Soluble sugars are the key photo-assimilates in higher plants, playing critical roles in growth, development, and stress regulation. The transport of sugars in plants involves the coordinated action between several sugar transporter families, including the SUT, STP, pGlcT, VGT, TMT, INT, PLT, SFP, and SWEET families. Over recent decades, numerous studies have elucidated the molecular functions of major sugar transporters. Phylogenetic and evolutionary analyses support the conservation of substrate specificity and transport direction, at least to some extent. Structural analyses have provided key insights into the structural-function relationships of important transporters (e.g., OsSWEET2b and AtSTP10), which can be effectively leveraged for artificial intelligence (AI)-enabled protein structure prediction and rational design. Advances in omics technologies now enable low-cost, routine transcriptome profiling and cutting-edge techniques (e.g., single-cell multi-omics and spatiotemporal RNA-seq), providing unprecedented ways to understand how sugar transporters function coordinately at multiple levels. Here, we describe the classification of major sugar transporters in plants and summarize established functional knowledge. We emphasize that recent groundbreaking advances in AI-enabled protein analyses and multi-omics will revolutionize molecular physiology in crops. Specifically, the integration of functional knowledge, AI-based protein analyses, and multi-omics will help unravel the orchestration of different sugar transporters, thereby enhancing our understanding of how sugar transportation and source-sink interactions contribute to crop development, yield formation, and beyond, ultimately boosting carbohydrate transport- related crop improvement.

Gene duplication is a primary evolutionary driver of gene family expansion and functional diversification in plants, yet how different duplication processes reshape the evolutionary architecture of transcription factor repertoires remains poorly resolved in lineage-specific genomic contexts. Here, we performed a comprehensive evolutionary and transcriptomic analysis of the basic leucine zipper (bZIP) family across 17 representative species, with a focus on Pooideae. We identified 1878 bZIP genes and found that, although copy numbers were relatively conserved in most diploid grasses, polyploid Triticeae showed substantial expansion. Genome-wide and Ks analyses indicated that bZIP genes were preferentially retained after whole-genome/segmental duplication, with many copies tracing back to the ancient grass-specific ρ-WGD event, the most recent shared polyploidization event in Poaceae. Phylogenetic analyses and orthology inference further resolved four evolutionary models linking ancient duplication with lineage-specific retention and expansion. Transcriptome analyses revealed structured expression divergence across developmental and stress-related contexts, and wheat homoeologous triads exhibited widespread subgenome expression bias that was dynamically reconfigured under stress and hormone treatments. Differences in transposable element landscapes among duplication models and subgenomes further suggest a role for local genomic context in regulatory divergence. Together, these findings establish a unified framework linking ancient duplication, selective retention, and transcriptional diversification of the bZIP family in Pooideae.

Systematically characterized the ARF family in Triticeae revealed its evolutionary expansion patterns and validated that TaARF4.1 acts as a repressor enhancing salt/alkali tolerance potentially by regulating cell wall metabolism and ROS homeostasis. Auxin response factors (ARFs) are core transcription factor families mediating auxin signaling, which not only regulate plant growth and development but also bridge the trade-off between growth and stress adaptation. However, their roles in responding to abiotic stresses—particularly salt/alkali stress, a major constraint to global wheat production—remain poorly understood in wheat (Triticum aestivum). To address this, we integrated evolutionary genomics, multi-tissue expression profiling, and functional validation across 10 Poaceae species (including wheat, rice, maize, and other Triticeae crops) to systematically identify stress-regulatory wheat ARFs (TaARFs). We identified 349 ARF members and reconstructed the evolutionary trajectory across 10 species, clarified orthologous relationships between TaARFs and rice ARFs (OsARFs), and revealed that TaARF expansion is driven by two mechanisms: ancient whole-genome duplication (WGD) conserving core ARF functions and recent gene duplication burst (RBGD) generating Triticeae-specific duplicates (e.g., TaARF4.1/4.2). GO enrichment and stress-induced expression analyses highlighted Group IV repressor ARFs (TaARF4.1/4.2/9) as candidate regulators of abiotic stress responses. Transcriptome integration across salt/alkali-treated wheat leaves and roots identified stably stress-responsive TaARFs, while functional assays confirmed TaARF4.1, as a repressor ARF with the whole-cell localization, was associated with key genes involved in stress signaling, cell wall metabolism, and reactive oxygen species (ROS) homeostasis. This study demonstrates that underutilized genome evolution data aids gene mining in complex crop genomes, providing novel genetic resources for wheat salt/alkali tolerance breeding and insights into auxin-mediated stress adaptation mechanisms.

