The integrated genomics of crop domestication and breeding.

As a major event in human civilization, wild plants were successfully domesticated to be crops, largely owing to continuing artificial selection. Here, we summarize new discoveries made during the past decade in crop domestication and breeding. The construction of crop genome maps and the functional characterization of numerous trait genes provide foundational information. Approaches to read, interpret, and write complex genetic information are being leveraged in many plants for highly efficient de novo or re-domestication. Understanding the underlying mechanisms of crop microevolution and applying the knowledge to agricultural productions will give possible solutions for future challenges in food security.

A route to de novo domestication of wild allotetraploid rice.

Cultivated rice varieties are all diploid, and polyploidization of rice has long been desired because of its advantages in genome buffering, vigorousness, and environmental robustness. However, a workable route remains elusive. Here, we describe a practical strategy, namely de novo domestication of wild allotetraploid rice. By screening allotetraploid wild rice inventory, we identified one genotype of Oryza alta (CCDD), polyploid rice 1 (PPR1), and established two important resources for its de novo domestication: (1) an efficient tissue culture, transformation, and genome editing system and (2) a high-quality genome assembly discriminated into two subgenomes of 12 chromosomes apiece. With these resources, we show that six agronomically important traits could be rapidly improved by editing O. alta homologs of the genes controlling these traits in diploid rice. Our results demonstrate the possibility that de novo domesticated allotetraploid rice can be developed into a new staple cereal to strengthen world food security.

Pan-Genome of Wild and Cultivated Soybeans.

Soybean is one of the most important vegetable oil and protein feed crops. To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using these assembled genomes together with three previously reported genomes, we constructed a graph-based genome and performed pan-genome analysis, which identified numerous genetic variations that cannot be detected by direct mapping of short sequence reads onto a single reference genome. The structural variations from the 2,898 accessions that were genotyped based on the graph-based genome and the RNA sequencing (RNA-seq) data from the representative 26 accessions helped to link genetic variations to candidate genes that are responsible for important traits. This pan-genome resource will promote evolutionary and functional genomics studies in soybean.

NLRs guard metabolism to coordinate pattern- and effector-triggered immunity.

Pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) in plants enable them to respond to pathogens by activating the production of defence metabolites that orchestrate immune responses1-4. How the production of defence metabolites is promoted by immune receptors and coordinated with broad-spectrum resistance remains elusive. Here we identify the deubiquitinase PICI1 as an immunity hub for PTI and ETI in rice (Oryza sativa). PICI1 deubiquitinates and stabilizes methionine synthetases to activate methionine-mediated immunity principally through biosynthesis of the phytohormone ethylene. PICI1 is targeted for degradation by blast fungal effectors, including AvrPi9, to dampen PTI. Nucleotide-binding domain, leucine-rich-repeat-containing receptors (NLRs) in the plant immune system, such as PigmR, protect PICI1 from effector-mediated degradation to reboot the methionine-ethylene cascade. Natural variation in the PICI1 gene contributes to divergence in basal blast resistance between the rice subspecies indica and japonica. Thus, NLRs govern an arms race with effectors, using a competitive mode that hinges on a critical defence metabolic pathway to synchronize PTI with ETI and ensure broad-spectrum resistance.

The WD40 domain-containing protein Ehd5 positively regulates flowering in rice (Oryza sativa).

Heading date (flowering time), which greatly influences regional and seasonal adaptability in rice (Oryza sativa), is regulated by many genes in different photoperiod pathways. Here, we characterized a heading date gene, Early heading date 5 (Ehd5), using a modified bulked segregant analysis method. The ehd5 mutant showed late flowering under both short-day and long-day conditions, as well as reduced yield, compared to the wild type. Ehd5, which encodes a WD40 domain-containing protein, is induced by light and follows a circadian rhythm expression pattern. Transcriptome analysis revealed that Ehd5 acts upstream of the flowering genes Early heading date 1 (Ehd1), RICE FLOWERING LOCUS T 1 (RFT1), and Heading date 3a (Hd3a). Functional analysis showed that Ehd5 directly interacts with Rice outermost cell-specific gene 4 (Roc4) and Grain number, plant height, and heading date 8 (Ghd8), which might affect the formation of Ghd7-Ghd8 complexes, resulting in increased expression of Ehd1, Hd3a, and RFT1. In a nutshell, these results demonstrate that Ehd5 functions as a positive regulator of rice flowering and provide insight into the molecular mechanisms underlying heading date.

