Citrus (Rutaceae) SNP markers based on Competitive Allele‐Specific PCR; transferability across the Aurantioideae subfamily

Abstract

• Premise of the study: Single nucleotide polymorphism (SNP) markers based on Competitive Allele‐Specific PCR (KASPar) were developed from sequences of three Citrus species. Their transferability was tested in 63 Citrus genotypes and 19 relative genera of the subfamily Aurantioideae to estimate the potential of SNP markers, selected from a limited intrageneric discovery panel, for ongoing broader diversity analysis at the intra‐ and intergeneric levels and systematic germplasm bank characterization. • Methods and Results: Forty‐two SNP markers were developed using KASPar technology. Forty‐one were successfully genotyped in all of the Citrus germplasm, where intra‐ and interspecific polymorphisms were observed. The transferability and diversity decreased with increasing taxonomic distance. • Conclusions: SNP markers based on the KASPar method developed from sequence data of a limited intrageneric discovery panel provide a valuable molecular resource for genetic diversity analysis of germplasm within a genus and should be useful for germplasm fingerprinting at a much broader diversity level.