The wall-associated kinase GWN1 controls grain weight and grain number in rice.

Grain size is a crucial agronomic trait that determines grain weight and final yield. Although several genes have been reported to regulate grain size in rice (Oryza sativa), the function of Wall-Associated Kinase family genes affecting grain size is still largely unknown. In this study, we identified GRAIN WEIGHT AND NUMBER 1 (GWN1) using map-based cloning. GWN1 encodes the OsWAK74 protein kinase, which is conserved in plants. GWN1 negatively regulates grain length and weight by regulating cell proliferation in spikelet hulls. We also found that GWN1 negatively influenced grain number by influencing secondary branch numbers and finally increased plant grain yield. The GWN1 gene was highly expressed in inflorescences and its encoded protein is located at the cell membrane and cell wall. Moreover, we identified three haplotypes of GWN1 in the germplasm. GWN1hap1 showing longer grain, has not been widely utilized in modern rice varieties. In summary, GWN1 played a very important role in regulating grain length, weight and number, thereby exhibiting application potential in molecular breeding for longer grain and higher yield.

Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding.

Upland rice is a distinctive drought-aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought-aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high-quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought-resistant rice and the "blue revolution" in agriculture.

Genome-Wide Association Study Reveals the Genetic Basis of Total Flavonoid Content in Brown Rice.

Flavonoids have anti-inflammatory, antioxidative, and anticarcinogenic effects. Breeding rice varieties rich in flavonoids can prevent chronic diseases such as cancer and cardio-cerebrovascular diseases. However, most of the genes reported are known to regulate flavonoid content in leaves or seedlings. To further elucidate the genetic basis of flavonoid content in rice grains and identify germplasm rich in flavonoids in grains, a set of rice core collections containing 633 accessions from 32 countries was used to determine total flavonoid content (TFC) in brown rice. We identified ten excellent germplasms with TFC exceeding 300 mg/100 g. Using a compressed mixed linear model, a total of 53 quantitative trait loci (QTLs) were detected through a genome-wide association study (GWAS). By combining linkage disequilibrium (LD) analysis, location of significant single nucleotide polymorphisms (SNPs), gene expression, and haplotype analysis, eight candidate genes were identified from two important QTLs (qTFC1-6 and qTFC9-7), among which LOC_Os01g59440 and LOC_Os09g24260 are the most likely candidate genes. We also analyzed the geographic distribution and breeding utilization of favorable haplotypes of the two genes. Our findings provide insights into the genetic basis of TFC in brown rice and could facilitate the breeding of flavonoid-rich varieties, which may be a prevention and adjuvant treatment for cancer and cardio-cerebrovascular diseases.

RRS1 shapes robust root system to enhance drought resistance in rice.

A strong root system facilitates the absorption of water and nutrients from the soil, to improve the growth of crops. However, to date, there are still very few root development regulatory genes that can be used in crop breeding for agriculture. In this study, we cloned a negative regulator gene of root development, Robust Root System 1 (RRS1), which encodes an R2R3-type MYB family transcription factor. RRS1 knockout plants showed enhanced root growth, including longer root length, longer lateral root length, and larger lateral root density. RRS1 represses root development by directly activating the expression of OsIAA3 which is involved in the auxin signaling pathway. A natural variation in the coding region of RRS1 changes the transcriptional activity of its protein. RRS1T allele, originating from wild rice, possibly increases root length by means of weakening regulation of OsIAA3. Knockout of RRS1 enhances drought resistance by promoting water absorption and improving water use efficiency. This study provides a new gene resource for improving root systems and cultivating drought-resistant rice varieties with important values in agricultural applications.

Variations in OsSPL10 confer drought tolerance by directly regulating OsNAC2 expression and ROS production in rice.

Drought is a major factor restricting the production of rice (Oryza sativa L.). The identification of natural variants for drought stress-related genes is an important step toward developing genetically improved rice varieties. Here, we characterized a member of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) family, OsSPL10, as a transcription factor involved in the regulation of drought tolerance in rice. OsSPL10 appears to play a vital role in drought tolerance by controlling reactive oxygen species (ROS) production and stomatal movements. Haplotype and allele frequency analyses of OsSPL10 indicated that most upland rice and improved lowland rice varieties harbor the OsSPL10Hap1 allele, whereas the OsSPL10Hap2 allele was mainly present in lowland and landrace rice varieties. Importantly, we demonstrated that the varieties with the OsSPL10Hap1 allele showed low expression levels of OsSPL10 and its downstream gene, OsNAC2, which decreases the expression of OsAP37 and increases the expression of OsCOX11, thus preventing ROS accumulation and programmed cell death (PCD). Furthermore, the knockdown or knockout of OsSPL10 induced fast stomatal closure and prevented water loss, thereby improving drought tolerance in rice. Based on these observations, we propose that OsSPL10 confers drought tolerance by regulating OsNAC2 expression and that OsSPL10Hap1 could be a valuable haplotype for the genetic improvement of drought tolerance in rice.

