SNP Discovery of Nine Drought-Responsive Genes in Genus Populus and Development of SNP Genotyping Assays By TaqMan Probe-Based Real-Time PCR

We discovered a total of 346 SNPs from the re-sequencing of partial genomic sequences of nine drought-responsive genes (dehydrin, alternative oxidase 1a, amino acid permease I, galactinol synthase, transcription factor like protein, ethylene-responsive element-binding factor 1, 4-hydroxyphenylpyruvate dioxygenase, leucoanthocyanidin dioxygenase-like protein and putative Zinc finger protein) in genus Populus. Fifty-seven panels of SNP genotyping assay by TaqMan probe-based real-time PCR were developed from the SNPs. The panels successfully generated a total of 155 SNP types for 100 samples of 9 species (P. tremula var. davidiana, P. tremula var. glandulosa, P. alba, P. alba x P. tremula var. glandulosa, P. maximowizii, P. nigra, P. deltoids and P. euramericana). Seventy-eight haplotypes were reconstructed from the SNP typing results of nine genes over the species using an EM algorithm function implemented in the PowerMarker v.3.25 program. The number of haplotypes varied in genes and species with an average of 8.67 haplotypes per gene. Species-specific haplotypes were also found in two species, P. tremula var. davidiana and P. maximowiczii. The panels were also applied to 58 samples from five natural populations of P. tremula var. davidiana in Korea. The mean values of number of alleles per gene and observed heterozygosity were 5.33 and 0.6609. The Wright’s F-statisitics(F_IS, F_IT and F_ST) were 0.2601, -0.1007 and 0.1317. The results indicated relatively high level of genetic variation and heterozygote excess, and a considerable genetic differentiation among the populations of P. tremula var. davidiana in Korea for the 9 drought-responsive genes, in particular.