Knockout of two BnaMAX1 homologs by CRISPR/Cas9-targeted mutagenesis improves plant architecture and increases yield in rapeseed (Brassica napus L.)

Integrative analyses reveal Bna-miR397a-BnaLAC2 as a potential modulator of low-temperature adaptability in Brassica napus L

Brassica napus L. (B. napus) is a major edible oil crop grown around the southern part of China, which often faces cold stress, posing potential damage to vegetative tissues. To sustain growth and reproduction, a detailed understanding of fundamental regulatory processes in B. napus against long-term low temperature (LT) stress is necessary for breeders to adjust the level of LT adaption in a given region and is therefore of great economic importance. Till now, studies on microRNAs (miRNAs) in coping with LT adaption in B. napus are limited. Here, we performed an in-depth analysis on two B. napus varieties with distinct adaptability to LT stress. Through integration of RNA sequencing (RNA-seq) and small RNA-sequencing (sRNA-seq), we identified 106 modules comprising differentially expressed miRNAs and corresponding potential targets based on strong negative correlations between their dynamic expression patterns. Specifically, we demonstrated that Bna-miR397a post-transcriptionally regulates a LACCASE (LAC) gene, BnaLAC2, to enhance the adaption to LT stresses in B. napus by reducing the total lignin remodelling and ROS homeostasis. In addition, the miR397-LAC2 module was also proved to improve freezing tolerance of Arabidopsis, indicating a conserved role of miR397-LAC2 in Cruciferae plants. Overall, this work provides the first description of a miRNA-mediated-module signature for LT adaption and highlights the prominent role of laccase in future breeding programme of LT tolerant B. napus.

Unlocking genetic potential: a review of the role of CRISPR/Cas technologies in rapeseed improvement

Rapeseed (Brassica napus L.) is a globally important oil crop, providing edible vegetable oil and other valuable sources for humans. Being an allotetraploid, rapeseed has a complex genome that has undergone whole-genome duplication, making molecular breeding rather difficult. Fortunately, clustered regularly interspacedshort palindromic repeat (CRISPR)/CRISPR-associated (Cas) technologies have emerged as a potent tool in plant breeding, providing unprecedented accuracy as well as effectiveness in genome editing. This review focuses on the application and progresses of CRISPR/Cas technologies in rapeseed. We discussed the principles and mechanisms of CRISPR/Cas systems focusing on their use in rapeseed improvement such as targeted gene knockout, gene editing and transcriptional regulation. Furthermore, we summarized the regulatory frameworks governing CRISPR-edited crops as well as the challenges and opportunities for their commercialization and adoption. The potential advantages of CRISPR-mediated traits in rapeseed such as increased yield, disease and stress resistance and oil quality are discussed along with biosafety and environmental implications. The purpose of this review is to provide insights into the transformative role of CRISPR/Cas technologies in rapeseed breeding and its potential to address global agricultural challenges while ensuring sustainable crop production.

Mapping and molecular marker development for the BnaSBT gene controlling inflorescence and plant architectures in B. napus

Exploring the molecular mechanism underlying plant architecture and breeding new varieties suitable for mechanized harvesting are primary objectives for rapeseed breeders in China. However, few genes controlling plant architecture have been cloned in Brassica napus. In this study, SX3, a scattered-bud B. napus line with a dwarf and compact plant architecture, was characterized. To identify the genes underlying bud arrangement, plant height and branch angle, segregating populations were constructed by crossing SX3 with two clustered-bud lines with a tall and loose plant architecture. Genetic analysis revealed that the scattered-bud trait (SBT) was controlled by a single dominant gene, BnaSBT. BnaSBT is likely a pleiotropic gene that simultaneously controls plant height and branch angle. Using BSA-seq analysis, BnaSBT was mapped to a 4.15 Mb region on ChrA10. Owing to the lack of recombinants within this region, it was infeasible to finely map BnaSBT. RNA-seq analysis of BC2 plants with contrasting inflorescence and plant architectures revealed that the upregulation of genes involved in amino acid and lipid metabolism and genes encoding MADS-box transcription factors is related to the the phenotype of SX3. These findings together with comparative sequencing indicated that BnaA10.SEP1, BnaA10.AGL15, BnaA10.GLN1-4 and BnaA10.AGP15 are candidate genes for BnaSBT. Markers closely linked to the scattered-bud trait were developed for selecting dwarf and compact plants. These findings provide molecular markers and germplasms for breeding new varieties with ideal plant types and lay a theoretical foundation for cloning key genes and elucidating the genetic basis of inflorescence and plant architectures in B. napus.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01556-2.

A glycogen synthase kinase-3 gene enhances grain yield heterosis in semi-dwarf rapeseed

Optimizing plant height is a key breeding objective in Brassica napus to enhance lodging resistance and increase yield potential. In the present study, we identified a semi-dwarf gene in rapeseed, BnDWARF5 (BnDF5), which encodes a glycogen synthase kinase 3, BRASSINOSTEROID-INSENSITIVE 2 (BnaC03.BIN2), primarily controlling the elongation of basal internodes by inhibiting the elongation of internode cells. Genetic mapping and cloning revealed that BnDF5 is governed by a semi-dominant/dominant gene located on chromosome C03. Sequencing uncovered an SNP in BnaC03.BIN2 due to an amino acid substitution, which was confirmed via kompetitive allele-specific polymerase chain reaction marker analysis, and expressing the mutated BnaC03.BIN2 in the wild type resulted in decreased plant height. Practical breeding applications showed that heterozygous BnDF5 plants exhibited optimal intermediate height and strong yield heterosis, making the semi-dwarf mutant a valuable genetic resource for developing semi-dwarf rapeseed varieties with improved lodging resistance and yield.

Manipulation of seed coat content for increasing oil content via modulating BnaMYB52 in Brassica napus

Seed oil is synthesized in the embryo, which is surrounded by the seed coat. However, the genetic and molecular mechanisms of how seed coat development affects seed oil content (SOC) remains less studied. Through genome-wide association studies in Brassica napus accessions, we identify BnaA09.MYB52 transcription factor as a candidate gene underlying ZS11_qSCC.A09. Knocking out BnaMYB52 results in a 7.7%-8.2% reduction in seed coat content (SCC) but a 12.3%-13.4% increase in SOC, whereas overexpression of BnaA09.MYB52 leads to the opposite effects. Intriguingly, BnaA09.MYB52 has predominant expression in seed coat during seed development. BnaA09.MYB52 activates the expression of PMEI14 and BAN. Mutant analyses indicate that the SOC is increased by 4.3%-7.7%, while seed coat thickness shows a 12.9%-22.8% reduction in the ban and pmei14 mutants. Thus, our findings identify the molecular mechanism of MYB52-BAN/PMEI14 modules regulating SCC and SOC and provide a potential target for oil content improvement in B. napus.