Uncovering Hierarchical Regulation among MYB-bHLH-WD40 Proteins and Manipulating Anthocyanin Pigmentation in Rice.

Anthocyanins accumulate in various organs of rice, and the regulatory genes involved in pigmentation of specific organs, such as pericarp, hull, leaf, apiculus, and stigma have been elucidated. However, the corresponding gene for rice culm pigmentation has not been clarified. The well-known MYB-bHLH-WD40 (MBW) complex plays vital role in regulating the anthocyanin biosynthesis pathway in plants. However, the core members of MBW and the hierarchical regulation between these members are not fully elucidated in rice. Here, by map-based cloning, we identified the culm-specific pigmentation gene S1 whose alleles are also known for hull/pericarp pigmentation. We also clarified that one WD40 protein encoding gene, WA1, is indispensable for anthocyanin biosynthesis in rice. In the cascading regulation among MBW members, S1 (bHLH) acts as the master gene by activating the expression of C1 (MYB), and then C1 activates the expression of WA1 (WD40), which is unique in plant species. This enables MBW members to be coordinated in a common way to efficiently regulate anthocyanin biosynthesis genes. Based on these studies, we explored the minimal gene set required for anthocyanin biosynthesis in rice. These findings will help us design new rice varieties with anthocyanin accumulation in specific organs as needed.

Natural variation of DROT1 confers drought adaptation in upland rice.

Upland rice is a distinct ecotype that grows in aerobic environments and tolerates drought stress. However, the genetic basis of its drought resistance is unclear. Here, using an integrative approach combining a genome-wide association study with analyses of introgression lines and transcriptomic profiles, we identify a gene, DROUGHT1 (DROT1), encoding a COBRA-like protein that confers drought resistance in rice. DROT1 is specifically expressed in vascular bundles and is directly repressed by ERF3 and activated by ERF71, both drought-responsive transcription factors. DROT1 improves drought resistance by adjusting cell wall structure by increasing cellulose content and maintaining cellulose crystallinity. A C-to-T single-nucleotide variation in the promoter increases DROT1 expression and drought resistance in upland rice. The potential elite haplotype of DROT1 in upland rice could originate in wild rice (O. rufipogon) and may be beneficial for breeding upland rice varieties.

Genome-Wide Identification of MDH Family Genes and Their Association with Salt Tolerance in Rice.

Malate dehydrogenase (MDH) is widely present in nature and regulates plant growth and development, as well as playing essential roles, especially in abiotic stress responses. Nevertheless, there is no comprehensive knowledge to date on MDH family members in rice. In this study, a total of 12 MDH members in rice were identified through genome-wide analysis and divided into three groups on the basis of their phylogenetic relationship and protein-conserved motifs. Evolutionary analysis showed that MDH proteins from rice, maize and wheat shared a close phylogenetic relationship, and the MDH family was conserved in the long-term process of domestication. We identified two segmental duplication events involving four genes, which could be the major force driving the expansion of the OsMDH family. The expression profile, cis-regulatory elements and qRT-PCR results of these genes revealed that a few OsMDH showed high tissue specificity, almost all of which had stress response elements in the promoter region, and ten MDH members were significantly induced by salt stress. Through gene-based association analysis, we found a significant correlation between salt tolerance at the seedling stage and the genetic variation of OsMDH8.1 and OsMDH12.1. Additionally, we found that the polymorphism in the promoter region of OsMDH8.1 might be related to the salt tolerance of rice. This study aimed to provide valuable information on the functional study of the rice MDH gene family related to salt stress response and revealed that OsMDH8.1 might be an important gene for the cultivar improvement of salt tolerance in rice.

RGN1 controls grain number and shapes panicle architecture in rice.

Yield in rice is determined mainly by panicle architecture. Using map-based cloning, we identified an R2R3 MYB transcription factor REGULATOR OF GRAIN NUMBER1 (RGN1) affecting grain number and panicle architecture. Mutation of RGN1 caused an absence of lateral grains on secondary branches. We demonstrated that RGN1 controls lateral grain formation by regulation of LONELY GUY (LOG) expression, thus controlling grain number and shaping panicle architecture. A novel favourable allele, RGN1C , derived from the Or-I group in wild rice affected panicle architecture by means longer panicles. Identification of RGN1 provides a theoretical basis for understanding the molecular mechanism of lateral grain formation in rice; RGN1 will be an important gene resource for molecular breeding for higher yield.

