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Background: Small-secreted peptides are increasingly recognized as a novel class of intracellular signal molecules, playing crucial roles in plant growth and development. However, the precise role and mechanism governed by peptides containing Tyrosine Sulfation (PSY) are still under investigation. Currently, there is a lack of accessible information concerning the PSY gene family in wheat. Results: Therefore, in this investigation, we identified 29 PSY genes in Triticum aestivum, with the aim of unraveling their significance in plant development processes and their response to a variety of stress conditions. Phylogenetic analysis showed that TaPSY genes clustered into five groups. Additionally, an analysis of the gene structure of TaPSYs displayed a conserved evolutionary path. The syntenic relationship demonstrated the 69 orthologous gene pairs in T. dicoccoides, Ae. tauschii, T. turgidum, and H. vulgare, respectively. Furthermore, the Ka/Ks analysis indicated that TaPSY genes have experienced purifying selection during their evolutionary processes. The promoters of TaPSY genes were found to contain numerous CAREs, and these elements are known to perform essential functions in various development processes, phytohormone responses, as well as defense and stress mechanisms. In addition, the identification of potential miRNAs targeting TaPSY genes was followed by an examination of their expression patterns across various tissues. Among the 29 TaPSY genes, twenty miRNAs were discovered to target eighteen of them. Moreover, TaPSY genes displayed a distinct expression across different tissues and stress conditions. Conclusions: Hence, these discoveries offer a significant reference point for forthcoming molecular investigations and hold promise for bolstering wheat yield and stress resilience through targeted genetic enhancements and strategic breeding approaches. Highlights: ➢ Signaling peptides, particularly those with Tyrosine Sulfation (PSY) gene family members, have been extensively researched in Arabidopsis. However, there is scarce information available regarding PSY genes in other crops such as wheat. ➢ In this study, we have identified 29 PSY genes in wheat for the first time, shedding light on their significance in plant development and stress response. ➢ Phylogenetic analysis categorized TaPSY genes into five clusters, exhibiting conserved gene structures and notable purifying selection. ➢ Further, the presence of multiple cis-acting regulatory elements (CAREs) in TaPSY promoters and out of the 29 TaPSY genes, 18 TaPSY genes were targeting by miRNAs highlight their roles in various developmental and stress processes. ➢ These discoveries offer invaluable insights for future molecular investigations aimed at boosting wheat yield and enhancing stress tolerance through targeted genetic improvements. [ABSTRACT FROM AUTHOR]

Global warming is a serious threat to food security and severely affects plant growth, developmental processes, and, eventually, crop productivity. Respiratory metabolism plays a critical role in the adaptation of diverse stress in plants. Aconitase (ACO) is the main enzyme, which catalyzes the revocable isomerization of citrate to isocitrate in the Krebs cycle. The function of ACO gene family members has been extensively studied in model plants, for instance Arabidopsis. However, their role in plant developmental processes and various stress conditions largely remained unknown in other plant species. Thus, we identified 15 ACO genes in wheat to elucidate their function in plant developmental processes and different stress environments. The phylogenetic tree revealed that TaACO genes were classified into six groups. Further, gene structure analysis of TaACOs has shown a distinctive evolutionary path. Synteny analysis showed the 84 orthologous gene pairs in Brachypodium distachyon, Aegilops tauschii, Triticum dicoccoides, Oryza sativa, and Arabidopsis thaliana. Furthermore, Ka/Ks ratio revealed that most TaACO genes experienced strong purifying selection during evolution. Numerous cis-acting regulatory elements were detected in the TaACO promoters, which play a crucial role in plant development processes, phytohormone signaling, and are related to defense and stress. To understand the function of TaACO genes, the expression profiling of TaACO genes were investigated in different tissues, developmental stages, and stress conditions. The transcript per million values of TaACOs genes were retrieved from the Wheat Expression Browser Database. We noticed the differential expression of the TaACO genes in different tissues and various stress conditions. Moreover, gene ontology analysis has shown enrichment in the tricarboxylic acid metabolic process (GO:0072350), citrate metabolic process (GO:0006101), isocitrate metabolic process GO:0006102, carbohydrate metabolic (GO:0005975), and glyoxylate metabolic process (GO:0046487). Therefore, this study provided valuable insight into the ACO gene family in wheat and contributed to the further functional characterization of TaACO during different plant development processes and various stress conditions. [ABSTRACT FROM AUTHOR]

Background: IDA (INFLORESCENCE DEFICIENT IN ABSCISSION)-like signaling peptides and the associated HAE (HAESA)-like family of receptor kinases were originally reported in the model plant Arabidopsis thaliana (Arabidopsis) to be deeply involved in the regulation of abscission. Actually, IDA peptides, as cell-to-cell communication elements, appear to be implicated in many developmental processes that rely on cell separation events, and even in the responses to abiotic stresses. However, the knowledge related to the molecular machinery regulating abscission in economically important crops is scarce. In this work, we determined the conservation and phylogeny of the IDA-like and HAE-like gene families in relevant species of the Solanaceae family and analyzed the expression of these genes in the allopolyploid Nicotiana benthamiana, in order to identify members involved in abscission, stem growth and in the response to drought conditions. Results: The phylogenetic relationships among the IDA-like members of the Solanaceae studied, grouped the two pairs of NbenIDA1 and NbenIDA2 protein homeologs with the Arabidopsis prepropeptides related to abscission. Analysis of promoter regions searching for regulatory elements showed that these two pairs of homeologs contained both hormonal and drought response elements, although NbenIDA2A lacked the hormonal regulatory elements. Expression analyses showed that the pair of NbenIDA1 homeologs were upregulated during corolla abscission. NbenIDA1 and NbenIDA2 pairs showed tissue differential expression under water stress conditions, since NbenIDA1 homeologs were highly expressed in stressed leaves while NbenIDA2 homeologs, especially NbenIDA2B, were highly expressed in stressed roots. In non-stressed active growing plants, nodes and internodes were the tissues with the highest expression levels of all members of the IDA-like family and their putative HAE-like receptors. Conclusion: Our results suggest that the pair of NbenIDA1 homeologs are involved in the natural process of corolla abscission while both pairs of NbenIDA1 and NbenIDA2 homeologs are implicated in the response to water stress. The data also suggest that IDA peptides may be important during stem growth and development. These results provide additional evidence that the functional module formed by IDA peptides and its receptor kinases, as defined in Arabidopsis, may also be conserved in Solanaceae. [ABSTRACT FROM AUTHOR]