Dwarfs standing tall: breeding towards the 'Yellow revolution' through insights into plant height regulation

High oilseed production is an exigency due to the increasing edible oil consumption of the growing population. Rapeseed and mustard are cultivated worldwide and contribute significantly to the world's total oilseed production. Already a plateau is reached in terms of area and yield in most of the existing cultivars. Most of the commercially cultivated high yielding rapeseed and mustard varieties are tall, mainly due to a wider use of heterosis. However, they are susceptible to lodging and consequent yield losses. Plant yield is strongly dependent upon its architecture; therefore, 'ideotype breeding' is the key approach adopted to develop new varieties with enhanced yield potential, which is less explored in these crops. Dwarf/ semi dwarf plant type varieties has shown its improved yield potential over tall plant type in cereals which further leads to 'Green revolution' in Asian countries. Although, many induced dwarf mutants in rapeseed and mustard were isolated, unlike dwarf green-revolution varieties of cereals, most of them had undesirable plant types with defects including extreme dwarfism and sterility, leading to poor yield potential. Understanding the genetic and molecular mechanisms governing plant height and its correlation with yield and yield contributing characters is crucial. In this review, recent insights into genetic, molecular, and anatomical regulation of plant height have been discussed. The role of hormones, their crosstalk, and hormonal control for cell division and expansion have been delineated with respect to plant architecture. Many dwarfing genes are identified as being part of various phytohormone pathways. Parallelly, molecular links between plant height and flowering time have been explored. The overall synthesis of the review points out some key target pathways and genes that will be useful for plant breeders as well as biotechnologists for targeted genome editing for improving plant architecture without a yield penalty.

Synthetic biology and artificial intelligence in crop improvement

Synthetic biology plays a pivotal role in improving crop traits and increasing bioproduction through the use of engineering principles that purposefully modify plants through "design, build, test, and learn" cycles, ultimately resulting in improved bioproduction based on an input genetic circuit (DNA, RNA, and proteins). Crop synthetic biology is a new tool that uses circular principles to redesign and create innovative biological components, devices, and systems to enhance yields, nutrient absorption, resilience, and nutritional quality. In the digital age, artificial intelligence (AI) has demonstrated great strengths in design and learning. The application of AI has become an irreversible trend, with particularly remarkable potential for use in crop breeding. However, there has not yet been a systematic review of AI-driven synthetic biology pathways for plant engineering. In this review, we explore the fundamental engineering principles used in crop synthetic biology and their applications for crop improvement. We discuss approaches to genetic circuit design, including gene editing, synthetic nucleic acid and protein technologies, multi-omics analysis, genomic selection, directed protein engineering, and AI. We then outline strategies for the development of crops with higher photosynthetic efficiency, reshaped plant architecture, modified metabolic pathways, and improved environmental adaptability and nutrient absorption; the establishment of trait networks; and the construction of crop factories. We propose the development of SMART (self-monitoring, adapted, and responsive technology) crops through AI-empowered synthetic biotechnology. Finally, we address challenges associated with the development of synthetic biology and offer potential solutions for crop improvement.

Advancing vegetable genetics with gene editing: a pathway to food security and nutritional resilience in climate-shifted environments

As global populations grow and climate change increasingly disrupts agricultural systems, ensuring food security and nutritional resilience has become a critical challenge. In addition to grains and legumes, vegetables are very important for both human and animals because they contain vitamins, minerals, and fibre. Enhancing the ability of vegetables to withstand climate change threats is essential; however, traditional breeding methods face challenges due to the complexity of the genomic clonal multiplication process. In the postgenomic era, gene editing (GE) has emerged as a powerful tool for improving vegetables. GE can help to increase traits such as abiotic stress tolerance, herbicide tolerance, and disease resistance; improve agricultural productivity; and improve nutritional content and shelf-life by fine-tuning key genes. GE technologies such as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR-Cas9) have revolutionized vegetable breeding by enabling specific gene modifications in the genome. This review highlights recent advances in CRISPR-mediated editing across various vegetable species, highlighting successful modifications that increase their resilience to climatic stressors. Additionally, it explores the potential of GE to address malnutrition by increasing the nutrient content of vegetable crops, thereby contributing to public health and food system sustainability. Additionally, it addresses the implementation of GE-guided breeding strategies in agriculture, considering regulatory, ethical, and public acceptance issues. Enhancing vegetable genetics via GE may provide a reliable and nutritious food supply for an expanding global population under more unpredictable environmental circumstances.

Gibberellin-Induced Transcription Factor SmMYB71 Negatively Regulates Salvianolic Acid Biosynthesis in Salvia miltiorrhiza

Salvia miltiorrhiza, the valuable traditional Chinese medicinal plant, has been used in clinics for thousands of years. The water-soluble salvianolic acid compounds are bioactive substances used in treating many diseases. Gibberellins (GAs) are growth-promoting phytohormones that regulate plant growth and development. Previous studies have demonstrated that GAs can promote salvianolic acid accumulation in S. miltiorrhiza; however, the underlying mechanism requires further investigation. Here, we identified a GA-induced R2R3MYB transcription factor (TF), SmMYB71, from a transcriptome library of GA-treated S. miltiorrhiza. SmMYB71 was highly expressed in the root of S. miltiorrhiza and localized to the nucleus. SmMYB71-knockout hairy roots showed higher salvianolic acid accumulation compared to wild lines. Overexpressing SmMYB71 in S. miltiorrhiza hairy roots significantly decreased the content of salvianolic acid by downregulating key salvianolic acid biosynthesis enzymes such as SmRAS and SmCYP98A14. The GCC box in the promoter of SmMYB71 can bind with SmERF115, suggesting that SmMYB71 is regulated by SmERF115 in salvianolic acid biosynthesis. These findings demonstrate a novel regulatory role of SmMYB71 in GA-mediated phenolic acid biosynthesis. With the development of CRISPR/Cas9-based genome editing technology, the SmMYB71 regulation mechanism of salvianolic acid biosynthesis provides a potential target gene for metabolic engineering to increase the quality of S. miltiorrhiza.

Functional characterisation of BnaA02.TOP1α and BnaC02.TOP1α involved in true leaf biomass accumulation in Brassica napus L

Leaves, as primary photosynthetic organs essential for high crop yield and quality, have attracted significant attention. The functions of DNA topoisomerase 1α (TOP1α) in various biological processes, including leaf development, in Brassica napus remain unknown. Here, four paralogs of BnaTOP1α, namely BnaA01.TOP1α, BnaA02.TOP1α, BnaC01.TOP1α and BnaC02.TOP1α, were identified and cloned in the B. napus inbred line 'K407'. Expression pattern analysis revealed that BnaA02.TOP1α and BnaC02.TOP1α, but not BnaA01.TOP1α and BnaC01.TOP1α, were persistently and highly expressed in B. napus true leaves. Preliminary analysis in Arabidopsis thaliana revealed that BnaA02.TOP1α and BnaC02.TOP1α paralogs, but not BnaA01.TOP1α and BnaC01.TOP1α, performed biological functions. Targeted mutations of four BnaTOP1α paralogs in B. napus using the CRISPR-Cas9 system revealed that BnaA02.TOP1α and BnaC02.TOP1α served as functional paralogs and redundantly promoted true leaf number and size, thereby promoting true leaf biomass accumulation. Moreover, BnaA02.TOP1α modulated the levels of endogenous gibberellins, cytokinins and auxins by indirectly regulating several genes related to their metabolism processes. BnaA02.TOP1α directly activated BnaA03.CCS52A2 and BnaC09.AN3 by facilitating the recruitment of RNA polymerase II and modulating H3K27me3, H3K36me2 and H3K36me3 levels at these loci and indirectly activated the BnaA08.PARL1 expression, thereby positively controlling the true leaf size in B. napus. Additionally, BnaA02.TOP1α indirectly activated the BnaA07.PIN1 expression to positively regulate the true leaf number. These results reveal the important functions of BnaTOP1α and provide insights into the regulatory network controlling true leaf biomass accumulation in B. napus.

Allelic Variation of BnaFTA2 and BnaFTC6 Is Associated With Flowering Time and Seasonal Crop Type in Rapeseed (Brassica napus L.)