Efficient Construction of Near-Infrared Absorption Donor-Acceptor Copolymers with and without Pt(II)-Incorporation toward Broadband Nonlinear Optical Materials.

Organic nonlinear optical (NLO) materials have attracted immense scientific interest in various fields. Broadband NLO response extending to near-infrared (NIR) region is extremely important and remains challenging. Herein, two diketopyrrolopyrrole (DPP)-based donor-acceptor (D-A)-type π-conjugated copolymers with and without Pt(II) incorporation are rationally designed and synthesized toward broadband NLO response materials. The broad intramolecular charge transfer (ICT) absorption reaching 1000 nm due to the strong D-A interaction is well demonstrated by photophysical characterizations. The NLO properties of copolymers are studied using Z-scan technology. Owing to their extended π-conjugated D-A systems and near-infrared ICT absorption properties, both copolymers exhibit laser-induced NLO response to nanosecond as well as picosecond laser pulses upon the wavelengths of 532 and 1064 nm. Interestingly, introducing Pt(II) into the copolymer backbone can evidently improve the NLO property or unexpectedly switch the NLO response from saturable absorption to reverse saturable absorption. Meanwhile, both copolymers are successfully employed as optical limiting materials and exhibit broadband optical limiting abilities. Therefore, we present an efficient strategy toward broadband NLO materials, which may significantly facilitate the understanding of organic molecular structure-property relationship and promote their practical application.

New alleles for chlorophyll content and stay-green traits revealed by a genome wide association study in rice (Oryza sativa).

Higher chlorophyll content (CC) and strong stay-green (SG) traits are conducive for improvement of photosynthetic efficiency in plants. Exploration of natural elite alleles for CC and SG, and highly resolved gene haplotypes are beneficial to rational design of breeding for high-photosynthetic efficiency. Phenotypic analysis of 368 rice accessions showed no significant correlation between CC and SG, and higher CC and stronger SG in japonica than in indica. Genome-wide association studies of six indices for CC and SG identified a large number of association signals, among which 14 were identified as pleiotropic regions for CC and SG. Twenty-five known genes and pleiotropic candidate gene OsSG1 accounted for natural variation in CC and SG. Further analysis indicated that 20 large-effect, non-synonymous SNPs within six known genes around GWAS signals and three SNPs in the promoter of OsSG1 could be functional causing significant phenotypic differences between alleles. Superior haplotypes were identified based on these potentially functional SNPs. Population analyses of 368 cultivated accessions and 446 wild accessions based on SNPs within genes for CC and SG suggested that these genes had been subjected to strong positive selection in japonica in the process of spreading from its subtropical origin to the North China temperate zone. Our studies point to important genes that account for natural variation and provide superior haplotypes of possible functional SNPs that will be beneficial in breeding for high-photosynthetic efficiency in rice.

Natural alleles of GLA for grain length and awn development were differently domesticated in rice subspecies japonica and indica.

Rice (Oryza sativa L.) cultivars harbour morphological and physiological traits different from those of wild rice (O. rufipogon Griff.), but the molecular mechanisms underlying domestication remain controversial. Here, we show that awn and long grain traits in the near-isogenic NIL-GLA are separately controlled by variations within the GLA (Grain Length and Awn Development) gene, a new allele of GAD1/RAE2, which encodes one member of the EFPL (epidermal patterning factor-like protein) family. Haplotype analyses and transgenic studies revealed that InDel1 (variation for grain length, VGL) in the promoter region of GLA (GLAVGL ) increases grain length by promoting transcription of GLA. Absence of InDel3 (variation for awn formation, VA) in the coding region (CDS) of GLA (GLAva ) results in short awn or no awn phenotypes. Analyses of minimum spanning trees and introgression regions demonstrated that An-1, an important gene for awn formation, was preferentially domesticated and its mutation to an-1 was followed by GLA and An-2. Gene flow then occurred between the evolved japonica and indica populations. Quality analysis showed that GLA causes poor grain quality. During genetic improvement, awnlessness was selected in ssp. indica, whereas short-grained and awnless phenotypes with good quality were selected in japonica. Our findings facilitate an understanding of rice domestication and provide a favourable allele for rice breeding.

Gnp4/LAX2, a RAWUL protein, interferes with the OsIAA3-OsARF25 interaction to regulate grain length via the auxin signaling pathway in rice.

