Search

The utilization of reduced plant height genes Rht-B1b and Rht-D1b, encoding homeologous DELLA proteins, led to the wheat Green Revolution (GR). However, the specific functions of GR genes in yield determination and the underlying regulatory mechanisms remained unknown. Here, we validated that Rht-B1b, as a representative of GR genes, affects plant architecture and yield component traits. Upregulation of Rht-B1b reduced plant height, leaf size and grain weight, but increased tiller number, tiller angle, spike number per unit area, and grain number per spike. Dynamic investigations showed that Rht-B1b increased spike number by improving tillering initiation rather than outgrowth, and enhanced grain number by promoting floret fertility. Rht-B1b reduced plant height by reducing cell size in the internodes, and reduced grain size or weight by decreasing cell number in the pericarp. Transcriptome analyses uncovered that Rht-B1b regulates many homologs of previously reported key genes for given traits and several putative integrators for different traits. These findings specify the pleiotropic functions of Rht-B1b in improving yield and provide new insights into the regulatory mechanisms underlying plant morphogenesis and yield formation.

The breeding of crops with improved nitrogen use efficiency (NUE) is crucial for sustainable agriculture. Despite its importance, the way in which epigenetic modifications regulate cultivar-specific responses to low nitrogen (LN) constraints is not yet well understood. Here, we analyzed the chromatin landscapes in the roots, leaves, and seeds of two wheat cultivars (KN9204 and J411) that differ radically in NUE under varied nitrogen conditions. The chromatin regions responsible for regulating gene transcription exhibited clear cultivar-specificity between the two cultivars, and the regulation of nitrogen metabolism genes (NMGs) was closely linked to variation in histone modification levels instead of differences in DNA sequence. We also found that cultivar-specific histone modification regions contribute to the genetic regulation of NUE-related traits, such as the QTL locus of maximum root length of qMRL-7B. Additionally, LN-induced H3K27ac and H3K27me3 dynamics enhanced root growth more significantly in KN9204, while strengthened the nitrogen uptake system remarkably in J411. Evidence from histone deacetylase inhibitor treatment and transgenic plants with loss function of the H3K27me3 methyltransferase further showed that changes in epigenetic modifications can alter the strategy for root development and nitrogen uptake in response to LN constraint. Taken together, our data highlight the importance of epigenetic regulation in mediating cultivar-specific adaptation to LN in wheat.

The Green Revolution of the 1960s improved crop yields in part through the widespread cultivation of semidwarf plant varieties, which resist lodging but require a high-nitrogen (N) fertilizer input. Because environmentally degrading synthetic fertilizer use underlies current worldwide cereal yields, future agricultural sustainability demands enhanced N use efficiency (NUE). Here, we summarize the current understanding of how plants sense, uptake, and respond to N availability in the model plants that can be used to improve sustainable productivity in agriculture. Recent progress in unlocking the genetic basis of NUE within the broader context of plant systems biology has provided insights into the coordination of plant growth and nutrient assimilation and inspired the implementation of a new breeding strategy to cut fertilizer use in high-yield cereal crops. We conclude that identifying fresh targets for N sensing and response in crops would simultaneously enable improved grain productivity and NUE to launch a new Green Revolution and promote future food security.

The breeding of crops with improved nitrogen use efficiency (NUE) is crucial for sustainable agriculture. However, the role of epigenetic modification in the regulation of cultivar-specific responses to low nitrogen (LN) constraint is not well understood. Here, we analyzed the chromatin landscapes in roots, leaves, and seeds in two wheat cultivars (KN9204 and J411) that differ radically in NUE under normal and nitrogen-limited conditions. Transcriptional regulatory chromatin regions exhibited a clear cultivar-specificity between KN9204 and J411. Cultivar-specific regulation of nitrogen metabolism genes (NMGs) is linked to variation in histone modification levels, rather than differences in DNA sequence. Cultivar-specific histone modification regions were found to contribute to the genetic regulation of NUE-related traits, such as QTL locus of maximum root length of qMRL-7B. Furthermore, LN-induced H3K27ac and H3K27me3 dynamics enhanced root growth more in KN9204, while strengthened the nitrogen uptake system more in J411. Evidence from histone deacetylase inhibitor treatment and transgenic plants with loss-of-function of the H3K27me3 methyltransferase further showed that changes in epigenetic modifications can alter the strategy for root development and nitrogen uptake in response to LN constraint. Taken together, the results of our study highlight the importance of epigenetic regulation in mediating cultivar-specific root development and metabolic adaptation to LN in wheat.

