SiASR4, the Target Gene of SiARDP from Setaria italica, Improves Abiotic Stress Adaption in Plants

Genome-wide identification and functional analysis of the SiCIN gene family in foxtail millet (Setaria italica L.)

Cell wall invertase (CIN) is a vital member of plant invertase (INV) and plays a key role in the breakdown of sucrose. This enzyme facilitates the hydrolysis of sucrose into glucose and fructose, which is crucial for various aspects of plant growth and development. However, the function of CIN genes in foxtail millet (Setaria italica) is less studied. In this research, we used the blast-p of NCBI and TBtools for bidirectional comparison, and a total of 13 CIN genes (named SiCINs) were identified from foxtail millet by using Arabidopsis and rice CIN sequences as reference sequences. The phylogenetic tree analysis revealed that the CIN genes can be categorized into three subfamilies: group 1, group 2, and group 3. Furthermore, upon conducting chromosomal localization analysis, it was observed that the 13 SiCINs were distributed unevenly across five chromosomes. Cis-acting elements of SiCIN genes can be classified into three categories: plant growth and development, stress response, and hormone response. The largest number of cis-acting elements were those related to light response (G-box) and the cis-acting elements related to seed-specific regulation (RY-element). qRT-PCR analysis further confirmed that the expression of SiCIN7 and SiCIN8 in the grain was higher than that in any other tissues. The overexpression of SiCIN7 in Arabidopsis improved the grain size and thousand-grain weight, suggesting that SiCIN7 could positively regulate grain development. Our findings will help to further understand the grain-filling mechanism of SiCIN and elucidate the biological mechanism underlying the grain development of SiCIN.

Drought resistance strategies in minor millets: a review

MAIN CONCLUSION

The review discusses growth and drought-response mechanisms in minor millets under three themes: drought escape, drought avoidance and drought tolerance. Drought is one of the most prominent abiotic stresses impacting plant growth, performance, and productivity. In the context of climate change, the prevalence and severity of drought is expected to increase in many agricultural regions worldwide. Millets (coarse grains) are a group of small-seeded grasses cultivated in arid and semi-arid regions throughout the world and are an important source of food and feed for humans and livestock. Although minor millets, i.e., foxtail millet, finger millet, proso millet, barnyard millet, kodo millet and little millet are generally hardier and more drought-resistant than cereals and major millets (sorghum and pearl millet), understanding their responses, processes and strategies in response to drought is more limited. Here, we review drought resistance strategies in minor millets under three themes: drought escape (e.g., short crop cycle, short vegetative period, developmental plasticity and remobilization of assimilates), drought avoidance (e.g., root traits for better water absorption and leaf traits to control water loss), and drought tolerance (e.g., osmotic adjustment, maintenance of photosynthetic ability and antioxidant potential). Data from 'omics' studies are summarized to provide an overview of the molecular mechanisms important in drought tolerance. In addition, the final section highlights knowledge gaps and challenges to improving minor millets. This review is intended to enhance major cereals and millet per se in light of climate-related increases in aridity.

ZmASR1 negatively regulates drought stress tolerance in maize

Abscisic acid-, stress-, and ripening-induced (ASR) proteins in plants play a significant role in plant response to diverse abiotic stresses. However, the functions of ASR genes in maize remain unclear. In the present study, we identified a novel drought-induced ASR gene in maize (ZmASR1) and functionally characterized its role in mediating drought tolerance. The transcription of ZmASR1 was upregulated under drought stress and abscisic acid (ABA) treatment, and the ZmASR1 protein was observed to exhibit nuclear and cytoplasmic localization. Moreover, ZmASR1 knockout lines generated with the CRISPR-Cas9 system showed lower ROS accumulation, higher ABA content, and a higher degree of stomatal closure than wild-type plants, leading to higher drought tolerance. Transcriptome sequencing data indicated that the significantly differentially expressed genes in the drought treatment group were mainly enriched in ABA signal transduction, antioxidant defense, and photosynthetic pathway. Taken together, the findings suggest that ZmASR1 negatively regulates drought tolerance and represents a candidate gene for genetic manipulation of drought resistance in maize.

Major transcription factor families at the nexus of regulating abiotic stress response in millets: a comprehensive review

Millets stand out as a sustainable crop with the potential to address the issues of food insecurity and malnutrition. These small-seeded, drought-resistant cereals have adapted to survive a broad spectrum of abiotic stresses. Researchers are keen on unravelling the regulatory mechanisms that empower millets to withstand environmental adversities. The aim is to leverage these identified genetic determinants from millets for enhancing the stress tolerance of major cereal crops through genetic engineering or breeding. This review sheds light on transcription factors (TFs) that govern diverse abiotic stress responses and play role in conferring tolerance to various abiotic stresses in millets. Specifically, the molecular functions and expression patterns of investigated TFs from various families, including bHLH, bZIP, DREB, HSF, MYB, NAC, NF-Y and WRKY, are comprehensively discussed. It also explores the potential of TFs in developing stress-tolerant crops, presenting a comprehensive discussion on diverse strategies for their integration.

