An informational view of accession rarity and allele specificity in germplasm banks for management and conservation

PloS One
M Humberto Reyes-ValdésCarolina Paola Sansaloni

Abstract

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 mathematica...Continue Reading

References

Aug 22, 1997·Science·S D Tanksley, S R McCouch
Aug 11, 2005·Genetical Research·M Humberto Reyes-Valdés, Claire G Williams
Feb 2, 2008·Science·David B LobellRosamond L Naylor
Jul 9, 2008·Proceedings of the National Academy of Sciences of the United States of America·Octavio Martínez, M Humberto Reyes-Valdés
Jan 19, 2010·Neural Networks : the Official Journal of the International Neural Network Society·Pierre Baldi, Laurent Itti
May 11, 2010·PloS One·Octavio MartínezLuis Herrera-Estrella
Feb 9, 2012·American Journal of Botany·Susan R McCouchRuaraidh Sackville Hamilton
Nov 22, 2013·PloS One·M Humberto Reyes-ValdésCelso Cortés-Romero

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Methods Mentioned

BETA
genotyping

Software Mentioned

MSTRAT
MixRep
Core Hunter
R
HCore
REMC
Bio
R environment for statistical computing

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