Genome-Wide Survey and Expression Analysis of B-Box Family Genes in Cucumber Reveal Their Potential Roles in Response to Diverse Abiotic and Biotic Stresses

Abstract

As a class of zinc finger transcription factors, B-box (BBX) proteins play diverse roles in numerous biological processes, and they have been identified in a series of plant species in recent years. However, the roles of BBX genes in regulating cucumber growth regulation and stress response have not yet been established. Here, a total of 22 BBX family genes were identified via an analysis of the latest cucumber genome data, which were classified into five groups (I–V) on the basis of their phylogenetic features and number of B-box domains and CCT domains. The CsBBX genes were unevenly distributed across the seven cucumber chromosomes, and segmental duplication was found to play a significant role in the expansion of the cucumber BBX gene family. Gene structure and motif composition analysis suggested that the evolutionarily close CsBBXs have similar conserved motif composition and gene structure. Most CsBBX genes possessed 1–3 introns, and intron gain rather than intron loss could contribute to the different structures of CsBBX genes across different groups during their evolution. Promoter analysis revealed the presence of 13 kinds of hormone-related and nine kinds of stress-related cis-regulatory elements in the promoter regions of these CsBBX genes. Expression analysis via RNA-seq and qRT-PCR suggested that the CsBBX genes exhibit differential expression in different tissues and in response to various abiotic and biotic stresses. This work constitutes a starting point for further revealing the function of the CsBBX genes and sheds light on the potential molecular mechanism of stress resistance in cucumber.

Molecular Cloning, Characterization, and Expression Analysis of SIMILAR TO RCD-ONE (SRO) Family Genes Responding to Abiotic and Biotic Stress in Cucumber

“…Cucumber seedlings were soaked in Hoagland nutrient solution for hydroponics with a 16:8 h light: dark photoperiod. We transferred the two-leaf stage seedlings to a nutrition solution containing NaCl (200 mM) and PEG6000 (10%), for salt stress and drought stress, respectively, as described previously [4]. The leaf tissues were harvested for each stress condition with three biological replicates at 0, 3, 6, and 12 h after treatment.…”

“…The physical locations of CsSRO genes were illustrated with the MapInspect software according to the initial position information provided in CuGenDB. Moreover, these genes involved in the tandem or segmental duplications were analyzed with MCScanX on the basis of the criterion in our previous report [4]. The 2000 bp promoter sequences located upstream of the initiation codon (ATG) of the cucumber SRO genes were retrieved from CuGenDB, and various cis-regulatory elements related to stresses and hormones were determined using PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/, accessed on 19 June 2022) [40].…”

“…The total qRT-PCR mixture was 20 µL including 10 µL 2 × ChamQ Universal SYBR qPCR Master Mix, 0.4 µL forward primer, 0.4 µL reverse primer, 7.2 µL ddH 2 O, and 2 µL template cDNA. The reaction conditions were as follows: 95 • C for 30 s, followed by 40 cycles of 95 • C for 10 s, and 60 • C for 30 s. All reactions were performed in triplicate, and CsAct3 was used as the reference gene to determine the relative expression with the 2 −∆∆Ct method [4]. qRT-PCR-specific primers used for expression analysis of each CsSRO gene were listed in Table S1.…”

“…Plants have produced a series of regulatory networks through the transcriptional control of numerous stress-responsive genes to protect themselves from adverse environmental effects [1,2]. Transcription factors (TFs) are a class of proteins that can bind to the cis-regulatory elements in promoters of target genes and thus to activate or inhibit their expression, thereby regulating plant development and the response to various stresses [3,4]. SIMILAR TO RCD-ONE (SRO) is a unique type of small TF proteins in plants, which can act as key regulators involved in regulation of many biological pathways.…”

“…Cucumber is an important vegetable crop with great economic value in the world, but it always encounters a variety of environmental stimulus (such as drought, salt, and pathogens) during its growth cycle [4,28]. In recent years, many stress-responsive TF gene families have been identified in cucumber, such as GARS [29,30], bHLH [31], WRKY [32], VQ [33], and TIFY [34], and some members of them were proven to function in stress responses [35,36].…”