Objectives Gatifloxacin (GAT), as one of the representatives of the fourth-generation fluoroquinolones (FQs) has been used to treat drug-resistant tuberculosis. Although DNA gyrase mutations are the leading cause of FQs resistance, mutations conferring resistance to GAT remain inadequately characterized. Methods In the present study, GAT-resistant mutants were selected from 7H10 agar plates containing 0.5 mg/L GAT (the critical concentration). Mutations involved in GAT resistance were identified through whole-genome sequence. Results A total of 123 isolates were demonstrated to resistance to GAT. Among those isolates, 55.3% (68/123) mutants had gyrA gene mutations (G280A (D94N), A281G (D94G), G280T (D94Y) and G262T (G88C)). The remain (44.7%, 55/123) harbored gyrB gene mutations (A1495G (N499D), C1497A (N499K), C1497G (N499K) and A1503C (E501D)). Conclusions In summary, mutations in gyrA and gyrB are the primary mechanism of GAT resistance. The findings provides new insight of resistance to GAT and contribute to molecular diagnosis of GAT resistance in the clinical setting.

Summary The AGAMOUS‐LIKE6 (AGL6)‐like genes are ancient MADS‐box genes and are functionally studied in a few model plants. The knowledge of these genes in wheat remains limited. Here, by studying a ‘double homoeolog mutant’ of the AGL6 gene in tetraploid wheat, we showed that AGL6 was required for the development of all four whorls of floral organs with dosage‐dependent effect on floret fertility. Yeast two‐hybrid analyses detected interactions of AGL6 with all classes of MADS‐box proteins in the ABCDE model for floral organ development. AGL6 was found to interact with several additional proteins, including the G protein β and γ (DEP1) subunits. Analysis of the DEP1‐B mutant showed a significant reduction in spikelet number per spike in tetraploid wheat, while overexpression of AGL6 in common wheat increased the spikelet number per spike and hence the grain number per spike. RNA‐seq analysis identified the regulation of several meristem activity genes by AGL6, such as FUL2 and TaMADS55. Our work therefore extensively updated the wheat ABCDE model and proposed an alternative approach to improve wheat grain yield by manipulating the AGL6 gene.

G-protein signaling and ubiquitin-dependent degradation are both involved in grain development in rice, but how these pathways are coordinated in regulating this process is unknown. Here, we show that Chang Li Geng 1 (CLG1), which encodes an E3 ligase, regulates grain size by targeting the Gγ protein GS3, a negative regulator of grain length, for degradation. Overexpression of CLG1 led to increased grain length, while overexpression of mutated CLG1 with changes in three conserved amino acids decreased grain length. We found that CLG1 physically interacts with and ubiquitinats GS3which is subsequently degraded through the endosome degradation pathway, leading to increased grain size. Furthermore, we identified a critical SNP in the exon 3 of CLG1 that is significantly associated with grain size variation in a core collection of cultivated rice. This SNP results in an amino acid substitution from Arg to Ser at position 163 of CLG1 that enhances the E3 ligase activity of CLG1 and thus increases rice grain size. Both the expression level of CLG1 and the SNP CLG1163S may be useful variations for manipulating grain size in rice.

Objective With the widespread application of CRISPR/Cas9 gene editing technology, new methods are needed to screen mutants quickly and effectively. Here, we aimed to develop a simple and cost-effective method to screen CRISPR/Cas9-induced mutants. Result We report a novel method to identify CRISPR/Cas9-induced mutants through a DNA-guided Argonaute nuclease derived from the archaeon Pyrococcus furiosus. We demonstrated that the Pyrococcus furiosus Argonaute (PfAgo)-based method could distinguish among biallelic mutants, monoallelic mutants and wild type (WT). Furthermore, this method was able to identify 1 bp indel mutations. Conclusion The PfAgo-based method is simple to implement and can be applied to screen biallelic mutants and mosaic mutants generated by CRISPR-Cas9 or other kinds of gene editing tools. Supplementary Information The online version contains supplementary material available at 10.1007/s10529-021-03177-z.

Climate change negatively affects crop yield, which hinders efforts to reach agricultural sustainability and food security. Here, we show that a previously unidentified allele of the nitrate transporter gene OsNRT2.3 is required to maintain high yield and high nitrogen use efficiency under high temperatures. We demonstrate that this tolerance to high temperatures in rice accessions harboring the HTNE-2 (high temperature resistant and nitrogen efficient-2) alleles from enhanced translation of the OsNRT2.3b mRNA isoform and the decreased abundance of a unique small RNA (sNRT2.3-1) derived from the 5′ untranslated region of OsNRT2.3 . sNRT2.3-1 binds to the OsNRT2.3a mRNA in a temperature-dependent manner. Our findings reveal that allelic variation in the 5′ untranslated region of OsNRT2.3 leads to an increase in OsNRT2.3b protein levels and higher yield during high-temperature stress. Our results also provide a breeding strategy to produce rice varieties with higher grain yield and lower N fertilizer input suitable for a sustainable agriculture that is resilient against climate change.

