Identification of the PvIQD Gene Family and Its Expression Analysis Under Abiotic Stress in Common Bean (Phaseolus vulgaris)
DONG Xue1, ZHAO Min2, LI Jia2, QIU Fu-Yi2, WANG Yan1, ZHAO Jian-Dong1, CHANG Jian-Wu1,*, HAO Xiao-Peng1,*
1 Center for Agricultural Genetic Resources Research/Ministry of Agriculture/Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Shanxi Agricultural University, Taiyuan 030031, China; 2 College of Agriculture, Shanxi Agricultural University, Taiyuan 030031, China
Abstract：The IQ67 domain (IQD) genes encode a class of calmodulin-binding proteins that contain the conserved IQ67 domain. These proteins play important roles in regulating plant organ morphology and responding to adversity stress. In this study, 34 PvIQD genes were identified in the genome of common bean (Phaseolus vulgaris) through bioinformatics analysis. Their physicochemical properties, gene duplication events, phylogenetic evolution, gene structures, and expression patterns were analyzed. The study showed, PvIQD genes were unevenly distributed on 11 chromosomes. There were 2 segmentally duplicated gene pairs and no tandem duplicate gene pairs. The Ka/Ks ratios were all less than 1, indicating that PvIQD gene pairs have been under purification selection pressure during evlution. In the phylogenetic analysis, the PvIQD gene family members were divided into 4 subfamilies (Ⅰ~Ⅳ), with 28 PvIQD genes exhibiting a one-to-two clustering relationship with IQD genes from soybean (Glycine max). Gene structure analysis revealed that PvIQD genes contained 2~6 exons, and most PvIQD protein sequences contained motif1 and motif7. PvIQD genes in the same subfamily had similar gene structures and conserved motifs. Gln7, Arg11, Gly12, Leu14, and Arg16 in the IQ motif were highly conserved amino acids. Collinearity analysis showed that common bean had a closer genetic relationship between common bean and dicotyledonous plants (Arabidopsis thaliana and Glycine max), compared with monocotyledonous plants (Oryza sativa and Zea mays), and the closest relationship. Analysis of RNA-seq data showed that 6 PvIQD genes were highly expressed in multiple tissues at different developmental stages. The tissue-specific genes, PvIQD2 and PvIQD19, showed the highest transcript levels in green mature pods and nodules, respectively. The results of qRT-PCR analysis showed that 8 PvIQD genes exhibited distinct expression patterns in response to drought and salt stress. This study provides a reference for exploring the regulatory mechanisms of PvIQD genes in resistance to abiotic stress in common bean.
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