Cellular and Biophysical Applications of Genetic Code Expansion.

Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.

Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation.

Understanding the genetic mechanisms of phenotypic variation in hybrids between domestic animals and their wild relatives may aid germplasm innovation. Here, we report the high-quality genome assemblies of a male Pamir argali (O ammon polii, 2n = 56), a female Tibetan sheep (O aries, 2n = 54), and a male hybrid of Pamir argali and domestic sheep, and the high-throughput sequencing of 425 ovine animals, including the hybrids of argali and domestic sheep. We detected genomic synteny between Chromosome 2 of sheep and two acrocentric chromosomes of argali. We revealed consistent satellite repeats around the chromosome breakpoints, which could have resulted in chromosome fusion. We observed many more hybrids with karyotype 2n = 54 than with 2n = 55, which could be explained by the selfish centromeres, the possible decreased rate of normal/balanced sperm, and the increased incidence of early pregnancy loss in the aneuploid ewes or rams. We identified genes and variants associated with important morphological and production traits (e.g., body weight, cannon circumference, hip height, and tail length) that show significant variations. We revealed a strong selective signature at the mutation (c.334C > A, p.G112W) in TBXT and confirmed its association with tail length among sheep populations of wide geographic and genetic origins. We produced an intercross population of 110 F2 offspring with varied number of vertebrae and validated the causal mutation by whole-genome association analysis. We verified its function using CRISPR-Cas9 genome editing. Our results provide insights into chromosomal speciation and phenotypic evolution and a foundation of genetic variants for the breeding of sheep and other animals.

Unlocking the mystery of heterosis opens the era of intelligent rice breeding.

Heterosis refers to the phenomenon where the first filial offspring (F1) from genetically diverse parents displays advantages in growth rate, yield, and adaptability compared with its parents. The exploitation of heterosis in rice breeding has greatly increased the productivity, making a significant contribution to food security in the last half of the century. Conventional hybrid rice breeding highly relies on the breeder's experience on random crossing and comprehensive field selection. This process is time-consuming and labor-intensive. In recent years, rice hybrid breeding has encountered challenges stemming from limited germplasm resource, low breeding efficiency, and high uncertainty, which constrain the progress in yield increase, coupled with difficulties in balancing grain yield, quality, and resistance. Understanding the genetic basis of rice heterosis could lead to significant advancements in breeding concepts and methods. This will fully unleash the advantages of heterosis. In this review, we focus on the research progress of the genetic dissection of crop heterosis and briefly introduce some key advancements in modern intelligent breeding of rice hybrid.

Simultaneous knockout of cytosolic and plastidial disproportionating enzymes disrupts grain setting and filling in rice.

Rice (Oryza sativa) plants contain plastidial and cytosolic disproportionating enzymes (DPE1 and DPE2). Our previous studies showed that DPE2 acts on maltose, the major product of starch degradation in pollens, releasing one glucose to fuel pollen tube growth and fertilization, whereas DPE1 participates in endosperm starch synthesis by transferring maltooligosyl groups from amylose to amylopectin, and removing excess short maltooligosaccharides. However, little is known about their integrated function. Here, we report that the coordinated actions of DPE1 and DPE2 contribute to grain setting and filling in rice. The dpe1dpe2 mutants could not be isolated from the progeny of heterozygous parental plants but were obtained via anther culture. Unlike that reported in Arabidopsis (Arabidopsis thaliana) and potato (Solanum tuberosum), the dpe1dpe2 rice plants grew normally but only yielded a small number of empty, unfilled seeds. In the dpe1dpe2 seeds, nutrient accumulation was substantially reduced, and dorsal vascular bundles were also severely malnourished. Zymogram analyses showed that changes in the activities of the major starch-synthesizing enzymes matched well with various endosperm phenotypes of mutant seeds. Mechanistically, DPE1 deficiency allowed normal starch mobilization in leaves and pollens but affected starch synthesis in endosperm, while DPE2 deficiency blocked starch degradation, resulting in substantially decreased levels of the sugars available for pollen tube growth and grain filling. Overall, our results demonstrate the great potential of DPE1-DPE2 as an important regulatory module to realize higher crop yields and present a promising target for regulating nutrient accumulation in cereal crop endosperm.