Spike architecture largely affects grain number embraced, which is an important trait to optimize during wheat breeding process. In this study, we incorporated multi-omic data and investigated the genetic regulation of wheat spike development. We generated transcriptome and epigenome profiles of shoot apex at eight developmental stages and observed that chromatin accessibility and H3K27me3 abundance coordinated with transcriptome alteration for flowering transition. A core transcriptional regulatory network (TRN) that drove the formation of the wheat spike was constructed. Integration of the TRN and genome-wide association analysis (GWAS) led to the identification of 227 transcription factors (TFs) with both known (42) and unknown (185) functions. Multi-layer regulatory module among TaSPL6, TaMADS34 and TaMADS15 identified by TRN was validated experimentally. Of the 85 novel TFs with homozygous mutant lines in TILLING library, 38 showed altered spike architecture or flowering time, including bHLH, MYB, and WRKY. Furthermore, we demonstrated that TaMYB4-A regulates fertile spikelet number likely via regulating hormones homeostasis and signaling, and is downstream of, and repressed by WFZP. The elite allele of TaMYB4-A, with a C-SNP at the WFZP binding site, was selected for balancing spikelet number and fertility during breeding process in China. Collectively, our findings provide high-confidence novel regulators and an efficient strategy for studying the genetic basis of wheat spike development for practical breeding applications.

Herein, Polyester woven fabrics as the matrices for the experimental group, while cotton knitted fabrics, cotton woven fabrics, and Polyethylene terephthalate (PET) mesh cloth used as the matrices for the control groups, at 40 °e, using 3,4-ethoxylene dioxy thiophene (EDOT)as the polymer monomer, FeCl3as the oxidant, and poly(sodium-p-styrenesulfonate) (PSS) as the dopant, are separately coated with PEDOT:PSS polymer to prepare flexible conductive composite fabrics. The influences of the fabric pattern, oxidant concentration, and monomer concentration on the electrical performance of composite fabrics are optimized. The maximal electrical conductivity of PET-based composite fabrics (218 S/m) occurs when monomer concentration is 0.035 mol/L, the molar ratio of oxidant to monomer is 2.5, and the dopant concentration is 2.5 g/L. Moreover, bacteriostasis rate of this composite fabric reaches 71.8%. Furthermore, by electrocardiogram (ECG) simulated human body unit test as well as human body ECG test, the optimal PET-based composite fabric electrode both has a lower impedance which helps form the stabilized ECG signal. The resulting fabric electrodes retain the soft and breathable advantages from fabrics and reduce the discomfort for a long-term use of conventional electrographic gel, thereby validating the empirical evidence for mobile, portable, wearable ECG electrodes.

Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.

Deep knowledge of crop biodiversity is essential to improve global food security. Despite bread wheat serving as a keystone crop worldwide, the population history of bread wheat and its wild relatives (a.k.a. wheats) remains elusive. By analyzing whole-genome sequences of 795 wheats, we found that bread wheat originated southwest of the Caspian Sea ∼11,700 years ago and underwent a slow speciation process, lasting ∼3,300 years due to persistent gene flow from wild relatives. Soon after, bread wheat spread across Eurasia and reached Europe, South Asia, and East Asia ∼7,000 to ∼5,000 years ago, shaping a diversified but occasionally convergent adaptive landscape of bread wheat in novel environments. Opposite to cultivated wheat, wild wheat populations have declined by ∼82% in the past ∼2,000 years due to the food choice shift of humans, and likely continue to drop because of the changing climate. These findings will guide future efforts in protecting and utilizing wheat biodiversity to improve global food security.

