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An efficient single nucleotide polymorphism assay to diagnose the genomic identity of poplar species and hybrids on the Canadian prairies

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Abstract:

Hybridization frequently occurs among poplars, both naturally and artificially, hindering identification. Over 32 million clonal poplars, predominantly hybrids, have been planted throughout the Canadian prairies over the past century, making confirmation of genomic identity important. We developed a genotyping assay that rapidly diagnoses four compatible Populus species (Populus balsamifera L. and Populus deltoides Bartr. ex Marsh.: indigenous, Populus laurifolia Ledeb. and Populus nigra L.: exotics) and their hybrids found throughout this ecozone. First, we sequenced 23 genes from representative provenances of the four Populus species to discover single nucleotide polymorphisms (SNPs). Second, we developed and validated a medium-throughput genotyping assay of 26 diagnostic SNPs within these genes. We used this assay to genotype 198 trees from natural populations as well as 30 clones (pure species and hybrids), including those broadly distributed by Agriculture and Agri-Food Canada’s Agroforestry Development Centre since 1910. This suite of SNPs has the resolving power to correctly identify pure species and hybrids of Populus. We confirmed the identity of clones of well-documented origin, complex hybrids with exotic components, and paternity of open-pollinated progenies from breeding programs. This diagnostic tool should prove useful for efficient molecular fingerprinting of breeding material and for further studies of interspecific gene flow on the Canadian prairies.

Document Type: Research Article

DOI: http://dx.doi.org/10.1139/x11-025

Affiliations: 1: Département des sciences du bois et de la forêt, Université Laval, 2325 rue de l’Université, Québec, QC G1V 0A6, Canada. 2: Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, 1055 rue du PEPS, Québec, QC G1V 4C7, Canada. 3: Agroforestry Development Centre, AAFC Agri-Environment Services Branch, P.O. Box 940, No. 2 Government Road, Indian Head, SK S0G 2K0, Canada.

Publication date: May 28, 2011

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