Engineering the Interfacing of Molecules with 2D Transition Metal Dichalcogenides: Enhanced Multifunctional Electronics.

ConspectusEngineering all interfaces between different components in electronic devices is the key to control and optimize fundamental physical processes such as charge injection at metal-semiconductor interfaces, gate modulation at the dielectric-semiconductor interface, and carrier modulation at semiconductor-environment interfaces. The use of two-dimensional (2D) crystals as semiconductors, by virtue of their atomically flat dangling bond-free structures, can facilitate the tailoring of such interfaces effectively. In this context, 2D transition metal dichalcogenides (TMDs) have garnered tremendous attention over the past two decades owing to their exclusive and outstanding physical and chemical characteristics such as their strong light-matter interactions and high charge mobility. These properties position them as promising building blocks for next-generation semiconductor materials. The combination of their large specific surface area, unique electronic structure, and properties highly sensitive to environmental changes makes 2D TMDs appealing platforms for applications in optoelectronics and sensing. While a broad arsenal of TMDs has been made available that exhibit a variety of electronic properties, the latter are unfortunately hardly tunable. To overcome this problem, the controlled functionalization of TMDs with molecules and assemblies thereof represents a most powerful strategy to finely tune their surface characteristics for electronics. Such functionalization can be used not only to encapsulate the electronic material, therefore enhancing its stability in air, but also to impart dynamic, stimuli-responsive characteristics to TMDs and to selectively recognize the presence of a given analyte in the environment, demonstrating unprecedented application potential.In this Account, we highlight the most enlightening recent progress made on the interface engineering in 2D TMD-based electronic devices via covalent and noncovalent functionalization with suitably designed molecules, underlining the remarkable synergies achieved. While electrode functionalization allows modulating charge injection and extraction, the functionalization of the dielectric substrate enables tuning of the carrier concentration in the device channel, and the functionalization of the upper surface of 2D TMDs allows screening the interaction with the environment and imparts molecular functionality to the devices, making them versatile for various applications. The tailored interfaces enable enhanced device performance and open up avenues for practical applications. This Account specifically focuses on our recent endeavor in the unusual properties conferred to 2D TMDs through the functionalization of their interfaces with stimuli-responsive molecules or molecular assemblies. This includes electrode-functionalized devices with modulable performance and charge carriers, molecular-bridged TMD network devices with overall enhanced electrical properties, sensor devices that are highly responsive to changes in the external environment, in particular, electrochemically switchable transistors that react to external electrochemical signals, optically switchable transistors that are sensitive to external light inputs, and multiresponsive transistors that simultaneously respond to multiple external stimuli including optical, electrical, redox, thermal, and magnetic inputs and their application in the development of unprecedented memories, artificial synapses, and logic inverters. By presenting the current challenges, opportunities, and prospects in this blooming research field, we will discuss the powerful integration of such strategies for next-generation electronic digital devices and logic circuitries, outlining future directions and potential breakthroughs in interface engineering.

Model fusion for predicting unconventional proteins secreted by exosomes using deep learning.