The role of NaHS pretreatment in improving salt stress resistance in foxtail millet seedlings: physiological and molecular mechanisms

Salt stress is a prevailing abiotic stress in nature, with soil salinization becoming a pressing issue worldwide. High soil salinity severely hampers plant growth and leads to reduced crop yields. Hydrogen sulfide (H2S), a gas signal molecule, is known to be synthesized in plants exposed to abiotic stress, contributing to enhanced plant stress resistance. To investigate the impact of sodium hydrosulfide hydrate (NaHS, a H2S donor) on millet's response to salt stress, millet seedlings were subjected to pretreatment with 200 μM NaHS, followed by 100 mM NaCl stress under soil culture conditions. The growth, osmotic adjustment substances, antioxidant characteristics, membrane damage, and expression levels of related genes in millet seedlings were detected and analyzed. The results showed that NaHS pretreatment alleviated the inhibition of salt stress on the growth of foxtail millet seedlings, increased the proline content and antioxidant enzyme activities, as well as the expression levels of SiASR4, SiRPLK35 and SiHAK23 genes under salt stress. These findings demonstrated that NaHS pretreatment can enhance salt tolerance in foxtail millet seedlings by regulating the content of osmotic adjustment substances and antioxidant enzyme activity, reducing electrolyte permeability, and activating the expression of salt-resistant genes.

Genetic enhancement of climate-resilient traits in small millets: A review

Agriculture is facing the challenge of feeding the ever-growing population that is projected to reach ten billion by 2050. While improving crop yield and productivity can address this challenge, the increasing effects of global warming and climate change seriously threaten agricultural productivity. Thus, genomics and genome modification technologies are crucial to improving climate-resilient traits to enable sustained yield and productivity; however, significant research focuses on staple crops such as rice, wheat, and maize. Crops that are naturally climate-resilient and nutritionally superior to staple cereals, such as small millets, remain neglected and underutilized by mainstream research. The ability of small millets to grow in marginal regions having limited irrigation and poor soil fertility makes these crops a better choice for cultivation in arid and semi-arid areas. Hence, mainstreaming small millets for cultivation and using omics technologies to dissect the climate-resilient traits to identify the molecular determinants underlying these traits are imperative for addressing food and nutritional security. In this context, the review discusses the genomics and genome modification approaches for dissecting key traits in small millets and their application for improving these traits in cultivated germplasm. The review also discusses biofortification for nutritional security and machine-learning approaches for trait improvement in small millets. Altogether, the review provides a roadmap for the effective use of next-generation approaches for trait improvement in small millets. This will lead to the development of improved varieties for addressing multiple insecurities prevailing in the present climate change scenario.

Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects

Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C₄ photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.

Regulation of Drought and Salt Tolerance by OsSKL2 and OsASR1 in Rice

Abiotic stresses such as salinity and drought greatly impact the growth and production of crops worldwide. Here, a shikimate kinase-like 2 (SKL2) gene was cloned from rice and characterized for its regulatory function in salinity and drought tolerance. OsSKL2 was localized in the chloroplast, and its transcripts were significantly induced by drought and salinity stress as well as H₂O₂ and abscisic acid (ABA) treatment. Meanwhile, overexpression of OsSKL2 in rice increased tolerance to salinity, drought and oxidative stress by increasing antioxidant enzyme activity, and reducing levels of H₂O₂, malondialdehyde, and relative electrolyte leakage. In contrast, RNAi-induced suppression of OsSKL2 increased sensitivity to stress treatment. Interestingly, overexpression of OsSKL2 also increased sensitivity to exogenous ABA, with an increase in reactive oxygen species (ROS) accumulation. Moreover, OsSKL2 was found to physically interact with OsASR1, a well-known chaperone-like protein, which also exhibited positive roles in salt and drought tolerance. A reduction in ROS production was also observed in leaves of Nicotiana benthamiana showing transient co-expression of OsSKL2 with OsASR1. Taken together, these findings suggest that OsSKL2 together with OsASR1 act as important regulatory factors that confer salt and drought tolerance in rice via ROS scavenging.

