Towards a molecular taxonomic key of the Aurantioideae subfamily using chloroplastic SNP diagnostic markers of the main clades genotyped by competitive allele-specific PCR

• DOI: 10.1186/s12863-016-0426-x
• Publication Date: 2016-08-18T07:17:03Z
• Authors: Amel Oueslati; Frederique Ollitr...; Ghada Baraket; Amel Salhi-Hannachi; Luis Navarro; Patrick Ollitrault
• Keywords: Subfamily; Monophyly; Subspecies

Chloroplast DNA is a primary source of molecular variations for phylogenetic analysis photosynthetic eukaryotes. However, the sequencing and multiple chloroplastic regions difficult to apply large collections or samples natural populations. The objective our work was demonstrate that taxonomic key based on easy, scalable low-cost genotyping method should be developed from set Single Nucleotide Polymorphisms (SNPs) diagnostic well-established clades. It applied Aurantioideae subfamily, largest group Rutaceae family includes cultivated citrus species.The publicly available nucleotide sequences eight plastid genomic were compared 79 accessions subfamily search SNPs revealing differentiation at inter-tribe, inter-subtribe, inter-genus interspecific levels. Diagnostic (DSNPs) found 46 54 clade levels analysed. Forty DSNPs selected develop KASPar markers their value tested by 108 subfamily. Twenty-seven 24 clades validated they displayed very high rate transferability in (only 1.2 % missing data average). UPGMA produced cladistic organisation highly coherent with previous sequence plasmid regions. In particular, monophyletic origin "true citrus" genera plus Oxanthera validated. some clarification remains necessary regarding other wild species Citreae tribe.We concept clades, can efficiently transformed into competitive allele-specific PCR (KASPar method) allowing cost-effective efficient level. robustness this an additional decisive advantage network collaborative research. availability WGS main soon make it possible DSNP fine resolution important horticultural group.