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
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...
| Autores principales: | , , , , , , , |
|---|---|
| Formato: | Artículo |
| Lenguaje: | Inglés |
| Publicado: |
Springer Nature
2019
|
| Materias: | |
| Acceso en línea: | 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 |
| _version_ | 1855483509321236480 |
|---|---|
| author | Tagliotti, Martín Deperi, Sofia Bedogni, Maria Cecilia Zhang, Roufang Manrique Carpintero, Norma C. Coombs, Joseph Douches, David Huarte, Marcelo Atilio |
| author_browse | Bedogni, Maria Cecilia Coombs, Joseph Deperi, Sofia Douches, David Huarte, Marcelo Atilio Manrique Carpintero, Norma C. Tagliotti, Martín Zhang, Roufang |
| author_facet | Tagliotti, Martín Deperi, Sofia Bedogni, Maria Cecilia Zhang, Roufang Manrique Carpintero, Norma C. Coombs, Joseph Douches, David Huarte, Marcelo Atilio |
| author_sort | Tagliotti, Martín |
| collection | INTA Digital |
| 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. |
| format | Artículo |
| id | INTA4849 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Springer Nature |
| publisherStr | Springer Nature |
| record_format | dspace |
| spelling | INTA48492019-04-09T11:33:40Z 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 Deperi, Sofia Bedogni, Maria Cecilia Zhang, Roufang Manrique Carpintero, Norma C. Coombs, Joseph Douches, David Huarte, Marcelo Atilio Papa Solanun tuberosum Fenotipos Diversidad Genética Estructura de la Población Potatoes Phenotypes Genetic Divergence Population Structure 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. 2019-04-09T11:25:04Z 2019-04-09T11:25:04Z 2018-01-16 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng 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) application/pdf Springer Nature BMC Genetics 19 (1) : 8 (January 2018) |
| spellingShingle | Papa Solanun tuberosum Fenotipos Diversidad Genética Estructura de la Población Potatoes Phenotypes Genetic Divergence Population Structure Tagliotti, Martín Deperi, Sofia Bedogni, Maria Cecilia Zhang, Roufang Manrique Carpintero, Norma C. Coombs, Joseph Douches, David Huarte, Marcelo Atilio 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 |
| 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_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_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 |
| topic | Papa Solanun tuberosum Fenotipos Diversidad Genética Estructura de la Población Potatoes Phenotypes Genetic Divergence Population Structure |
| 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 |
| work_keys_str_mv | AT tagliottimartin useofeasymeasurablephenotypictraitsasacomplementaryapproachtoevaluatethepopulationstructureanddiversityinahighheterozygouspaneloftetraploidclonesandcultivars AT deperisofia useofeasymeasurablephenotypictraitsasacomplementaryapproachtoevaluatethepopulationstructureanddiversityinahighheterozygouspaneloftetraploidclonesandcultivars AT bedognimariacecilia useofeasymeasurablephenotypictraitsasacomplementaryapproachtoevaluatethepopulationstructureanddiversityinahighheterozygouspaneloftetraploidclonesandcultivars AT zhangroufang useofeasymeasurablephenotypictraitsasacomplementaryapproachtoevaluatethepopulationstructureanddiversityinahighheterozygouspaneloftetraploidclonesandcultivars AT manriquecarpinteronormac useofeasymeasurablephenotypictraitsasacomplementaryapproachtoevaluatethepopulationstructureanddiversityinahighheterozygouspaneloftetraploidclonesandcultivars AT coombsjoseph useofeasymeasurablephenotypictraitsasacomplementaryapproachtoevaluatethepopulationstructureanddiversityinahighheterozygouspaneloftetraploidclonesandcultivars AT douchesdavid useofeasymeasurablephenotypictraitsasacomplementaryapproachtoevaluatethepopulationstructureanddiversityinahighheterozygouspaneloftetraploidclonesandcultivars AT huartemarceloatilio useofeasymeasurablephenotypictraitsasacomplementaryapproachtoevaluatethepopulationstructureanddiversityinahighheterozygouspaneloftetraploidclonesandcultivars |