OsASR6 Enhances Salt Stress Tolerance in Rice

High salinity seriously affects crop growth and yield. Abscisic acid-, stress-, and ripening-induced (ASR) proteins play an important role in plant responses to multiple abiotic stresses. In this study, we identified a new salt-induced ASR gene in rice (OsASR6) and functionally characterized its role in mediating salt tolerance. Transcript levels of OsASR6 were upregulated under salinity stress, H₂O₂ and abscisic acid (ABA) treatments. Nuclear and cytoplasmic localization of the OsASR6 protein were confirmed. Meanwhile, a transactivation activity assay in yeast demonstrated no self-activation ability. Furthermore, transgenic rice plants overexpressing OsASR6 showed enhanced salt and oxidative stress tolerance as a result of reductions in H₂O₂, malondialdehyde (MDA), Na/K and relative electrolyte leakage. In contrast, OsASR6 RNAi transgenic lines showed opposite results. A higher ABA content was also measured in the OsASR6 overexpressing lines compared with the control. Moreover, OsNCED1, a key enzyme of ABA biosynthesis, was found to interact with OsASR6. Collectively, these results suggest that OsASR6 serves primarily as a functional protein, enhancing tolerance to salt stress, representing a candidate gene for genetic manipulation of new salinity-resistant lines in rice.

Regulatory network established by transcription factors transmits drought stress signals in plant

Plants are sessile organisms that evolve with a flexible signal transduction system in order to rapidly respond to environmental changes. Drought, a common abiotic stress, affects multiple plant developmental processes especially growth. In response to drought stress, an intricate hierarchical regulatory network is established in plant to survive from the extreme environment. The transcriptional regulation carried out by transcription factors (TFs) is the most important step for the establishment of the network. In this review, we summarized almost all the TFs that have been reported to participate in drought tolerance (DT) in plant. Totally 466 TFs from 86 plant species that mostly belong to 11 families are collected here. This demonstrates that TFs in these 11 families are the main transcriptional regulators of plant DT. The regulatory network is built by direct protein-protein interaction or mutual regulation of TFs. TFs receive upstream signals possibly via post-transcriptional regulation and output signals to downstream targets via direct binding to their promoters to regulate gene expression.

Genetic Mechanisms of Cold Signaling in Wheat (Triticum aestivum L.)

Cold stress is a major environmental factor affecting the growth, development, and productivity of various crop species. With the current trajectory of global climate change, low temperatures are becoming more frequent and can significantly decrease crop yield. Wheat (Triticum aestivum L.) is the first domesticated crop and is the most popular cereal crop in the world. Because of a lack of systematic research on cold signaling pathways and gene regulatory networks, the underlying molecular mechanisms of cold signal transduction in wheat are poorly understood. This study reviews recent progress in wheat, including the ICE-CBF-COR signaling pathway under cold stress and the effects of cold stress on hormonal pathways, reactive oxygen species (ROS), and epigenetic processes and elements. This review also highlights possible strategies for improving cold tolerance in wheat.

Time-series transcriptomics reveals a drought-responsive temporal network and crosstalk between drought stress and the circadian clock in foxtail millet

Drought stress is a serious factor affecting crop growth and production worldwide. The circadian clock has been identified as key to improving regional adaptability of plants. However, our understanding of the contribution of the circadian clock to drought response and the impacts of drought stress on the circadian clock in plants is still limited. To explore the interactions between the circadian clock and drought stress, foxtail millet seedlings were treated with simulated drought (20% polyethylene glycol-6000) treatment starting at the day (DD) onset zeitgeber time 0 (ZT0, lights on) and at the night (DN) onset zeitgeber time 16 (ZT16, lights off). A high temporal-resolution transcriptomic investigation was performed using DD and DN samples collected at intervals of 2 or 4 h within a 24-h drought-treatment period. Overall, we identified 13 294 drought-responsive genes (DRGs). Among these DRGs, 7931 were common between DD and DN samples, 2638 were specific to DD, and 2725 were specific to DN. Additionally, we identified 1257 circadian genes, of which 67% were DRGs. Interestingly, with drought treatment starting at the day for 8, 12 or 16 h, the circadian phase shifted to 12 h. We also found that the circadian clock led to different day and night drought-responsive pathways. The identification of DRG_Clock (DRG and circadian clock) and DRG_NonClock (DRG and not circadian clock) genes provides a reference for selecting candidate drought resistance genes. Our work reveals the temporal drought-response process and crosstalk between drought stress and the circadian clock in foxtail millet.

