A set of Columbia-0-specific single nucleotide polymorphism markers for the genetic analysis of natural variation in Arabidopsis thaliana

Abstract

Genetic markers are important tools for the study of natural and induced genetic variation. Due to the strong increase in the number of genome sequences, an overview of the genomic diversity of many natural strains from individual species could be gained. This allows for the design of markers for flexible use and cost-efficient small scale genetic studies requiring minimal laboratory and bioinformatics effort. Here, we describe 140 single nucleotide polymorphism (SNP) markers with genome-wide distribution that discriminate between the genotype of the common Arabidopsis thaliana reference accession Columbia-0 (Col-0) and the majority of Arabidopsis thaliana accessions that have been sequenced to date. We designed, generated and validated the markers using the kompetitive allele-specific PCR (KASP) technology and made all 140SNPvCol marker assays publicly available through a service provider. Through the integration of available genomic SNP allele information of 1,135 accessions, we found that 120 of these 140 markers could detect non-reference alleles in 647 accessions and more than 100 markers showed non-reference alleles in 1,094 accessions. We further show that the marker set can be used for the verification or identification of accessions of unknown identity. As the KASP methodology is very flexible, an optimal marker subset can be easily selected among the available 140SNPvCol markers presented here to analyze genetic combinations of Col-0 with any other accession.