Roles of the Brassica napus DELLA Protein BnaA6.RGA, in Modulating Drought Tolerance by Interacting With the ABA Signaling Component BnaA10.ABF2

CRISPR-Cas9 mediated understanding of plants' abiotic stress-responsive genes to combat changing climatic patterns

Multiple abiotic stresses like extreme temperatures, water shortage, flooding, salinity, and exposure to heavy metals are confronted by crop plants with changing climatic patterns. Prolonged exposure to these adverse environmental conditions leads to stunted plant growth and development with significant yield loss in crops. CRISPR-Cas9 genome editing tool is being frequently employed to understand abiotic stress-responsive genes. Noteworthy improvements in CRISPR-Cas technology have been made over the years, including upgradation of Cas proteins fidelity and efficiency, optimization of transformation protocols for different crop species, base and prime editing, multiplex gene-targeting, transgene-free editing, and graft-based heritable CRISPR-Cas9 approaches. These developments helped to improve the knowledge of abiotic stress tolerance in crops that could potentially be utilized to develop knock-out varieties and over-expressed lines to tackle the adverse effects of altered climatic patterns. This review summarizes the mechanistic understanding of heat, drought, salinity, and metal stress-responsive genes characterized so far using CRISPR-Cas9 and provides data on potential candidate genes that can be exploited by modern-day biotechnological tools to develop transgene-free genome-edited crops with better climate adaptability. Furthermore, the importance of early-maturing crop varieties to withstand abiotic stresses is also discussed in this review.

Genome-wide identification and expression analysis of GRAS gene family in Eucalyptus grandis

BACKGROUND

The GRAS gene family is a class of plant-specific transcription factors with important roles in many biological processes, such as signal transduction, disease resistance and stress tolerance, plant growth and development. So far, no information available describes the functions of the GRAS genes in Eucalyptus grandis.

RESULTS

A total of 82 GRAS genes were identified with amino acid lengths ranging from 267 to 817 aa, and most EgrGRAS genes had one exon. Members of the GRAS gene family of Eucalyptus grandis are divided into 9 subfamilies with different protein structures, while members of the same subfamily have similar gene structures and conserved motifs. Moreover, these EgrGRAS genes expanded primarily due to segmental duplication. In addition, cis-acting element analysis showed that this family of genes was involved involved in the signal transduction of various plant hormones, growth and development, and stress response. The qRT-PCR data indicated that 18 EgrGRAS genes significantly responded to hormonal and abiotic stresses. Among them, the expression of EgrGRAS13, EgrGRAS68 and EgrGRAS55 genes was significantly up-regulated during the treatment period, and it was hypothesised that members of the EgrGRAS family play an important role in stress tolerance.

CONCLUSIONS

In this study, the phylogenetic relationship, conserved domains, cis-elements and expression patterns of GRAS gene family of Eucalyptus grandis were analyzed, which filled the gap in the identification of GRAS gene family of Eucalyptus grandis and laid the foundation for analyzing the function of EgrGRAS gene in hormone and stress response.

RING-type E3 ligase BnaJUL1 ubiquitinates and degrades BnaTBCC1 to regulate drought tolerance in Brassica napus L

Drought stress poses a persistent threat to field crops and significantly limits global agricultural productivity. Plants employ ubiquitin-dependent degradation as a crucial post-translational regulatory mechanism to swiftly adapt to changing environmental conditions. JUL1 is a RING-type E3 ligase related to drought stress in Arabidopsis. In this study, we explored the function of BnaJUL1 (a homologous gene of JUL1 in Brassica napus) and discovered a novel gene BnaTBCC1 participating in drought tolerance. First, we utilised BnaJUL1-cri materials through the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 system. Second, we confirmed that BnaJUL1 regulated drought tolerance through the drought tolerance assay and transcriptome analysis. Then, we identified a series of proteins interacting with BnaJUL1 through yeast library screening, including BnaTBCC1 (a tubulin binding cofactor C domain-containing protein); whose homologous gene TBCC1 knockdown mutants (tbcc1-1) exhibited ABA-sensitive germination in Arabidopsis, we then confirmed the involvement of BnaTBCC1 in drought tolerance in both Arabidopsis and Brassica. Finally, we established that BnaJUL1 could ubiquitinate and degrade BnaTBCC1 to regulate drought tolerance. Consequently, our study unveils BnaJUL1 as a novel regulator that ubiquitinates and degrades BnaTBCC1 to modulate drought tolerance and provided desirable germplasm for further breeding of drought tolerance in rapeseed.

BcABF1 Plays a Role in the Feedback Regulation of Abscisic Acid Signaling via the Direct Activation of BcPYL4 Expression in Pakchoi

Abscisic acid-responsive element-binding factor 1 (ABF1), a key transcription factor in the ABA signal transduction process, regulates the expression of downstream ABA-responsive genes and is involved in modulating plant responses to abiotic stress and developmental processes. However, there is currently limited research on the feedback regulation of ABF1 in ABA signaling. This study delves into the function of BcABF1 in Pakchoi. We observed a marked increase in BcABF1 expression in leaves upon ABA induction. The overexpression of BcABF1 not only spurred Arabidopsis growth but also augmented the levels of endogenous IAA. Furthermore, BcABF1 overexpression in Arabidopsis significantly decreased leaf water loss and enhanced the expression of genes associated with drought tolerance in the ABA pathway. Intriguingly, we found that BcABF1 can directly activate BcPYL4 expression, a critical receptor in the ABA pathway. Similar to BcABF1, the overexpression of BcPYL4 in Arabidopsis also reduces leaf water loss and promotes the expression of drought and other ABA-responsive genes. Finally, our findings suggested a novel feedback regulation mechanism within the ABA signaling pathway, wherein BcABF1 positively amplifies the ABA signal by directly binding to and activating the BcPYL4 promoter.

Natural variation in BnaA9.NF-YA7 contributes to drought tolerance in Brassica napus L

Rapeseed (Brassica napus) is one of the important oil crops worldwide. Its production is often threatened by drought stress. Here, we identify a transcription factor (BnaA9.NF-YA7) that negatively regulates drought tolerance through genome-wide association study in B. napus. The presence of two SNPs within a CCAAT cis element leads to downregulation of BnaA9.NF-YA7 expression. In addition, the M63I (G-to-C) substitution in the transactivation domain can activate low level expression of BnaA4.DOR, which is an inhibitory factor of ABA-induced stomatal closure. Furthermore, we determine that Bna.ABF3/4s directly regulate the expression of BnaA9.NF-YA7, and BnaA9.NF-YA7 indirectly suppresses the expression of Bna.ABF3/4s by regulation of Bna.ASHH4s. Our findings uncover that BnaA9.NF-YA7 serves as a supplementary role for ABA signal balance under drought stress conditions, and provide a potential molecular target to breed drought-tolerant B. napus cultivars.