Improvement of millets in the post-genomic era

Millets are food and nutrient security crops in the semi-arid tropics of developing countries. Crop improvement using modern tools is one of the priority areas of research in millets. The whole-genome sequence (WGS) of millets provides new insight into understanding and studying the genes, genome organization and genomic-assisted improvement of millets. The WGS of millets helps to carry out genome-wide comparison and co-linearity studies among millets and other cereal crops. This approach might lead to the identification of genes underlying biotic and abiotic stress tolerance in millets. The available genome sequence of millets can be used for SNP identification, allele discovery, association and linkage mapping, identification of valuable candidate genes, and marker-assisted breeding (MAB) programs. Next generation sequencing (NGS) technology provides opportunities for genome-assisted breeding (GAB) through genomic selection (GS) and genome-wide association studies (GAWS) for crop improvement. Clustered, regularly interspaced, short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) genome editing (GE) system provides new opportunities for millet improvement. In this review, we discuss the details on the WGS available for millets and highlight the importance of utilizing such resources in the post-genomic era for millet improvement. We also draw inroads on the utilization of various approaches such as GS, GWAS, functional genomics, gene validation and GE for millet improvement. This review might be helpful for understanding the developments in the post-genomic era of millet improvement.

Abscisic Acid-Stress-Ripening Genes Involved in Plant Response to High Salinity and Water Deficit in Durum and Common Wheat

In the dry and hot Mediterranean regions wheat is greatly susceptible to several abiotic stresses such as extreme temperatures, drought, and salinity, causing plant growth to decrease together with severe yield and quality losses. Thus, the identification of gene sequences involved in plant adaptation to such stresses is crucial for the optimization of molecular tools aimed at genetic selection and development of stress-tolerant varieties. Abscisic acid, stress, ripening-induced (ASR) genes act in the protection mechanism against high salinity and water deficit in several plant species. In a previous study, we isolated for the first time the TtASR1 gene from the 4A chromosome of durum wheat in a salt-tolerant Tunisian landrace and assessed its involvement in plant response to some developmental and environmental signals in several organs. In this work, we focused attention on ASR genes located on the homoeologous chromosome group 4 and used for the first time a Real-Time approach to "in planta" to evaluate the role of such genes in modulating wheat adaptation to salinity and drought. Gene expression modulation was evaluated under the influence of different variables - kind of stress, ploidy level, susceptibility, plant tissue, time post-stress application, gene chromosome location. ASR response to abiotic stresses was found only slightly affected by ploidy level or chromosomal location, as durum and common wheat exhibited a similar gene expression profile in response to salt increase and water deficiency. On the contrary, gene activity was more influenced by other variables such as plant tissue (expression levels were higher in roots than in leaves), kind of stress [NaCl was more affecting than polyethylene glycol (PEG)], and genotype (transcripts accumulated differentially in susceptible or tolerant genotypes). Based on such experimental evidence, we confirmed Abscisic acid, stress, ripening-induced genes involvement in plant response to high salinity and drought and suggested the quantification of gene expression variation after long salt exposure (72 h) as a reliable parameter to discriminate between salt-tolerant and salt-susceptible genotypes in both Triticum aestivum and Triticum durum.

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

Cultivating new crop cultivars with multiple abiotic stress tolerances is important for crop production. The abscisic acid-stress-ripening (ASR) protein has been shown to confer abiotic stress tolerance in plants. However, the mechanisms of ASR function under stress condition remain largely unclear. In this study, we characterized all ASR family members in common wheat and constitutively overexpressed TaASR1-D in a commercial hexaploid wheat cultivar Zhengmai 9023. The transgenic wheat plants exhibited increased tolerance to multiple abiotic stresses and increased grain yields under salt stress condition. Overexpression of TaASR1-D conferred enhanced antioxidant capacity and ABA sensitivity in transgenic wheat plants. Further, RNA in situ hybridization results showed that TaASR1-D had higher expression levels in the vascular tissues of leaves and the parenchyma cells around the vascular tissues of roots and stems. Yeast one-hybrid and electrophoretic mobility shift assays revealed that TaASR1-D could directly bind the specific cis-elements in the promoters of TaNCED1 and TaGPx1-D. In conclusion, our findings suggest that TaASR1-D can be used to breed new wheat cultivars with increased multiple abiotic stress tolerances, and TaASR1-D enhances abiotic stress tolerances by reinforcing antioxidant capacity and ABA signalling.