Proline-rich extensin-like receptor kinases (PERKs) play a crucial role in a wide range of biological processes in plants. In model plants like Arabidopsis, the PERK gene family has been well investigated. Conversely, no information available on the PERK gene family and their biological functions largely remained unknown in rice. This study analyzed the basic physicochemical properties, phylogeny, gene structure, cis-acting elements, Gene ontology (GO) annotation and protein-protein interaction of OsPERK gene family members using various bioinformatics tools based on the whole-genome data of O. sativa. Thus, in this work, 8 PERK genes in rice were identified, and their roles in plant development, growth, and response to various stresses were studied. A phylogenetic study revealed that OsPERKs are grouped into seven classes. Chromosomal mapping also displayed that 8 PERK genes were unevenly distributed on 12 chromosomes. Further, the prediction of subcellular localization indicated that OsPERKs were mainly located at the endomembrane system. Gene structure analysis of OsPERKs has shown a distinctive evolutionary path. In addition, synteny analysis exhibited the 40 orthologous gene pairs in Arabidopsis thaliana, Triticum aestivum, Hordeum vulgare and Medicago truncatula. Furthermore, Ka to Ks proportion shows that most OsPERK genes experienced resilient purifying selection during evolutionary processes. The OsPERK promoters contained several cis-acting regulatory, which are crucial for plant development processes, phytohormone signaling, stress, and defense response. Moreover, the expression pattern of OsPERK family members showed differential expression patterns in different tissues and various stress conditions. Taken together, these results provide clear messages for a better understanding the roles of OsPERK genes in various development stages, tissues, and multifactorial stress as well as enriched the related research of OsPERK family members in rice. • In this work, 8 PERK genes were identified, and their roles in plant growth and development and response to various stresses were studied in rice. • Phylogenetic analysis revealed that OsPERKs are grouped into seven classes. In addition, gene structure analysis of OsPERKs has shown a distinctive evolutionary path. • Further, Synteny analysis exhibited the 40 orthologous gene pairs in Arabidopsis thaliana, Triticum aestivum, Hordeum vulgare and Medicago truncatula. • Moreover, Ka to Ks proportion shows that most OsPERK genes experienced a strong purifying selection during evolutionary processes. • The OsPERK promoters contained several cis-acting regulatory, which are crucial for plant development processes, phytohormone signaling, stress, and defense response. • The expression pattern of OsPERK family members showed differential expression patterns in different tissues and various stress conditions. [ABSTRACT FROM AUTHOR]

Brassinosteroids (BRs) play crucial roles in various biological processes, including plant developmental processes and response to diverse biotic and abiotic stresses. However, no information is currently available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the BZR gene family in wheat to understand the evolution and their role in diverse developmental processes and under different stress conditions. In this study, we performed the genome-wide analysis of the BZR gene family in the bread wheat and identified 20 TaBZR genes through a homology search and further characterized them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses lead to the classification of TaBZR genes into five different groups or subfamilies, providing evidence of evolutionary relationship with Arabidopsis thaliana, Zea mays, Glycine max, and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, and cis-acting regulatory elements were also examined using various computational approaches. In addition, an analysis of public RNA-seq data also shows that TaBZR genes may be involved in diverse developmental processes and stress tolerance mechanisms. Moreover, qRT-PCR results also showed similar expression with slight variation. Collectively, these results suggest that TaBZR genes might play an important role in plant developmental processes and various stress conditions. Therefore, this work provides valuable information for further elucidate the precise role of BZR family members in wheat. [ABSTRACT FROM AUTHOR]

PIN-FORMED (PIN) genes play a crucial role in regulating polar auxin distribution in diverse developmental processes, including tropic responses, embryogenesis, tissue differentiation, and organogenesis. However, the role of PIN-mediated auxin transport in various plant species is poorly understood. Currently, no information is available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the PIN gene family in wheat to understand the evolution of PIN-mediated auxin transport and its role in various developmental processes and under different biotic and abiotic stress conditions. In this study, we performed genome-wide analysis of the PIN gene family in common wheat and identified 44 TaPIN genes through a homology search, further characterizing them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses led to the classification of TaPIN genes into seven different groups, providing evidence of an evolutionary relationship with Arabidopsis thaliana and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, transmembrane domains, and three-dimensional (3D) structure were also examined using various computational approaches. Cis-elements analysis of TaPIN genes showed that TaPIN promoters consist of phytohormone, plant growth and development, and stress-related cis-elements. In addition, expression profile analysis also revealed that the expression patterns of the TaPIN genes were different in different tissues and developmental stages. Several members of the TaPIN family were induced during biotic and abiotic stress. Moreover, the expression patterns of TaPIN genes were verified by qRT-PCR. The qRT-PCR results also show a similar expression with slight variation. Therefore, the outcome of this study provides basic genomic information on the expression of the TaPIN gene family and will pave the way for dissecting the precise role of TaPINs in plant developmental processes and different stress conditions. [ABSTRACT FROM AUTHOR]