Different ecological types of rapeseed (Brassica napus L.), including winter, spring, and semi-winter cultivars, exhibit varying flowering times and cannot be planted in the same cultivation areas. FLOWERING LOCUS T (FT) plays a key role in regulating flowering. In allotetraploid B. napus six copies of FT (BnaFT) have been reported. However, there is uncertainty about how the translated products of each paralog, as well as cis-allelic variations at each locus, contribute functionally to flowering time and define specific crop types. In this study, we confirm that BnaFT exhibit distinct expression patterns in different crop types of rapeseed. Using the CRISPR/Cas9 gene editing system, we provide functional evidence that the mutants between Bnaft paralogues affects the regulation of flowering time. Furthermore, we identify a new haplotype of BnaFT.A2 that is associated with early flowering time, although this appears necessary but not sufficient to confer a spring type phenotype. Three haplotypes of BnaFT.C6 were further identified and associated with both flowering time and crop types. We speculate that variations in both BnaFT.A2 and BnaFT.C6 may have undergone diversifying selection during the divergence of seasonal crop types in rapeseed.

Integrating GWAS, RNA-Seq and functional analysis revealed that BnaA02.SE mediates silique elongation by affecting cell proliferation and expansion in Brassica napus

Rapeseed (Brassica napus) silique is the major carbohydrate source for seed development, and the final silique length has attracted great attention from breeders. However, no studies had focused on the dynamic character of silique elongation length (SEL). Here, the dynamic SEL investigation in a natural population including 588 lines over two years indicate that dynamic SEL during 0-20 days after flowering was the most essential stage associated with seed number per silique (SPS) and thousand seed weight (TSW). Then, nine loci were identified to be associated with SEL based on GWAS analysis, among which five SNPs (over 50%) distributed on the A02 chromosome within 6.08 to 6.48 Mb. Subsequently, we screened 5078 differentially expressed genes between two extreme materials. An unknown protein, BnaA02.SE, was identified combining with GWAS and RNA-Seq analysis. Subcellular localization and expression profiles analysis demonstrated that BnaA02.SE is a chloroplast- and nucleus-localized protein mainly expressed in pericarps and leaves. Furthermore, transgenic verification and dynamic cytological observation reveal that overexpressed BnaA02.SE can promote silique elongation by regulating JA and IAA contents, affecting cell proliferation and expansion, respectively, and finally enhance seed yield by influencing SPS and TSW. Haplotype analysis reveal that the homologs of BnaA02.SE may also be involved in silique elongation regulation. Our findings provided comprehensive insights into a newly SEL trait, and cloned the first gene (BnaA02.SE) controlling silique elongation in B. napus. The identified BnaA02.SE and its homologs can offer a valuable target for improving B. napus yield.

Exploring silique number in Brassica napus L.: Genetic and molecular advances for improving yield

Silique number is a crucial yield-related trait for the genetic enhancement of rapeseed (Brassica napus L.). The intricate molecular process governing the regulation of silique number involves various factors. Despite advancements in understanding the mechanisms regulating silique number in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the molecular processes involved in controlling silique number in rapeseed remain largely unexplored. In this review, we identify candidate genes and review the roles of genes and environmental factors in regulating rapeseed silique number. We use genetic regulatory networks for silique number in Arabidopsis and grain number in rice to uncover possible regulatory pathways and molecular mechanisms involved in regulating genes associated with rapeseed silique number. A better understanding of the genetic network regulating silique number in rapeseed will provide a theoretical basis for the genetic improvement of this trait and genetic resources for the molecular breeding of high-yielding rapeseed.

BnaC06.WIP2-BnaA09.STM transcriptional regulatory module promotes leaf lobe formation in Brassica napus

The lobed leaves of rapeseed (Brassica napus L.) offer significant advantages in dense planting, leading to increased yield. Although AtWIP2, a C2H2 zinc finger transcription factor, acts as a regulator of leaf development in Arabidopsis thaliana, the function and regulatory mechanisms of BnaWIP2 in B. napus remain unclear. Here, constitutive expression of the BnaC06.WIP2 paralog, predominantly expressed in leaf serrations, produced lobed leaves in both A. thaliana and B. napus. We demonstrated that BnaC06.WIP2 directly repressed the expression of BnaA01.TCP4, BnaA03.TCP4, and BnaC03.TCP4 and indirectly inhibited the expression of BnaA05.BOP1 and BnaC02.AS2 to promote leaf lobe formation. On the other hand, we discovered that BnaC06.WIP2 modulated the levels of endogenous gibberellin, cytokinin, and auxin, and controlled the auxin distribution in B. napus leaves, thus accelerating leaf lobe formation. Meanwhile, we revealed that BnaA09.STM physically interacted with BnaC06.WIP2, and ectopic expression of BnaA09.STM generated smaller and lobed leaves in B. napus. Furthermore, we found that BnaC06.WIP2 and BnaA09.STM synergistically promoted leaf lobe formation through forming transcriptional regulatory module. Collectively, our findings not only facilitate in-depth understanding of the regulatory mechanisms underlying lobed leaf formation, but also are helpful for guiding high-density breeding practices through improving leaf morphology in B. napus.

The story of a decade: Genomics, functional genomics, and molecular breeding in Brassica napus

Rapeseed (Brassica napus L.) is one of the major global sources of edible vegetable oil and is also used as a feed and pioneer crop and for sightseeing and industrial purposes. Improvements in genome sequencing and molecular marker technology have fueled a boom in functional genomic studies of major agronomic characters such as yield, quality, flowering time, and stress resistance. Moreover, introgression and pyramiding of key functional genes have greatly accelerated the genetic improvement of important traits. Here we summarize recent progress in rapeseed genomics and genetics, and we discuss effective molecular breeding strategies by exploring these findings in rapeseed. These insights will extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture throughout the world.

Crop bioengineering via gene editing: reshaping the future of agriculture

Genome-editing technologies have revolutionized research in plant biology, with major implications for agriculture and worldwide food security, particularly in the face of challenges such as climate change and increasing human populations. Among these technologies, clustered regularly interspaced short palindromic repeats [CRISPR]-CRISPR-associated protein [Cas] systems are now widely used for editing crop plant genomes. In this review, we provide an overview of CRISPR-Cas technology and its most significant applications for improving crop sustainability. We also review current and potential technological advances that will aid in the future breeding of crops to enhance food security worldwide. Finally, we discuss the obstacles and challenges that must be overcome to realize the maximum potential of genome-editing technologies for future crop and food production.

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.

Biotechnology and urban agriculture: A partnership for the future sustainability

The global population is growing rapidly, and with it, the demand for food. In the coming decades, more and more people will be living in urban areas, where land for traditional agriculture is scarce. Urban agriculture can help to meet this growing demand for food in a sustainable way. Urban agriculture is the practice of growing food in urban areas. It can be done on rooftops, balconies, vacant lots, and even in alleyways. Urban agriculture can produce a variety of crops, including fruits, vegetables, and herbs. It can also help to improve air quality, reduce stormwater runoff, and create jobs. Biotechnology can be used to improve the efficiency and sustainability of urban agriculture. Biotechnological tools can be used to develop crops that are resistant to pests and diseases, that are more tolerant of drought and heat, and that have higher yields. Biotechnology can also be used to improve the nutritional value of crops. This review article discusses the need for and importance of urban agriculture, biotechnology, and genome editing in meeting the growing demand for food in urban areas. It also discusses the potential of biotechnology to improve the sustainability of urban agriculture.