Grain length is one of the determinants of yield in rice and auxin plays an important role in regulating it by mediating cell growth. Although several genes in the auxin pathway are involved in regulating grain length, the underlying molecular mechanisms remain unclear. In this study we identify a RING-finger and wd40-associated ubiquitin-like (RAWUL) domain-containing protein, Gnp4/LAX2, with a hitherto unknown role in regulation of grain length by its influence on cell expansion. Gnp4/LAX2 is broadly expressed in the plant and subcellular localization analysis shows that it encodes a nuclear protein. Overexpression of Gnp4/LAX2 can significantly increase grain length and thousand-kernel weight. Moreover, Gnp4/LAX2 physically interacts with OsIAA3 and consequently interferes with the OsIAA3-OsARF25 interaction in vitro and in vivo. OsIAA3 RNAi plants consistently exhibit longer grains, while the mutant osarf25 has small grains. In addition, OsARF25 binds to the promoter of OsERF142/SMOS1, a regulator of organ size, and positively regulates its expression. Taken together, the results reveal that Gnp4/LAX2 functions as a regulator of grain length through participation in the OsIAA3-OsARF25-OsERF142 pathway and that it has potential value for molecular breeding in rice.

Highly Efficient Carbon Dots with Reversibly Switchable Green-Red Emissions for Trichromatic White Light-Emitting Diodes.

Carbon dots (CDs) have potentials to be utilized in optoelectronic devices, bioimaging, and photocatalysis. The majority of the current CDs with high quantum yield to date were limited in the blue light emission region. Herein, on the basis of surface electron-state engineering, we report a kind of CDs with reversible switching ability between green and red photoluminescence with a quantum yield (QY) of both up to 80%. Highly efficient green and red solid-state luminescence is realized by doping CDs into a highly transparent matrix of methyltriethoxysilane and 3-triethoxysilylpropylamine to form CDs/gel glasses composites with QYs of 80 and 78%. The CDs/gel glasses show better transmittance in visible light bands and excellent thermal stability. A blue-pumped CDs/gel glasses phosphor-based trichromatic white light-emitting diode (WLED) is realized, whose color rendering index is 92.9. The WLED gets the highest luminous efficiency of 71.75 lm W-1 in CDs-based trichromatic WLEDs. This work opens a door for developing highly efficient green- and red-emissive switching CDs which were used as phosphors for WLEDs and have the tendency for applications in other fields, such as sensing, bioimaging, and photocatalysis.

Alternative splicing of OsLG3b controls grain length and yield in japonica rice.

Grain size, one of the important components determining grain yield in rice, is controlled by the multiple quantitative trait loci (QTLs). Intensive artificial selection for grain size during domestication is evidenced in modern cultivars compared to their wild relatives. Here, we report the molecular cloning and characterization of OsLG3b, a QTL for grain length in tropical japonica rice that encodes MADS-box transcription factor 1 (OsMADS1). Six SNPs in the OsLG3b region led to alternative splicing, which were associated with grain length in an association analysis of candidate region. Quantitative PCR analysis indicated that OsLG3b expression was higher during the panicle and seed development stages. Analysis of haplotypes and introgression regions revealed that the long-grain allele of OsLG3b might have arisen after domestication of tropical japonica and spread to subspecies indica or temperate japonica by natural crossing and artificial selection. OsLG3b is therefore a target of human selection for adaptation to tropical regions during domestication and/or improvement of rice. Phylogenetic analysis and pedigree records showed that OsLG3b had been employed by breeders, but the gene still has much breeding potential for increasing grain length in indica. These findings will not only aid efforts to elucidate the molecular basis of grain development and domestication, but also facilitate the genetic improvement of rice yield.

Ultra-broadband nonlinear optical response of two-dimensional h-BN nanosheets and their hybrid gel glasses.

Hydrophilic hydroxylated hexagonal boron nitride nanosheets (BNNSs), also called 'white graphene', exhibit high water solubility, compatibility, dispersity with physical and/or chemical effects on the gel matrix, and unexpected but outstanding near-infrared adsorption and nonlinear optical limiting properties. These properties mean that hydroxylated BNNSs are suitable for practical applications in solidification and devices. Hydroxylated BNNSs are doped into an organically modified silicate matrix through a facile sol-gel process. The resulting BNNS-organically modified silicate glass hybrids demonstrate various solid structures (glass, coating, and film), good uniformity, thermostability, toughness, and high linear transmittance in the visible and near-infrared regions. Hybrid glasses showed large optical limiting effects and high doping concentrations without the addition of a compatibiliser, and their limiting thresholds and concentration exceed those of the corresponding suspensions by factors of 1.3-2 and 20-130, respectively. The optical limiting performance of BNNSs is almost equal to or may exceed those of graphene oxide and graphene in solutions and doped glasses. The combined mechanisms of nonlinear absorption, refraction, and scattering are deduced. A solid organically modified silicate hybrid transparent system doped with BNNSs is a promising candidate material for optical limiters and nonlinear optical devices. This system could be an efficient solid-state optical limiter in the visible and long-wavelength near-infrared regions (532-2000 nm).

