Genome-Wide Mining of Wheat DUF966 Gene Family Provides New Insights Into Salt Stress Responses

Abstract

Domain of unknown function (DUF) proteins constitute a great deal of families of functionally uncharacterized proteins in eukaryotes. The DUF966 gene family is found in monocotyledons, dicotyledons, mosses, and other species. However, little is known about the functions of DUF966 genes in wheat (Triticum aestivum L.). In this study, we identified and characterized the TaDUF966 gene family members in wheat by in silico analysis. A total of 28 TaDUF966 proteins were identified in wheat. Phylogenetic analysis divided these proteins into two groups (Groups I and II). Proteins in each group showed a highly conserved DUF966 domain and conserved motif distribution, implying their functional conservation. Analysis of gene expression profiling data showed that some TaDUF966 genes were induced by salt stress. We further confirmed the role of TaDUF966-9B in salt stress using virus induced gene silencing (VIGS) assay. Compared with the empty vector control, the TaDUF966-9B knockdown plants exhibited severe leaf curling at 10 days post-inoculation with BSMV under salt stress, suggesting that TaDUF966 genes play a vital role in salt stress tolerance in wheat. Taken together, these results expand our knowledge of the evolution of the DUF966 gene family in wheat and promote the potential application of these genes in wheat genetic improvement.

Genome-Wide Identification and Characterization of Wheat 14-3-3 Genes Unravels the Role of TaGRF6-A in Salt Stress Tolerance by Binding MYB Transcription Factor

“…Reference genome sequences of wheat sub-genome donors were downloaded from NCBI, and 14-3-3 genes of each species were identified using the same methods as those used for determining the TaGRFs . To determine the paralogous or orthologous relationship between wheat TaGRFs and 14-3-3 genes of its sub-genome donors, the general tool “all against all BLAST searches” was used, with an E -value of 1 × 10 −10 and sequence similarity > 75% [ 59 ]. The “circlize” package of the R program was used to draw the relationship between wheat TaGRFs and 14-3-3 genes of its sub-genome donors [ 60 ].…”

Capturing Wheat Phenotypes at the Genome Level

“…For instance, in silico analyses of the published wheat reference genome, IWGSC RefSeq v1 (Appels et al, 2018), have allowed the identification and characterization of the gene families. They include: (i) Domain of Unknown Function (DUF-966, TaDUF966) gene family, involved in salinity-stress tolerance (Zhou et al, 2020); (ii) MADS-Box gene (TaMADS-box) family members, involved in wheat growth, development, and abiotic stresses (Raza et al, 2021); (iii) Gretchen Hagen3 (TaGH3) gene family, important in various biological processes, including phytohormone responses, growth, development, metabolism, defense, and abiotic-stress tolerance, such as salinity and osmotic ones, with polyploidization contributing to their high number (Jiang et al, 2020); (iv) superoxide dismutase (SOD) gene (TaSOD) family, encoding antioxidant enzymes scavenging reactive oxygen species (ROS), also involved in plant growth, development, and abioticstress tolerance, including drought and salinity (Jiang et al, 2019); (v) non-specific lipid transfer proteins (nsLTP/LTP) gene (TansLTP/TaLTP) family, involved in transporting phospholipids across membranes, growth, development, and abiotic stresses, such as drought and salinity, showing high numbers, due to gene duplications (Fang et al, 2020a); (vi) REMorin (REM) gene (TaREM) family, involved in vernalization, plant-microbe interactions, hormonal regulation, development, and tolerance to biotic and abiotic stresses, including cold acclimation (Badawi et al, 2019); (vii) S-phase Kinase-associated Protein 1 (SKP1) gene (TaSKP1) family, encoding core subunits of the Ubiquitin Proteasome 26S (UPS) and have expanded through duplications, being involved in development and stress signaling (El Beji et al, 2019); (viii) subtilase or subtilisin-like protease (SBT) genes (TaSBT), involved in many biological functions, such as defense and tolerance to biotic stresses caused by pathogens, among which are Puccinia striiformis f. sp. tritici, which is the fungus generating the wheat stripe-rust disease (Yang et al, 2020); (ix) highly and structurally conserved "Soluble N-ethylmaleimide Sensitive Factor (NSF; SNF) Attachment Protein (SNAP) REceptor" (SNARE) and Novel Plant SNare (NPSN) gene families (TaSNARE and TaNPSN, respectively), involved in growth and development, regulating vesicle trafficking, fusion, and targeting to vacuoles and exocytosis (Gaggar et al, 2020); (x) "DNA binding with one finger" (Dof) gene (TaDof) family, encoding zinc-finger transcription factors (TaDof), involved in phytohormone response, growth, development, metabolism, defense, and stress responses, including both abiotic (such as salinity and drought) and biotic ones, with their high numbers due to polyploidization, showing many segmental duplications and both miRNA and cis-regulators involvement in modulating their gene expression profiles (Fang et al, 2020b); and (xi) basic leucine ZIPper (bZIP) gene (TabZIP) family, encoding transcription factor, being involved in plant growth, development, metabolism, chlorophyll content, photosynthesis, membrane stability, and ...…”

Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis

“…Tauschii) were identified by BLASTp analysis, and the cutoff values (e-value < 10 −10 , identity > 80%) were used to ensure the reliability of orthologs. The homology relationships were displayed using the R package 'circlize' [39]. In addition, basing on the multiple alignments among wheat and other species (Arabidopsis, S. lycopersicum, Z. mays, and O. sativa), the synteny relationship within species of ZF-HDs was analyzed using MCScanX [40].…”