Introduction Dehydration-responsive element-binding (DREB) transcription factors, members of the AP2/ERF superfamily, are pivotal regulators of stress-responsive gene expression by binding to DRE/CRT cis-elements. They represent promising targets for engineering crop resilience. Objectives This study aims to elucidate the molecular mechanisms underlying ABA-mediated transcription and growth inhibition during drought stress in wheat, with the goal of identifying key drought-resistance genes. Methods The reverse genetics was employed in both Arabidopsis and wheat to investigate the drought-resistance function of TaDREB26-B. The regulatory interplay between TaDREB26-B and abscisic acid-responsive element-binding factors (ABFs), central components of ABA signaling, was dissected using Y1H, LUC, and EMSA assays. Results Co-localization with drought-related QTLs and stress-responsive expression profiles nominated TaDREB26 as a strong candidate drought-tolerance gene. Phylogenetic analysis revealed a Poaceae-specific clade within the DREB-A6 group harboring multiple stress-responsive DREBs. TaDREB26-B expression was rapidly upregulated by drought and ABA. Transgenic plants overexpressing TaDREB26-B exhibited enhanced drought tolerance and heightened ABA sensitivity. Mechanistically, TaDREB26-B activated AtABI4 in Arabidopsis and directly bound the promoter of TaABF2 to amplify the ABA signaling cascade in wheat. Furthermore, we identified a potential feedback regulatory module wherein TaDREB26-B activates TaABF2, while TaABF3 represses TaDREB26-B expression, fine-tuning ABA-responsive transcription. Conclusion This work delineates a Poaceae-specific DREB clade and establishes TaDREB26-B as a prime regulator for improving drought tolerance. These findings provide novel molecular insights into the ABA-dependent transcriptional network governing stress responses and growth in wheat.

GATA transcription factors (TFs) are essential regulators of plant development and stress adaptation. Although certain GATA genes have been functionally characterized in model species and identified in staple crops, the evolutionary history and divergence of this gene family within the Triticeae tribe remain largely unexplored. In this study, we identified 318 GATA genes across seven Triticeae species, classifying them into seven subgroups (I-VII). Comparative phylogenetic analysis revealed that the family's expansion was driven by ancient whole-genome duplication (WGD) and lineage-specific gene duplication events. Comprehensive transcriptomics profiling revealed divergent expression patterns among the duplicated TaGATA members and highlighted TaGATA26-5A as a drought-responsive gene. Heterologous expression of TaGATA26-5A in Arabidopsis significantly enhanced drought tolerance of transgenic plants by modulating stomatal aperture and increasing antioxidant enzyme activities in leaves. Additionally, we characterized the Triticeae-specific tandemly duplicated TaGATA31 copies, among which the ancestral copy TaGATA31.1 showed specific responsiveness to low-phosphate (LP) stress. Functional validation through dual-luciferase and yeast assays confirmed TaGATA31.1-2B as a positive regulator of LP tolerance. This study elucidates the evolutionary dynamics of Triticeae GATA genes and identifies TaGATA26-5A and TaGATA31.1-2B as promising candidates for breeding stress-resilient wheat varieties.

Floret fertility is a key determinant of grain number per spike and an important factor in cereal crop yield. However, the mechanisms by which phytohormone signalling and transcription factors coordinately regulate floret fertility and spikelet development are not well understood, especially in wheat. In this study, we identified the role of jasmonic acid (JA) in the regulation of floret fertility in wheat. TaSPL13-2B, a JA-responsive regulator, directly represses the gene expression of the key JA signalling factor TaJAZ1 to improve floret fertility and increase the number of florets and grains per spikelet. The TaSPL13-2B-regulated JA signalling module (TaJAZ1-TaMYC2) contributes to floret fertility by inducing the expression of TaMADS1, an E-class gene critical for floral organ identity and floret meristem activity, and increasing the content of jasmonoyl-isoleucine (JA-Ile) by upregulating the expression of genes involved in JA biosynthesis. We further demonstrated that TaSPL13-2B is a potential target for yield improvement through field trials. Our work provides mechanistic insights into floret fertility and demonstrates that improving floret fertility could be a promising strategy to increase yield.

