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Presize: an approach for precise estimation of core collection size using the Similarity Elimination (SimEli) method

Published online by Cambridge University Press:  16 September 2014

R. Ramesh Krishnan ,
B. B. Bindroo  and
V. Girish Naik
R. Ramesh Krishnan
Affiliation:
Molecular Biology Laboratory-1, Host Plant Improvement, Central Sericultural Research and Training Institute, Srirampura, Manandavadi Road, Mysore 570008, Karnataka, India
B. B. Bindroo
Affiliation:
Director, Central Sericultural Research and Training Institute, Srirampura, Manandavadi Road, Mysore 570008, India
V. Girish Naik*
Affiliation:
Molecular Biology Laboratory-1, Host Plant Improvement, Central Sericultural Research and Training Institute, Srirampura, Manandavadi Road, Mysore 570008, Karnataka, India
*
*Corresponding author. E-mail: vgirishnaik@yahoo.com
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Abstract

Core collections are the integral part of biotechnology-aided modern-day crop improvement programmes and utilized for a variety of applications including conventional plant breeding, association mapping, resequencing, among others. Since their advent, determination of core collection size has been based on the size of the whole collection. In this study, we precisely estimated the size of the core collection based on the diversity of the whole collection using the Similarity Elimination method. For each of the elimination cycle, allele retention and pairwise and mean genetic distances were calculated and used as the criteria for the precise estimation of the core collection size. We sampled a coconut core collection with 266 entries by retaining the diversity of the whole collection. During the elimination process, accessions with very rare alleles were eliminated first when compared with those having rare and common alleles. Therefore, our results support the hypothesis that the less frequent alleles seldom contribute to the genetic distance when compared with common alleles. In conclusion, presize can be efficiently utilized in any crop for the precise estimation of core collection size.

Keywords

core collectioncrop improvementSimilarity Eliminationsize
Type
Short Communication
Information
Plant Genetic Resources , Volume 13 , Issue 3 , November 2015 , pp. 282 - 285
Copyright
Copyright © NIAB 2014 

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