Identification of single nucleotide polymorphisms in different Populus species

Partial sequences of six genes in 54 trees belonging to five different Populus species were analyzed for occurrence of single nucleotide polymorphisms (SNPs). Genes selected are involved in wood formation and quality (CAD), defence reactions (PPO), hormone biosynthesis (GA20ox), or transcription factors (CBF1, TB1, LFY). The number of polymorphisms identified for each gene fragment varied between different genes, and also between exon and intron regions. The six genes resolved the phylogenetic relationships between the five species to different degrees. Only PPO is resolving all five Populus species as monophyletic in all three phylogenetic approaches. CAD resolves all species with the exception of Populus tremula. For CBF1 and TB1, a monophyletic group consisting of P. tremula and P. tremuloides is resolved by some of the reconstruction approaches. Indels in three out of the six genes analyzed were detected in “consensus”-sequence comparisons between the Populus species. In the CAD-like and LFY genes, these were found only in introns but in the case of TB1 gene these were also found in coding regions. Sizes of the indels range from 1 up to 8 nucleotides. This study confirms the main split between section Leuce and a group-combining sections Aigeiros and Tacamahaca that is perfectly supported with 100% bootstrap supports and 1.0 posterior probability. The SNP markers developed as well as the indels identified can be used for differentiation of Populus species and characterization of hybrids.