Genome-Wide Analysis of the Late Embryogenesis Abundant (LEA) and Abscisic Acid-, Stress-, and Ripening-Induced (ASR) Gene Superfamily from Canavalia rosea and Their Roles in Salinity/Alkaline and Drought Tolerance

Canavalia rosea (bay bean), distributing in coastal areas or islands in tropical and subtropical regions, is an extremophile halophyte with good adaptability to seawater and drought. Late embryogenesis abundant (LEA) proteins typically accumulate in response to various abiotic stresses, including dehydration, salinity, high temperature, and cold, or during the late stage of seed development. Abscisic acid-, stress-, and ripening-induced (ASR) genes are stress and developmentally regulated plant-specific genes. In this study, we reported the first comprehensive survey of the LEA and ASR gene superfamily in C. rosea. A total of 84 CrLEAs and three CrASRs were identified in C. rosea and classified into nine groups. All CrLEAs and CrASRs harbored the conserved motif for their family proteins. Our results revealed that the CrLEA genes were widely distributed in different chromosomes, and all of the CrLEA/CrASR genes showed wide expression features in different tissues in C. rosea plants. Additionally, we introduced 10 genes from different groups into yeast to assess the functions of the CrLEAs/CrASRs. These results contribute to our understanding of LEA/ASR genes from halophytes and provide robust candidate genes for functional investigations in plant species adapted to extreme environments.

Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping-by-sequencing

Foxtail millet [Setaria italica (L.) P. Beauv.] is the second most important millet species globally and is adapted to cultivation in diverse environments. Like its wild progenitor, green foxtail [S. viridis (L.) P. Beauv.], it is a model species for C4 photosynthetic pathways and stress tolerance genes in related bioenergy crops. We addressed questions regarding the evolution and spread of foxtail millet through a population genomic study of landraces from across its cultivated range in Europe, Asia, and Africa. We sought to determine population genomic structure and the relationship of domesticated lineages relative to green foxtail. Further, we aimed to identify genes involved in environmental stress tolerance that have undergone differential selection between geographical and genetic groups. Foxtail millet landrace accessions (n = 328) and green foxtail accessions (n = 12) were sequenced by genotyping-by-sequencing (GBS). After filtering, 5,677 single nucleotide polymorphisms (SNPs) were retained for the combined foxtail millet-green foxtail dataset and 5,020 for the foxtail millet dataset. We extended geographic coverage of green foxtail by including previously published GBS sequence tags, yielding a 4,515-SNP dataset for phylogenetic reconstruction. All foxtail millet samples were monophyletic relative to green foxtail, suggesting a single origin of foxtail millet, although no group of foxtail millet was clearly the most ancestral. Four genetic clusters were found within foxtail millet, each with a distinctive geographical distribution. These results, together with archaeobotanical evidence, suggest plausible routes of spread of foxtail millet. Selection scans identified nine candidate genes potentially involved in environmental adaptations, particularly to novel climates encountered, as domesticated foxtail millet spread to new altitudes and latitudes.

A novel wheat ASR gene, TaASR2D, enhances drought tolerance in Brachypodium distachyon

Abscisic acid-, stress-, and ripening-induced (ASR) proteins play an important role in protecting plants against adverse environmental conditions. Here, we identified 24 ASR genes in the wheat genome and analyzed their characteristics. Among these, five ASR genes highly induced by abscisic acid (ABA) and polyethylene glycol were cloned and further characterized. The TaASR genes were expressed in response to different abiotic stresses and ABA and were found to be localized in the nucleus and plasma membrane of transformed tobacco cells. Brachypodium distachyon transgenic plants overexpressing TaASR2D showed enhanced drought tolerance by regulating leaf transpiration. The expression levels of stress-related and ABA-responsive genes were higher in transgenic plants than in wild-type plants under drought stress conditions. Moreover, overexpression of TaASR2D increased the levels of both endogenous ABA and hydrogen peroxide in response to drought stress, and these plants showed hypersensitivity to exogenous ABA at the germination stage. Furthermore, plants overexpressing TaASR2D showed increased stomatal closure. Further analysis revealed that TaASR2D interacts with ABA biosynthesis and stress-related proteins in yeast and tobacco plants. Collectively, these findings indicate that TaASR2D plays an important role in the response of plants to drought stress by regulating the ABA biosynthesis pathway and redox homeostasis system.

Transcriptome analysis reveals the tolerant mechanisms to cobalt and copper in barley

Cobalt (Co) and copper (Cu) co-exist commonly in the contaminated soils and at excessive levels, they are toxic to plants. However, their joint effect and possible interaction have not been fully addressed. In this work, a hydroponic experiment was performed to investigate the combined effects of Co and Cu on two barley genotypes at transcriptional level by RNA-seq analysis. The results identified 358 genes inclusively expressed in both genotypes under single and combined treatments of Co and Cu, with most of them being related to metal transport, stress response and transcription factor. The combined treatment induced more differently expressed genes (DEGs) than the single treatment, with Yan66, a metal tolerant genotype having more DEGs than Ea52, a sensitive genotype. The pathways associated with anthocyanin biosynthesis, MAPK signaling, glutathione biosynthesis, phenylalanine metabolism, photosynthesis, arginin biosynthesis, fatty acid elongation, and plant hormone signal transduction biosynthesis were induced and inhibited in Yan66 and Ea52, respectively. Furthermore, flavonoid biosynthesis was much more largely enhanced and accordingly more free flavonoid components (naringin, narirutin and neohesperidin) were accumulated in Yan66 than in Ea52. It may be suggested that high tolerance to both Co and Cu in Yan66 is attributed to its high gene regulatory ability.

