Development of a minimal KASP marker panel for distinguishing genotypes in apple collections.

Mark Winfield,Danny Thorogood,Gary Barker,Paul Wilkinson,Helen Harper,Matthew Ordidge,Amanda Burridge,Liz Copas,Keith Edwards,Tzen-Yuh Chiang

doi:10.1371/journal.pone.0242940

Abstract

Accurate identification of named accessions in germplasm collections is extremely important, especially for vegetatively propagated crops which are expensive to maintain. Thus, an inexpensive, reliable, and rapid genotyping method is essential because it avoids the need for laborious and time-consuming morphological comparisons. Single Nucleotide Polymorphism (SNP) marker panels containing large numbers of SNPs have been developed for many crop species, but such panels are much too large for basic cultivar identification. Here, we have identified a minimum set of SNP markers sufficient to distinguish apple cultivars held in the English and Welsh national collections providing a cheaper and automatable alternative to the markers currently used by the community. We show that SNP genotyping with a small set of well selected markers is equally efficient as microsatellites for the identification of apple cultivars and has the added advantage of automation and reduced cost when screening large numbers of samples.

Highlights

Accurate identification of plant material within germplasm collections is of utmost importance, especially for vegetatively propagated crops which are expensive to maintain
In many crop species microsatellites have been replaced with Single Nucleotide Polymorphism (SNP) markers which are more amenable to high throughput
In our attempt to develop a minimal marker set capable of discriminating all unique accessions held in U.K. collections, we considered that the markers chosen should fulfil various characteristics: they should be reliable with low fail and error rates; they should produce distinct genotypes for most, if not all, varieties; they must produce identical SNP profiles for replicates of the same variety

Summary

Introduction

Accurate identification of plant material within germplasm collections is of utmost importance, especially for vegetatively propagated crops which are expensive to maintain. Genotyping of plant genetic resources, is an essential task for any gene bank to ensure the preservation of maximum genetic diversity whilst, at the same time, avoiding the waste of resources by carrying unknown duplicates. In addition to phenotyping to determine trueness-to-type, cultivars need to be genetically fingerprinted using an appropriate tool. In apple, traditionally this tool has been microsatellite markers [2, 4, 5]. In many crop species microsatellites have been replaced with Single Nucleotide Polymorphism (SNP) markers which are more amenable to high throughput

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Conclusion