A second-generation diagnostic single nucleotide polymorphism (SNP)-based assay, optimized to distinguish among eight poplar (Populus L.) species and their early hybrids
2012 (English)In: Tree Genetics & Genomes, ISSN 1614-2942, Vol. 9, no 2, 621-626 p.Article in journal (Refereed) Published
Rapid identification of Populus L. species and hybrids can be achieved with relatively little effort through the use of primer extension-based single nucleotide poly- morphism (SNP) genotyping assays. We present an opti- mized set of 36 SNP markers from 28 gene regions that diagnose eight poplar species (Populus angustifolia James, Populus balsamifera L., Populus deltoides Bartram, Popu- lus fremontii Watson, Populus laurifolia Ledeb., Populus maximowiczii Henry, Populus nigra L., and Populus tricho- carpa Torr. & Gray). A total of 700 DNA sequences from six Populus species (1–15 individuals per species) were used to construct the array. A set of flanking and probe oligonucleotides was developed and tested. The accuracy of the SNP assay was validated by genotyping 448 putative- ly “pure” individuals from 14 species of Populus. Overall, the SNP assay had a high success rate (97.6 %) and will prove useful for the identification of all Aigeiros Duby and Tacamahaca Spach. species and their early-generation hybrids within natural populations and breeding programs. Null alleles and intraspecific polymorphisms were detected for a few locus/species combinations in the Aigeiros and Tacamahaca sections. When we attempted to genotype aspens of the section Populus (Populus alba L., Populus grandidentata Michx., Populus tremula L., and Populus tremuloides Michx.), the success rate of the SNP array decreased by 13 %, demonstrating moderate cross- sectional transferability.
Place, publisher, year, edition, pages
Springer Berlin/Heidelberg, 2012. Vol. 9, no 2, 621-626 p.
Genotyping array, Hybridization, Marker development, Poplars, Clone certification, Species identification
IdentifiersURN: urn:nbn:se:umu:diva-67088DOI: 10.1007/s11295-012-0569-5OAI: oai:DiVA.org:umu-67088DiVA: diva2:610620