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
Abstract 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 s...
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BMC
2018-01-01
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Online Access: | http://link.springer.com/article/10.1186/s12863-017-0556-9 |
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author | Martin E. Tagliotti Sofia I. Deperi Maria C. Bedogni Ruofang Zhang Norma C. Manrique Carpintero Joseph Coombs David Douches Marcelo A. Huarte |
author_facet | Martin E. Tagliotti Sofia I. Deperi Maria C. Bedogni Ruofang Zhang Norma C. Manrique Carpintero Joseph Coombs David Douches Marcelo A. Huarte |
author_sort | Martin E. Tagliotti |
collection | DOAJ |
description | Abstract 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. |
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issn | 1471-2156 |
language | English |
last_indexed | 2024-04-13T04:23:22Z |
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series | BMC Genetics |
spelling | doaj.art-bb2db6cad4fe44f6904a282fe2aedfc52022-12-22T03:02:39ZengBMCBMC Genetics1471-21562018-01-0119111210.1186/s12863-017-0556-9Use 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 cultivarsMartin E. Tagliotti0Sofia I. Deperi1Maria C. Bedogni2Ruofang Zhang3Norma C. Manrique Carpintero4Joseph Coombs5David Douches6Marcelo A. Huarte7Potato Research Group, Estación Experimental Agropecuaria Balcarce, Instituto Nacional de Tecnología Agropecuaria (INTA)Potato Research Group, Estación Experimental Agropecuaria Balcarce, Instituto Nacional de Tecnología Agropecuaria (INTA)Potato Research Group, Estación Experimental Agropecuaria Balcarce, Instituto Nacional de Tecnología Agropecuaria (INTA)Potato Engineering and Technology Research Centre, Inner Mongolia UniversityDepartment of Plant, Molecular Plant Sciences Bldg., Michigan State UniversityDepartment of Plant, Molecular Plant Sciences Bldg., Michigan State UniversityDepartment of Plant, Molecular Plant Sciences Bldg., Michigan State UniversityPotato Research Group, Estación Experimental Agropecuaria Balcarce, Instituto Nacional de Tecnología Agropecuaria (INTA)Abstract 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.http://link.springer.com/article/10.1186/s12863-017-0556-9Potato breedingPhenotypic traitGenetic diversitySNPPopulation structure |
spellingShingle | Martin E. Tagliotti Sofia I. Deperi Maria C. Bedogni Ruofang Zhang Norma C. Manrique Carpintero Joseph Coombs David Douches Marcelo A. Huarte 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 BMC Genetics Potato breeding Phenotypic trait Genetic diversity SNP Population structure |
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 | Potato breeding Phenotypic trait Genetic diversity SNP Population structure |
url | http://link.springer.com/article/10.1186/s12863-017-0556-9 |
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