Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultiv...

Autores
Tagliotti, Martín; Deperi, Sofia; Bedogni, Maria Cecilia; Zhang, Roufang; Manrique Carpintero, Norma C.; Coombs, Joseph; Douches, David; Huarte, Marcelo Atilio
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: Diversity in crops is fundamental for plant breeding efforts. An accurate assessment of genetic diversity, using molecular markers, such as single nucleotide polymorphism (SNP), must be able to reveal the structure of the population under study. A characterization of population structure using easy measurable phenotypic traits could be a preliminary and low-cost approach to elucidate the genetic structure of a population. A potato population of 183 genotypes was evaluated using 4859 high-quality SNPs and 19 phenotypic traits commonly recorded in potato breeding programs. A Bayesian approach, Minimum Spanning Tree (MST) and diversity estimator, as well as multivariate analysis based on phenotypic traits, were adopted to assess the population structure. Results: Analysis based on molecular markers showed groups linked to the phylogenetic relationship among the germplasm as well as the link with the breeding program that provided the material. Diversity estimators consistently structured the population according to a priori group estimation. The phenotypic traits only discriminated main groups with contrasting characteristics, as different subspecies, ploidy level or membership in a breeding program, but were not able to discriminate within groups. A joint molecular and phenotypic characterization analysis discriminated groups based on phenotypic classification, taxonomic category, provenance source of genotypes and genetic background. Conclusions: This paper shows the significant level of diversity existing in a parental population of potato as well as the putative phylogenetic relationships among the genotypes. The use of easily measurable phenotypic traits among highly contrasting genotypes could be a reasonable approach to estimate population structure in the initial phases of a potato breeding program.
EEA Balcarce
Fil: Tagliotti, Martín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.
Fil: Deperi, Sofía. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.
Fil: Bedogni, María Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina.
Fil: Zhang, R. Inner Mongolia University. Potato Engineering and Technology Research Centre; China
Fil: Manrique Carpintero, Norma C. Michigan State University. Department of Plant, Molecular Plant Sciences Bldg; Estados Unidos
Fil: Coombs, Joseph. Michigan State University. Department of Plant, Molecular Plant Sciences Bldg; Estados Unidos
Fil: Douches, David. Michigan State University. Department of Plant, Molecular Plant Sciences Bldg; Estados Unidos
Fil: Huarte, Marcelo Atilio. INTA, Estación Experimental Agropecuaria Balcarce; Argentina.
Fuente
BMC Genetics 19 (1) : 8 (January 2018)
Materia
Papa
Solanun tuberosum
Fenotipos
Diversidad Genética
Estructura de la Población
Potatoes
Phenotypes
Genetic Divergence
Population Structure
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/4849
Acceder
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oai_identifier_str oai:localhost:20.500.12123/4849
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network_name_str INTA Digital (INTA)
spelling Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivarsTagliotti, MartínDeperi, SofiaBedogni, Maria CeciliaZhang, RoufangManrique Carpintero, Norma C.Coombs, JosephDouches, DavidHuarte, Marcelo AtilioPapaSolanun tuberosumFenotiposDiversidad GenéticaEstructura de la PoblaciónPotatoesPhenotypesGenetic DivergencePopulation StructureBackground: Diversity in crops is fundamental for plant breeding efforts. An accurate assessment of genetic diversity, using molecular markers, such as single nucleotide polymorphism (SNP), must be able to reveal the structure of the population under study. A characterization of population structure using easy measurable phenotypic traits could be a preliminary and low-cost approach to elucidate the genetic structure of a population. A potato population of 183 genotypes was evaluated using 4859 high-quality SNPs and 19 phenotypic traits commonly recorded in potato breeding programs. A Bayesian approach, Minimum Spanning Tree (MST) and diversity estimator, as well as multivariate analysis based on phenotypic traits, were adopted to assess the population structure. Results: Analysis based on molecular markers showed groups linked to the phylogenetic relationship among the germplasm as well as the link with the breeding program that provided the material. Diversity estimators consistently structured the population according to a priori group estimation. The phenotypic traits only discriminated main groups with contrasting characteristics, as different subspecies, ploidy level or membership in a breeding program, but were not able to discriminate within groups. A joint molecular and phenotypic characterization analysis discriminated groups based on phenotypic classification, taxonomic category, provenance source of genotypes and genetic background. Conclusions: This paper shows the significant level of diversity existing in a parental population of potato as well as the putative phylogenetic relationships among the genotypes. The use of easily measurable phenotypic traits among highly contrasting genotypes could be a reasonable approach to estimate population structure in the initial phases of a potato breeding program.EEA BalcarceFil: Tagliotti, Martín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Deperi, Sofía. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Bedogni, María Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina.Fil: Zhang, R. Inner Mongolia University. Potato Engineering and Technology Research Centre; ChinaFil: Manrique Carpintero, Norma C. Michigan State University. Department of Plant, Molecular Plant Sciences Bldg; Estados UnidosFil: Coombs, Joseph. Michigan State University. Department of Plant, Molecular Plant Sciences Bldg; Estados UnidosFil: Douches, David. Michigan State University. Department of Plant, Molecular Plant Sciences Bldg; Estados UnidosFil: Huarte, Marcelo Atilio. INTA, Estación Experimental Agropecuaria Balcarce; Argentina.Springer Nature2019-04-09T11:25:04Z2019-04-09T11:25:04Z2018-01-16info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttps://bmcgenet.biomedcentral.com/articles/10.1186/s12863-017-0556-9http://hdl.handle.net/20.500.12123/48491471-2156https://doi.org/10.1186/s12863-017-0556-9BMC Genetics 19 (1) : 8 (January 2018)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-10-23T11:16:54Zoai:localhost:20.500.12123/4849instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-10-23 11:16:54.974INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars
title Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars
spellingShingle Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars
Tagliotti, Martín
Papa
Solanun tuberosum
Fenotipos
Diversidad Genética
Estructura de la Población
Potatoes
Phenotypes
Genetic Divergence
Population Structure
title_short Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars
title_full Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars
title_fullStr Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars
title_full_unstemmed Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars
title_sort Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars
dc.creator.none.fl_str_mv Tagliotti, Martín
Deperi, Sofia
Bedogni, Maria Cecilia
Zhang, Roufang
Manrique Carpintero, Norma C.
