Investigation and computational analysis of the IQD gene family in common bean ( Phaseolus vulgaris L.): expression profiling under salt stress

Common bean is one of the most nutritionally important legumes because of its high-quality protein content. While its genome has been widely studied, the IQ67 domain (IQD) gene family has not been extensively investigated in common bean to date. IQD proteins, a type of calmodulin-binding protein, are involved in plant growth and development, as well as the plant's response to environmental stressors. In this study, 36 Phaseolus vulgaris IQD ( PvIQD ) genes were identified, and their proteins were classified into four groups according to the phylogenetic tree. The proteins, which were encoded by PvIQD genes with similar exon-intron patterns, were located in the same groups of the phylogenetic tree. Duplication events revealed the importance of segmental duplication under purifying selection in the expansion of the PvIQD gene family. Furthermore, the detected miRNAs and cis-acting elements were assumed to play a crucial role in the regulation of PvIQD genes. RNA-seq data analysis and reverse-transcription quantitative polymerase chain reaction (RT-qPCR) reactions showed the contribution of certain PvIQD genes to salt stress responses in common bean. The consistent upregulation of PvIQD4, PvIQD10, PvIQD14, and PvIQD32 across both RNA-seq and RT-qPCR data might suggest a reliable and potentially significant role of these genes in salt stress response. These findings shed light on IQD genes in common bean and could potentially serve as a reference for future research studies.