Unconventional secretory proteins (USPs) are vital for cell-to-cell communication and are necessary for proper physiological processes. Unlike classical proteins that follow the conventional secretory pathway via the Golgi apparatus, these proteins are released using unconventional pathways. The primary modes of secretion for USPs are exosomes and ectosomes, which originate from the endoplasmic reticulum. Accurate and rapid identification of exosome-mediated secretory proteins is crucial for gaining valuable insights into the regulation of non-classical protein secretion and intercellular communication, as well as for the advancement of novel therapeutic approaches. Although computational methods based on amino acid sequence prediction exist for predicting unconventional proteins secreted by exosomes (UPSEs), they suffer from significant limitations in terms of algorithmic accuracy. In this study, we propose a novel approach to predict UPSEs by combining multiple deep learning models that incorporate both protein sequences and evolutionary information. Our approach utilizes a convolutional neural network (CNN) to extract protein sequence information, while various densely connected neural networks (DNNs) are employed to capture evolutionary conservation patterns.By combining six distinct deep learning models, we have created a superior framework that surpasses previous approaches, achieving an ACC score of 77.46% and an MCC score of 0.5406 on an independent test dataset.

Enzyme Activity-Based Optical Probe: Imaging Aminopeptidases N in Vulnerable Plaque and Serum.

Cardiovascular disease, a chronic and progressive arterial wall disease, is increasingly recognized for its clinical significance. Aminopeptidases N (APN), crucial in the pathophysiological processes of vulnerable plaque, have been linked to endothelial dysfunction, oxidative stress, and plaque formation, thus highlighting their potential as biomarkers for disease progression. However, current detection methods for APN in body fluids and in vivo have limitations, including insufficient sensitivity and specificity, time delays, and the inability to directly reflect enzyme activity in plaques. To address these challenges, we developed an optical probe, HD-APN, for in vivo imaging of aminopeptidases, providing a potential implementation in cardiovascular disease. Our work demonstrated the applicability of HD-APN for specific monitoring of aminopeptidase levels in plaques and serum, shedding light on its potential for further research in cardiovascular disease.

Light-Modulated Humidity Sensing in Spiropyran Functionalized MoS2 Transistors.

The optically tuneable nature of hybrid organic/inorganic heterostructures tailored by interfacing photochromic molecules with 2D semiconductors (2DSs) can be exploited to endow multi-responsiveness to the exceptional physical properties of 2DSs. In this study, a spiropyran-molybdenum disulfide (MoS2) light-switchable bi-functional field-effect transistor is realized. The spiropyran-merocyanine reversible photo-isomerization has been employed to remotely control both the electron transport and wettability of the hybrid structure. This manipulation is instrumental for tuning the sensitivity in humidity sensing. The hybrid organic/inorganic heterostructure is subjected to humidity testing, demonstrating its ability to accurately monitor relative humidity (RH) across a range of 10%-75%. The electrical output shows good sensitivity of 1.0% · (%) RH-1. The light-controlled modulation of the sensitivity in chemical sensors can significantly improve their selectivity, versatility, and overall performance in chemical sensing.

A Universal Strategy for Constructing Hydrogel Assemblies Enabled by PAA Hydrogel Adhesive.

Hydrogel is a significant type of building block for constructing macroscopic assemblies, the construction of which usually entails the incorporation of supramolecular groups. However, supramolecular group recognition is specific and only suitable for assembling two particular modified hydrogels, but not a versatile strategy. Herein, a universal strategy without modification process is proposed using polyacrylic acid (PAA) hydrogel as the adhesive layer to assemble different kinds of hydrogels. Furthermore, hydrogel assemblies with various shapes and multi-stimuli responsiveness are constructed by assembling different stimuli-responsive hydrogels with PAA hydrogel. Therefore, hydrogel assemblies are able to complete bending motions upon applying corresponding stimuli. This strategy provides a universal approach for constructing hydrogel assemblies, and also shows the potential for developing soft robots with versatile functions.

Constructing 2D Phthalocyanine Covalent Organic Framework with Enhanced Stability and Conductivity via Interlayer Hydrogen Bonding as Electrocatalyst for CO2 Reduction.