TaGF14g enhances drought and salt tolerance by reducing ROS levels and increasing osmoprotectants content through the activation of stress-related genes and ABA signaling. Drought and high salinity severely constrain plant growth. The 14-3-3 proteins, a family of phosphopeptide-binding proteins, play pivotal roles in various signaling pathways. However, their functional mechanisms underlying drought and salt stress adaptation remain poorly understood, particularly in crop plant wheat (Triticum aestivum L.). Here, we identified a wheat 14-3-3 protein, TaGF14g, which positively modulates drought and salt tolerance. Spatiotemporal expression profiling revealed that TaGF14g is expressed in a variety of organs and tissues. Moreover, the expression of TaGF14g was significantly upregulated in response to treatments with polyethylene glycol 6000 (simulating drought), NaCl (simulating salt stress), and abscisic acid (ABA). Ectopic expression of TaGF14g exhibited improved abiotic stress resilience in transgenic tobacco (Nicotiana tabacum L.), with seedlings developing longer roots under drought and high-salinity conditions compared to control plants. Physiological analysis further showed that overexpression of TaGF14g in tobacco enhanced the activity and transcriptional levels of antioxidant enzymes, thereby improving reactive oxygen species (ROS) scavenging capacity and alleviating oxidative damage to plants. Meanwhile, TaGF14g overexpression improved drought stress tolerance by improving water retention and the accumulation of osmolytes. Under salt stress, transgenic lines showed improved tolerance through the upregulation of genes related to ion transporters. Furthermore, TaGF14b increased ABA sensitivity in transgenic tobacco and induced stress-responsive gene expression under stress conditions. Our findings demonstrate that TaGF14g confers drought and salt stress resilience by modulating physiological processes and ABA signaling pathways, thus positioning it as a promising candidate for developing stress-resistant crop varieties.

Due to lack gluten and bioactive ingredients, making gluten-free flour (GFF) difficult to meet consumer demand for higher quality and healthier food. This work studied the effects of tannic acid (TA) addition on the physicochemical properties of GFF and explored the underlying mechanisms of this improvement. The addition of TA improved the mixing properties, antioxidant capacity, pasting properties, water binding capacity, swelling power, enthalpy of gelatinization, microstructure and rheological properties of GFF. When TA was added at 0.3%–0.6% percentages of GFF in weight, the binding rate of TA and GFF, and the complex index of TA-starch complexes significantly increased from 5% to 15%, and 45%–65%, respectively. The results of the molecular force analysis and iodine binding analysis demonstrated that hydrogen bonds and hydrophobic interactions were formed between TA and starch, particularly hydrophobic interactions, and TA mainly interacted with amylose molecules. These results discovered the underlying mechanisms of TA interacting with starch and enriched the technology for improving GFF and demonstrated that TA can expand the function of GFF.

Modern wheat cultivation requires seed to germinate rapidly and uniformly with weak dormancy. However, such varieties tend to undergo pre-harvest sprouting (PHS) if the harvest overlaps with the rainy season, causing substantial yield losses. Knowledge regarding the mechanisms of seed dormancy in wheat (Triticum aestivum L.) is limited, with only a few causal genes of the many PHS quantitative trait loci (QTLs) characterized. Here, we emphasize the involvement of ABA signalling core components in regulating seed dormancy and germination in wheat. TaPP2C-a6 was identified as the likely causal gene of wheat PHS-QTLs QPhs.wsu-1A/1B and QPhs1D.1_nwafu loci. Both TaPP2C-a6 and TaPP2C-a7 were highly expressed at embryonic developmental stages and germinating seeds, whereas TaPP2C-a6 was up-regulated during embryo maturation and seed germination. TaPP2C-a6 and TaPP2C-a7 were clade-A PP2Cs that interacted with TaPYLs and class III TaSnRK2s; however, TaPP2C-a6 showed stronger interactions with TaDOG1L members than those of TaPP2C-a7. TaPP2C-a6 overexpression in transgenic Arabidopsis thaliana caused a more severe reduction in ABA sensitivity than TaPP2C-a7 overexpression. Overexpression of TaPP2C-a6 in transgenic A. thaliana and wheat increased PHS levels, whereas TaPP2C-a7 transgenic A. thaliana did not affect PHS levels, confirming that TaPP2C-a6 is a novel regulator of wheat seed dormancy and germination. In summary, we demonstrated that leveraging the knowledge of seed dormancy and germination from model species could rapidly identify the causal genes of PHS-QTLs in wheat. Significantly, we showed that the TaPP2C-TaDOG1L interactions, particularly the interaction strength, could be a new aspect in the regulation of seed dormancy and germination.