Functional genomics of Brassica napus: Progresses, challenges, and perspectives

Brassica napus, commonly known as rapeseed or canola, is a major oil crop contributing over 13% to the stable supply of edible vegetable oil worldwide. Identification and understanding the gene functions in the B. napus genome is crucial for genomic breeding. A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in B. napus. In this review, we present an overview of the progress made in the functional genomics of B. napus, including the availability of germplasm resources, omics databases and cloned functional genes. Based on the current progress, we also highlight the main challenges and perspectives in this field. The advances in the functional genomics of B. napus contribute to a better understanding of the genetic basis underlying the complex agronomic traits in B. napus and will expedite the breeding of high quality, high resistance and high yield in B. napus varieties.

Advancements and prospects of CRISPR/Cas9 technologies for abiotic and biotic stresses in sugar beet

Sugar beet is a crop with high sucrose content, known for sugar production and recently being considered as an emerging raw material for bioethanol production. This crop is also utilized as cattle feed, mainly when animal green fodder is scarce. Bioethanol and hydrogen gas production from this crop is an essential source of clean energy. Environmental stresses (abiotic/biotic) severely affect the productivity of this crop. Over the past few decades, the molecular mechanisms of biotic and abiotic stress responses in sugar beet have been investigated using next-generation sequencing, gene editing/silencing, and over-expression approaches. This information can be efficiently utilized through CRISPR/Cas 9 technology to mitigate the effects of abiotic and biotic stresses in sugar beet cultivation. This review highlights the potential use of CRISPR/Cas 9 technology for abiotic and biotic stress management in sugar beet. Beet genes known to be involved in response to alkaline, cold, and heavy metal stresses can be precisely modified via CRISPR/Cas 9 technology for enhancing sugar beet's resilience to abiotic stresses with minimal off-target effects. Similarly, CRISPR/Cas 9 technology can help generate insect-resistant sugar beet varieties by targeting susceptibility-related genes, whereas incorporating Cry1Ab and Cry1C genes may provide defense against lepidopteron insects. Overall, CRISPR/Cas 9 technology may help enhance sugar beet's adaptability to challenging environments, ensuring sustainable, high-yield production.

Genetic Databases and Gene Editing Tools for Enhancing Crop Resistance against Abiotic Stress

Abiotic stresses extensively reduce agricultural crop production globally. Traditional breeding technology has been the fundamental approach used to cope with abiotic stresses. The development of gene editing technology for modifying genes responsible for the stresses and the related genetic networks has established the foundation for sustainable agriculture against environmental stress. Integrated approaches based on functional genomics and transcriptomics are now expanding the opportunities to elucidate the molecular mechanisms underlying abiotic stress responses. This review summarizes some of the features and weblinks of plant genome databases related to abiotic stress genes utilized for improving crops. The gene-editing tool based on clustered, regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has revolutionized stress tolerance research due to its simplicity, versatility, adaptability, flexibility, and broader applications. However, off-target and low cleavage efficiency hinder the successful application of CRISPR/Cas systems. Computational tools have been developed for designing highly competent gRNA with better cleavage efficiency. This powerful genome editing tool offers tremendous crop improvement opportunities, overcoming conventional breeding techniques' shortcomings. Furthermore, we also discuss the mechanistic insights of the CRISPR/Cas9-based genome editing technology. This review focused on the current advances in understanding plant species' abiotic stress response mechanism and applying the CRISPR/Cas system genome editing technology to develop crop resilience against drought, salinity, temperature, heavy metals, and herbicides.

Mutating BnEOD1s via CRISPR-Cas9 increases the seed size and weight in Brassica napus

Seed weight, which is highly correlated to seed size, is a critical agronomic trait that determines the yield of Brassica napus. However, there have been limited researches on the genes involved in regulating seed size. In Arabidopsis thaliana, ENHANCER OF DA1 (EOD1), an E3 ubiquitin ligase gene, has been identified as a significant negative regulator in controlling organ size, but the function of its homologs in rapeseed remains unknown. Only two homologous of EOD1, BnaEOD1.A04 and BnaEOD1.C04, have been found in B. napus and were mutated using the CRISPR-Cas9 system. Three T-DNA-free lines, T2-157-1-C8, T2-390-2-B8, and T2-397-2-E2, were identified from the homozygous T2 mutant lines. The BnaEOD1.A04 showed a similar type of editing in these mutants, whereas the BnaEOD1.C04 in T2-397-2-E2 was only missing 26 amino acids, and the translation was not prematurely terminated, which was different from the other two mutants. In parallel, mutation of BnaEOD1s resulted in a noteworthy increase in both seed size and seed weight in the three editing lines. Additionally, there was a significant decline in the number of seeds per silique (SPS) and silique length (SL) in T2-157-1-C8 and T2-390-2-B8, but T2-397-2-E2 did not show any significant changes in the SPS and SL, possibly due to distinct types of editing in the three lines. The above results indicate the conserved function of EOD1 homologs and provides promising germplasm for breeding novel high-yield rapeseed varieties by improving seed size and thousand-seed weight.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01430-z.

The transcription factor BnaWRKY10 regulates cytokinin dehydrogenase BnaCKX2 to control cytokinin distribution and seed size in Brassica napus

Cytokinins (CKs) are phytohormones that promote cell division and differentiation. However, the regulation of CK distribution and homeostasis in Brassica napus is poorly understood. Here, the endogenous CKs were first quantified by LC-ESI-MS/MS in rapeseed tissues and visualized by TCSn::GUS reporter lines. Interestingly, the cytokinin oxidase/dehydrogenase BnaCKX2 homologs were mainly expressed in reproductive organs. Subsequently, the quadruple mutants of the four BnaCKX2 homologs were generated. Endogenous CKs were increased in the seeds of the BnaCKX2 quadruple mutants, resulting in a significantly reduced seed size. In contrast, overexpression of BnaA9.CKX2 resulted in larger seeds, probably by delaying endosperm cellularization. Furthermore, the transcription factor BnaC6.WRKY10b, but not BnaC6.WRKY10a, positively regulated BnaA9.CKX2 expression by binding directly to its promoter region. Overexpression of BnaC6.WRKY10b rather than BnaC6.WRKY10a resulted in lower concentration of CKs and larger seeds by activating BnaA9.CKX2 expression, indicating that the functional differentiation of BnaWRKY10 homologs might have occurred during B. napus evolution or domestication. Notably, the haploid types of BnaA9.CKX2 were associated with 1000-seed weight in the natural B. napus population. Overall, the study reveals the distribution of CKs in B. napus tissues, and shows that BnaWRKY10-mediated BnaCKX2 expression is essential for seed size regulation, providing promising targets for oil crop improvement.