Coombs, Joseph
Douches, David
Huarte, Marcelo Atilio
author Tagliotti, Martín
author_facet Tagliotti, Martín
Deperi, Sofia
Bedogni, Maria Cecilia
Zhang, Roufang
Manrique Carpintero, Norma C.
Coombs, Joseph
Douches, David
Huarte, Marcelo Atilio
author_role author
author2 Deperi, Sofia
Bedogni, Maria Cecilia
Zhang, Roufang
Manrique Carpintero, Norma C.
Coombs, Joseph
Douches, David
Huarte, Marcelo Atilio
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Papa
Solanun tuberosum
Fenotipos
Diversidad Genética
Estructura de la Población
Potatoes
Phenotypes
Genetic Divergence
Population Structure
topic Papa
Solanun tuberosum
Fenotipos
Diversidad Genética
Estructura de la Población
Potatoes
Phenotypes
Genetic Divergence
Population Structure
dc.description.none.fl_txt_mv Background: Diversity in crops is fundamental for plant breeding efforts. An accurate assessment of genetic diversity, using molecular markers, such as single nucleotide polymorphism (SNP), must be able to reveal the structure of the population under study. A characterization of population structure using easy measurable phenotypic traits could be a preliminary and low-cost approach to elucidate the genetic structure of a population. A potato population of 183 genotypes was evaluated using 4859 high-quality SNPs and 19 phenotypic traits commonly recorded in potato breeding programs. A Bayesian approach, Minimum Spanning Tree (MST) and diversity estimator, as well as multivariate analysis based on phenotypic traits, were adopted to assess the population structure. Results: Analysis based on molecular markers showed groups linked to the phylogenetic relationship among the germplasm as well as the link with the breeding program that provided the material. Diversity estimators consistently structured the population according to a priori group estimation. The phenotypic traits only discriminated main groups with contrasting characteristics, as different subspecies, ploidy level or membership in a breeding program, but were not able to discriminate within groups. A joint molecular and phenotypic characterization analysis discriminated groups based on phenotypic classification, taxonomic category, provenance source of genotypes and genetic background. Conclusions: This paper shows the significant level of diversity existing in a parental population of potato as well as the putative phylogenetic relationships among the genotypes. The use of easily measurable phenotypic traits among highly contrasting genotypes could be a reasonable approach to estimate population structure in the initial phases of a potato breeding program.
EEA Balcarce
Fil: Tagliotti, Martín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.
Fil: Deperi, Sofía. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.
Fil: Bedogni, María Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina.
Fil: Zhang, R. Inner Mongolia University. Potato Engineering and Technology Research Centre; China
Fil: Manrique Carpintero, Norma C. Michigan State University. Department of Plant, Molecular Plant Sciences Bldg; Estados Unidos
Fil: Coombs, Joseph. Michigan State University. Department of Plant, Molecular Plant Sciences Bldg; Estados Unidos
Fil: Douches, David. Michigan State University. Department of Plant, Molecular Plant Sciences Bldg; Estados Unidos
Fil: Huarte, Marcelo Atilio. INTA, Estación Experimental Agropecuaria Balcarce; Argentina.
description Background: Diversity in crops is fundamental for plant breeding efforts. An accurate assessment of genetic diversity, using molecular markers, such as single nucleotide polymorphism (SNP), must be able to reveal the structure of the population under study. A characterization of population structure using easy measurable phenotypic traits could be a preliminary and low-cost approach to elucidate the genetic structure of a population. A potato population of 183 genotypes was evaluated using 4859 high-quality SNPs and 19 phenotypic traits commonly recorded in potato breeding programs. A Bayesian approach, Minimum Spanning Tree (MST) and diversity estimator, as well as multivariate analysis based on phenotypic traits, were adopted to assess the population structure. Results: Analysis based on molecular markers showed groups linked to the phylogenetic relationship among the germplasm as well as the link with the breeding program that provided the material. Diversity estimators consistently structured the population according to a priori group estimation. The phenotypic traits only discriminated main groups with contrasting characteristics, as different subspecies, ploidy level or membership in a breeding program, but were not able to discriminate within groups. A joint molecular and phenotypic characterization analysis discriminated groups based on phenotypic classification, taxonomic category, provenance source of genotypes and genetic background. Conclusions: This paper shows the significant level of diversity existing in a parental population of potato as well as the putative phylogenetic relationships among the genotypes. The use of easily measurable phenotypic traits among highly contrasting genotypes could be a reasonable approach to estimate population structure in the initial phases of a potato breeding program.
publishDate 2018
dc.date.none.fl_str_mv 2018-01-16
2019-04-09T11:25:04Z
2019-04-09T11:25:04Z
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-017-0556-9
http://hdl.handle.net/20.500.12123/4849
1471-2156
https://doi.org/10.1186/s12863-017-0556-9
url https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-017-0556-9
http://hdl.handle.net/20.500.12123/4849
https://doi.org/10.1186/s12863-017-0556-9
identifier_str_mv 1471-2156
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv BMC Genetics 19 (1) : 8 (January 2018)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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score 12.982451

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