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A second-generation diagnostic single nucleotide polymorphism (SNP)-based assay, optimized to distinguish among eight poplar (Populus L.) species and their early hybrids
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
2012 (English)In: Tree Genetics & Genomes, ISSN 1614-2942, Vol. 9, no 2, 621-626 p.Article in journal (Refereed) Published
Abstract [en]

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.
Keyword [en]
Genotyping array, Hybridization, Marker development, Poplars, Clone certification, Species identification
National Category
Biological Sciences
URN: urn:nbn:se:umu:diva-67088DOI: 10.1007/s11295-012-0569-5OAI: diva2:610620
Available from: 2013-03-12 Created: 2013-03-12 Last updated: 2013-04-25Bibliographically approved

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Thompson, Stacey Lee
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