Recent Developments in CRISPR/Cas9 Genome-Editing Technology Related to Plant Disease Resistance and Abiotic Stress Tolerance

The revolutionary CRISPR/Cas9 genome-editing technology has emerged as a powerful tool for plant improvement, offering unprecedented precision and efficiency in making targeted gene modifications. This powerful and practical approach to genome editing offers tremendous opportunities for crop improvement, surpassing the capabilities of conventional breeding techniques. This article provides an overview of recent advancements and challenges associated with the application of CRISPR/Cas9 in plant improvement. The potential of CRISPR/Cas9 in terms of developing crops with enhanced resistance to biotic and abiotic stresses is highlighted, with examples of genes edited to confer disease resistance, drought tolerance, salt tolerance, and cold tolerance. Here, we also discuss the importance of off-target effects and the efforts made to mitigate them, including the use of shorter single-guide RNAs and dual Cas9 nickases. Furthermore, alternative delivery methods, such as protein- and RNA-based approaches, are explored, and they could potentially avoid the integration of foreign DNA into the plant genome, thus alleviating concerns related to genetically modified organisms (GMOs). We emphasize the significance of CRISPR/Cas9 in accelerating crop breeding processes, reducing editing time and costs, and enabling the introduction of desired traits at the nucleotide level. As the field of genome editing continues to evolve, it is anticipated that CRISPR/Cas9 will remain a prominent tool for crop improvement, disease resistance, and adaptation to challenging environmental conditions.

Genome Editing and Improvement of Abiotic Stress Tolerance in Crop Plants

Genome editing aims to revolutionise plant breeding and could assist in safeguarding the global food supply. The inclusion of a 12-40 bp recognition site makes mega nucleases the first tools utilized for genome editing and first generation gene-editing tools. Zinc finger nucleases (ZFNs) are the second gene-editing technique, and because they create double-stranded breaks, they are more dependable and effective. ZFNs were the original designed nuclease-based approach of genome editing. The Cys2-His2 zinc finger domain's discovery made this technique possible. Clustered regularly interspaced short palindromic repeats (CRISPR) are utilized to improve genetics, boost biomass production, increase nutrient usage efficiency, and develop disease resistance. Plant genomes can be effectively modified using genome-editing technologies to enhance characteristics without introducing foreign DNA into the genome. Next-generation plant breeding will soon be defined by these exact breeding methods. There is abroad promise that genome-edited crops will be essential in the years to come for improving the sustainability and climate-change resilience of food systems. This method also has great potential for enhancing crops' resistance to various abiotic stressors. In this review paper, we summarize the most recent findings about the mechanism of abiotic stress response in crop plants and the use of the CRISPR/Cas mediated gene-editing systems to improve tolerance to stresses including drought, salinity, cold, heat, and heavy metals.

Transcriptomic Profiling Highlights the ABA Response Role of BnSIP1-1 in Brassica napus

BnSIP1-1 is the first identified SIP1 (6b Interacting Protein1) subfamily gene of the trihelix transcription factor family from Brassica napus (B. napus). We previously used a reverse genetic method to reveal its abiotic stress response function in endowing plants resistance to drought and salinity, as well as ABA (Abscisic acid). However, the molecular mechanisms of BnSIP1-1 are unclear. In this study, the global transcriptome files of BnSIP1-1-overexpressing transgenic and wildtype B. napus seedlings under ABA treatment were constructed using RNA-seq. A total of 1823 and 5512 DEGs (Differentially Expressed Genes) were identified in OE vs. WT and OE_ABA vs. WT_ABA comparison groups, which included 751 and 2567 up-regulated DEGs, and 1072 and 2945 down-regulated DEGs, separately. The impact of overexpressed BnSIP1-1 on plants was amplified by ABA, indicating BnSIP1-1 was an ABA-conditioned responsive gene. More interestingly, we found the reasons for BnSIP1-1 increasing plants' insensitivity to ABA were not by regulating ABA synthesis and catabolism, but by manipulating ABA transportation, ABA signal perception and transduction, inositol phosphate metabolism, as well as endomembrane trafficking, indirectly suggesting this gene may play roles upstream of the core ABA response pathway. Our results provided new insights into improving the knowledge about the function of BnSIP1-1 and the ABA signaling mechanism in B. napus.

Targeted genome editing in polyploids: lessons from Brassica

CRISPR-mediated genome editing has emerged as a powerful tool for creating targeted mutations in the genome for various applications, including studying gene functions, engineering resilience against biotic and abiotic stresses, and increasing yield and quality. However, its utilization is limited to model crops for which well-annotated genome sequences are available. Many crops of dietary and economic importance, such as wheat, cotton, rapeseed-mustard, and potato, are polyploids with complex genomes. Therefore, progress in these crops has been hampered due to genome complexity. Excellent work has been conducted on some species of Brassica for its improvement through genome editing. Although excellent work has been conducted on some species of Brassica for genome improvement through editing, work on polyploid crops, including U's triangle species, holds numerous implications for improving other polyploid crops. In this review, we summarize key examples from genome editing work done on Brassica and discuss important considerations for deploying CRISPR-mediated genome editing more efficiently in other polyploid crops for improvement.

Enhancing Crop Resilience to Drought Stress through CRISPR-Cas9 Genome Editing

With increasing frequency and severity of droughts in various parts of the world, agricultural productivity may suffer major setbacks. Among all the abiotic factors, drought is likely to have one of the most detrimental effects on soil organisms and plants. Drought is a major problem for crops because it limits the availability of water, and consequently nutrients which are crucial for plant growth and survival. This results in reduced crop yields, stunted growth, and even plant death, according to the severity and duration of the drought, the plant's developmental stage, and the plant's genetic background. The ability to withstand drought is a highly complex characteristic that is controlled by multiple genes, making it one of the most challenging attributes to study, classify, and improve. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) technology has opened a new frontier in crop enhancement, revolutionizing plant molecular breeding. The current review provides a general understanding of principles as well as optimization of CRISPR system, and presents applications on genetic enhancement of crops, specifically in terms of drought resistance and yield. Moreover, we discuss how innovative genome editing techniques can aid in the identification and modification of genes conferring drought tolerance.

Comparative transcriptome profiling reveals the multiple levels of crosstalk in phytohormone networks in Brassica napus

Plant hormones are the intrinsic factors that control plant development. The integration of different phytohormone pathways in a complex network of synergistic, antagonistic and additive interactions has been elucidated in model plants. However, the systemic level of transcriptional responses to hormone crosstalk in Brassica napus is largely unknown. Here, we present an in-depth temporal-resolution study of the transcriptomes of the seven hormones in B. napus seedlings. Differentially expressed gene analysis revealed few common target genes that co-regulated (up- and down-regulated) by seven hormones; instead, different hormones appear to regulate distinct members of protein families. We then constructed the regulatory networks between the seven hormones side by side, which allowed us to identify key genes and transcription factors that regulate the hormone crosstalk in B. napus. Using this dataset, we uncovered a novel crosstalk between gibberellin and cytokinin in which cytokinin homeostasis was mediated by RGA-related CKXs expression. Moreover, the modulation of gibberellin metabolism by the identified key transcription factors was confirmed in B. napus. Furthermore, all data were available online from http://yanglab.hzau.edu.cn/BnTIR/hormone. Our study reveals an integrated hormone crosstalk network in Brassica napus, which also provides a versatile resource for future hormone studies in plant species.