Ubiquitination, an essential post-transcriptional modification (PTM), plays a vital role in nearly every biological process, including development and growth. Despite its functions in plant reproductive development, its targets in rice panicles remain unclear. In this study, we used proteome-wide profiling of lysine ubiquitination in rice (O. sativa ssp. indica) young panicles. We created the largest ubiquitinome dataset in rice to date, identifying 1638 lysine ubiquitination sites on 916 unique proteins. We detected three conserved ubiquitination motifs, noting that acidic glutamic acid (E) and aspartic acid (D) were most frequently present around ubiquitinated lysine. Enrichment analysis of Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of these ubiquitinated proteins revealed that ubiquitination plays an important role in fundamental cellular processes in rice young panicles. Interestingly, enrichment analysis of protein domains indicated that ubiquitination was enriched on a variety of receptor-like kinases and cytoplasmic tyrosine and serine-threonine kinases. Furthermore, we analyzed the crosstalk between ubiquitination, acetylation, and succinylation, and constructed a potential protein interaction network within our rice ubiquitinome. Moreover, we identified ubiquitinated proteins related to pollen and grain development, indicating that ubiquitination may play a critical role in the physiological functions in young panicles. Taken together, we reported the most comprehensive lysine ubiquitinome in rice so far, and used it to reveal the functional role of lysine ubiquitination in rice young panicles.

Embryogenesis represents the beginning of life cycle, but our understanding of the regulatory circuitry in plants is far lagged to animals. Here, we draw a transcriptome trajectory and chromatin landscape profile during embryogenesis of most cultivated crop hexaploid wheat, highlighting large-scale chromatin reconfiguration and distinct proximal and distal transcriptional regulation in defining cell fate transition. Upon fertilization, H3K27ac and H3K4me3 resetting were correlated with maternal genome silence, while de novo building of chromatin accessibility activated zygotic genome. Global depletion of H3K27me3 in pre-embryo results in a permissive chromatin environment with gain-of-chromatin accessibility, allowing subsequent hierarchical cis- and trans-regulation network mediated by key factors, such as LEC1, MYB, ZHD, LEC2, governing embryo pattern formation. By contrast, H3K27me3 restoration coordinating with chromatin compaction in developmental genes attenuated totipotency and prohibited extensive organogenesis during embryo maturation. In addition, dynamic biased expression of homeolog triads and diverse expression profiles after polyploidization were observed. This is correlated with asymmetric transposon elements insertion in accessible proximal and distal regions. Thus, our study revealed a plant-specific chromatin reprogramming process in facilitating the hierarchical transcription regulation circuits mediated “inverse hourglass model” and unveiled epigenetic regulation of evolutionary divergence among different sub-genome in shaping embryogenesis in polyploidy wheat.

BackgroundStructural variations (SVs) pervade the genome and contribute substantially to the phenotypic diversity of species. However, most SVs were ineffectively assayed because of the complexity of plant genomes and the limitations of sequencing technologies. Recent advancement of third-generation sequencing technologies, particularly the PacBio high-fidelity (HiFi) sequencing, which generates both long and highly accurate reads, offers an unprecedented opportunity to characterize SVs and reveal their functionality. Since HiFi sequencing is new, it is crucial to evaluate HiFi reads in SV detection before applying the technology at scale.ResultsWe sequenced wheat genomes using HiFi, then conducted a comprehensive evaluation of SV detection using mainstream long-read aligners and SV callers. The results showed the accuracy of SV discovery depends more on aligners rather than callers. For aligners, pbmm2 and NGMLR provided the most accurate results while detecting deletion and insertion, respectively. Likewise, cuteSV and SVIM achieved the best performance across all SV callers. We demonstrated that the combination of the aligners and callers mentioned above is optimal for SV detection. Furthermore, we evaluated the impact of sequencing depth on the accuracy of SV detection. The results showed that low-coverage HiFi sequencing is capable of generating high-quality SV genotyping.ConclusionsThis study provides a robust benchmark of SV discovery with HiFi reads, showing the remarkable potential of long-read sequencing to investigate structural variations in plant genomes. The high accuracy SV discovery from low-coverage HiFi sequencing indicates that skim HiFi sequencing is an ideal approach to study structural variations at the population level.

Diversity surveys of crop germplasm are important for gaining insights into the genomic basis for plant architecture and grain yield improvement, which is still poorly understood in wheat. In this study, we exome sequenced 287 wheat accessions that were collected in the past 100 years. Population genetics analysis identified that 6.7% of the wheat genome falls within the selective sweeps between landraces and cultivars, which harbors the genes known for yield improvement. These regions were asymmetrically distributed on the A and B subgenomes with regulatory genes being favorably selected. Genome-wide association study (GWAS) identified genomic loci associated with traits for yield potential, and two underlying genes, TaARF12 encoding an auxin response factor and TaDEP1 encoding the G-protein γ-subunit, were located and characterized to pleiotropically regulate both plant height and grain weight. Elite single-nucleotide haplotypes with increased allele frequency in cultivars relative to the landraces were identified and found to have accumulated over the course of breeding. Interestingly, we found that TaARF12 and TaDEP1 function in epistasis with the classical plant height Rht-1 locus, leading to propose a "Green Revolution"-based working model for historical wheat breeding. Collectively, our study identifies selection signatures that fine-tune the gibberellin pathway during modern wheat breeding and provides a wealth of genomic diversity resources for the wheat research community.

