Genome-wide association study for morphological, physiological, and productive traits in Coffea arabica using structural equation models.
Autor(a) principal: | |
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Data de Publicação: | 2023 |
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/1157822 https://doi.org/10.1007/s11295-023-01597-8 |
Resumo: | Yield is one of the most important traits of arabica coffee. Plant breeders seek to maximize yield directly or indirectly, using other related traits. The standard multi-trait genome-wide association study (MTM-GWAS) does not accommodate the network structure of phenotypes, therefore, does not address how traits are interrelated. We applied structural equation modeling (SEM) to GWAS to explore interrelated dependencies between phenotypes related to morphology (fruit size and number of reproductive nodes), physiology (vegetative vigor), and productivity (yield) traits using 195 Coffea arábica individuals genotyped with 21,211 single-nucleotide polymorphism markers. We inferred the probabilistic phenotypic network by the Hill-Climbing algorithm to estimate the structural coefficients. The integration of multivariate GWAS and SEM (SEM-GWAS) identified a positive interrelationship between vegetative vigor and yield, and vegetative vigor and the number of reproductive nodes. Among those traits, yield and number of reproductive nodes presented indirect SNP effects. There was no evidence of a single quantitative trait locus controlling all the traits jointly. We identified three genes (Stress enhanced protein 1, Abscisic stress-ripening protein 5, and SAR?SNI1) that acted directly on yield. In summary, SEM-GWAS offered new insights into the relationship between the traits linked to coffee yield, providing useful information for arabica coffee breeding programs. |
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Genome-wide association study for morphological, physiological, and productive traits in Coffea arabica using structural equation models.Structural equation modelingGenome-wide association studySingle nucleotide polymorphismCoffea arabica var. arabicaYield is one of the most important traits of arabica coffee. Plant breeders seek to maximize yield directly or indirectly, using other related traits. The standard multi-trait genome-wide association study (MTM-GWAS) does not accommodate the network structure of phenotypes, therefore, does not address how traits are interrelated. We applied structural equation modeling (SEM) to GWAS to explore interrelated dependencies between phenotypes related to morphology (fruit size and number of reproductive nodes), physiology (vegetative vigor), and productivity (yield) traits using 195 Coffea arábica individuals genotyped with 21,211 single-nucleotide polymorphism markers. We inferred the probabilistic phenotypic network by the Hill-Climbing algorithm to estimate the structural coefficients. The integration of multivariate GWAS and SEM (SEM-GWAS) identified a positive interrelationship between vegetative vigor and yield, and vegetative vigor and the number of reproductive nodes. Among those traits, yield and number of reproductive nodes presented indirect SNP effects. There was no evidence of a single quantitative trait locus controlling all the traits jointly. We identified three genes (Stress enhanced protein 1, Abscisic stress-ripening protein 5, and SAR?SNI1) that acted directly on yield. In summary, SEM-GWAS offered new insights into the relationship between the traits linked to coffee yield, providing useful information for arabica coffee breeding programs.MATHEUS MASSARIOL SUELA, UNIVERSIDADE FEDERAL DE VIÇOSA; CAMILA FERREIRA AZEVEDO, UNIVERSIDADE FEDERAL DE VIÇOSA; ANA CAROLINA CAMPANA NASCIMENTO, UNIVERSIDADE FEDERAL DE VIÇOSA; MEHDI MOMEN, UNIVERSITY OF WISCONSIN-MADISON; ANTONIO CARLOS BAIAO DE OLIVEIRA, CNPCa; EVELINE TEIXEIRA CAIXETA MOURA, CNPCa; GOTA MOROTA, VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY; MOYSÉS NASCIMENTO, UNIVERSIDADE FEDERAL DE VIÇOSA.SUELA, M. M.AZEVEDO, C. F.NASCIMENTO, A. C. C.MOMEN, M.OLIVEIRA, A. C. B. deCAIXETA, E. T.MOROTA, G.NASCIMENTO, M.2023-11-06T18:31:29Z2023-11-06T18:31:29Z2023-11-062023info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article17 p.Tree Genetics & Genomes, v. 19, n. 3, 2023.http://www.alice.cnptia.embrapa.br/alice/handle/doc/1157822https://doi.org/10.1007/s11295-023-01597-8enginfo: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:EMBRAPA2023-11-06T18:31:29Zoai:www.alice.cnptia.embrapa.br:doc/1157822Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542023-11-06T18:31:29falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542023-11-06T18:31:29Repositório 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 |
Genome-wide association study for morphological, physiological, and productive traits in Coffea arabica using structural equation models. |
title |