The Oryza genus serves not only as a gene pool for rice improvement but also as a model system for plant evolutionary research. Calcium-dependent protein kinases (CPKs) function as both effectors and sensors in calcium signaling and play versatile roles in plant development and stress responses. Four kinase families, namely CPK-related kinases (CRKs), phosphoenolpyruvate carboxylase kinases (PPCKs), PPCK-related kinases (PEPRKs), and calcium- and calmodulin-dependent kinases (CCaMKs), are frequently called CPK-related kinases. This study utilized evolutionary genomics approaches and provided the pan-genome repertoires of CPKs and their related kinases in 34 Oryza genomes by leveraging the rich genomics resources of the Orzya genus. Gene duplication analysis revealed that distinct duplication types contributed to expanding CPKs and their related kinases in wild rice. We depicted the protein domain architectures of CPKs and their related kinases, highlighting the complexity of EF-hand motifs in CPKs and CCaMKs. Transcriptome analysis determined that alternative splicing was a mechanism contributing to the diversity in the domain architectures of CPKs and CCaMKs. We also generated the expression atlas of CPKs and their related kinases in multiple species of Oryza genus, emphasizing divergent homoeolog expression patterns across tissues and species in allotetraploid wild rice. Collectively, our Oryza-wide analysis of CPKs and their related kinases revealed their evolutionary trajectories and highlighted their diversified domain architectures and expression dynamics, providing gene resources of wild relatives for rice improvement.

Introduction The sessile plants often experience environmental conditions not ideal for growth, and therefore have evolved strategies to survive and adapt to stress conditions. Abscisic acid (ABA) regulates plant development and abiotic stress response. Clade A type 2C protein phosphatases (PP2Cs), act as co-receptors of ABA, negatively regulate ABA signalling. However, the biological function and detailed molecular mechanism of clade A PP2Cs in ABA signalling pathway remain to be elucidated in wheat. Objectives To analyze the mechanisms of stress response and development mediated by ABA signal precisely regulated by TaPP2C-a5 at the post-transcriptional level in wheat, providing candidate genes for wheat improvement. Methods Based on our previous results of TaPP2Cs gene family analysis, the function and detailed regulation mechanisms of TaPP2C-a5 gene in seed dormancy and germination as well as drought response mediated by ABA signaling pathway were explored through reverse genetics technology. Results We found that class A TaPP2C-a5 underwent alternative splicing (AS) to produce two transcripts encoding TaPP2C-a5.1 and TaPP2C-a5.2, respectively. Both TaPP2C-a5.1 and TaPP2C-a5.2 were highly expressed in mature seeds, and were upregulated by exogenous ABA in seedlings. Overexpression of TaPP2C-a5.1 and TaPP2C-a5.2 coordinately negatively regulated seed dormancy and ABA-mediated seed germination as well as post-germination developmental arrest in wheat. TaPP2C-a5.1 negatively regulated drought stress response, while TaPP2C-a5.2 did not participate in drought stress response. The homologous genes of TaPP2C-a5 underwent the same AS as TaPP2C-a5 in tetraploid wheat, but not in rice. Conclusion Our results revealed that TaPP2C-a5 gene underwent AS and was involved in the regulation of seed dormancy and germination, as well as drought stress response mediated by the ABA signaling at the post-transcriptional level. Our work not only provide a potential target gene to improve PHS resistance, but also emphasize alternative splicing as a strategy with evolution contexts to fine-tune ABA signaling and its involvement in certain biological process.