The Potential of CRISPR/Cas Technology to Enhance Crop Performance on Adverse Soil Conditions

Worldwide food security is under threat in the actual scenery of global climate change because the major staple food crops are not adapted to hostile climatic and soil conditions. Significant efforts have been performed to maintain the actual yield of crops, using traditional breeding and innovative molecular techniques to assist them. However, additional strategies are necessary to achieve the future food demand. Clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) technology, as well as its variants, have emerged as alternatives to transgenic plant breeding. This novelty has helped to accelerate the necessary modifications in major crops to confront the impact of abiotic stress on agriculture systems. This review summarizes the current advances in CRISPR/Cas applications in crops to deal with the main hostile soil conditions, such as drought, flooding and waterlogging, salinity, heavy metals, and nutrient deficiencies. In addition, the potential of extremophytes as a reservoir of new molecular mechanisms for abiotic stress tolerance, as well as their orthologue identification and edition in crops, is shown. Moreover, the future challenges and prospects related to CRISPR/Cas technology issues, legal regulations, and customer acceptance will be discussed.

Transcriptomic profiling of near-isogenic lines reveals candidate genes for a significant locus conferring metribuzin resistance in wheat

BACKGROUND

Weeds reduce wheat yields in dryland farming systems. Herbicides such as metribuzin are commonly used to control weeds. However, wheat has a narrow safety margin against metribuzin. Standing crops such as wheat with weeds in the same field can also be killed by the same dose of metribuzin. Therefore, it is important to identify metribuzin resistance genes and understand the resistance mechanism in wheat for sustainable crop production. A previous study identified a significant metribuzin resistance wheat QTL, Qsns.uwa.4 A.2, explaining 69% of the phenotypic variance for metribuzin resistance.

RESULTS

Two NIL pairs with the most contrasting performance in the metribuzin treatment and different in genetic backgrounds were compared using RNA sequence analysis, identifying nine candidate genes underlying Qsns.uwa.4 A.2 responsible for metribuzin resistance. Quantitative RT-qPCR further validated the candidate genes, with TraesCS4A03G1099000 (nitrate excretion transporter), TraesCS4A03G1181300 (aspartyl protease), and TraesCS4A03G0741300 (glycine-rich proteins) identified as key factors for metribuzin resistance.

CONCLUSION

Identified markers and key candidate genes can be used for selecting metribuzin resistance in wheat.

OsNF-YA3 regulates plant growth and osmotic stress tolerance by interacting with SLR1 and SAPK9 in rice

The antagonism between gibberellin (GA) and abscisic acid (ABA) signaling pathways is vital to balance plant growth and stress response. Nevertheless, the mechanism by which plants determine the balance remains to be elucidated. Here, we report that rice NUCLEAR FACTOR-Y A3 (OsNF-YA3) modulates GA- and ABA-mediated balance between plant growth and osmotic stress tolerance. OsNF-YA3 loss-of-function mutants exhibit stunted growth, compromised GA biosynthetic gene expression, and decreased GA levels, while its overexpression lines have promoted growth and enhanced GA content. Chromatin immunoprecipitation-quantitative polymerase chain reaction analysis and transient transcriptional regulation assays demonstrate that OsNF-YA3 activates GA biosynthetic gene OsGA20ox1 expression. Furthermore, the DELLA protein SLENDER RICE1 (SLR1) physically interacts with OsNF-YA3 and thus inhibits its transcriptional activity. On the other side, OsNF-YA3 negatively regulates plant osmotic stress tolerance by repressing ABA response. OsNF-YA3 reduces ABA levels by transcriptionally regulating ABA catabolic genes OsABA8ox1 and OsABA8ox3 by binding to their promoters. Furthermore, OSMOTIC STRESS/ABA-ACTIVATED PROTEIN KINASE 9 (SAPK9), the positive component in ABA signaling, interacts with OsNF-YA3 and mediates OsNF-YA3 phosphorylation, resulting in its degradation in plants. Collectively, our findings establish OsNF-YA3 as an important transcription factor that positively modulates GA-regulated plant growth and negatively controls ABA-mediated water-deficit and salt tolerance. These findings shed light on the molecular mechanism underlying the balance between the growth and stress response of the plant.

Two aspartic proteases, BnaAP36s and BnaAP39s, regulate pollen tube guidance in Brassica napus

Pollen tube (PT) growth towards the micropyle is critical for successful double fertilization. However, the mechanism of micropyle-directed PT growth is still unclear in Brassica napus. In this study, two aspartate proteases, BnaAP36s and BnaAP39s, were identified in B. napus. BnaAP36s and BnaAP39s were localized to the plasma membrane. The homologues of BnaAP36 and BnaAP39 were highly expressed in flower organs, especially in the anther. Sextuple and double mutants of BnaAP36s and BnaAP39s were then generated using CRISPR/Cas9 technology. Compared to WT, the seed-set of cr-bnaap36 and cr-bnaap39 mutants was reduced by 50% and 60%, respectively. The reduction in seed-set was also found when cr-bnaap36 and cr-bnaap39 were used as the female parent in a reciprocal cross assay. Like WT, cr-bnaap36 and cr-bnaap39 pollen were able to germinate and the relative PTs were able to elongate in style. Approximately 36% and 33% of cr-bnaap36 and cr-bnaap39 PTs, respectively, failed to grow towards the micropyle, indicating that BnaAP36s and BnaAP39s are essential for micropyle-directed PT growth. Furthermore, Alexander's staining showed that 10% of cr-bnaap39 pollen grains were aborted, but not cr-bnaap36, suggesting that BnaAP39s may also affect microspore development. These results suggest that BnaAP36s and BnaAP39s play a critical role in the growth of micropyle-directed PTs in B. napus.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01377-1.

CRISPR/Cas genome editing in plants: Dawn of Agrobacterium transformation for recalcitrant and transgene-free plants for future crop breeding

Genome editing tools based on CRISPR/Cas system have been posed to solve many issues in agriculture and improve food production. Genetic engineering by Agrobacterium-mediated transformation has helped to impart specific traits straightaway in many crops. Many GM crops have also reached the field for commercial cultivation. Genetic engineering requires mostly a transformation protocol often mediated by Agrobacterium to insert a specific gene at a random locus. Genome editing with CRISPR/Cas system is a more precise technique for the targeted modification of genes/bases in the host plant genome. Unlike the conventional transformation system, wherein elimination of marker/foreign gene was possible only post-transformation, CRISPR/Cas system could generate transgene-free plants by delivering CRISPR/Cas reagents such as the Cas protein and guide RNAs gRNA(s) preassembled to form ribonucleoproteins (RNPs) into plant cells. CRISPR reagent delivery might be helpful to overcome issues with plants that are recalcitrant to Agrobacterium transformation and the legal hurdles due to the presence of the foreign gene. More recently, the grafting of wild-type shoots to transgenic donor rootstocks developed by the CRISPR/Cas system has reported transgene-free genome editing. CRISPR/Cas system also requires only a small piece of gRNA besides Cas9 or other effectors to target a specific region in the genome. So this system has been projected to be a key contributor to future crop breeding. In this article, we recap the main events of plant transformation, compare the difference between genetic transformation and CRISPR/Cas-mediated genome editing, and draw insights into the future application of the CRISPR/Cas system.

