Identification, Evolutionary Relationship Analysis of the Trehalose-6-Phosphate Synthase (TPS) Gene Family in Common Bean (Phaseolus vulgaris) and Their Expression in Response to Cold Stress

Trehalose-6-phosphate synthases (TPS) are the family of enzymes in plant involved in the synthesis of trehalose and play critical roles in regulating development and abiotic stress response but the available information about the TPS family in common bean (Phaseolus vulgaris) is very limited. Here, we provide a comprehensive genome-wide analysis of the TPS family in P. vulgaris genome, identifying 12 TPS genes clustered into two major groups. The characteristics of both gene structures and motif compositions supported the reliability of the phylogenetic relationship. Collinearity analysis indicated that the PvTPS gene family is evolutionarily conserved and formed orthologous pairs with the TPS genes of Arabidopsis thaliana (14), Oryza sativa (5), and Glycine max (34). Segmental duplication was the major driving force of expansion for the PvTPS genes family. Promoter analysis revealed numerous cis-acting elements related to hormone and abiotic stress-responsiveness. RNA-seq data elucidated that PvTPS12/8/6/5 exhibited tissue specificity expression as compared to PvTPS1/4/9/11preferring expression in multiple tissues. Protein interaction network analysis showed the PvTPS proteins were involved in metabolisms of stress and development. Furthermore, qRT-PCR analysis indicated that all PvTPSs except PvTPS7 respond significantly to cold stress in different organs of two varieties. Notably, PvTPS2, PvTPS5, and PvTPS10 were constitutively elevated expression in the roots, stems, and leaves during cold stress, which might play important roles in the protective response to cold stress. This study provided extensive information about the TPS family in common bean and contribute to further functional verification and application in cold resistance breeding.