Double B-box (DBB) proteins, a plant-specific subgroup of the B-box (BBX) transcription factors, have been implicated in light signaling and stress responses. However, their evolutionary trajectory and functional divergence remain unexplored in the common wheat (Triticum aestivum L.), hindering the identification of stress-involved TaDBB candidates and the stress-responsive gene networks. Here, we performed a genome-wide identification and comparative analysis of DBB genes across 10 Poaceae species, with a focus on wheat and its relatives. Phylogenetic and duplication analysis, and expression profiling were integrated to re-construct the evolutionary patterns and to pinpoint the stress-responsive roles of several DBB genes. Candidate TaDBBs were further validated through qRT-PCR, protein subcellular localization, and transactivation assays. A total of 136 DBB genes were identified, including 29 TaDBBs from the common wheat genome forming nine triads. Dispersed duplication was the primary driver of DBB expansion in Triticeae. Expression profiling revealed that DBB genes exhibit tissue-specific and stress-responsive expression patterns. Notably, TaDBB4.1 and TaDBB4.2, derived from segmental duplication, showed divergent regulatory roles under saline/alkaline stress. TaDBB4.1 was found to negatively regulate photosynthesis-related genes, while TaDBB4.2 targeted ion transport and redox processes. Both localized to the nucleus and exhibited distinct transactivation activities. This study provides the first comprehensive analysis of DBB genes in wheat and highlights TaDBB4 as a key regulator of saline-alkaline stress responses. Our findings offer valuable genetic resources for improving wheat stress tolerance through molecular breeding.

Introduction: Drought poses a significant environmental challenge, disrupting plant growth and reducing crop productivity. As sensors and effectors in calcium signaling, calcium-dependent protein kinases (CPKs) regulate plant development and environmental adaptation. However, the specific roles and molecular networks of many OsCPKs in rice adaptation to abiotic stress remain to be elucidated. Objectives: Drought-tolerant rice holds significant potential for enhancing yield stability and global food security. The study aimed to isolate drought-responsive OsCPKs and explore their molecular mechanisms. Methods: To elucidate the mechanisms underlying OsCPK9-mediated drought tolerance, we integrated assays of Co-immunoprecipitation, yeast two-hybrid, GST pull-down and bimolecular fluorescence complementation to validate the OsCPK9-interacting proteins. In vitro protein phosphorylation analysis was conducted to identify phosphorylated substrates and sites. Rice yield performance was evaluated through three-year field trials. Results: OsCPK9 overexpressing plants enhanced drought tolerance in rice, accompanied by lower H2O2 content and higher catalase activity than wild-type (WT) plants. Conversely, OsCPK9 knockout plants exhibited sensitive to drought stress compared with WT plants. Myristoylation and palmitoylation contributed to plasma membrane localization of OsCPK9, which is required for drought tolerance. OsCPK9 interacts with and phosphorylates Catalase C (OsCATC) at the plasma membrane. Phosphorylation of OsCATC at the highly conserved Thr105 enhanced its self-interaction, promoting oligomer formation and thereby increasing catalytic activity. OsCATC overexpressing plants showed higher catalase activity and improved drought tolerance compared to WT plants. Moreover, OsCPK9 overexpressing plants mitigated a 17.6% average yield loss per plant relative to WT plants. Conclusion: This study reveals that myristoylation and palmitoylation of OsCPK9 contribute to its plasma membrane localization and drought tolerance. The post-translational regulatory mechanism mediated by OsCPK9 enhances environmental adaptability and provides a promising strategy to improve rice grain yield under drought stress conditions.

Drought is a major abiotic stress that severely constrains plant growth, development, and crop productivity. Identifying key drought-tolerance genes and deciphering their regulatory mechanisms are critical for enhancing crop resilience. The 14-3-3 proteins, a family of phosphopeptide-binding proteins, play pivotal roles in diverse signaling pathways, thereby influencing metabolism, development, and stress responses. However, their detailed mechanism in mediating drought tolerance in wheat (Triticum aestivum L.) remains largely elusive. In this study, we demonstrate that TaGF14b, a 14-3-3 family member in wheat, functions as a positive regulator of drought stress tolerance. Mechanistically, TaGF14b enhances abscisic acid (ABA) responses by interacting with the ABA-responsive element binding factor TaABF2, thereby amplifying the transactivation activity of downstream drought-responsive genes. Metabolomic profiling revealed that overexpression of TaGF14b mitigates drought-induced metabolic perturbations in wheat. Furthermore, we identified a novel regulatory mechanism wherein TaGF14b interacts with sucrose phosphate synthase TaSPS2, modulating its enzymatic activity to alleviate the perturbations in sugar metabolism under stress conditions. Intriguingly, TaSPS2 weakens the TaGF14b-TaABF2 interaction, thereby fine-tuning the transcriptional activation of ABA-responsive genes and preventing overactivation of the ABA signaling pathway. Our findings uncover a dual role of TaGF14b in coordinating drought tolerance through ABA-dependent gene regulation and the maintenance of sugar metabolism, providing novel insights into strategies for improving drought tolerance in wheat. Through integrated multi-omics and biochemical analyses, we demonstrate the significance of TaGF14b in maintaining metabolic homeostasis and mediating drought stress response, thereby highlighting its potential as a novel target for improving drought tolerance in wheat.