Gene Editing for Plant Resistance to Abiotic Factors: A Systematic Review

Agricultural crops are exposed to various abiotic stresses, such as salinity, water deficits, temperature extremes, floods, radiation, and metal toxicity. To overcome these challenges, breeding programs seek to improve methods and techniques. Gene editing by Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR/Cas-is a versatile tool for editing in all layers of the central dogma with focus on the development of cultivars of plants resistant or tolerant to multiple biotic or abiotic stresses. This systematic review (SR) brings new contributions to the study of the use of CRISPR/Cas in gene editing for tolerance to abiotic stress in plants. Articles deposited in different electronic databases, using a search string and predefined inclusion and exclusion criteria, were evaluated. This SR demonstrates that the CRISPR/Cas system has been applied to several plant species to promote tolerance to the main abiotic stresses. Among the most studied crops are rice and Arabidopsis thaliana, an important staple food for the population, and a model plant in genetics/biotechnology, respectively, and more recently tomato, whose number of studies has increased since 2021. Most studies were conducted in Asia, specifically in China. The Cas9 enzyme is used in most articles, and only Cas12a is used as an additional gene editing tool in plants. Ribonucleoproteins (RNPs) have emerged as a DNA-free strategy for genome editing without exogenous DNA. This SR also identifies several genes edited by CRISPR/Cas, and it also shows that plant responses to stress factors are mediated by many complex-signaling pathways. In addition, the quality of the articles included in this SR was validated by a risk of bias analysis. The information gathered in this SR helps to understand the current state of CRISPR/Cas in the editing of genes and noncoding sequences, which plays a key role in the regulation of various biological processes and the tolerance to multiple abiotic stresses, with potential for use in plant genetic improvement programs.

Cell dehydration of intergeneric hybrid induces subgenome-related specific responses

The aim was to identify subgenome-related specific responses in two types of triticale, that is, of the wheat-dominated genome (WDG) and rye-dominated genome (RDG), to water stress induced in the early phase (tillering) of plant growth. Higher activity of the primary metabolism of carbohydrates is a feature of the WDG type, while the dominance of the rye genome is associated with a higher activity of the secondary metabolism of phenolic compounds in the RDG type. The study analyzed carbohydrates and key enzymes of their synthesis, free phenolic compounds and carbohydrate-related components of the cell wall, monolignols, and shikimic acid (ShA), which is a key link between the primary and secondary metabolism of phenolic compounds. Under water stress, dominance of the wheat genome in the WDG type was manifested by an increased accumulation of the large subunit of Rubisco and sucrose phosphate synthase and a higher content of raffinose and stachyose compared with the RDG type. In dehydrated RDG plants, higher activity of L-phenylalanine ammonia lyase (PAL) and L-tyrosine ammonia lyase (TAL), as well as a higher level of ShA, free and cell wall-bound p-hydroxybenzoic acid, free homovanillic acid, free sinapic acid, and cell wall-bound syringic acid can be considered biochemical indicators of the dominance of the rye genome.

Application of CRISPR/Cas9-mediated gene editing for abiotic stress management in crop plants

Abiotic stresses, including drought, salinity, cold, heat, and heavy metals, extensively reducing global agricultural production. Traditional breeding approaches and transgenic technology have been widely used to mitigate the risks of these environmental stresses. The discovery of engineered nucleases as genetic scissors to carry out precise manipulation in crop stress-responsive genes and associated molecular network has paved the way for sustainable management of abiotic stress conditions. In this context, the clustered regularly interspaced short palindromic repeat-Cas (CRISPR/Cas)-based gene-editing tool has revolutionized due to its simplicity, accessibility, adaptability, flexibility, and wide applicability. This system has great potential to build up crop varieties with enhanced tolerance against abiotic stresses. In this review, we summarize the latest findings on understanding the mechanism of abiotic stress response in plants and the application of CRISPR/Cas-mediated gene-editing system towards enhanced tolerance to a multitude of stresses including drought, salinity, cold, heat, and heavy metals. We provide mechanistic insights on the CRISPR/Cas9-based genome editing technology. We also discuss applications of evolving genome editing techniques such as prime editing and base editing, mutant library production, transgene free and multiplexing to rapidly deliver modern crop cultivars adapted to abiotic stress conditions.

USDA's revised biotechnology regulation's contribution to increasing agricultural sustainability and responding to climate change

Biotechnology can provide a valuable tool to meet UN Sustainable Development Goals and U.S. initiatives to find climate solutions and improve agricultural sustainability. The literature contains hundreds of examples of crops that may serve this purpose, yet most remain un-launched due to high regulatory barriers. Recently the USDA revised its biotechnology regulations to make them more risk-proportionate, science-based, and streamlined. Here, we review some of the promising leads that may enable agriculture to contribute to UN sustainability goals. We further describe and discuss how the revised biotechnology regulation would hypothetically apply to these cases.

Engineering drought and salinity tolerance traits in crops through CRISPR-mediated genome editing: Targets, tools, challenges, and perspectives

Prolonged periods of drought triggered by climate change hamper plant growth and cause substantial agricultural yield losses every year. In addition to drought, salinity is one of the major abiotic stresses that severely affect crop health and agricultural production. Plant responses to drought and salinity involve multiple processes that operate in a spatiotemporal manner, such as stress sensing, perception, epigenetic modifications, transcription, post-transcriptional processing, translation, and post-translational changes. Consequently, drought and salinity stress tolerance are polygenic traits influenced by genome-environment interactions. One of the ideal solutions to these challenges is the development of high-yielding crop varieties with enhanced stress tolerance, together with improved agricultural practices. Recently, genome-editing technologies, especially clustered regularly interspaced short palindromic repeats (CRISPR) tools, have been effectively applied to elucidate how plants deal with drought and saline environments. In this work, we aim to portray that the combined use of CRISPR-based genome engineering tools and modern genomic-assisted breeding approaches are gaining momentum in identifying genetic determinants of complex traits for crop improvement. This review provides a synopsis of plant responses to drought and salinity stresses at the morphological, physiological, and molecular levels. We also highlight recent advances in CRISPR-based tools and their use in understanding the multi-level nature of plant adaptations to drought and salinity stress. Integrating CRISPR tools with modern breeding approaches is ideal for identifying genetic factors that regulate plant stress-response pathways and for the introgression of beneficial traits to develop stress-resilient crops.

Engineering Abiotic Stress Tolerance in Crop Plants through CRISPR Genome Editing

Environmental abiotic stresses challenge food security by depressing crop yields often exceeding 50% of their annual production. Different methods, including conventional as well as genomic-assisted breeding, mutagenesis, and genetic engineering have been utilized to enhance stress resilience in several crop species. Plant breeding has been partly successful in developing crop varieties against abiotic stresses owning to the complex genetics of the traits as well as the narrow genetic base in the germplasm. Irrespective of the fact that genetic engineering can transfer gene(s) from any organism(s), transgenic crops have become controversial mainly due to the potential risk of transgene-outcrossing. Consequently, the cultivation of transgenic crops is banned in certain countries, particularly in European countries. In this scenario, the discovery of the CRISPR tool provides a platform for producing transgene-free genetically edited plants-similar to the mutagenized crops that are not extensively regulated such as genetically modified organisms (GMOs). Thus, the genome-edited plants without a transgene would likely go into the field without any restriction. Here, we focused on the deployment of CRISPR for the successful development of abiotic stress-tolerant crop plants for sustaining crop productivity under changing environments.