Biotechnological approaches to dissect climate-resilient traits in millets and their application in crop improvement

'Small millets' is a generic term that includes all the millets except pearl millet and sorghum. These small or minor millets constitute eleven species that are marginally cultivated and consumed worldwide. These small millets possess excellent agronomic-, climate-resilient, and nutritional traits, although they lack popularity. Small millets withstand a broad spectrum of environmental stresses and possess better water-use and nitrogen-use efficiencies. Of note, small millets are five- to seven-fold nutritionally rich in terms of protein, bioactive compounds, micro- and macro-nutrients as compared to major cereals. Irrespective of these merits, small millets have received little research attention compared to major millets and cereals. However, the knowledge generated from such studies is significant for the improvement of millets per se and for translating the information to improve major cereals through breeding and transgene-based approaches. Given this, the review enumerates the efforts invested in dissecting the climate-resilient traits in small millets and provides a roadmap for deploying the information in crop improvement of millets as well as cereals in the scenario of climate change.

Novel ASR isolated from drought stress responsive SSH library in pearl millet confers multiple abiotic stress tolerance in PgASR3 transgenic Arabidopsis

A genomic resource of drought stress responsive genes/ESTs was generated using Suppression Subtractive Hybridization (SSH) approach in a drought stress tolerant Pennisetum glaucum genotype 841B. Fifty five days old plants were subjected to drought stress after withholding water for different time intervals (10 days, 15 days, 20 days and 25 days). A forward subtractive cDNA library was prepared from isolated RNA of leaf tissue. Differential gene expression under drought stress was validated for selected nine contigs by RT-qPCR. A transcript homologous to Setaria italica ASR3 upregulated under drought stress was isolated from genotype 841B and characterized. Heterologous expression of PgASR3 was validated in Arabidopsis and confirmed under multiple abiotic stress conditions. A total of four independent transgenic lines overexpressing gene PgASR3 were analyzed by Southern blot at T₁ stage. For drought stress tolerance, three independent lines (T₂ stage) were analyzed by biochemical and physiological assays at seedling stage. The growth rate (shoot and root length) of transgenic seedlings improved as compared to WT seedling under differenct abiotic stress conditions. The three transgenic lines were also validated for drought stress tolerance and RT-qPCR analysis, at maturity stage. Under drought stress conditions, the mature transgenic lines showed higher levels of RWC, chlorophyll and proline but lower levels of MDA as compared to WT plants. PgASR3 gene isolated and validated in this study can be utilized for developing abiotic stress tolerant crops.

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

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.

The functional identification of glycine-rich TtASR from Tetragonia tetragonoides (Pall.) Kuntze involving in plant abiotic stress tolerance

In this study, we reported on an ASR gene (TtASR) related to salt/drought tolerance from the edible halophyte Tetragonia tetragonoides (Pall.) Kuntze (Aizoaceae). A phylogenetic analysis revealed that TtASR was evolutionarily close to other two halophytic glycine-rich ASR members, SbASR-1 (from Salicornia brachiate) and SlASR (from Suaeda liaotungensis), with a typical abscisic acid (ABA)/water-deficit stress (WDS) domain at C-terminal. Quantitative RT-PCR analyses showed that TtASR was expressed in all tested different organs of the T. tetragonoides plant and that expression levels were apparently induced after salt, osmotic stress, and ABA treatments in T. tetragonoides seedlings. An induction of TtASR improved the growth performance of yeast and bacteria more than the control under high salinity, osmotic stress, and oxidative stress. TtASR was not a nuclear-specific protein in plant, and the transcriptional activation assay also demonstrated that TtASR could not activate reporter gene's expression in yeast. TtASR overexpressed Arabidopsis plants exhibited higher tolerance for salt/drought and oxidative stresses and lower ROS accumulation than wild type (WT) plants, accompanied by increased CAT, SOD activities, higher proline content, and lower MDA content in vivo. The results indicated that the TtASR was involved in plant responses to salt and drought, probably by mediating water homeostasis or by acting as ROS scavengers, and that it decreased the membrane damage and improved cellular osmotic adjustment that respond to abiotic stresses in microorganisms and plants.