Auxin Response Factors (ARFs) make up a plant-specific transcription factor family that mainly couples perception of the phytohormone, auxin, and gene expression programs and plays an important and multi-faceted role during plant growth and development. Lemongrass (Cymbopogon flexuosus) is a representative Cymbopogon species widely used in gardening, beverages, fragrances, traditional medicine, and heavy metal phytoremediation. Biomass yield is an important trait for several agro-economic purposes of lemongrass, such as landscaping, essential oil production, and phytoremediation. Therefore, we performed gene mining of CfARFs and identified 26 and 27 CfARF-encoding genes in each of the haplotype genomes of lemongrass, respectively. Phylogenetic and domain architecture analyses showed that CfARFs can be divided into four groups, among which groups 1, 2, and 3 correspond to activator, repressor, and ETTN-like ARFs, respectively. To identify the CfARFs that may play major roles during the growth of lemongrass plants, RNA-seq was performed on three tissues (leaf, stem, and root) and four developmental stages (3-leaf, 4-leaf, 5-leaf. and mature stages). The expression profiling of CfARFs identified several highly expressed activator and repressor CfARFs and three CfARFs (CfARF3, 18, and 35) with gradually increased levels during leaf growth. Haplotype-resolved transcriptome analysis revealed that biallelic expression dominance is frequent among CfARFs and contributes to their gene expression patterns. In addition, co-expression network analysis identified the modules enriched with CfARFs. By establishing orthologous relationships among CfARFs, sorghum ARFs, and maize ARFs, we showed that CfARFs were mainly expanded by whole-genome duplications, and that the duplicated CfARFs might have been divergent due to differential expression and variations in domains and motifs. Our work provides a detailed catalog of CfARFs in lemongrass, representing a first step toward characterizing CfARF functions, and may be useful in molecular breeding to enhance lemongrass plant growth.

Sorghum ( Sorghum bicolor L. Moench), a monocot C4 crop, is an important staple crop for many countries in arid and semi-arid regions worldwide. Because sorghum has outstanding tolerance and adaptability to a variety of abiotic stresses, including drought, salt, and alkaline, and heavy metal stressors, it is valuable research material for better understanding the molecular mechanisms of stress tolerance in crops and for mining new genes for their genetic improvement of abiotic stress tolerance. Here, we compile recent progress achieved using physiological, transcriptome, proteome, and metabolome approaches; discuss the similarities and differences in how sorghum responds to differing stresses; and summarize the candidate genes involved in the process of responding to and regulating abiotic stresses. More importantly, we exemplify the differences between combined stresses and a single stress, emphasizing the necessity to strengthen future studies regarding the molecular responses and mechanisms of combined abiotic stresses, which has greater practical significance for food security. Our review lays a foundation for future functional studies of stress-tolerance-related genes and provides new insights into the molecular breeding of stress-tolerant sorghum genotypes, as well as listing a catalog of candidate genes for improving the stress tolerance for other key monocot crops, such as maize, rice, and sugarcane.

