Development of chloroplast single nucleotide polymorphisms (SNPs) as a tool towards interspecies typing of Anthurium germplasm

J.Y. Suzuki, S.M. Geib, M.M. Carlsen, C.L. Henriquez, T.D. Amore, S.B. Sim, T.K. Matsumoto, L.M. Keith, R.Y. Myers
Hybridization between Anthurium species, especially from within the subgeneric section Calomystrium, has played an important role in the development of commercially important ornamental traits in modern Anthurium cultivars, including spathe and spadix color, scent and form, plant shape, and bacterial blight tolerance. Recent advances in our understanding of the phylogenetic relationships within this most species-rich genus of the Araceae family has laid the foundation for further development of molecular tools for Anthurium species and cultivar identification to aid in germplasm preservation and parental selection. In this study, next generation DNA sequencing techniques enabled assembly and a first examination of the chloroplast genomes of Anthurium, including three closely related species, A. hoffmannii Schott, A. huixtlense Matuda, and the horticultural cultivar 'New Pahoa Red' (A. andraeanum Hort.) of section Calomystrium, as well as A. flexile Schott from section Polyphyllium, one of the earliest diverging lineages within this genus. Whole chloroplast genome comparisons between the species from section Calomystrium indicated greater than 99.67% identity, while the lowest similarity (98.44%) was observed between the chloroplast genomes of A. flexile and the cultivar 'New Pahoa Red'. From these comparisons, SNP assays were designed to distinguish between the three Calomystrium chloroplast genomes. Thirty-twoSNP assays were effective in identifying corresponding chloroplast SNP genotypes in Anthurium species within and outside section Calomystrium and distinguishing chloroplast SNP genotypes and their inheritance patterns among different cultivar family groups. Six of the 32 SNP assays each individually specifically distinguished a single species or accession. The results demonstrate the potential of chloroplast SNPs as a supplementary tool for molecular characterization of species across the genus Anthurium as well as cultivars in germplasm collections through genotyping of their chloroplast genomes.
Suzuki, J.Y., Geib, S.M., Carlsen, M.M., Henriquez, C.L., Amore, T.D., Sim, S.B., Matsumoto, T.K., Keith, L.M. and Myers, R.Y. (2017). Development of chloroplast single nucleotide polymorphisms (SNPs) as a tool towards interspecies typing of Anthurium germplasm. Acta Hortic. 1167, 257-270
DOI: 10.17660/ActaHortic.2017.1167.39
Araceae, Calomystrium, genotype, maternal inheritance, next generation sequencing, plastome

Acta Horticulturae