Over-expression of the Brachypodium ASR gene, BdASR4, enhances drought tolerance in Brachypodium distachyon

BdASR4 expression was up-regulated during abiotic stress and hormone treatments. Plants over-expressing BdASR4 improved drought tolerant. BdASR4 may regulate antioxidant activities and transcript levels of stress-related and abscisic acid-responsive genes. Abiotic stress conditions negatively affect plant growth and developmental processes, causing a reduction in crop productivity. The abscisic acid-, stress-, ripening-induced (ASR) proteins play important roles in the protection of plants from abiotic stress. Brachypodium distachyon L. is a well-studied monocot model plant. However, ASR proteins of Brachypodium have not been widely studied. In this study, five ASR genes of Brachypodium plant were cloned and characterized. The BdASR genes were expressed in response to various abiotic stresses and hormones. In particular, BdASR4 was shown to encode a protein containing a nuclear localization signal in its C-terminal region, which enabled protein localization in the nucleus. To further examine functions of BdASR4, transgenic Brachypodium plants harboring BdASR4 were generated. Over-expression of BdASR4 was associated with strong drought tolerance, and plants over-expressing BdASR4 preserved more water and displayed higher antioxidant enzyme activities than did the wild-type plants. The transcript levels of stress-responsive genes, reactive oxygen species scavenger-associated genes, and abscisic acid-responsive genes tended to be higher in transgenic plants than in WT plants. Moreover, plants over-expressing BdASR4 were hypersensitive to exogenous abscisic acid at the germination stage. Taken together, these findings suggest multiple roles for BdASR4 in the plant response to drought stress by regulating antioxidant enzymes and the transcription of stress- and abscisic acid-responsive genes.

Transcriptome analysis reveals potential roles of a barley ASR gene that confers stress tolerance in transgenic rice

Control of gene expression and induction of cellular protection mechanisms are two important processes that plants employ to protect themselves against abiotic stresses. ABA-, stress, and ripening-induced (ASR) proteins have been identified to participate in such responses. Previous studies have proposed that these proteins can act as transcription factors and as molecular chaperones protecting transgenic plants against stresses; however a gene network regulated by ASRs has not been explored. To expand our knowledge on the function of these proteins in cereals, we present the functional characterization of a barley ASR gene. Expression of HvASR5 was almost ubiquitous in different organs and responded to ABA and to different stress treatments. When expressed ectopically, HvASR5 was able to confer drought and salt stress tolerance to Arabidopsis thaliana and to improve growth performance of rice plants under stress conditions. A transcriptomic analysis with two transgenic rice lines overexpressing HvASR5 helped to identify potential downstream targets and understand ASR-regulated cellular processes. HvASR5 up-regulated the expression of a distinct set of genes associated with stress responses, metabolic processes (particularly carbohydrate metabolism), as well as reproduction and development. These data, together with the confirmed nuclear and cytoplasmic localization of HvASR5, further support the hypothesis that HvASR5 can also carry out roles as molecular protector and transcriptional regulator.

Parallelism and convergence in post-domestication adaptation in cereal grasses

The selection of desirable traits in crops during domestication has been well studied. Many crops share a suite of modified phenotypic characteristics collectively known as the domestication syndrome. In this sense, crops have convergently evolved. Previous work has demonstrated that, at least in some instances, convergence for domestication traits has been achieved through parallel molecular means. However, both demography and selection during domestication may have placed limits on evolutionary potential and reduced opportunities for convergent adaptation during post-domestication migration to new environments. Here we review current knowledge regarding trait convergence in the cereal grasses and consider whether the complexity and dynamism of cereal genomes (e.g., transposable elements, polyploidy, genome size) helped these species overcome potential limitations owing to domestication and achieve broad subsequent adaptation, in many cases through parallel means. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.

Multi-omics approaches for strategic improvement of stress tolerance in underutilized crop species: A climate change perspective

For several decades, researchers are working toward improving the "major" crops for better adaptability and tolerance to environmental stresses. However, little or no research attention is given toward neglected and underutilized crop species (NUCS) which hold the potential to ensure food and nutritional security among the ever-growing global population. NUCS are predominantly climate resilient, but their yield and quality are compromised due to selective breeding. In this context, the importance of omics technologies namely genomics, transcriptomics, proteomics, phenomics and ionomics in delineating the complex molecular machinery governing growth, development and stress responses of NUCS is underlined. However, gaining insights through individual omics approaches will not be sufficient to address the research questions, whereas integrating these technologies could be an effective strategy to decipher the gene function, genome structures, biological pathways, metabolic and regulatory networks underlying complex traits. Given this, the chapter enlists the importance of NUCS in food and nutritional security and provides an overview of deploying omics approaches to study the NUCS. Also, the chapter enumerates the status of crop improvement programs in NUCS and suggests implementing "integrating omics" for gaining a better understanding of crops' response to abiotic and biotic stresses.

