Genome-Wide Identification and Expression Profiling of DUF221 Gene Family Provides New Insights Into Abiotic Stress Responses in Potato

Abstract

The domain of the unknown function 221 proteins regulate several processes in plants, including development, growth, hormone transduction mechanism, and abiotic stress response. Therefore, a comprehensive analysis of the potato genome was conducted to identify the deafness-dystonia peptide (DDP) proteins’ role in potatoes. In the present study, we performed a genome-wide analysis of the potato domain of the unknown function 221 (DUF221) genes, including phylogenetic inferences, chromosomal locations, gene duplications, gene structures, and expression analysis. In our results, we identified 10 DDP genes in the potato genome. The phylogenetic analysis results indicated that StDDPs genes were distributed in all four clades, and clade IV was the largest clade. The gene duplication under selection pressure analysis indicated various positive and purifying selections in StDDP genes. The putative stu-miRNAs from different families targeting StDDPs were also predicted in the present study. Promoter regions of StDDP genes contain different cis-acting components involved in multiple stress responses, such as phytohormones and abiotic stress-responsive factors. The analysis of the tissue-specific expression profiling indicated the StDDPs gene expression in stem, root, and leaf tissues. We subsequently observed that StDDP4, StDDP5, and StDDP8 showed higher expressions in roots, stems, and leaves. StDDP5 exhibited high expression against heat stress response, and StDDP7 showed high transcript abundance against salt stress in potatoes. Under abscisic acid (ABA) and indole acetic acid (IAA) treatments, seven StDDP genes’ expressions indicated that ABA and IAA performed important roles in immunity response. The expression profiling and real-time qPCR of stems, roots, and leaves revealed StDDPs’ significant role in growth and development. These expression results of DDPs are primary functional analysis and present basic information for other economically important crops.

Identification and Expression Profile Analysis of the OSCA Gene Family Related to Abiotic and Biotic Stress Response in Cucumber

“…Moreover, nearly all CsOSCAs had a consistent conserved motif arrangement ( Figure 2 A). Gene structure analysis revealed that the CsOSCA genes had clade-specific exon-intron patterns, and some genes had similar exon/intron structures but different sequence lengths ( Figure 2 B), which is also the case in rice [ 15 ], G. hirsutum [ 16 ], and potato [ 30 ]. The highly conserved evolutionary relationship, conserved motif and exon-intron arrangement of the OSCA genes indicated that the members in the same group probably have conserved functions after gene duplication and phylogenetic diversification events [ 14 ].…”

“…In this study, various stress- and hormone-responsive cis -elements that play essential roles in stress response through regulation of stress-responsive genes were found in the promoter regions of CsOSCA genes ( Figure 4 ), implying the possible roles of CsOSCA genes in stress response. Multiple cis -elements involved in multiple stress responses (hormones and abiotic stresses) have also been identified in the promoters of OSCA genes in other plant species, such as G. hirsutum [ 16 ], maize [ 18 ], soybean [ 9 ], tomato [ 28 ], and potato [ 30 ]. We then examined the transcript levels of seven selected CsOSCA genes under three osmotic-related abiotic stresses including drought, salt and ABA by qRT-PCR.…”

Genome-wide characterization and analysis of rice DUF247 gene family

“…Expression pro ling of ATDUF4228 genes under abiotic stresses such as osmotic, salt, and cold stress suggested that some ATDUF4228 genes may be involved in plant resistance pathways against abiotic stresses [16]. Furthermore, StDDP5 and StDDP7, both of which belong to the DUF221 gene family, exhibited high expression against heat and salt stress, respectively, in potatoes [17].…”

Genome-wide characterization and analysis of rice DUF247 gene family

“…Expression profiling of ATDUF4228 genes under abiotic stresses such as osmotic, salt, and cold stress suggested that some ATDUF4228 genes may be involved in plant resistance pathways against abiotic stresses [16]. Furthermore, StDDP5 and StDDP7, both of which belong to the DUF221 gene family, exhibited high expression against heat and salt stress, respectively, in potatoes [17].…”