sets and high-resolution melting (HRM). Single nucleotide polymorphisms (SNPs) variants were studied in coding regions of genes implicated in sucrose accumulation in the seed, Sucrose synthase 2 (SUS2), Ent-kaurene oxidase 1 (CaKO1), and Caffeoyl-coenzyme A 3-O-methyltransferase (CcOAOMT). The non-coding Internal transcribed spacer 2 (ITS2) region was also studied. Variability was shown at 103 positions both at the interspecies level (15 loci) and among varieties of Coffea arabica L. (4 loci). The HMR technique for identification of variants in genes CaKO1, SUS2, CcoAOMT, as well as in the ITS2 region proved to be a robust technique for germplasm characterization. More important this technique can be used for fingerprinting and traceability of coffee grain exports which is an increasing market-consumer demand. |
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SNP markers found in non-coding regions can distinguish among low-variant genotypes of arabica and other coffee species.Coffea ArábicaGenotypeSingle nucleotide polymorphismDevelopment of efficient and scalable methods for molecular identification of Coffea spp. are necessary to accelerate studies related to the characterization of germplasm for both conservation or breeding purposes, and the validation of coffee germplasm. The low genetic diversity of coffee hinders the establishment of protocols that facilitate the molecular characterization of a given genotype. In this study, nucleotide variability was analyzed at 22 loci in the genome of 19 coffee accessions using de novo primer sets and high-resolution melting (HRM). Single nucleotide polymorphisms (SNPs) variants were studied in coding regions of genes implicated in sucrose accumulation in the seed, Sucrose synthase 2 (SUS2), Ent-kaurene oxidase 1 (CaKO1), and Caffeoyl-coenzyme A 3-O-methyltransferase (CcOAOMT). The non-coding Internal transcribed spacer 2 (ITS2) region was also studied. Variability was shown at 103 positions both at the interspecies level (15 loci) and among varieties of Coffea arabica L. (4 loci). The HMR technique for identification of variants in genes CaKO1, SUS2, CcoAOMT, as well as in the ITS2 region proved to be a robust technique for germplasm characterization. More important this technique can be used for fingerprinting and traceability of coffee grain exports which is an increasing market-consumer demand.ALEJANDRO BOLÍVAR-GONZÁLEZ, UNIVERSIDAD DE COSTA RICA; RAMÓN MOLINA-BRAVO, UNIVERSIDAD NACIONAL; WILLIAM SOLANO-SÁNCHEZ, CENTRO AGRONÓMICO TROPICAL DE INVESTIGACIÓN Y ENSEÑANZA; EMANUEL ARAYA-VALVERDE, CENTRO NACIONAL DE INNOVACIONES BIOTECNOLÓGICAS; SUZANA T. IVAMOTO-SUZUKI, INSTITUTO DE DESENVOLVIMENTO RURAL DO PARANÁ; LUIZ FILIPE PROTASIO PEREIRA, CNPCa; ANDRÉS GATICA-ARIAS, UNIVERSIDAD DE COSTA RICA.BOLÍVAR-GONZÁLEZ, L.MOLINA-BRAVO, R.SOLANO-SÁNCHEZ, W.ARAYA-VALVERDE, E.IVAMOTO-SUZUKI, S. T.PEREIRA, L. F. P.GATICA-ARIAS, A.2023-01-09T20:01:32Z2023-01-09T20:01:32Z2023-01-092022info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleGenetic Resources and Crop Evolution, Dec. 2022.http://www.alice.cnptia.embrapa.br/alice/handle/doc/1150820https://doi.org/10.1007/s10722-022-01498-0enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2023-01-09T20:01:32Zoai:www.alice.cnptia.embrapa.br:doc/1150820Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542023-01-09T20:01:32falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542023-01-09T20:01:32Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false |
dc.title.none.fl_str_mv |
SNP markers found in non-coding regions can distinguish among low-variant genotypes of arabica and other coffee species. |
title |
SNP markers found in non-coding regions can distinguish among low-variant genotypes of arabica and other coffee species. |
spellingShingle |
SNP markers found in non-coding regions can distinguish among low-variant genotypes of arabica and other coffee species. BOLÍVAR-GONZÁLEZ, L. Coffea Arábica Genotype Single nucleotide polymorphism |
title_short |
SNP markers found in non-coding regions can distinguish among low-variant genotypes of arabica and other coffee species. |
title_full |