Comprehensive Analysis of the Cadmium Tolerance of Abscisic Acid-, Stress- and Ripening-Induced Proteins (ASRs) in Maize

In plants, abscisic acid-, stress-, and ripening-induced (ASR) proteins have been shown to impart tolerance to multiple abiotic stresses such as drought and salinity. However, their roles in metal stress tolerance are poorly understood. To screen plant Cd-tolerance genes, the yeast-based gene hunting method which aimed to screen Cd-tolerance colonies from maize leaf cDNA library hosted in yeast was carried out. Here, maize ZmASR1 was identified to be putative Cd-tolerant through this survival screening strategy. In silico analysis of the functional domain organization, phylogenetic classification and tissue-specific expression patterns revealed that maize ASR1 to ASR5 are typical ASRs with considerable expression in leaves. Further, four of them were cloned for testifying Cd tolerance using yeast complementation assay. The results indicated that they all confer Cd tolerance in Cd-sensitive yeast. Then they were transiently expressed in tobacco leaves for subcellular localization analysis and for Cd-challenged lesion assay, continuously. The results demonstrated that all 4 maize ASRs tested are localized to the cell nucleus and cytoplasm in tobacco leaves. Moreover, they were confirmed to be Cd-tolerance genes in planta through lesion analysis in Cd-infiltrated leaves transiently expressing them. Taken together, our results demonstrate that maize ASRs play important roles in Cd tolerance, and they could be used as promising candidate genes for further functional studies toward improving the Cd tolerance in plants.

Genomic, expressional, protein-protein interactional analysis of Trihelix transcription factor genes in Setaria italia and inference of their evolutionary trajectory

Background

Trihelix transcription factors (TTF) play important roles in plant growth and response to adversity stress. Until now, genome-wide identification and analysis of this gene family in foxtail millet has not been available. Here, we identified TTF genes in the foxtail millet and its grass relatives, and characterized their functional domains.

Results

As to sequence divergence, TTF genes were previously divided into five subfamilies, I-V. We found that Trihelix family members in foxtail millet and other grasses mostly preserved their ancestral chromosomal locations during millions of years’ evolution. Six amino acid sites of the SIP1 subfamily possibly were likely subjected to significant positive selection. Highest expression level was observed in the spica, with the SIP1 subfamily having highest expression level. As to the origination and expansion of the gene family, notably we showed that a subgroup of subfamily IV was the oldest, and therefore was separated to define a new subfamily O. Overtime, starting from the subfamily O, certain genes evolved to form subfamilies III and I, and later from subfamily I to develop subfamilies II and V. The oldest gene, Si1g016284, has the most structural changes, and a high expression in different tissues. What’s more interesting is that it may have bridge the interaction with different proteins.

Conclusions

By performing phylogenetic analysis using non-plant species, notably we showed that a subgroup of subfamily IV was the oldest, and therefore was separated to define a new subfamily O. Starting from the subfamily O, certain genes evolved to form other subfamilies. Our work will contribute to understanding the structural and functional innovation of Trihelix transcription factor, and the evolutionary trajectory.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5051-9) contains supplementary material, which is available to authorized users.

Ipomoea pes-caprae IpASR Improves Salinity and Drought Tolerance in Transgenic Escherichia coli and Arabidopsis

Ipomoea pes-caprae L. is an extremophile halophyte with strong adaptability to seawater and drought. It is widely used in the ecological restoration of coastal areas or degraded islands in tropical and subtropical regions. In this study, a new abscisic acid, stressandripening (ASR) gene, IpASR, was reported, and is mainly associated with biological functions involved in salt and drought tolerance. Sequence analysis of IpASR showed that this protein contains an ABA/WDS (abscisic acid/water deficit stress) domain, which is a common feature of all plant ASR members. Overexpression of IpASR improved Escherichia coli growth performance compared with the control under abiotic stress treatment. The transgenic overexpressing IpASR Arabidopsis showed higher tolerance to salt and drought stress than the wild type and lower accumulation of hydrogen peroxide (H₂O₂) and superoxide (O₂⁻) accompanied by increased antioxidant enzyme activity in vivo. IpASR exhibits transcription factor’s activity. Therefore, the overexpression of IpASR in Arabidopsis is supposed to influence the expression of some genes involved in anti-oxidative and abiotic stresses. The results indicate that IpASR is involved in the plant response to salt and drought and probably acts as a reactive oxygen species scavenger or transcription factor, and therefore influences physiological processes associated with various abiotic stresses in plants.