Rhizosphere bacterial communities are vital for plants, yet the composition of rhizobacterial communities and the complex interactions between roots and microbiota, or between microbiota, are largely unknown. In this study, we investigated the structure and composition of rhizobacterial communities in two soybean cultivars and their recombinant inbred lines contrasting in nodulation through 16S rRNA amplicon sequencing in two years of field trials. Our results demonstrate that soybean plants are able to select microbes from bulk soils at the taxonomic and functional level. Soybean genotype significantly influenced the structure of rhizobacterial communities and resulted in dramatically different co-occurrence networks of rhizobacterial communities between different genotypes of soybean plants. Furthermore, the introduction of exogenous rhizobia through inoculation altered soybean rhizobacterial communities in genotype-dependent manner. Rhizobium inoculation not only stimulated the proliferation of potential beneficial microbes but also increased connections in rhizobacterial networks and changed the hub microbes, all of which led to the association of distinctive bacterial communities. Taken together, we demonstrated that the assembly of soybean rhizobacterial communities was determined by both genotype and the introduction of exogenous rhizobia. These findings bolster the feasibility of root microbiome engineering through inoculation of specific microbial constituents.

Linear (Met1-linked) ubiquitination is involved inflammatory and innate immune signaling. Previous studies have characterized enzymes regulating the addition and removal of this modification in mammalian systems. However, only a few plant-derived deubiquitinases targeting Met1-linked ubiquitin chains have been reported and their mechanism of action remains elusive. Here, using a dehydroalanine-bearing Met1-diubiquitin suicide probe, we discover OTUB1 from Oryza sativa (OsOTUB1) as a Met1-linked ubiquitin chain-targeting deubiquitinase. By solving crystal structures of apo OsOTUB1 and an OsOTUB1/Met1-diubiquitin complex, we find that Met1 activity is conferred by Met1-specific motifs in the S1’ pocket of OsOTUB1. Large-scale sequence alignments and hydrolysis experiments provide evidence that these motifs are a general determinant of Met1 activity in the OTUB subfamily across species. Analysis of the species distribution of OTUBs capable of hydrolysing Met1-linked ubiquitin chains shows that this activity is conserved in green plants (Viridiplantae) and does not exist in metazoans, providing insights into the evolutionary differentiation between primitive plants and animals.

Background Cellulose synthase (CESA) mutants have potential use in straw processing due to their lower cellulose content, but almost all of the mutants exhibit defective phenotypes in plant growth and development. Balancing normal plant growth with reduced cellulose content remains a challenge, as cellulose content and normal plant growth are typically negatively correlated with one another. Result Here, the rice (Oryza sativa) semi-dominant brittle culm (sdbc) mutant Sdbc1, which harbors a substitution (D387N) at the first conserved aspartic acid residue of OsCESA9, exhibits lower cellulose content and reduced secondary wall thickness as well as enhanced biomass enzymatic saccharification compared with the wild type (WT). Further experiments indicated that the OsCESA9D387N mutation may compete with the wild-type OsCESA9 for interacting with OsCESA4 and OsCESA7, further forming non-functional or partially functional CSCs. The OsCESA9/OsCESA9D387N heterozygous plants increase salt tolerance through scavenging and detoxification of ROS and indirectly affecting related gene expression. They also improve rice straw return to the field due to their brittle culms and lower cellulose content without any negative effects in grain yield and lodging. Conclusion Hence, OsCESA9D387N allele can improve rice salt tolerance and provide the prospect of the rice straw for biofuels and bioproducts due to its improved enzymatic saccharification.

The Green Revolution of the 1960s boosted cereal crop yields in part through widespread adoption of semi-dwarf plant varieties, many of which were later found to have mutations in either gibberellins (GAs) homeostasis or DELLA proteins. GA is essential for plant growth and developmental regulation and plays an important role in improving crop plant architecture for enhanced grain yield under high nitrogen conditions. A complex regulatory network governs the spatially and temporally controlled genes expression through integrative GA signaling in response to multiple endogenous and environmental cues. In this review, we summarize current advances in understanding the molecular mechanisms of DELLA-dependent and DELLA-independent GA signaling pathways and their contributions to plant developmental and metabolic adaptations to changes in nitrogen availability. The progress in molecular understanding of the plant growth-metabolic coordination will facilitate breeding strategies for future sustainable agriculture and a new Green Revolution.