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The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections

BACKGROUND: Germplasm banks maintain collections representing the most comprehensive catalogue of native genetic diversity available for crop improvement. Users of germplasm banks are interested in a fixed number of samples representing as broadly as possible the diversity present in the wider colle...

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Autores principales: Franco-Duran, Jorge, Crossa, José, Chen, Jiafa, Hearne, Sarah Jane
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6882233/
https://www.ncbi.nlm.nih.gov/pubmed/31775638
http://dx.doi.org/10.1186/s12870-019-2142-y
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author Franco-Duran, Jorge
Crossa, José
Chen, Jiafa
Hearne, Sarah Jane
author_facet Franco-Duran, Jorge
Crossa, José
Chen, Jiafa
Hearne, Sarah Jane
author_sort Franco-Duran, Jorge
collection PubMed
description BACKGROUND: Germplasm banks maintain collections representing the most comprehensive catalogue of native genetic diversity available for crop improvement. Users of germplasm banks are interested in a fixed number of samples representing as broadly as possible the diversity present in the wider collection. A relevant question is whether it is necessary to develop completely independent germplasm samples or it is possible to select nested sets from a pre-defined core set panel not from the whole collection. We used data from 15,384, maize landraces stored in the CIMMYT germplasm bank to study the impact on 8 diversity criteria and the sample representativeness of: (1) two core selection strategies, a statistical sampling (DM), or a numerical maximization method (CH); (2) selecting samples of varying sizes; and (3) selecting samples of different sizes independently of each other or in a nested manner. RESULTS: Sample sizes greater than 10% of the whole population size retained more than 75% of the polymorphic markers for all selection strategies and types of sample; lower sample sizes showed more variability (instability) among repetitions; the strongest effect of sample size was observed on the CH-independent combination. Independent and nested samples showed similar performance for all the criteria for the DM method, but there were differences between them for the CH method. The DM method achieved better approximations to the known values in the population than the CH method; 2-d multidimensional scaling plots of the collection and samples highlighted tendency of sample selection towards the extremes of diversity in the CH method, compared with sampling more representative of the overall genotypic distribution of diversity under the DM method. CONCLUSIONS: The use of core subsets of size greater than or equal to 10% of the whole collection satisfied well the requirement of representativeness and diversity. Nested samples showed similar diversity and representativeness characteristics as independent samples offering a cost effective method of sample definition for germplasm banks. For most criteria assessed the DM method achieved better approximations to the known values in the whole population than the CH method, that is, it generated more statistically representative samples from collections.
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spelling pubmed-68822332019-12-03 The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections Franco-Duran, Jorge Crossa, José Chen, Jiafa Hearne, Sarah Jane BMC Plant Biol Research Article BACKGROUND: Germplasm banks maintain collections representing the most comprehensive catalogue of native genetic diversity available for crop improvement. Users of germplasm banks are interested in a fixed number of samples representing as broadly as possible the diversity present in the wider collection. A relevant question is whether it is necessary to develop completely independent germplasm samples or it is possible to select nested sets from a pre-defined core set panel not from the whole collection. We used data from 15,384, maize landraces stored in the CIMMYT germplasm bank to study the impact on 8 diversity criteria and the sample representativeness of: (1) two core selection strategies, a statistical sampling (DM), or a numerical maximization method (CH); (2) selecting samples of varying sizes; and (3) selecting samples of different sizes independently of each other or in a nested manner. RESULTS: Sample sizes greater than 10% of the whole population size retained more than 75% of the polymorphic markers for all selection strategies and types of sample; lower sample sizes showed more variability (instability) among repetitions; the strongest effect of sample size was observed on the CH-independent combination. Independent and nested samples showed similar performance for all the criteria for the DM method, but there were differences between them for the CH method. The DM method achieved better approximations to the known values in the population than the CH method; 2-d multidimensional scaling plots of the collection and samples highlighted tendency of sample selection towards the extremes of diversity in the CH method, compared with sampling more representative of the overall genotypic distribution of diversity under the DM method. CONCLUSIONS: The use of core subsets of size greater than or equal to 10% of the whole collection satisfied well the requirement of representativeness and diversity. Nested samples showed similar diversity and representativeness characteristics as independent samples offering a cost effective method of sample definition for germplasm banks. For most criteria assessed the DM method achieved better approximations to the known values in the whole population than the CH method, that is, it generated more statistically representative samples from collections. BioMed Central 2019-11-27 /pmc/articles/PMC6882233/ /pubmed/31775638 http://dx.doi.org/10.1186/s12870-019-2142-y Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Franco-Duran, Jorge
Crossa, José
Chen, Jiafa
Hearne, Sarah Jane
The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections
title The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections
title_full The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections
title_fullStr The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections
title_full_unstemmed The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections
title_short The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections
title_sort impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6882233/
https://www.ncbi.nlm.nih.gov/pubmed/31775638
http://dx.doi.org/10.1186/s12870-019-2142-y
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