The C-S-A gene system regulates hull pigmentation and reveals evolution of anthocyanin biosynthesis pathway in rice.

Floral organs in rice (Oryza sativa) can be purple, brown, or red in color due to the accumulation of flavonoids, but the molecular mechanism underlying specific organ pigmentation is not clear. Here, we propose a C-S-A gene model for rice hull pigmentation and characterize it through genetic, molecular, and metabolomic approaches. Furthermore, we conducted phylogenetic studies to reveal the evolution of rice color. In this gene system, C1 encodes a R2R3-MYB transcription factor and acts as a color-producing gene, and S1 encodes a bHLH protein that functions in a tissue-specific manner. C1 interacts with S1 and activates expression of A1, which encodes a dihydroflavonol reductase. As a consequence, the hull is purple where functional A1 participation leads to high accumulation of cyanidin 3-O-glucoside. Loss of function of A1 leads to a brown hull color due to accumulation of flavonoids such as hesperetin 5-O-glucoside, rutin, and delphinidin 3-O-rutinoside. This shows a different evolutionary pathway of rice color in japonica and indica, supporting independent origin of cultivars in each subspecies. Our findings provide a complete perspective on the gene regulation network of rice color formation and supply the theoretical basis for extended application of this beneficial trait.

Natural variation in CTB4a enhances rice adaptation to cold habitats.

Low temperature is a major factor limiting rice productivity and geographical distribution. Improved cold tolerance and expanded cultivation to high-altitude or high-latitude regions would help meet growing rice demand. Here we explored a QTL for cold tolerance and cloned the gene, CTB4a (cold tolerance at booting stage), encoding a conserved leucine-rich repeat receptor-like kinase. We show that different CTB4a alleles confer distinct levels of cold tolerance and selection for variation in the CTB4a promoter region has occurred on the basis of environmental temperature. The newly generated cold-tolerant haplotype Tej-Hap-KMXBG was retained by artificial selection during temperate japonica evolution in cold habitats for low-temperature acclimation. Moreover, CTB4a interacts with AtpB, a beta subunit of ATP synthase. Upregulation of CTB4a correlates with increased ATP synthase activity, ATP content, enhanced seed setting and improved yield under cold stress conditions. These findings suggest strategies to improve cold tolerance in crop plants.

Airline Passenger Profiling Based on Fuzzy Deep Machine Learning.

Passenger profiling plays a vital part of commercial aviation security, but classical methods become very inefficient in handling the rapidly increasing amounts of electronic records. This paper proposes a deep learning approach to passenger profiling. The center of our approach is a Pythagorean fuzzy deep Boltzmann machine (PFDBM), whose parameters are expressed by Pythagorean fuzzy numbers such that each neuron can learn how a feature affects the production of the correct output from both the positive and negative sides. We propose a hybrid algorithm combining a gradient-based method and an evolutionary algorithm for training the PFDBM. Based on the novel learning model, we develop a deep neural network (DNN) for classifying normal passengers and potential attackers, and further develop an integrated DNN for identifying group attackers whose individual features are insufficient to reveal the abnormality. Experiments on data sets from Air China show that our approach provides much higher learning ability and classification accuracy than existing profilers. It is expected that the fuzzy deep learning approach can be adapted for a variety of complex pattern analysis tasks.

Structural Minimax Probability Machine.

Minimax probability machine (MPM) is an interesting discriminative classifier based on generative prior knowledge. It can directly estimate the probabilistic accuracy bound by minimizing the maximum probability of misclassification. The structural information of data is an effective way to represent prior knowledge, and has been found to be vital for designing classifiers in real-world problems. However, MPM only considers the prior probability distribution of each class with a given mean and covariance matrix, which does not efficiently exploit the structural information of data. In this paper, we use two finite mixture models to capture the structural information of the data from binary classification. For each subdistribution in a finite mixture model, only its mean and covariance matrix are assumed to be known. Based on the finite mixture models, we propose a structural MPM (SMPM). SMPM can be solved effectively by a sequence of the second-order cone programming problems. Moreover, we extend a linear model of SMPM to a nonlinear model by exploiting kernelization techniques. We also show that the SMPM can be interpreted as a large margin classifier and can be transformed to support vector machine and maxi-min margin machine under certain special conditions. Experimental results on both synthetic and real-world data sets demonstrate the effectiveness of SMPM.