Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L.)

Abstract

Background: Abscisic acid-, stress-, and ripening-induced (ASR) genes are a class of plant specific transcription factors (TFs), which play important roles in plant development, growth and abiotic stress responses. The wheat ASRs have not been described in genome-wide yet. Methods: We predicted the transmembrane regions and subcellular localization using the TMHMM server, and Plant-mPLoc server and CELLO v2.5, respectively. Then the phylogeny tree was built by MEGA7. The exon-intron structures, conserved motifs and TFs binding sites were analyzed by GSDS, MEME program and PlantRegMap, respectively. Results: In wheat, 33ASR genes were identified through a genome-wide survey and classified into six groups. Phylogenetic analyses revealed that the TaASR proteins in the same group tightly clustered together, compared with those from other species. Duplication analysis indicated that the TaASR gene family has expanded mainly through tandem and segmental duplication events. Similar gene structures and conserved protein motifs of TaASRs in wheat were identified in the same groups. ASR genes contained various TF binding cites associated with the stress responses in the promoter region. Gene expression was generally associated with the expected group-specific expression pattern in five tissues, including grain, leaf, root, spike and stem, indicating the broad conservation of ASR genes function during wheat evolution. The qRT-PCR analysis revealed that several ASRs were up-regulated in response to NaCl and PEG stress. Conclusion: We identified ASR genes in wheat and found that gene duplication events are the main driving force for ASR gene evolution in wheat. The expression of wheat ASR genes was modulated in responses to multiple abiotic stresses, including drought/osmotic and salt stress. The results provided important information for further identifications of the functions of wheat ASR genes and candidate genes for high abiotic stress tolerant wheat breeding.

Genome-Wide Identification and Comparative Analysis of the ASR Gene Family in the Rosaceae and Expression Analysis of PbrASRs During Fruit Development

“…These results suggested that the ASR gene family is small and evolutionarily conserved. Furthermore, these ASR genes from Rosaceae species were classified into four clades in the phylogenetic tree constructed, namely I, II, III, and IV, a finding that is consistent with the classification of ASR genes from other plant species ( Li et al, 2020 ). Of these, six ASR genes were classified into each of clades IV, III, and II, with nine ASR genes classified into clade I.…”

“…In order to adapt to the natural environment, a set of signal transduction pathways has evolved in plants to cope with responses to the complex and changeable environment. ASR proteins are small, hydrophilic plant-specific proteins that are widely involved in fruit ripening, sugar metabolism, and particularly in plant response to various biotic and abiotic stresses ( Cakir et al, 2003 ; Liu et al, 2010 ; Saumonneau et al, 2012 ; Jia et al, 2016 ; Li et al, 2020 ). It is possible to comprehensively analyze the potential functions of a gene family from the genomic perspective as entire genome sequencing has been carried out on more and more plant species.…”

“…The adaptation of plants to various stressful environmental conditions are associated with changes in morphological traits, physiological and biochemical pathways, and expression of related genes to mitigate the damage caused by such biological and abiotic stresses. The ABA, Stress, and Ripening ( ASR ) genes encode a small, plant-specific, hydrophilic protein, which is involved not only in the response of plants to drought, high salt, low temperature, and abscisic acid stresses, but also in many plant metabolic processes, such as fruit development, maturation, and sugar metabolism ( Iusem et al, 1993 ; Cakir et al, 2003 ; Saumonneau et al, 2012 ; Jia et al, 2016 ; Li et al, 2020 ). With the development of molecular biology methodologies and transcriptome sequencing technology, the first ASR gene was cloned and characterized from tomato ( Solanum lycopersicum L.) in 1993 ( Iusem et al, 1993 ), with further ASR gene members having subsequently been identified in, and cloned from, dicotyledons and monocotyledons.…”

TaASR1‐D confers abiotic stress resistance by affecting ROS accumulation and ABA signalling in transgenic wheat

“…Currently, two studies have identified 29 and 33 ASR genes in wheat, respectively (Li et al, 2020 ; Zan et al, 2020 ). However, in this study, we identified 36 genes in wheat (Table S1 ), and all genes except TaASR8‐U are located on chromosome groups 2, 3, and 4 (Figure S1 a).…”

Characterization and Stress Response of the JmjC Domain-Containing Histone Demethylase Gene Family in the Allotetraploid Cotton Species Gossypium hirsutum

“…Physicochemical parameters of G. hirsutum JmjC genes, including molecular weight (Mw) and isoelectric point (pI), were calculated using the compute pI/Mw tool in EXPASy [ 77 ], with the parameter set to average. Subcellular localization predictions of G. hirsutum JmjC proteins were carried out online using CELLO v2.5 [ 78 ].…”