Genome‐Wide Identification and Characterization of the Wheat Remorin (TaREM) Family during Cold Acclimation

Abstract

Core Ideas Twenty different wheat remorin (TaREM) genes were identified and classified into six phylogenetic groups. TaREM gene expression was measured in plants grown under both field and controlled cold conditions and in response to hormone treatment. Twelve TaREM were regulated during cold acclimation in four different tissues (roots, crowns, stems, and leaves). Several TaREM genes are implicated in cold response and tolerance. Eight genes were induced in response to abscisic acid and methyl jasmonate treatment. Remorins (REMs) are plant‐specific proteins that play an essential role in plant–microbe interactions. However, their roles in vernalization and abiotic stress responses remain speculative. Most remorins have a variable proline‐rich N‐half and a more conserved C‐half that is predicted to form coils. A search of the wheat (Triticum aestivum L.) database revealed the existence of 20 different REM genes, which we classified into six groups on the basis of whether they shared a common phylogenetic and structural origin. Analysis of the physical genomic distributions demonstrated that REM genes are dispersed in the wheat genome and have one to seven introns. Promoter analysis of TaREM genes revealed the presence of putative cis‐elements related to diverse functions like development, hormonal regulation, and biotic and abiotic stress responsiveness. Expression levels of TaREM genes were measured in plants grown under field and controlled conditions and in response to hormone treatment. Our analyses revealed that 12 members of the REM family are regulated during cold acclimation in wheat in four different tissues (roots, crowns, stems, and leaves), with the highest expression in roots. Differential gene expression was found between wheat cultivars with contrasting degrees of cold tolerance, suggesting the implication of TaREM genes in cold response and tolerance. Additionally, eight genes were induced in response to abscisic acid and methyl jasmonate treatment. This genome‐wide analysis of TaREM genes provides valuable resources for functional analysis aimed at understanding their role in stress adaptation.

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 ...…”

“…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 abiotic-stress 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.…”

Genome-Wide Identification and Expression Analysis of VviYABs Family Reveal Its Potential Functions in the Developmental Switch and Stresses Response During Grapevine Development

“…unipd.it/grape/) in this study. The upstream 1,500-bp region from the translation initiation site for all VviYABs was regarded as the putative promoter sequence (Badawi et al, 2019;Feng et al, 2021). The cis-acting elements of VviYAB genes were predicted using PlantCARE tool (http:// bioinformatics.psb.ugent.be/webtools/plantcare/html/; Postel et al, 2002).…”

Wheat genomics and breeding: bridging the gap.

“…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 [281].…”