Modification of Fatty Acid Profile and Oil Contents Using Gene Editing in Oilseed Crops for a Changing Climate

Mutation breeding based on various chemical and physical mutagens induces and disrupts non-target loci. Hence, large populations were required for visual screening, but desired plants were rare and it was a further laborious task to identify desirable mutants. Generated mutant had high defect due to non-targeted mutation, with poor agronomic performance. Mutation techniques were augmented by targeted induced local lesions in genome (TILLING) facilitating the selection of desirable germplasm. On the other hand, gene editing through CRISPR/Cas9 allows knocking down genes for site-directed mutation. This handy technique has been exploited for the modification of fatty acid profile. High oleic acid genetic stocks were obtained in a broad range of crops. Moreover, genes involved in the accumulation of undesirable seed components such as starch, polysaccharide, and flavors were knocked down to enhance seed quality, which helps to improve oil contents and reduces the anti-nutritional component.

Progress in gene editing tools, implications and success in plants: a review

Genetic modifications are made through diverse mutagenesis techniques for crop improvement programs. Among these mutagenesis tools, the traditional methods involve chemical and radiation-induced mutagenesis, resulting in off-target and unintended mutations in the genome. However, recent advances have introduced site-directed nucleases (SDNs) for gene editing, significantly reducing off-target changes in the genome compared to induced mutagenesis and naturally occurring mutations in breeding populations. SDNs have revolutionized genetic engineering, enabling precise gene editing in recent decades. One widely used method, homology-directed repair (HDR), has been effective for accurate base substitution and gene alterations in some plant species. However, its application has been limited due to the inefficiency of HDR in plant cells and the prevalence of the error-prone repair pathway known as non-homologous end joining (NHEJ). The discovery of CRISPR-Cas has been a game-changer in this field. This system induces mutations by creating double-strand breaks (DSBs) in the genome and repairing them through associated repair pathways like NHEJ. As a result, the CRISPR-Cas system has been extensively used to transform plants for gene function analysis and to enhance desirable traits. Researchers have made significant progress in genetic engineering in recent years, particularly in understanding the CRISPR-Cas mechanism. This has led to various CRISPR-Cas variants, including CRISPR-Cas13, CRISPR interference, CRISPR activation, base editors, primes editors, and CRASPASE, a new CRISPR-Cas system for genetic engineering that cleaves proteins. Moreover, gene editing technologies like the prime editor and base editor approaches offer excellent opportunities for plant genome engineering. These cutting-edge tools have opened up new avenues for rapidly manipulating plant genomes. This review article provides a comprehensive overview of the current state of plant genetic engineering, focusing on recently developed tools for gene alteration and their potential applications in plant research.

Integrated analysis of transcriptome and metabolome reveals insights for low-temperature germination in hybrid rapeseeds (Brassica napus L.)

Rapeseed (Brassica napus L.) is an important oil-producing crop in China. However, cold stress in winter can adversely affect rapeseed germination and subsequently result in poor seed yield at the mature stage. Studies of differences in the transcriptional and metabolic levels of rapeseed under cold stress can improve our understanding of low-temperature germination (LTG). The current study aimed to identify the cold stress-responsive genes, metabolites, and metabolic pathways based on a combined transcriptome and metabolome analysis to understand the difference of LTG and tolerance mechanisms in the cold-tolerant (Yueyou1301, YY1301) and cold-normal (Fengyou737, FY737) rapeseed varieties. Compared to FY737, YY1301 had a higher germination rate, indole acetic acid (IAA) and gibberellic acid (GA)/(abscisic acid) ABA levels at 7.5 °C. A total of 951 differentially expressed genes (DEGs) and 86 differentially accumulated metabolites (DAMs) were identified in two rapeseed varieties. Conjoint analysis revealed 12 DAMs and 5 DEGs that were strongly correlated in inducing rapeseed LTG, which were mainly related to carbohydrate and amino acid metabolism, specifically the pathway of glutathione metabolism and starch and sucrose metabolism. These results suggest that the DAMs and DEGs involved in crucial biological pathways may regulate the LTG of rapeseed. It increases the understanding of the molecular mechanisms underlying the adaptation of rapeseed to LTG.

CRISPR-Cas technology secures sustainability through its applications: a review in green biotechnology

The CRISPR-Cas system's applications in biotechnology offer a promising avenue for addressing pressing global challenges, such as climate change, environmental pollution, the energy crisis, and the food crisis, thereby advancing sustainability. The ever-growing demand for food due to the projected population of around 9.6 billion by 2050 requires innovation in agriculture. CRISPR-Cas technology emerges as a powerful solution, enhancing crop varieties, optimizing yields, and improving resilience to stressors. It offers multiple gene editing, base editing, and prime editing, surpassing conventional methods. CRISPR-Cas introduces disease and herbicide resistance, high-yielding, drought-tolerant, and water-efficient crops to address rising water utilization and to improve the efficiency of agricultural practices which promise food sustainability and revolutionize agriculture for the benefit of future generations. The application of CRISPR-Cas technology extends beyond agriculture to address environmental challenges. With the adverse impacts of climate change and pollution endangering ecosystems, there is a growing need for sustainable solutions. The technology's potential in carbon capture and reduction through bio-sequestration is a pivotal strategy for combating climate change. Genomic advancements allow for the development of genetically modified organisms, optimizing biofuel and biomaterial production, and contributing to a renewable and sustainable energy future. This study reviews the multifaceted applications of CRISPR-Cas technology in the agricultural and environmental fields and emphasizes its potential to secure a sustainable future.

The current scenario and future perspectives of transgenic oilseed mustard by CRISPR-Cas9

PURPOSE

Production of a designer crop having added attributes is the primary goal of all plant biotechnologists. Specifically, development of a crop with a simple biotechnological approach and at a rapid pace is most desirable. Genetic engineering enables us to displace genes among species. The newly incorporated foreign gene(s) in the host genome can create a new trait(s) by regulating the genotypes and/or phenotypes. The advent of the CRISPR-Cas9 tools has enabled the modification of a plant genome easily by introducing mutation or replacing genomic fragment. Oilseed mustard varieties (e.g., Brassica juncea, Brassica nigra, Brassica napus, and Brassica carinata) are one such plants, which have been transformed with different genes isolated from the wide range of species. Current reports proved that the yield and value of oilseed mustard has been tremendously improved by the introduction of stably inherited new traits such as insect and herbicide resistance. However, the genetic transformation of oilseed mustard remains incompetent due to lack of potential plant transformation systems. To solve numerous complications involved in genetically modified oilseed mustard crop varieties regeneration procedures, scientific research is being conducted to rectify the unwanted complications. Thus, this study provides a broader overview of the present status of new traits introduced in each mentioned varieties of oilseed mustard plant by different genetical engineering tools, especially CRISPR-Cas9, which will be useful to improve the transformation system of oilseed mustard crop plants.

METHODS

This review presents recent improvements made in oilseed mustard genetic engineering methodologies by using CRISPR-Cas9 tools, present status of new traits introduced in oilseed mustard plant varieties.

RESULTS

The review highlighted that the transgenic oilseed mustard production is a challenging process and the transgenic varieties of oilseed mustard provide a powerful tool for enhanced mustard yield. Over expression studies and silencing of desired genes provide functional importance of genes involved in mustard growth and development under different biotic and abiotic stress conditions. Thus, it can be expected that in near future CRISPR can contribute enormously in improving the mustard plant's architecture and develop stress resilient oilseed mustard plant species.

