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

Abstract

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.

Keywords

• calcium channel
• calcium pump
• calcium exchanger
• cyclic nucleotide-gated ion channel (CNGC)
• OSCA
• glutamate receptor-like protein (GLR)