An integrated transcriptome mapping the regulatory network of coding and long non-coding RNAs provides a genomics resource in chickpea

Large-scale transcriptome analysis can provide a systems-level understanding of biological processes. To accelerate functional genomic studies in chickpea, we perform a comprehensive transcriptome analysis to generate full-length transcriptome and expression atlas of protein-coding genes (PCGs) and long non-coding RNAs (lncRNAs) from 32 different tissues/organs via deep sequencing. The high-depth RNA-seq dataset reveal expression dynamics and tissue-specificity along with associated biological functions of PCGs and lncRNAs during development. The coexpression network analysis reveal modules associated with a particular tissue or a set of related tissues. The components of transcriptional regulatory networks (TRNs), including transcription factors, their cognate cis-regulatory motifs, and target PCGs/lncRNAs that determine developmental programs of different tissues/organs, are identified. Several candidate tissue-specific and abiotic stress-responsive transcripts associated with quantitative trait loci that determine important agronomic traits are also identified. These results provide an important resource to advance functional/translational genomic and genetic studies during chickpea development and environmental conditions.

A full-length transcriptome and expression atlas of protein-coding genes and long non-coding RNAs is generated in chickpea. Components of transcriptional regulatory networks and candidate tissue-specific transcripts associated with quantitative trait loci are identified.

Genome-Wide Identification of Brassicaceae Hormone-Related Transcription Factors and Their Roles in Stress Adaptation and Plant Height Regulation in Allotetraploid Rapeseed

Phytohormone-related transcription factors (TFs) are involved in regulating stress responses and plant growth. However, systematic analysis of these TFs in Brassicaceae is limited, and their functions in stress adaptation and plant height (PH) regulation remain unclear. In this study, 2115 hormone-related TFs were identified in nine Brassicaceae species. Specific domains were found in several Brassicaceae hormone-related TFs, which may be associated with diverse functions. Syntenic analysis indicated that expansion of these genes was mainly caused by segmental duplication, with whole-genome duplication occurring in some species. Differential expression analysis and gene co-expression network analysis identified seven phytohormone-related TFs (BnaWRKY7, 21, 32, 38, 52, BnaGL3-4, and BnaAREB2-5) as possible key genes for cadmium (Cd) toxicity, salinity stress, and potassium (K) and nitrogen (N) deficiencies. Furthermore, BnaWRKY42 and BnaARR21 may play essential roles in plant height. Weighted gene co-expression network analysis (WGCNA) identified 15 phytohormone-related TFs and their potential target genes regulating stress adaptation and plant height. Among the above genes, BnaWRKY56 and BnaWRKY60 responded to four different stresses simultaneously, and BnaWRKY42 was identified in two dwarf rapeseeds. In summary, several candidate genes for stress resistance (BnaWRKY56 and BnaWRKY60) and plant height (BnaWRKY42) were identified. These findings should help elucidate the biological roles of Brassicaceae hormone-related TFs, and the identified candidate genes should provide a genetic resource for the potential development of stress-tolerant and dwarf oilseed plants.

Advances in Crop Breeding Through Precision Genome Editing

The global climate change and unfavourable abiotic and biotic factors are limiting agricultural productivity and therefore intensifying the challenges for crop scientists to meet the rising demand for global food supply. The introduction of applied genetics to agriculture through plant breeding facilitated the development of hybrid varieties with improved crop productivity. However, the development of new varieties with the existing gene pools poses a challenge for crop breeders. Genetic engineering holds the potential to broaden genetic diversity by the introduction of new genes into crops. But the random insertion of foreign DNA into the plant's nuclear genome often leads to transgene silencing. Recent advances in the field of plant breeding include the development of a new breeding technique called genome editing. Genome editing technologies have emerged as powerful tools to precisely modify the crop genomes at specific sites in the genome, which has been the longstanding goal of plant breeders. The precise modification of the target genome, the absence of foreign DNA in the genome-edited plants, and the faster and cheaper method of genome modification are the remarkable features of the genome-editing technology that have resulted in its widespread application in crop breeding in less than a decade. This review focuses on the advances in crop breeding through precision genome editing. This review includes: an overview of the different breeding approaches for crop improvement; genome editing tools and their mechanism of action and application of the most widely used genome editing technology, CRISPR/Cas9, for crop improvement especially for agronomic traits such as disease resistance, abiotic stress tolerance, herbicide tolerance, yield and quality improvement, reduction of anti-nutrients, and improved shelf life; and an update on the regulatory approval of the genome-edited crops. This review also throws a light on development of high-yielding climate-resilient crops through precision genome editing.

Genome-Wide Identification and Expressional Profiling of the Metal Tolerance Protein Gene Family in Brassica napus

The Cation Diffusion Facilitator (CDF) family, also named Metal Tolerance Protein (MTP), is one of the gene families involved in heavy metal transport in plants. However, a comprehensive study of MTPs in Brassica napus has not been reported yet. In the present study, we identified 33 BnMTP genes from the rapeseed genome using bioinformatic analyses. Subsequently, we analyzed the phylogenetic relationship, gene structure, chromosome distribution, conserved domains, and motifs of the BnMTP gene family. The 33 BnMTPs were phylogenetically divided into three major clusters (Zn-CDFs, Fe/Zn-CDFs, and Mn-CDFs) and seven groups (group 1, 5, 6, 7, 8, 9, and 12). The structural characteristics of the BnMTP members were similar in the same group, but different among groups. Evolutionary analysis indicated that the BnMTP gene family mainly expanded through whole-genome duplication (WGD) and segmental duplication events. Moreover, the prediction of cis-acting elements and microRNA target sites suggested that BnMTPs might be involved in plant growth, development, and stress responses. In addition, we found the expression of 24 BnMTPs in rapeseed leaves or roots could respond to heavy metal ion treatments. These results provided an important basis for clarifying the biological functions of BnMTPs, especially in heavy metal detoxification, and will be helpful in the phytoremediation of heavy metal pollution in soil.

The potential of dynamic physiological traits in young tomato plants to predict field-yield performance

To address the challenge of predicting tomato yields in the field, we used whole-plant functional phenotyping to evaluate water relations under well-irrigated and drought conditions. The genotypes tested are known to exhibit variability in their yields in wet and dry fields. The examined lines included two lines with recessive mutations that affect carotenoid biosynthesis, zeta z²⁰⁸³ and tangerine t³⁴⁰⁶, both isogenic to the processing tomato variety M82. The two mutant lines were reciprocally grafted onto M82, and multiple physiological characteristics were measured continuously, before, during and after drought treatment in the greenhouse. A comparative analysis of greenhouse and field yields showed that the whole-canopy stomatal conductance (g_sc) in the morning and cumulative transpiration (CT) were strongly correlated with field measurements of total yield (TY: r² = 0.9 and 0.77, respectively) and plant vegetative weight (PW: r² = 0.6 and 0.94, respectively). Furthermore, the minimum CT during drought and the rate of recovery when irrigation was resumed were both found to predict resilience.