Integrated approaches for increasing plant yield under salt stress

Salt stress affects large cultivated areas worldwide, thus causing remarkable reductions in plant growth and yield. To reduce the negative effects of salt stress on plant growth and yield, plant hormones, nutrient absorption, and utilization, as well as developing salt-tolerant varieties and enhancing their morpho-physiological activities, are some integrative approaches to coping with the increasing incidence of salt stress. Numerous studies have been conducted to investigate the critical impacts of these integrative approaches on plant growth and yield. However, a comprehensive review of these integrative approaches, that regulate plant growth and yield under salt stress, is still in its early stages. The review focused on the major issues of nutrient absorption and utilization by plants, as well as the development of salt tolerance varieties under salt stress. In addition, we explained the effects of these integrative approaches on the crop's growth and yield, illustrated the roles that phytohormones play in improving morpho-physiological activities, and identified some relevant genes involve in these integrative approaches when the plant is subjected to salt stress. The current review demonstrated that HA with K enhance plant morpho-physiological activities and soil properties. In addition, NRT and NPF genes family enhance nutrients uptake, NHX1, SOS1, TaNHX, AtNHX1, KDML, RD6, and SKC1, maintain ion homeostasis and membrane integrity to cope with the adverse effects of salt stress, and sd1/Rht1, AtNHX1, BnaMAX1s, ipal-1D, and sft improve the plant growth and yield in different plants. The primary purpose of this investigation is to provide a comprehensive review of the performance of various strategies under salt stress, which might assist in further interpreting the mechanisms that plants use to regulate plant growth and yield under salt stress.

Synthetic developmental biology: molecular tools to re-design plant shoots and roots

Plant morphology and anatomy strongly influence agricultural yield. Crop domestication has strived for desirable growth and developmental traits, such as larger and more fruits and semi-dwarf architecture. Genetic engineering has accelerated rational, purpose-driven engineering of plant development, but it can be unpredictable. Developmental pathways are complex and riddled with environmental and hormonal inputs, as well as feedback and feedforward interactions, which occur at specific times and places in a growing multicellular organism. Rational modification of plant development would probably benefit from precision engineering based on synthetic biology approaches. This review outlines recently developed synthetic biology technologies for plant systems and highlights their potential for engineering plant growth and development. Streamlined and high-capacity genetic construction methods (Golden Gate DNA Assembly frameworks and toolkits) allow fast and variation-series cloning of multigene transgene constructs. This, together with a suite of gene regulation tools (e.g. cell type-specific promoters, logic gates, and multiplex regulation systems), is starting to enable developmental pathway engineering with predictable outcomes in model plant and crop species.

The genetic basis of shoot architecture in soybean

Shoot architecture refers to the three-dimensional body plan of the above ground organs of the plant. The patterning of this body plan results from the tight genetic control of the size and maintenance of meristems, the initiation of axillary growth, and the timing of developmental phase transition. Variation in shoot architecture can result in dramatic differences in plant productivity and/or grain yield due to their effects on light interception, photosynthetic efficiency, response to agronomic inputs, and environmental adaptation. The fine-tuning of shoot architecture has consequently been of great interest to plant breeders, driving the need for deeper understanding of the genes and molecular mechanisms governing these traits. In soybean, the world's most important oil and protein crop, major components of shoot architecture include stem growth habit, plant height, branch angle, branch number, leaf petiole angle, and the size and shape of leaves. Key genes underlying some of these traits have been identified to integrate hormonal, developmental, and environmental signals modulating the growth and orientation of shoot organs. Here we summarize the current knowledge and recent advances in the understanding of the genetic control of these important architectural traits in soybean.

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.

Fine mapping of BnDM1-the gene regulating indeterminate inflorescence in Brassica napus

KEY MESSAGE

A candidate gene Bndm1 related to determinate inflorescence was mapped to a 128-kb interval on C02 in Brassica napus. Brassica napus plants with determinate inflorescence exhibit improved traits in field production, such as lower plant height, improved lodging resistance, and consistent maturity. Compared to plants with indeterminate inflorescence, such features are favorable for mechanized harvesting techniques. Here, using a natural mutant 6138 with determinate inflorescence, it is demonstrated that determinate inflorescence reduces plant height significantly without affecting thousand-grain weight and yield per plant. Determinacy was regulated by a single recessive gene, Bndm1. Using a combination of SNP arrays and map-based cloning, we mapped the locus of determinacy to a 128-kb region on C02. Based on sequence comparisons and the reported functions of candidate genes in this region, we predicted BnaC02.knu (a homolog of KNU in Arabidopsis) as a possible candidate gene of Bndm1 for controlling determinate inflorescence. We found a 623-bp deletion in a region upstream of the KNU promoter in the mutant. This deletion led to the significant overexpression of BnaC02.knu in the mutant compared to that in the ZS11 line. The correlation between this deletion and determinate inflorescence was examined in natural populations. The results indicated that the deletion affected the normal transcription of BnaC02.knu in the plants with determinate inflorescence and played an important role in maintaining flower development. This study presents as a new material for optimizing plant architecture and breeding novel canola varieties suitable for mechanized production. Moreover, our findings provide a theoretical basis for analyzing the molecular mechanisms underlying the formation of determinate inflorescence in B. napus.

Genome-scale targeted mutagenesis in Brassica napus using a pooled CRISPR library

The recently constructed mutant libraries of diploid crops by the CRISPR-Cas9 system have provided abundant resources for functional genomics and crop breeding. However, because of the genome complexity, it is a big challenge to accomplish large-scale targeted mutagenesis in polyploid plants. Here, we demonstrate the feasibility of using a pooled CRISPR library to achieve genome-scale targeted editing in an allotetraploid crop of Brassica napus A total of 18,414 sgRNAs were designed to target 10,480 genes of interest, and afterward, 1104 regenerated transgenic plants harboring 1088 sgRNAs were obtained. Editing interrogation results revealed that 93 of the 178 genes were identified as mutated, thus representing an editing efficiency of 52.2%. Furthermore, we have discovered that Cas9-mediated DNA cleavages tend to occur at all the target sites guided by the same individual sgRNA, a novel finding in polyploid plants. Finally, we show the strong capability of reverse genetic screening for various traits with the postgenotyped plants. Several genes, which might dominate the fatty acid profile and seed oil content and have yet to be reported, were unveiled from the forward genetic studies. Our research provides valuable resources for functional genomics, elite crop breeding, and a good reference for high-throughput targeted mutagenesis in other polyploid plants.

Soil microbiome feedback to climate change and options for mitigation

Microbes are a critical component of soil ecosystems, performing crucial functions in biogeochemical cycling, carbon sequestration, and plant health. However, it remains uncertain how their community structure, functioning, and resultant nutrient cycling, including net GHG fluxes, would respond to climate change at different scales. Here, we review global and regional climate change effects on soil microbial community structure and functioning, as well as the climate-microbe feedback and plant-microbe interactions. We also synthesize recent studies on climate change impacts on terrestrial nutrient cycles and GHG fluxes across different climate-sensitive ecosystems. It is generally assumed that climate change factors (e.g., elevated CO₂ and temperature) will have varying impacts on the microbial community structure (e.g., fungi-to-bacteria ratio) and their contribution toward nutrient turnover, with potential interactions that may either enhance or mitigate each other's effects. Such climate change responses, however, are difficult to generalize, even within an ecosystem, since they are subjected to not only a strong regional influence of current ambient environmental and edaphic conditions, historical exposure to fluctuations, and time horizon but also to methodological choices (e.g., network construction). Finally, the potential of chemical intrusions and emerging tools, such as genetically engineered plants and microbes, as mitigation strategies against global change impacts, particularly for agroecosystems, is presented. In a rapidly evolving field, this review identifies the knowledge gaps complicating assessments and predictions of microbial climate responses and hindering the development of effective mitigation strategies.

