Comprehensive in Silico Characterization and Expression Profiling of Nine Gene Families Associated with Calcium Transport in Soybean

Calcium (Ca²⁺) plays a critical role in the regulation of growth and development and environmental stress responses in plants. The membrane-associated Ca²⁺ transport proteins are required to mediate Ca²⁺ signaling and maintain Ca²⁺ homeostasis. Ca²⁺ channels, pumps (ATPases), and antiporters are three major classes of Ca²⁺ transporters. Although the genome-wide analysis of Ca²⁺ transporters in model plants Arabidopsis and rice have been well documented, the identification, classification, phylogenesis, expression profiles, and physiological functions of Ca²⁺ transport proteins in soybean are largely unknown. In this study, a comprehensive in silico analysis of gene families associated with Ca²⁺ transport was conducted, and a total of 207 putative Ca²⁺ transporter genes have been identified in soybean. These genes belong to nine different families, such as Ca²⁺-ATPase, Ca²⁺/cation antiporter, cyclic nucleotide-gated ion channel (CNGC), and hyperosmolality induced cytosolic Ca²⁺ concentration channel (OSCA). Detailed analysis of these identified genes was performed, including their classification, phylogenesis, protein domains, chromosomal distribution, and gene duplication. Expression profiling of these genes was conducted in different tissues and developmental stages, as well as under stresses using publicly available RNA-seq data. Some genes were found to be predominantly expressed in specific tissues like flowers and nodules, and some genes were found to be expressed strongly during seed development. Seventy-four genes were found to be significantly and differentially expressed under abiotic and biotic stresses, such as salt, phosphorus deficiency, and fungal pathogen inoculation. In addition, hormonal signaling- and stress response-related cis-elements and potential microRNA target sites were analyzed. This study suggests the potential roles of soybean Ca²⁺ transporters in stress responses and growth regulation, and provides a basis for further functional characterization of putative Ca²⁺ transporters in soybean.