SNP markers found in non-coding regions can distinguish among low-variant genotypes of arabica and other coffee species. |
title_fullStr |
SNP markers found in non-coding regions can distinguish among low-variant genotypes of arabica and other coffee species. |
title_full_unstemmed |
SNP markers found in non-coding regions can distinguish among low-variant genotypes of arabica and other coffee species. |
title_sort |
SNP markers found in non-coding regions can distinguish among low-variant genotypes of arabica and other coffee species. |
author |
BOLÍVAR-GONZÁLEZ, L. |
author_facet |
BOLÍVAR-GONZÁLEZ, L. MOLINA-BRAVO, R. SOLANO-SÁNCHEZ, W. ARAYA-VALVERDE, E. IVAMOTO-SUZUKI, S. T. PEREIRA, L. F. P. GATICA-ARIAS, A. |
author_role |
author |
author2 |
MOLINA-BRAVO, R. SOLANO-SÁNCHEZ, W. ARAYA-VALVERDE, E. IVAMOTO-SUZUKI, S. T. PEREIRA, L. F. P. GATICA-ARIAS, A. |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
ALEJANDRO BOLÍVAR-GONZÁLEZ, UNIVERSIDAD DE COSTA RICA; RAMÓN MOLINA-BRAVO, UNIVERSIDAD NACIONAL; WILLIAM SOLANO-SÁNCHEZ, CENTRO AGRONÓMICO TROPICAL DE INVESTIGACIÓN Y ENSEÑANZA; EMANUEL ARAYA-VALVERDE, CENTRO NACIONAL DE INNOVACIONES BIOTECNOLÓGICAS; SUZANA T. IVAMOTO-SUZUKI, INSTITUTO DE DESENVOLVIMENTO RURAL DO PARANÁ; LUIZ FILIPE PROTASIO PEREIRA, CNPCa; ANDRÉS GATICA-ARIAS, UNIVERSIDAD DE COSTA RICA. |
dc.contributor.author.fl_str_mv |
BOLÍVAR-GONZÁLEZ, L. MOLINA-BRAVO, R. SOLANO-SÁNCHEZ, W. ARAYA-VALVERDE, E. IVAMOTO-SUZUKI, S. T. PEREIRA, L. F. P. GATICA-ARIAS, A. |
dc.subject.por.fl_str_mv |
Coffea Arábica Genotype Single nucleotide polymorphism |
topic |
Coffea Arábica Genotype Single nucleotide polymorphism |
description |
Development of efficient and scalable methods for molecular identification of Coffea spp. are necessary to accelerate studies related to the characterization of germplasm for both conservation or breeding purposes, and the validation of coffee germplasm. The low genetic diversity of coffee hinders the establishment of protocols that facilitate the molecular characterization of a given genotype. In this study, nucleotide variability was analyzed at 22 loci in the genome of 19 coffee accessions using de novo primer sets and high-resolution melting (HRM). Single nucleotide polymorphisms (SNPs) variants were studied in coding regions of genes implicated in sucrose accumulation in the seed, Sucrose synthase 2 (SUS2), Ent-kaurene oxidase 1 (CaKO1), and Caffeoyl-coenzyme A 3-O-methyltransferase (CcOAOMT). The non-coding Internal transcribed spacer 2 (ITS2) region was also studied. Variability was shown at 103 positions both at the interspecies level (15 loci) and among varieties of Coffea arabica L. (4 loci). The HMR technique for identification of variants in genes CaKO1, SUS2, CcoAOMT, as well as in the ITS2 region proved to be a robust technique for germplasm characterization. More important this technique can be used for fingerprinting and traceability of coffee grain exports which is an increasing market-consumer demand. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022 2023-01-09T20:01:32Z 2023-01-09T20:01:32Z 2023-01-09 |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
Genetic Resources and Crop Evolution, Dec. 2022. http://www.alice.cnptia.embrapa.br/alice/handle/doc/1150820 https://doi.org/10.1007/s10722-022-01498-0 |
identifier_str_mv |
Genetic Resources and Crop Evolution, Dec. 2022. |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1150820 https://doi.org/10.1007/s10722-022-01498-0 |
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.source.none.fl_str_mv |
reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA |
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Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
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EMBRAPA |
institution |
EMBRAPA |
reponame_str |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
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Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
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Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
repository.mail.fl_str_mv |
cg-riaa@embrapa.br |
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1794503537096392704 |