INTRODUCTION:Reverse genetic studies conducted in the plant with a complex or polyploidy genome enriched with large gene families (like wheat) often meet challenges in identifying the key candidate genes related to important traits and prioritizing the genes for functional experiments. OBJECTIVE:To overcome the above-mentioned challenges of reverse genetics, this work aims to establish an efficient multi-species strategy for genome-wide gene identification and prioritization of the key candidate genes. METHODS:We established the integrative gene duplication and genome-wide analysis (iGG analysis) as a strategy for pinpointing key candidate genes deserving functional research. The iGG captures the evolution, and the expansion/contraction of large gene families across phylogeny-related species and integrates spatial-temporal expression information for gene function inference. Transgenic approaches were also employed to functional validation. RESULTS:As a proof-of-concept for the iGG analysis, we took the wheat calcineurin B-like protein-interacting protein kinases (CIPKs) family as an example. We identified CIPKs from seven monocot species, established the orthologous relationship of CIPKs between rice and wheat, and characterized Triticeae-specific CIPK duplicates (e.g., CIPK4 and CIPK17). Integrated with our analysis of CBLs and CBL-CIPK interaction, we revealed that divergent expressions of TaCBLs and TaCIPKs could play an important role in keeping the stoichiometric balance of CBL-CIPK. Furthermore, we validated the function of TaCIPK17-A2 in the regulation of drought tolerance by using transgenic approaches. Overexpression of TaCIPK17 enhanced antioxidant capacity and improved drought tolerance in wheat. CONCLUSION:The iGG analysis leverages evolutionary and comparative genomics of crops with large genomes to rapidly highlight the duplicated genes potentially associated with speciation, domestication and/or particular traits that deserve reverse-genetic functional studies. Through the identification of Triticeae-specific TaCIPK17 duplicates and functional validation, we demonstrated the effectiveness of the iGG analysis and provided a new target gene for improving drought tolerance in wheat.

Valine-glutamine motif-containing (VQ) proteins are transcriptional cofactors widely involved in plant growth, development, and response to various stresses. Although the VQ family has been genome-wide identified in some species, but the knowledge regarding duplication-driven functionalization of VQ genes among evolutionarily related species is still lacking. Here, 952 VQ genes have been identified from 16 species, emphasizing seven Triticeae species including the bread wheat. Comprehensive phylogenetic and syntenic analyses allow us to establish the orthologous relationship of VQ genes from rice (Oryza sativa) to bread wheat (Triticum aestivum). The evolutionary analysis revealed that whole-genome duplication (WGD) drives the expansion of OsVQs, while TaVQs expansion is associated with a recent burst of gene duplication (RBGD). We also analyzed the motif composition and molecular properties of TaVQ proteins, enriched biological functions, and expression patterns of TaVQs. We demonstrate that WGD-derived TaVQs have become divergent in both protein motif composition and expression pattern, while RBGD-derived TaVQs tend to adopt specific expression patterns, suggesting their functionalization in certain biological processes or in response to specific stresses. Furthermore, some RBGD-derived TaVQs are found to be associated with salt tolerance. Several of the identified salt-related TaVQ proteins were located in the cytoplasm and nucleus and their salt-responsive expression patterns were validated by qPCR analysis. Yeast-based functional experiments confirmed that TaVQ27 may be a new regulator to salt response and regulation. Overall, this study lays the foundation for further functional validation of VQ family members within the Triticeae species.

The extensive use of fossil fuels and global climate change have raised ever-increasing attention to sustainable development, global food security and the replacement of fossil fuels by renewable energy. Several C4 monocot grasses have excellent photosynthetic ability, stress tolerance and may rapidly produce biomass in marginal lands with low agronomic inputs, thus representing an important source of bioenergy. Among these grasses, Sorghum bicolor has been recognized as not only a promising bioenergy crop but also a research model due to its diploidy, simple genome, genetic diversity and clear orthologous relationship with other grass genomes, allowing sorghum research to be easily translated to other grasses. Although sorghum molecular genetic studies have lagged far behind those of major crops (e.g., rice and maize), recent advances have been made in a number of biomass-related traits to dissect the genetic loci and candidate genes, and to discover the functions of key genes. However, molecular and/or targeted breeding toward biomass-related traits in sorghum have not fully benefited from these pieces of genetic knowledge. Thus, to facilitate the breeding and bioenergy applications of sorghum, this perspective summarizes the bioenergy applications of different types of sorghum and outlines the genetic control of the biomass-related traits, ranging from flowering/maturity, plant height, internode morphological traits and metabolic compositions. In particular, we describe the dynamic changes of carbohydrate metabolism in sorghum internodes and highlight the molecular regulators involved in the different stages of internode carbohydrate metabolism, which affects the bioenergy utilization of sorghum biomass. We argue the way forward is to further enhance our understanding of the genetic mechanisms of these biomass-related traits with new technologies, which will lead to future directions toward tailored designing sorghum biomass traits suitable for different bioenergy applications.