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 however, the IQD gene family has not been extensively investigated in common bean to date. The IQD proteins (IQ-67 domain), 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, thirty-six PvIQD genes were discovered and their proteins were found to be classified into four groups according to the phylogenetic tree. The proteins which are encoded by PvIQD genes with similar exon-intron pattern were found to be located in the same groups of the phylogenetic tree. Duplication events revealed the importance of segmental duplication under purifying selection in the expansion of PvIQD gene family. Furthermore, the detected miRNAs and cis-acting elements are assumed to play crucial role in the regulation of PvIQD genes. RNA-seq data analysis and 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 genes across both RNA-seq and RT-qPCR data might suggest a reliable and potentially significant role of these genes in salt stress response. In this regard, the findings shed light on IQD genes in common bean and could potentially serve as a reference for future research studies.