Genome-wide identification and expression analysis of the IQD gene family in Populus trichocarpa

IQD proteins are downstream targets of calcium sensors, which play important roles in development and responses to environmental cues in plants. Comprehensive analyses of IQD genes have been conducted in Arabidopsis, rice, tomato, and Brachypodium distachyon, but have not been reported from poplar. The availability of the Populus trichocarpa genome sequence allowed us to conduct phylogenetic, gene structure, chromosomal location, and microarray analyses of the predicted IQD genes in P. trichocarpa. We identified 40 IQD genes (PtIQD1-40) classified in four subfamilies (I-IV). Gene structure and protein motif analyses showed that these genes are relatively conserved within each subfamily. The 40 PtIQD genes are distributed on 18 of the 19 chromosomes, with 16 gene pairs involved in segmental duplication events. The Ka/Ks ratios of the 16 segmentally-duplicated gene pairs show that the duplicated pairs underwent purifying selection with restrictive functional divergence after the duplication events. Analyses of microarray data for 38 PtIQD genes showed tissue/organ-specific expression patterns. We also performed quantitative real-time RT-PCR (qRT-PCR) analyses of twelve selected PtIQD genes in plants treated with MeJA and PEG in order to explore their stress-related expression patterns. Our results will be valuable for further analysis of poplar IQD genes to characterize their important biological functions.