BnaC01.BIN2, a GSK3-like kinase, modulates plant height and yield potential in Brassica napus

Using map-based cloning and transgenic transformation, we revealed that glycogen kinase synthase 3-like kinase, BnaC01.BIN2, modulates plant height and yield in rapeseed. The modification of plant height is one of the most important goals in rapeseed breeding. Although several genes that regulate rapeseed plant height have been identified, the genetics mechanisms underlying rapeseed plant height regulation remain poorly understood, and desirable genetic resources for rapeseed ideotype breeding are scarce. Here, we map-based cloned and functionally verified that the rapeseed semi-dominant gene, BnDF4, greatly affects rapeseed plant height. Specifically, BnDF4 encodes brassinosteroid (BR)-insensitive 2, a glycogen synthase kinase 3 primarily expressed in the lower internodes to modulate rapeseed plant height by blocking basal internode-cell elongation. Transcriptome data showed that several cell expansion-related genes involving auxin and BRs pathways were significantly downregulated in the semi-dwarf mutant. Heterozygosity in the BnDF4 allele results in small stature with no marked differences in other agronomic traits. Using BnDF4 in the heterozygous condition, the hybrid displayed strong yield heterosis through optimum intermediate plant height. Our results provide a desirable genetic resource for breeding semi-dwarf rapeseed phenotypes and support an effective strategy for breeding rapeseed hybrid varieties with strong yield heterosis.

The soybean ubiquitin-proteasome system: Current knowledge and future perspective

Increasing soybean [Glycine max (L.) Merr.] yield has become a worldwide scientific problem in the world. Many studies have shown that ubiquitination plays a key role in stress response and yield formation. In the UniProtKB database, 2,429 ubiquitin-related proteins were predicted in soybean, however, <20 were studied. One key way to address this lack of progress in increasing soybean yield will be a deeper understanding of the ubiquitin-proteasome system (UPS) in soybean. In this review, we summarized the current knowledge about soybean ubiquitin-related proteins and discussed the method of combining phenotype, mutant library, transgenic system, genomics, and proteomics approaches to facilitate the exploration of the soybean UPS. We also proposed the strategy of applying the UPS in soybean improvement based on related studies in model plants. Our review will be helpful for soybean scientists to learn current research progress of the soybean UPS and further lay a theoretical reference for the molecular improvement of soybean in future research by use of this knowledge.

Direct access to millions of mutations by whole genome sequencing of an oilseed rape mutant population

Induced mutations are an essential source of genetic variation in plant breeding. Ethyl methanesulfonate (EMS) mutagenesis has been frequently applied, and mutants have been detected by phenotypic or genotypic screening of large populations. In the present study, a rapeseed M₂ population was derived from M₁ parent cultivar 'Express' treated with EMS. Whole genomes were sequenced from fourfold (4×) pools of 1988 M₂ plants representing 497 M₂ families. Detected mutations were not evenly distributed and displayed distinct patterns across the 19 chromosomes with lower mutation rates towards the ends. Mutation frequencies ranged from 32/Mb to 48/Mb. On average, 284 442 single nucleotide polymorphisms (SNPs) per M₂ DNA pool were found resulting from EMS mutagenesis. 55% of the SNPs were C → T and G → A transitions, characteristic for EMS induced ('canonical') mutations, whereas the remaining SNPs were 'non-canonical' transitions (15%) or transversions (30%). Additionally, we detected 88 725 high confidence insertions and deletions per pool. On average, each M₂ plant carried 39 120 canonical mutations, corresponding to a frequency of one mutation per 23.6 kb. Approximately 82% of such mutations were located either 5 kb upstream or downstream (56%) of gene coding regions or within intergenic regions (26%). The remaining 18% were located within regions coding for genes. All mutations detected by whole genome sequencing could be verified by comparison with known mutations. Furthermore, all sequences are accessible via the online tool 'EMSBrassica' (http://www.emsbrassica.plantbreeding.uni-kiel.de), which enables direct identification of mutations in any target sequence. The sequence resource described here will further add value for functional gene studies in rapeseed breeding.

Targeted mutagenesis with sequence-specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects

Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. The presence of a larger number of homoeologous copies of each gene makes random mutation breeding a daunting task for polyploids. Genome editing has revolutionized improvement of polyploid crops as multiple gene copies and/or alleles can be edited simultaneously while preserving the key attributes of elite cultivars. Most genome-editing platforms employ sequence-specific nucleases (SSNs) to generate DNA double-stranded breaks at their target gene. Such DNA breaks are typically repaired via the error-prone nonhomologous end-joining process, which often leads to frame shift mutations, causing loss of gene function. Genome editing has enhanced the disease resistance, yield components, and end-use quality of polyploid crops. However, identification of candidate targets, genotyping, and requirement of high mutagenesis efficiency remain bottlenecks for targeted mutagenesis in polyploids. In this review, we will survey the tremendous progress of SSN-mediated targeted mutagenesis in polyploid crop improvement, discuss its challenges, and identify optimizations needed to sustain further progress.

Genome-wide identification of MAXs genes for strigolactones synthesis/signaling in solanaceous plants and analysis of their potential functions in tobacco

The more axillary growth (MAX) gene family is a group of key genes involved in the synthesis and signal transduction of strigolactones (SLs) in plants. Although MAX genes play vital roles in plant growth and development, characterization of the MAX gene family has been limited in solanaceous crops, especially in tobacco. In this study, 74 members of the MAX family were identified in representative Solanaceae crops and classified into four groups. The physicochemical properties, gene structure, conserved protein structural domains, cis-acting elements, and expression patterns could be clearly distinguished between the biosynthetic and signal transduction subfamilies; furthermore, MAX genes in tobacco were found to be actively involved in the regulation of meristem development by responding to hormones. MAX genes involved in SL biosynthesis were more responsive to abiotic stresses than genes involved in SL signaling. Tobacco MAX genes may play an active role in stress resistance. The results of this study provide a basis for future in-depth analysis of the molecular mechanisms of MAX genes in tobacco meristem development and stress resistance.

Integrating GWAS, linkage mapping and gene expression analyses reveal the genetic control of first branch height in Brassica napus L

Rapeseed (Brassica napus L.) is a crucial oil crop cultivated worldwide. First branch height, an essential component of rapeseed plant architecture, has an important effect on yield and mechanized harvesting; however, the underlying genetic mechanism remains unclear. In this study, based on the 60K single nucleotide polymorphism array and a recombinant inbred lines population derived from M083 and 888-5, a total of 19 QTLs were detected in five environments, distributed on linkage groups A02, A09, A10, C06, and C07, which explained phenotypic variation ranging from 4.87 to 29.87%. Furthermore, 26 significant SNPs were discovered on Chr.A02 by genome-wide association study in a diversity panel of 324 re-sequencing accessions. The major QTL of the first branch height trait was co-located on Chr.A02 by integrating linkage mapping and association mapping. Eleven candidate genes were screened via allelic variation analysis, inter-subgenomic synteny analysis, and differential expression of genes in parental shoot apical meristem tissues. Among these genes, BnaA02g13010D, which encodes a TCP transcription factor, was confirmed as the target gene according to gene function annotation, haplotype analysis, and full-length gene sequencing, which revealed that TATA insertion/deletion in the promoter region was closely linked to significantly phenotypic differences BnaA02.TCP1 ^M083 overexpression resulted in decreased branch height and increased branch number in Arabidopsis. These results provide a genetic basis for first branch height and the ideal architecture of B. napus.