Fabricating COFs-based electrocatalysts with high stability and conductivity still remains a great challenge. Herein, 2D polyimide-linked phthalocyanine COF (denoted as NiPc-OH-COF) is constructed via solvothermal reaction between tetraanhydrides of 2,3,9,10,16,17,23,24-octacarboxyphthalocyaninato nickel(II) and 2,5-diamino-1,4-benzenediol (DB) with other two analogous 2D COFs (denoted as NiPc-OMe-COF and NiPc-H-COF) synthesized for reference. In comparison with NiPc-OMe-COF and NiPc-H-COF, NiPc-OH-COF exhibits enhanced stability, particularly in strong NaOH solvent and high conductivity of 1.5 × 10-3 S m-1 due to the incorporation of additional strong interlayer hydrogen bonding interaction between the O-H of DB and the hydroxy "O" atom of DB in adjacent layers. This in turn endows the NiPc-OH-COF electrode with ultrahigh CO2-to-CO faradaic efficiency (almost 100%) in a wide potential range from -0.7 to -1.1 V versus reversible hydrogen electrode (RHE), a large partial CO current density of -39.2 mA cm-2 at -1.1 V versus RHE, and high turnover number as well as turnover frequency, amounting to 45 000 and 0.76 S-1 at -0.80 V versus RHE during 12 h lasting measurement.

Hydrophilic 1T-WS2 Nanosheet Arrays toward Conductive Textiles for High-Efficient and Continuous Hydroelectric Generation and Storage.

Flexible hydroelectric generators (HEGs) are promising self-powered devices that spontaneously derive electrical power from moisture. However, achieving the desired compatibility between a continuous operating voltage and superior current density remains a significant challenge. Herein, a textile-based van der Waals heterostructure is rationally designed between conductive 1T phase tungsten disulfide@carbonized silk (1T-WS2@CSilk) and carbon black@cotton (CB@Cotton) fabrics with an asymmetric distribution of oxygen-containing functional groups, which enhances the proton concentration gradients toward high-performance wearable HEGs. The vertically staggered 1T-WS2 nanosheet arrays on the CSilk fabric provide abundant hydrophilic nanochannels for rapid carrier transport. Furthermore, the moisture-induced primary battery formed between the active aluminum (Al) electrode and the conductive textiles introduces the desired electric field to facilitate charge separation and compensate for the decreased streaming potential. These devices exhibit a power density of 21.6 µW cm-2, an open-circuit voltage (Voc) of 0.65 V sustained for over 10 000 s, and a current density of 0.17 mA cm-2. This performance makes them capable of supplying power to commercial electronics and human respiratory monitoring. This study presents a promising strategy for the refined design of wearable electronics.

Highly Emissive Lanthanide-Based 0D Metal Halide Nanocrystals for Efficient Ultraviolet Photodetector.

Recently, lanthanide-based 0D metal halides have attracted considerable attention for their applications in X-ray imaging, light-emitting diodes (LEDs), sensors, and photodetectors. Herein, lead-free 0D gadolinium-alloyed cesium cerium chloride (Gd3+-alloyed Cs3CeCl6) nanocrystals (NCs) are introduced as promising materials for optoelectronic application owing to their unique optical properties. The incorporation of Gd3+ in Cs3CeCl6 (CCC) NCs is proposed to increase the photoluminescence quantum yield (PLQY) from 57% to 96%, along with significantly enhanced phase and chemical stability. The structural analysis is performed by density functional theory (DFT) to confirm the effect of Gd3+ in Cs3Ce1- xGdxCl6 (CCGC) alloy system. Moreover, the CCGC NCs are applied as the active layer in UVPDs with different Gd3+ concentration. The excellent device performance is shown at 20% of Gd3+ in CCGC NCs with high detectivity (7.938 × 1011 Jones) and responsivity (0.195 A W-1) at -0.1 V at 310 nm. This study paves the way for the development of lanthanide-based metal halide NCs for next-generation UVPDs and other optoelectronic applications.

A higher-yield hybrid rice is achieved by assimilating a dominant heterotic gene in inbred parental lines.