Genome Editing in Crop Plant Research-Alignment of Expectations and Current Developments

The rapid development of genome editing and other new genomic techniques (NGT) has evoked manifold expectations on purposes of the application of these techniques to crop plants. In this study, we identify and align these expectations with current scientific development. We apply a semi-quantitative text analysis approach on political, economic, and scientific opinion papers to disentangle and extract expectations towards the application of NGT-based plants. Using the sustainable development goals (SDG) of the 2030 agenda as categories, we identify contributions to food security or adaptation to climatic changes as the most frequently mentioned expectations, accompanied by the notion of sustainable agriculture and food systems. We then link SDG with relevant plant traits and review existing research and commercial field trials for genome-edited crop plants. For a detailed analysis we pick as representative traits drought tolerance and resistance against fungal pathogens. Diverse genetic setscrews for both traits have been identified, modified, and tested under laboratory conditions, although there are only a few in the field. All in all, NGT-plants that can withstand more than one stressor or different environments are not documented in advanced development states. We further conclude that developing new plants with modified traits will not be sufficient to reach food security or adaption to climatic changes in a short time frame. Further scientific development of sustainable agricultural systems will need to play an important role to tackle SDG challenges, as well.

Genome-wide discovery of DNA polymorphisms via resequencing of chickpea cultivars with contrasting response to drought stress

Drought stress limits plant growth, resulting in a significant yield loss in chickpea. The diversification in genome sequence and selective sweep of allele(s) in different genotypes of a crop plant may play an important role in the determination of agronomic traits, including drought stress response. We investigated, via whole genome resequencing, the DNA polymorphisms between two sets of chickpea genotypes with contrasting drought stress responses (3 drought-sensitive vs. 6 drought-tolerant). In total, 36,406 single nucleotide polymorphisms (SNPs) and 3407 insertions or deletions (InDels) differentiating drought-sensitive and drought-tolerant chickpea genotypes were identified. Interestingly, most (91%) of these DNA polymorphisms were located in chromosomes 1 and 4. The genes harboring DNA polymorphisms in their promoter and/or coding regions and exhibiting differential expression under control and/or drought stress conditions between/within the drought-sensitive and tolerant genotypes were found implicated in the stress response. Furthermore, we identified DNA polymorphisms within the cis-regulatory motifs in the promoter region of abiotic stress-related and QTL-associated genes, which might contribute to the differential expression of the candidate drought-responsive genes. In addition, we revealed the effect of nonsynonymous SNPs on mutational sensitivity and stability of the encoded proteins. Taken together, we identified DNA polymorphisms having relevance in drought stress response and revealed candidate genes to engineer drought tolerance in chickpea.

Transcriptome and Metabolome Analyses Reveal Potential Salt Tolerance Mechanisms Contributing to Maintenance of Water Balance by the Halophytic Grass Puccinellia nuttalliana

Elevated soil salinity exacerbated by human activities and global climate change poses serious threats to plant survival. Although halophytes provide many important clues concerning salt tolerance in plants, some unanswered questions remain to be addressed, including the processes of water and solute transport regulation. We performed high-throughput RNA-sequencing in roots and metabolome characterizations in roots and leaves of Puccinellia nuttalliana halophytic grass subjected to 0 (control) and 150 mM NaCl. In RNAseq, a total of 31 Gb clean bases generated were de novo assembled into 941,894 transcripts. The PIP2;2 and HKT1;5 transcript levels increased in response to the NaCl treatment implying their roles in water and ion homeostasis. Several transcription factors, including WRKY39, DEK3, HY5, and ABF2, were also overexpressed in response to NaCl. The metabolomic analysis revealed that proline and dopamine significantly increased due to the upregulation of the pathway genes under salt stress, likely contributing to salt tolerance mechanisms. Several phosphatidylcholines significantly increased in roots suggesting that the alterations of membrane lipid composition may be an important strategy in P. nuttalliana for maintaining cellular homeostasis and membrane integrity under salt stress. In leaves, the TCA cycle was enriched suggesting enhanced energy metabolism to cope with salt stress. Other features contributing to the ability of P. nuttalliana to survive under high salinity conditions include salt secretion by the salt glands and enhanced cell wall lignification of the root cells. While most of the reported transcriptomic, metabolomics, and structural alterations may have consequences to water balance maintenance by plants under salinity stress, the key processes that need to be further addressed include the role of the changes in the aquaporin gene expression profiles in the earlier reported enhancement of the aquaporin-mediated root water transport.

DELLA proteins BnaA6.RGA and BnaC7.RGA negatively regulate fatty acid biosynthesis by interacting with BnaLEC1s in Brassica napus

Seed oil content (SOC) and fatty acid (FA) composition determine the quality and economic value of rapeseed (Brassica napus). Little is known about the role of gibberellic acid (GA) in regulating FA biosynthesis in B. napus. Here, we discovered that four BnaRGAs (B. napus REPRESSOR OF GA), encoding negative regulators of GA signalling, were suppressed during seed development. Compared to the wild type, SOC was reduced in gain-of-function mutants bnaa6.rga-D and ds-3, which also showed reduced oleic acid and increased linoleic acid contents. By contrast, the loss-of-function quadruple mutant bnarga displayed higher SOC during early seed development than the wild type, with increased oleic acid and reduced linoleic acid contents. Notably, only BnaA6.RGA and BnaC7.RGA physically interacted with two BnaLEC1s, which function as essential transcription factors in FA biosynthesis. The FA composition did not significantly differ between bnarga bnalec1 sextuple mutants and bnalec1, suggesting that BnaLEC1s are epistatic to BnaRGAs in the regulation of FA composition. Furthermore, BnaLEC1-induced activation of BnaABI3 expression was repressed by BnaA6.RGA, indicating that GA triggers the degradation of BnaRGAs to relieve their repression of BnaLEC1s, thus promoting the transcription of downstream genes to facilitate oil biosynthesis. Therefore, we uncovered a developmental stage-specific role of GA in regulating oil biosynthesis via the GA-BnaRGA-BnaLEC1 signalling cascade, providing a novel mechanistic understanding of how phytohormones regulate FA biosynthesis in seeds. BnaRGAs represent promising targets for oil crop improvement.

Exploring the gene pool of Brassica napus by genomics-based approaches

De novo allopolyploidization in Brassica provides a very successful model for reconstructing polyploid genomes using progenitor species and relatives to broaden crop gene pools and understand genome evolution after polyploidy, interspecific hybridization and exotic introgression. B. napus (AACC), the major cultivated rapeseed species and the third largest oilseed crop in the world, is a young Brassica species with a limited genetic base resulting from its short history of domestication, cultivation, and intensive selection during breeding for target economic traits. However, the gene pool of B. napus has been significantly enriched in recent decades that has been benefit from worldwide effects by the successful introduction of abundant subgenomic variation and novel genomic variation via intraspecific, interspecific and intergeneric crosses. An important question in this respect is how to utilize such variation to breed crops adapted to the changing global climate. Here, we review the genetic diversity, genome structure, and population-level differentiation of the B. napus gene pool in relation to known exotic introgressions from various species of the Brassicaceae, especially those elucidated by recent genome-sequencing projects. We also summarize progress in gene cloning, trait-marker associations, gene editing, molecular marker-assisted selection and genome-wide prediction, and describe the challenges and opportunities of these techniques as molecular platforms to exploit novel genomic variation and their value in the rapeseed gene pool. Future progress will accelerate the creation and manipulation of genetic diversity with genomic-based improvement, as well as provide novel insights into the neo-domestication of polyploid crops with novel genetic diversity from reconstructed genomes.

