Comparison of MatK Sequences and TRAP Molecular Markers for the Taxonomic Characterization of Six Species of the Allium Section Cepa (Mill.) Prokh. Complex

The USDA-ARS Western Regional Plant Introduction Station currently maintains 56 accessions in six of the nine wild species of Allium section Cepa (Mill.) Prokh. In 2003-2005 this collection was grown for characterization and to verify taxonomic identity. Taxonomic classification based solely on morphological characteristics can be difficult because the morphological features separating some species are slight (e.g., A. fistulosum and A. altaicum; A. galanthum and A. pskemeske). We sequenced a portion of the chloroplast maturase K gene (matK ) and employed targeted region amplified polymorphism (TRAP) molecular markers to verify taxonomic identity.  It was found that a few species-specific mutations in the matK sequences could be used to clarify the identity of these wild species.  Maximum likelihood and Bayesian phylogenetic analyses of matK sequences confirmed morphological characterization of the wild species and cluster analysis based on Jacard’s Similarity Coefficient from TRAP marker data agreed with these results, indicating that TRAP markers can be a quick and inexpensive tool for taxonomic characterization of this morphologically difficult group.