Genome-wide association study for morphological, physiological, and productive traits in Coffea arabica using structural equation models. |
spellingShingle |
Genome-wide association study for morphological, physiological, and productive traits in Coffea arabica using structural equation models. SUELA, M. M. Structural equation modeling Genome-wide association study Single nucleotide polymorphism Coffea arabica var. arabica |
title_short |
Genome-wide association study for morphological, physiological, and productive traits in Coffea arabica using structural equation models. |
title_full |
Genome-wide association study for morphological, physiological, and productive traits in Coffea arabica using structural equation models. |
title_fullStr |
Genome-wide association study for morphological, physiological, and productive traits in Coffea arabica using structural equation models. |
title_full_unstemmed |
Genome-wide association study for morphological, physiological, and productive traits in Coffea arabica using structural equation models. |
title_sort |
Genome-wide association study for morphological, physiological, and productive traits in Coffea arabica using structural equation models. |
author |
SUELA, M. M. |
author_facet |
SUELA, M. M. AZEVEDO, C. F. NASCIMENTO, A. C. C. MOMEN, M. OLIVEIRA, A. C. B. de CAIXETA, E. T. MOROTA, G. NASCIMENTO, M. |
author_role |
author |
author2 |
AZEVEDO, C. F. NASCIMENTO, A. C. C. MOMEN, M. OLIVEIRA, A. C. B. de CAIXETA, E. T. MOROTA, G. NASCIMENTO, M. |
author2_role |
author author author author author author author |
dc.contributor.none.fl_str_mv |
MATHEUS MASSARIOL SUELA, UNIVERSIDADE FEDERAL DE VIÇOSA; CAMILA FERREIRA AZEVEDO, UNIVERSIDADE FEDERAL DE VIÇOSA; ANA CAROLINA CAMPANA NASCIMENTO, UNIVERSIDADE FEDERAL DE VIÇOSA; MEHDI MOMEN, UNIVERSITY OF WISCONSIN-MADISON; ANTONIO CARLOS BAIAO DE OLIVEIRA, CNPCa; EVELINE TEIXEIRA CAIXETA MOURA, CNPCa; GOTA MOROTA, VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY; MOYSÉS NASCIMENTO, UNIVERSIDADE FEDERAL DE VIÇOSA. |
dc.contributor.author.fl_str_mv |
SUELA, M. M. AZEVEDO, C. F. NASCIMENTO, A. C. C. MOMEN, M. OLIVEIRA, A. C. B. de CAIXETA, E. T. MOROTA, G. NASCIMENTO, M. |
dc.subject.por.fl_str_mv |
Structural equation modeling Genome-wide association study Single nucleotide polymorphism Coffea arabica var. arabica |
topic |
Structural equation modeling Genome-wide association study Single nucleotide polymorphism Coffea arabica var. arabica |
description |
Yield is one of the most important traits of arabica coffee. Plant breeders seek to maximize yield directly or indirectly, using other related traits. The standard multi-trait genome-wide association study (MTM-GWAS) does not accommodate the network structure of phenotypes, therefore, does not address how traits are interrelated. We applied structural equation modeling (SEM) to GWAS to explore interrelated dependencies between phenotypes related to morphology (fruit size and number of reproductive nodes), physiology (vegetative vigor), and productivity (yield) traits using 195 Coffea arábica individuals genotyped with 21,211 single-nucleotide polymorphism markers. We inferred the probabilistic phenotypic network by the Hill-Climbing algorithm to estimate the structural coefficients. The integration of multivariate GWAS and SEM (SEM-GWAS) identified a positive interrelationship between vegetative vigor and yield, and vegetative vigor and the number of reproductive nodes. Among those traits, yield and number of reproductive nodes presented indirect SNP effects. There was no evidence of a single quantitative trait locus controlling all the traits jointly. We identified three genes (Stress enhanced protein 1, Abscisic stress-ripening protein 5, and SAR?SNI1) that acted directly on yield. In summary, SEM-GWAS offered new insights into the relationship between the traits linked to coffee yield, providing useful information for arabica coffee breeding programs. |
publishDate |
2023 |
dc.date.none.fl_str_mv |
2023-11-06T18:31:29Z 2023-11-06T18:31:29Z 2023-11-06 2023 |
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 |
Tree Genetics & Genomes, v. 19, n. 3, 2023. http://www.alice.cnptia.embrapa.br/alice/handle/doc/1157822 https://doi.org/10.1007/s11295-023-01597-8 |
identifier_str_mv |
Tree Genetics & Genomes, v. 19, n. 3, 2023. |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1157822 https://doi.org/10.1007/s11295-023-01597-8 |
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.format.none.fl_str_mv |
17 p. |
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 |
instname_str |
Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
instacron_str |
EMBRAPA |
institution |
EMBRAPA |
reponame_str |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
collection |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
repository.name.fl_str_mv |
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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1794503551390580736 |