An informational view of accession rarity and allele specificity in germplasm banks for management and conservation
Publication Date
February 28, 2018
Authors
M. Humberto Reyes Valdés, Juan Burgueño, Sukhwinder Singh, Octavio Martínez, et al
Volume
13
Issue
2
Pages
e0193346
DOI
https://dx.plos.org/10.1371/journal.pone.0193346
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0193346
Scopus
85042714450
Mendeley
http://www.mendeley.com/research/informational-view-accession-rarity-allele-specificity-germplasm-banks-management-conservation
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Mendeley | Further Information

{"title"=>"An informational view of accession rarity and allele specificity in germplasm banks for management and conservation", "type"=>"journal", "authors"=>[{"first_name"=>"M. Humberto", "last_name"=>"Reyes-Valdés", "scopus_author_id"=>"56013709200"}, {"first_name"=>"Juan", "last_name"=>"Burgueño", "scopus_author_id"=>"8237468600"}, {"first_name"=>"Sukhwinder", "last_name"=>"Singh", "scopus_author_id"=>"55945695500"}, {"first_name"=>"Octavio", "last_name"=>"Martínez", "scopus_author_id"=>"7103143863"}, {"first_name"=>"Carolina Paola", "last_name"=>"Sansaloni", "scopus_author_id"=>"36144381600"}], "year"=>2018, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "doi"=>"10.1371/journal.pone.0193346", "sgr"=>"85042714450", "scopus"=>"2-s2.0-85042714450", "isbn"=>"1111111111", "pui"=>"620895551"}, "id"=>"e03be241-9833-3d42-ae6a-0b8b8b21756e", "abstract"=>"Copyright: © 2018 Reyes-Valdés et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Germplasm banks are growing in their importance, number of accessions and amount of characterization data, with a large emphasis on molecular genetic markers. In this work, we offer an integrated view of accessions and marker data in an information theory framework. The basis of this development is the mutual information between accessions and allele frequencies for molecular marker loci, which can be decomposed in allele specificities, as well as in rarity and divergence of accessions. In this way, formulas are provided to calculate the specificity of the different marker alleles with reference to their distribution across accessions, accession rarity, defined as the weighted average of the specificity of its alleles, and divergence, defined by the Kullback-Leibler formula. Albeit being different measures, it is demonstrated that average rarity and divergence are equal for any collection. These parameters can contribute to the knowledge of the structure of a germplasm collection and to make decisions about the preservation of rare variants. The concepts herein developed served as the basis for a strategy for core subset selection called HCore, implemented in a publicly available R script. As a proof of concept, the mathematical view and tools developed in this research were applied to a large collection of Mexican wheat accessions, widely characterized by SNP markers. The most specific alleles were found to be private of a single accession, and the distribution of this parameter had its highest frequencies at low levels of specificity. Accession rarity and divergence had largely symmetrical distributions, and had a positive, albeit non-strictly linear relationship. Comparison of the HCore approach for core subset selection, with three state-of-the-art methods, showed it to be superior for average divergence and rarity, mean genetic distance and diversity. The proposed approach can be used for knowledge extraction and decision making in germplasm collections of diploid, inbred or outbred species.", "link"=>"http://www.mendeley.com/research/informational-view-accession-rarity-allele-specificity-germplasm-banks-management-conservation", "reader_count"=>4, "reader_count_by_academic_status"=>{"Researcher"=>2, "Other"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>2, "Other"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Mathematics"=>1, "Agricultural and Biological Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>2}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "group_count"=>0}

Scopus | Further Information

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