CRISPR/Cas Genome Editing Technologies for Plant Improvement against Biotic and Abiotic Stresses: Advances, Limitations, and Future Perspectives

Crossbreeding, mutation breeding, and traditional transgenic breeding take much time to improve desirable characters/traits. CRISPR/Cas-mediated genome editing (GE) is a game-changing tool that can create variation in desired traits, such as biotic and abiotic resistance, increase quality and yield in less time with easy applications, high efficiency, and low cost in producing the targeted edits for rapid improvement of crop plants. Plant pathogens and the severe environment cause considerable crop losses worldwide. GE approaches have emerged and opened new doors for breeding multiple-resistance crop varieties. Here, we have summarized recent advances in CRISPR/Cas-mediated GE for resistance against biotic and abiotic stresses in a crop molecular breeding program that includes the modification and improvement of genes response to biotic stresses induced by fungus, virus, and bacterial pathogens. We also discussed in depth the application of CRISPR/Cas for abiotic stresses (herbicide, drought, heat, and cold) in plants. In addition, we discussed the limitations and future challenges faced by breeders using GE tools for crop improvement and suggested directions for future improvements in GE for agricultural applications, providing novel ideas to create super cultivars with broad resistance to biotic and abiotic stress.

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.

Genetically engineered crops for sustainably enhanced food production systems

Genetic modification of crops has substantially focused on improving traits for desirable outcomes. It has resulted in the development of crops with enhanced yields, quality, and tolerance to biotic and abiotic stresses. With the advent of introducing favorable traits into crops, biotechnology has created a path for the involvement of genetically modified (GM) crops into sustainable food production systems. Although these plants heralded a new era of crop production, their widespread adoption faces diverse challenges due to concerns about the environment, human health, and moral issues. Mitigating these concerns with scientific investigations is vital. Hence, the purpose of the present review is to discuss the deployment of GM crops and their effects on sustainable food production systems. It provides a comprehensive overview of the cultivation of GM crops and the issues preventing their widespread adoption, with appropriate strategies to overcome them. This review also presents recent tools for genome editing, with a special focus on the CRISPR/Cas9 platform. An outline of the role of crops developed through CRSIPR/Cas9 in achieving sustainable development goals (SDGs) by 2030 is discussed in detail. Some perspectives on the approval of GM crops are also laid out for the new age of sustainability. The advancement in molecular tools through plant genome editing addresses many of the GM crop issues and facilitates their development without incorporating transgenic modifications. It will allow for a higher acceptance rate of GM crops in sustainable agriculture with rapid approval for commercialization. The current genetic modification of crops forecasts to increase productivity and prosperity in sustainable agricultural practices. The right use of GM crops has the potential to offer more benefit than harm, with its ability to alleviate food crises around the world.

Multiple Functions of MiRNAs in Brassica napus L

The worldwide climate changes every year due to global warming, waterlogging, drought, salinity, pests, and pathogens, impeding crop productivity. Brassica napus is one of the most important oil crops in the world, and rapeseed oil is considered one of the most health-beneficial edible vegetable oils. Recently, miRNAs have been found and confirmed to control the expression of targets under disruptive environmental conditions. The mechanism is through the formation of the silencing complex that mediates post-transcriptional gene silencing, which pairs the target mRNA and target cleavage and/or translation inhibition. However, the functional role of miRNAs and targets in B. napus is still not clarified. This review focuses on the current knowledge of miRNAs concerning development regulation and biotic and abiotic stress responses in B. napus. Moreover, more strategies for miRNA manipulation in plants are discussed, along with future perspectives, and the enormous amount of transcriptome data available provides cues for miRNA functions in B. napus. Finally, the construction of the miRNA regulatory network can lead to the significant development of climate change-tolerant B. napus through miRNA manipulation.

Regional association and transcriptome analysis revealed candidate genes controlling plant height in Brassica napus

Plant height is a key morphological trait in rapeseed, which not only plays an important role in determining plant architecture, but is also an important characteristic related to yield. Presently, the improvement of plant architecture is a major challenge in rapeseed breeding. This work was carried out to identify genetic loci related to plant height in rapeseed. In this study, a genome-wide association study (GWAS) of plant height was performed using a Brassica 60 K Illumina Infinium SNP array and 203 Brassica napus accessions. Eleven haplotypes containing important candidate genes were detected and significantly associated with plant height on chromosomes A02, A03, A05, A07, A08, C03, C06, and C09. Moreover, regional association analysis of 50 resequenced rapeseed inbred lines was used to further analyze these eleven haplotypes and revealed nucleotide variation in the BnFBR12-A08 and BnCCR1-C03 gene regions related to the phenotypic variation in plant height. Furthermore, coexpression network analysis showed that BnFBR12-A08 and BnCCR1-C03 were directly connected with hormone genes and transcription factors and formed a potential network regulating the plant height of rapeseed. Our results will aid in the development of haplotype functional markers to further improve plant height in rapeseed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01337-1.

Liriodendron chinense LcMAX1 regulates primary root growth and shoot branching in Arabidopsis thaliana

Strigolactones (SLs) play prominent roles in regulating shoot branching and root architecture in model plants. However, their roles in non-model (particularly woody) plants remain unclear. Liriodendron chinense is a timber tree species widely planted in southern China. The outturn percentage and wood quality of L. chinense are greatly affected by the branching characteristics of its shoot, and the rooting ability of the cuttings is key for its vegetative propagation. Here, we isolated and analyzed the function of the MORE AXILLARY GROWTH 1 (LcMAX1) gene, which is involved in L. chinense SL biosynthesis. RT-qPCR showed that LcMAX1 was highly expressed in the roots and axillary buds. LcMAX1 was located in the endoplasmic reticulum (ER) and nucleus. LcMAX1 ectopic expression promoted primary root growth, whereas there were no phenotypic differences in shoot branching between transgenic and wild-type (WT) A. thaliana plants. LcMAX1 overexpression in the max1 mutant restored them to the WT A. thaliana phenotypes. Additionally, AtPIN1, AtPIN2, and AtBRC1 expressions were significantly upregulated in transgenic A. thaliana and the max1 mutant. It was therefore speculated that LcMAX1 promotes primary root growth by regulating expression of auxin transport-related genes in A. thaliana, and LcMAX1 inhibits shoot branching by upregulating expression of AtBRC1 in the max1 mutant. Altogether, these results demonstrated that the root development and shoot branching functions of LcMAX1 were similar to those of AtMAX1. Our findings provide a foundation for obtaining further insights into root and branch development in L. chinense.

The Global Assessment of Oilseed Brassica Crop Species Yield, Yield Stability and the Underlying Genetics

The global demand for oilseeds is increasing along with the human population. The family of Brassicaceae crops are no exception, typically harvested as a valuable source of oil, rich in beneficial molecules important for human health. The global capacity for improving Brassica yield has steadily risen over the last 50 years, with the major crop Brassica napus (rapeseed, canola) production increasing to ~72 Gt in 2020. In contrast, the production of Brassica mustard crops has fluctuated, rarely improving in farming efficiency. The drastic increase in global yield of B. napus is largely due to the demand for a stable source of cooking oil. Furthermore, with the adoption of highly efficient farming techniques, yield enhancement programs, breeding programs, the integration of high-throughput phenotyping technology and establishing the underlying genetics, B. napus yields have increased by >450 fold since 1978. Yield stability has been improved with new management strategies targeting diseases and pests, as well as by understanding the complex interaction of environment, phenotype and genotype. This review assesses the global yield and yield stability of agriculturally important oilseed Brassica species and discusses how contemporary farming and genetic techniques have driven improvements.

