Investigation and utilization of intron length polymorphisms in conifers

Intron length polymorphisms (ILPs) are a new kind of molecular markers, which can be detected by PCR with specific primers designed on exons flanking the target introns. In this study, we identified 2300 putative introns and successfully designed primers for them in loblolly pine by comparing the cDNAs of loblolly pine with the homologous genes of Arabidopsis and rice, and experimentally examined 400 of them using 9 conifer species of two families (7 of Pinaceae and 2 of Cupressaceae) as materials. We found that about 88% of the predicted introns appeared to be correct, suggesting that the exon–intron structures are highly conservative in plants, even between Magnoliophyta and Coniferophyta. Therefore, prediction of introns in the species of Coniferophyta by referring to the model species of Magnoliophyta is feasible. Based on 39 ILP markers, a reasonable dendrogram of the 9 conifer species was constructed, demonstrating that ILP markers are quite suitable for phylogenetic studies involving distant species or higher taxonomic ranks.