Mechanistic insights of CRISPR/Cas-mediated genome editing towards enhancing abiotic stress tolerance in plants

Abiotic stresses such as temperature (high/low), drought, salinity, and others make the environment hostile to plants. Abiotic stressors adversely affect plant growth and development; and thereby makes a direct impact on overall plant productivity. Plants confront stress by developing an internal defense system orchestrated by compatible solutes, reactive oxygen species scavengers and phytohormones. However, routine exposure to unpredictable environmental stressors makes it essential to equip plants with a system that contributes to sustainable agricultural productivity, besides imparting multi-stress tolerance. The sustainable approach against abiotic stress is accomplished through breeding of tolerant cultivars. Though eco-friendly, tedious screening and crossing protocol limits its usage to overcome stress and in attaining the goal of global food security. Advancement on the technological front has enabled adoption of genomic engineering approaches to perform site-specific modification in the plant genome for improving adaptability, increasing the yield and in attributing resilience against different stressors. Of the different genome editing approaches, CRISPR/Cas has revolutionized biological research with wider applicability to crop plants. CRISPR/Cas emerged as a versatile tool in editing genomes for desired traits in highly accurate and precise manner. The present study summarizes advancement of the CRISPR/Cas genome editing tool in its adoption to manipulate plant genomes for novel traits towards developing high-yielding and climate-resilient crop varieties.

Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment

Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.

Omics: The way forward to enhance abiotic stress tolerance in Brassica napus L

Plant abiotic stresses negative affects growth and development, causing a massive reduction in global agricultural production. Rapeseed (Brassica napus L.) is a major oilseed crop because of its economic value and oilseed production. However, its productivity has been reduced by many environmental adversities. Therefore, it is a prime need to grow rapeseed cultivars, which can withstand numerous abiotic stresses. To understand the various molecular and cellular mechanisms underlying the abiotic stress tolerance and improvement in rapeseed, omics approaches have been extensively employed in recent years. This review summarized the recent advancement in genomics, transcriptomics, proteomics, metabolomics, and their imploration in abiotic stress regulation in rapeseed. Some persisting bottlenecks have been highlighted, demanding proper attention to fully explore the omics tools. Further, the potential prospects of the CRISPR/Cas9 system for genome editing to assist molecular breeding in developing abiotic stress-tolerant rapeseed genotypes have also been explained. In short, the combination of integrated omics, genome editing, and speed breeding can alter rapeseed production worldwide.

Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao

BACKGROUND

Giant Juncao is often used as feed for livestock because of its huge biomass. However, drought stress reduces forage production by affecting the normal growth and development of plants. Therefore, investigating the molecular mechanisms of drought tolerance will provide important information for the improvement of drought tolerance in this grass.

RESULTS

A total of 144.96 Gb of clean data was generated and assembled into 144,806 transcripts and 93,907 unigenes. After 7 and 14 days of drought stress, a total of 16,726 and 46,492 differentially expressed genes (DEGs) were observed, respectively. Compared with normal irrigation, 16,247, 23,503, and 11,598 DEGs were observed in 1, 5, and 9 days following rehydration, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed abiotic stress-responsive genes and pathways related to catalytic activity, methyltransferase activity, transferase activity, and superoxide metabolic process. We also identified transcription factors belonging to several families, including basic helix-loop-helix (bHLH), WRKY, NAM (no apical meristem), ATAF1/2 and CUC2 (cup-shaped cotyledon) (NAC), fatty acyl-CoA reductase (FAR1), B3, myeloblastosis (MYB)-related, and basic leucine zipper (bZIP) families, which are important drought-rehydration-responsive proteins. Weighted gene co-expression network analysis was also used to analyze the RNA-seq data to predict the interrelationship between genes. Twenty modules were obtained, and four of these modules may be involved in photosynthesis and plant hormone signal transduction that respond to drought and rehydration conditions.

CONCLUSIONS

Our research is the first to provide a more comprehensive understanding of DEGs involved in drought stress at the transcriptome level in Giant Juncao with different drought and recovery conditions. These results may reveal insights into the molecular mechanisms of drought tolerance in Giant Juncao and provide diverse genetic resources involved in drought tolerance research.

Detailed Genetic Analysis for Identifying QTLs Associated with Drought Tolerance at Seed Germination and Seedling Stages in Barley

Drought induces several challenges for plant development, growth, and production. These challenges become more severe, in particular, in arid and semiarid countries like Egypt. In terms of production, barley ranks fourth after wheat, maize, and rice. Seed germination and seedling stages are critical stages for plant establishment and growth. In the current study, 60 diverse barley genotypes were tested for drought tolerance using two different treatments: control (0-PEG) and drought (20%-PEG). Twenty-two traits were estimated for seed germination and seedling parameters. All traits were reduced under drought stress, and a significant variation was found among genotypes under control and stress conditions. The broad-sense heritability estimates were very high under both control and drought for all traits. It ranged from 0.63 to 0.97 under the control condition and from 0.89 to 0.97 under drought, respectively. These high heritabilities suggested that genetic improvement of drought tolerance in barley at both stages is feasible. The principal component analysis revealed that root-related parameters account for the largest portion of phenotypic variation in this collection. The single-marker analysis (SMA) resulted in 71 quantitative trait loci (QTLs) distributed across the seven chromosomes of barley. Thirty-three QTLs were detected for root-length-related traits. Many hotspots of QTLs were detected for various traits. Interestingly, some markers controlled many traits in a pleiotropic manner; thus, they can be used to control multiple traits at a time. Some QTLs were constitutive, i.e., they are mapped under control and drought, and targeting these QTLs makes the selection for drought tolerance a single-step process. The results of gene annotation analysis revealed very potential candidate genes that can be targeted to select for drought tolerance.

The Use of Genetic and Gene Technologies in Shaping Modern Rapeseed Cultivars (Brassica napus L.)

Since their domestication, Brassica oilseed species have undergone progressive transformation allied with the development of breeding and molecular technologies. The canola (Brassica napus) crop has rapidly expanded globally in the last 30 years with intensive innovations in canola varieties, providing for a wider range of markets apart from the food industry. The breeding efforts of B. napus, the main source of canola oil and canola meal, have been mainly focused on improving seed yield, oil quality, and meal quality along with disease resistance, abiotic stress tolerance, and herbicide resistance. The revolution in genetics and gene technologies, including genetic mapping, molecular markers, genomic tools, and gene technology, especially gene editing tools, has allowed an understanding of the complex genetic makeup and gene functions in the major bioprocesses of the Brassicales, especially Brassica oil crops. Here, we provide an overview on the contributions of these technologies in improving the major traits of B. napus and discuss their potential use to accomplish new improvement targets.