Integrated genetic mapping and transcriptome analysis reveal the BnaA03.IAA7 protein regulates plant architecture and gibberellin signaling in Brassica napus L

A novel mutation in the BnaA03.IAA7 protein reduces plant height and enhances gibberellin signaling in Brassica napus L. Rapeseed (Brassica napus) is an excellent and important source for vegetable oil production, but its production is severely affected by lodging. Lodging hinders mechanization and decreases yield, and an ideal solution is semidwarf breeding. Limited by germplasm resources, semidwarf breeding developed slowly in rapeseed. In the current study, a mutant called sdA03 was isolated from EMS-mutagenized lines of Zhongshuang 11 (ZS11). The inheritance analysis showed that phenotypes of sdA03 were controlled by a single semidominant gene. Genetic mapping, RNA-seq and candidate gene analysis identified BnaA03.IAA7 as a candidate gene, and a function test confirmed that the mutated BnaA03.iaa7 regulates plant architecture in a dose-dependent manner. Yeast two-hybrid and transient expression experiments illustrated the P87L substitution in the GWPPV/I degron motif of BnaA03.iaa7 impaired the interaction between BnaA03.IAA7 and TIR1 proteins, and BnaA03.iaa7 prevented ARF from activating the auxin signaling pathway.The gibberellin (GA) content was higher in sdA03 hypocotyls than in those of ZS11. Further expression analysis showed more active gibberellin signaling in hypocotyl and richer expression of GA synthetic genes in root and cotyledon of sdA03 seedlings. Finally, a marker was developed based on the SNP found in BnaA03.iaa7 and used in molecular breeding. The study enriched our understanding of the architectural regulation of rapeseed and provided germplasm resources for breeding.

CpMAX1a, a Cytochrome P450 Monooxygenase Gene of Chimonanthus praecox Regulates Shoot Branching in Arabidopsis

Strigolactones (SLs) are a class of important hormones in the regulation of plant branching. In the model plant Arabidopsis, AtMAX1 encodes a cytochrome P450 protein and is a crucial gene in the strigolactone synthesis pathway. Yet, the regulatory mechanism of MAX1 in the shoot branching of wintersweet (Chimonanthus praecox) remains unclear. Here we identified and isolated three MAX1 homologous genes, namely CpMAX1a, CpMAX1b, and CpMAX1c. Quantitative real-time PCR (qRT-PCR) revealed the expression of CpMAX1a in all tissues, being highest in leaves, whereas CpMAX1b was only expressed in stems, while CpMAX1c was expressed in both roots and stem tips. However, CpMAX1a’s expression decreased significantly after decapitation; hence, we verified its gene function. CpMAX1a was located in Arabidopsis chloroplasts. Overexpressing CpMAX1a restored the phenotype of the branching mutant max1−3, and reduced the rosette branch number, but resulted in no significant phenotypic differences from the wild type. Additionally, expression of AtBRC1 was significantly upregulated in transgenic lines, indicating that the CpMAX1a gene has a function similar to the homologous gene of Arabidopsis. In conclusion, our study shows that CpMAX1a plays a conserved role in regulating the branch development of wintersweet. This work provides a molecular and theoretical basis for better understanding the branch development of wintersweet.

Identification of Alkaline Salt Tolerance Genes in Brassica napus L. by Transcriptome Analysis

Soil salt alkalization is one major abiotic factor reducing the productivity of crops, including rapeseed, an indispensable oil crop and vegetable. The mechanism studies of alkali salt tolerance can help breed highly resistant varieties. In the current study, rapeseed (B. napus) line 2205 exhibited more tolerance to alkaline salt than line 1423 did. In line 2205, the lesser plasma membrane damage index, the accumulated osmotic solute, and higher antioxidant enzyme activities contributed to alkaline tolerance. A more integrated mesophyll-cell structure was revealed under alkali salt stress by ultrastructure observation in line 2205, which also implied a lesser injury. Transcriptome analysis showed that more genes responded to alkaline salt in line 2205. The expression of specific-response genes in line 1423 was lower than in line 2205. However, most of the specific-response genes in line 2205 had higher expression, which was mainly enriched in carbohydrate metabolism, photosynthetic processes, ROS regulating, and response to salt stress. It can be seen that the tolerance to alkaline salt is attributed to the high expression of some genes in these pathways. Based on these, twelve cross-differentially expressed genes were proposed as candidates. They provide clues for further analysis of the resistance mechanism of rapeseed.

Transcriptomic analysis of rapeseed (Brassica napus. L.) seed development in Xiangride, Qinghai Plateau, reveals how its special eco-environment results in high yield in high-altitude areas

As one of the most important oil crops, rapeseed (Brassica napus) is cultivated worldwide to produce vegetable oil, animal feed, and biodiesel. As the population grows and the need for renewable energy increases, the breeding and cultivation of high-yield rapeseed varieties have become top priorities. The formation of a high rapeseed yield is so complex because it is influenced not only by genetic mechanisms but also by many environmental conditions, such as climatic conditions and different farming practices. Interestingly, many high-yield areas are located in special eco-environments, for example, in the high-altitude Xiangride area of the Qinghai Plateau. However, the molecular mechanisms underlying the formation of high yields in such a special eco-environment area remain largely unknown. Here, we conducted field yield analysis and transcriptome analysis in the Xiangride area. Compared with the yield and environmental factors in the Xinning area (a low-yielding area), we found that the relatively longer daylight length is the key to high rapeseed yield in the Xiangride area, which leads up to a 52.1% increase in rapeseed yield, especially the increase in thousand seed weight and silique number (SN). Combined with transcriptome H-cluster analysis and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses, we can assume that the grain development of rapeseed in the Xiangride area is ahead of schedule and lasts for a long time, leading to the high-yield results in the Xiangride area, confirmed by the expression analysis by quantitative real-time polymerase chain reaction (qRT-PCR) of yield-related genes. Our results provide valuable information for further exploring the molecular mechanism underlying high yield in special ecological environments and provide a helpful reference for studying seed development characteristics in special-producing regions for Brassica napus.

Integrated strategies for increasing rapeseed yield

Over the past few years, rapeseed yields have been considerably lower than those of cereal crops, and progress has been slow due to its limitations for genetic improvement. Here, we propose a comprehensive strategy to consider the interactions between genetics, management practices, and environment, concentrating on using ideotype and heterosis to maximize yield.

CRISPR/Cas9-Mediated Efficient Targeted Mutagenesis in Sesame (Sesamum indicum L.)

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has been widely utilized for targeted genome modification in a wide range of species. It is a powerful genome editing technology, providing significant benefits for gene functional research and molecular breeding. However, to date, no study has applied this genome editing tool to sesame (Sesamum indicum L.), one of the most ancient and important oil crops used widely in diverse industries such as food and medicine. Herein, the CRISPR/Cas9 system along with hairy root transformation was used to induce targeted mutagenesis in sesame. Two single guide RNAs (sgRNAs) were designed to target two sesame cytochrome P450 genes (CYP81Q1 and CYP92B14), which are the key biosynthetic gene of sesamin and sesamolin, respectively. Sequencing data illustrated the expected InDel mutations at the target sites, with 90.63 and 93.33% mutation frequency in CYP81Q1 and CYP92B14, respectively. The most common editing event was single nucleotide deletion and insertion. Sequencing of potential off-target sites of CYP92B14-sgRNA showed no off-target events in cases of three mismatches. High-performance liquid chromatography analysis showed that sesamin and sesamolin biosynthesis was effectively disrupted in the mutated hairy roots, confirming the crucial role of CYP81Q1 and CYP92B14 in sesame lignan biosynthesis. These results demonstrated that targeted mutagenesis was efficiently created by the CRISPR/Cas9 system, and CRISPR/Cas9 coupled with hairy root transformation is an effective tool for assessing gene functions in sesame.