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Comparison Between Core Set Selection Methods Using Different Illumina Marker Platforms: A Case Study of Assessment of Diversity in Wheat
Collections of plant genetic resources stored in genebanks are an important source of genetic diversity for improvement in plant breeding programs and for conservation of natural variation. The establishment of reduced representative collections from a large set of genotypes is a valuable tool that...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7381318/ https://www.ncbi.nlm.nih.gov/pubmed/32754184 http://dx.doi.org/10.3389/fpls.2020.01040 |
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author | Soleimani, Behnaz Lehnert, Heike Keilwagen, Jens Plieske, Joerg Ordon, Frank Naseri Rad, Sara Ganal, Martin Beier, Sebastian Perovic, Dragan |
author_facet | Soleimani, Behnaz Lehnert, Heike Keilwagen, Jens Plieske, Joerg Ordon, Frank Naseri Rad, Sara Ganal, Martin Beier, Sebastian Perovic, Dragan |
author_sort | Soleimani, Behnaz |
collection | PubMed |
description | Collections of plant genetic resources stored in genebanks are an important source of genetic diversity for improvement in plant breeding programs and for conservation of natural variation. The establishment of reduced representative collections from a large set of genotypes is a valuable tool that provides cost-effective access to the diversity present in the whole set. Software like Core Hunter 3 is available to generate high quality core sets. In addition, general clustering approaches, e.g., k-medoids, are available to subdivide a large data set into small groups with maximum genetic diversity between groups. Illumina genotyping platforms are a very efficient tool for the assessment of genetic diversity of plant genetic resources. The accumulation of genotyping data over time using commercial genotyping platforms raises the question of how such huge amount of information can be efficiently used for creating core collections. In the present study, after developing a 15K wheat Infinium array with 12,908 SNPs and genotyping a set of 479 hexaploid winter wheat lines (Triticum aestivum), a larger data set was created by merging 411 lines previously genotyped with the 90K iSelect array. Overlaying the markers from the 15K and 90K arrays enabled the identification of a common set of 12,806 markers, suggesting that the 15K array is a valuable and cost-effective resource for plant breeding programs. Finally, we selected genetically diverse core sets out of these 890 wheat genotypes derived from five collections based on the common markers from the 15K and 90K SNP arrays. Two different approaches, k-medoids and Core Hunter 3 were compared,and k-medoids was identified as an efficient method for selecting small core sets out of a large collection of genotypes while retaining the genetic diversity of the original population. |
format | Online Article Text |
id | pubmed-7381318 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-73813182020-08-03 Comparison Between Core Set Selection Methods Using Different Illumina Marker Platforms: A Case Study of Assessment of Diversity in Wheat Soleimani, Behnaz Lehnert, Heike Keilwagen, Jens Plieske, Joerg Ordon, Frank Naseri Rad, Sara Ganal, Martin Beier, Sebastian Perovic, Dragan Front Plant Sci Plant Science Collections of plant genetic resources stored in genebanks are an important source of genetic diversity for improvement in plant breeding programs and for conservation of natural variation. The establishment of reduced representative collections from a large set of genotypes is a valuable tool that provides cost-effective access to the diversity present in the whole set. Software like Core Hunter 3 is available to generate high quality core sets. In addition, general clustering approaches, e.g., k-medoids, are available to subdivide a large data set into small groups with maximum genetic diversity between groups. Illumina genotyping platforms are a very efficient tool for the assessment of genetic diversity of plant genetic resources. The accumulation of genotyping data over time using commercial genotyping platforms raises the question of how such huge amount of information can be efficiently used for creating core collections. In the present study, after developing a 15K wheat Infinium array with 12,908 SNPs and genotyping a set of 479 hexaploid winter wheat lines (Triticum aestivum), a larger data set was created by merging 411 lines previously genotyped with the 90K iSelect array. Overlaying the markers from the 15K and 90K arrays enabled the identification of a common set of 12,806 markers, suggesting that the 15K array is a valuable and cost-effective resource for plant breeding programs. Finally, we selected genetically diverse core sets out of these 890 wheat genotypes derived from five collections based on the common markers from the 15K and 90K SNP arrays. Two different approaches, k-medoids and Core Hunter 3 were compared,and k-medoids was identified as an efficient method for selecting small core sets out of a large collection of genotypes while retaining the genetic diversity of the original population. Frontiers Media S.A. 2020-07-09 /pmc/articles/PMC7381318/ /pubmed/32754184 http://dx.doi.org/10.3389/fpls.2020.01040 Text en Copyright © 2020 Soleimani, Lehnert, Keilwagen, Plieske, Ordon, Naseri Rad, Ganal, Beier and Perovic http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Soleimani, Behnaz Lehnert, Heike Keilwagen, Jens Plieske, Joerg Ordon, Frank Naseri Rad, Sara Ganal, Martin Beier, Sebastian Perovic, Dragan Comparison Between Core Set Selection Methods Using Different Illumina Marker Platforms: A Case Study of Assessment of Diversity in Wheat |
title | Comparison Between Core Set Selection Methods Using Different Illumina Marker Platforms: A Case Study of Assessment of Diversity in Wheat |
title_full | Comparison Between Core Set Selection Methods Using Different Illumina Marker Platforms: A Case Study of Assessment of Diversity in Wheat |
title_fullStr | Comparison Between Core Set Selection Methods Using Different Illumina Marker Platforms: A Case Study of Assessment of Diversity in Wheat |
title_full_unstemmed | Comparison Between Core Set Selection Methods Using Different Illumina Marker Platforms: A Case Study of Assessment of Diversity in Wheat |
title_short | Comparison Between Core Set Selection Methods Using Different Illumina Marker Platforms: A Case Study of Assessment of Diversity in Wheat |
title_sort | comparison between core set selection methods using different illumina marker platforms: a case study of assessment of diversity in wheat |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7381318/ https://www.ncbi.nlm.nih.gov/pubmed/32754184 http://dx.doi.org/10.3389/fpls.2020.01040 |
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