The exploitation of heterosis to integrate parental advantages is one of the fastest and most efficient ways of rice breeding. The genomic architecture of heterosis suggests that the grain yield is strongly correlated with the accumulation of numerous rare superior alleles with positive dominance. However, the improvements in yield of hybrid rice have shown a slowdown or even plateaued due to the limited availability of complementary superior alleles. In this study, we achieved a considerable increase in grain yield of restorer lines by inducing an alternative splicing event in a heterosis gene OsMADS1 through CRISPR-Cas9, which accounted for approximately 34.1%-47.5% of yield advantage over their corresponding inbred rice cultivars. To achieve a higher yield in hybrid rice, we crossed the gene-edited restorer parents harbouring OsMADS1GW3p6 with the sterile lines to develop new rice hybrids. In two-line hybrid rice Guang-liang-you 676 (GLY676), the yield of modified hybrids carrying the homozygous heterosis gene OsMADS1GW3p6 significantly exceeded that of the original hybrids with heterozygous OsMADS1. Similarly, the gene-modified F1 hybrids with heterozygous OsMADS1GW3p6 increased grain yield by over 3.4% compared to the three-line hybrid rice Quan-you-si-miao (QYSM) with the homozygous genotype of OsMADS1. Our study highlighted the great potential in increasing the grain yield of hybrid rice by pyramiding a single heterosis gene via CRISPR-Cas9. Furthermore, these results demonstrated that the incomplete dominance of heterosis genes played a major role in yield-related heterosis and provided a promising strategy for breeding higher-yielding rice varieties above what is currently achievable.

Enhanced efficacy of glycoengineered rice cell-produced trastuzumab.

For several decades, a plant-based expression system has been proposed as an alternative platform for the production of biopharmaceuticals including therapeutic monoclonal antibodies (mAbs), but the immunogenicity concerns associated with plant-specific N-glycans attached in plant-based biopharmaceuticals has not been completely solved. To eliminate all plant-specific N-glycan structure, eight genes involved in plant-specific N-glycosylation were mutated in rice (Oryza sativa) using the CRISPR/Cas9 system. The glycoengineered cell lines, PhytoRice®, contained a predominant GnGn (G0) glycoform. The gene for codon-optimized trastuzumab (TMab) was then introduced into PhytoRice® through Agrobacterium co-cultivation. Selected cell lines were suspension cultured, and TMab secreted from cells was purified from the cultured media. The amino acid sequence of the TMab produced by PhytoRice® (P-TMab) was identical to that of TMab. The inhibitory effect of P-TMab on the proliferation of the BT-474 cancer cell line was significantly enhanced at concentrations above 1 µg/mL (****P < 0.0001). P-TMab bound to a FcγRIIIa variant, FcγRIIIa-F158, more than 2.7 times more effectively than TMab. The ADCC efficacy of P-TMab against Jurkat cells was 2.6 times higher than that of TMab in an in vitro ADCC assay. Furthermore, P-TMab demonstrated efficient tumour uptake with less liver uptake compared to TMab in a xenograft assay using the BT-474 mouse model. These results suggest that the glycoengineered PhytoRice® could be an alternative platform for mAb production compared to current CHO cells, and P-TMab has a novel and enhanced efficacy compared to TMab.

Functional diversity of oxidosqualene cyclases in genus Oryza.

Triterpene skeletons, catalyzing by 2,3-oxidosqualene cyclases (OSCs), are essential for synthesis of steroids and triterpenoids. In japonica rice cultivars Zhonghua11, a total of 12 OsOSCs have been found. While the catalytic functions of OsOSC1, 3, 4, 9, and 10 remain unclear, the functions of the other OsOSCs have been well studied. In this study, we conducted a comprehensive analysis of 12 OSC genes within genus Oryza with the aid of 63 genomes from cultivated and wild rice. We found that OSC genes are relatively conserved within genus Oryza with a few exceptions. Collinearity analysis further suggested that, throughout the evolutionary history of genus Oryza, the OSC genes have not undergone significant rearrangements or losses. Further functional analysis of 5 uncharacterized OSCs revealed that OsOSC10 was a friedelin synthase, which affected the development of rice grains. Additionally, the reconstructed ancestral sequences of Oryza OSC3 and Oryza OSC9 had lupeol synthase and poaceatapetol synthase activity, respectively. The discovery of friedelin synthase in rice unlocks a new catalytic path and biological function of OsOSC10. The pan-genome analysis of OSCs within genus Oryza gives insights into the evolutionary trajectory and products diversity of Oryza OSCs.