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Grain chalkiness is an important index of rice appearance quality and is negatively associated with rice processing and eating quality. However, the genetic mechanism underlying chalkiness formation is largely unknown. To identify the genetic basis of chalkiness, 410 recombinant inbred lines (RILs) derived from two representative indica rice varieties, Shuhui498 (R498) and Yihui3551 (R3551), were used to discover quantitative trait loci (QTLs). The two parental lines and RILs were grown in three locations in China under three controlled fertilizer application levels. Analyses indicated that chalkiness was significantly affected by genotype, the environment, and the interaction between the two, and that heritability was high. Several QTLs were isolated, including the two stable QTLs qCGP6 and qCGP8. Fine mapping and candidate gene verification of qCGP6 showed that Wx may play a key role in chalkiness formation. Chromosomal segment substitution lines (CSSLs) and near-isogenic lines (NILs) carrying the Wxa or Wxin allele produced more chalky grain than the R498 parent. A similar result was also observed in the 3611 background. Notably, the effect of the Wx genotype on rice chalkiness was shown to be dependent on environmental conditions, and Wx alleles exhibited different sensitivities to shading treatment. Using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9), the Wxa promoter region was successfully edited; down-regulating Wx alleviates chalkiness formation in NILR498-Wxa. This study developed a new strategy for synergistic improvement of eating and appearance qualities in rice, and created a novel Wx allele with great potential in breeding applications.

KEY MESSAGE: qGSN5, a novel quantitative trait locus coordinating grain size and grain number in rice, was fine-mapped to an 85.60-kb region. GS3 may be a suppressor of qGSN5. Grain size and grain number are two factors that directly determine rice grain yield; however, the underlying genetic mechanisms are complicated and remain largely unclear. In this study, a chromosome segment substitution line (CSSL), CSSL28, which showed increased grain size and decreased grain number per panicle, was identified in a set of CSSLs derived from a cross between 93-11 (recipient) and Nipponbare (donor). Four substitution segments were identified in CSSL28, and the substitution segment located on chromosome 5 was responsible for the phenotypes of CSSL28. Thus, we defined this quantitative trait locus (QTL) as grain size and grain number 5 (qGSN5). Cytological and quantitative PCR analysis showed that qGSN5 regulates the development of the spikelet hull by affecting cell proliferation. Genetic analysis showed that qGSN5 is a semi-dominant locus regulating grain size and grain number. Through map-based cloning and overlapping substitution segment analysis, qGSN5 was finally delimited to an 85.60-kb region. Based on sequence and quantitative PCR analysis, Os05g47510, which encodes a P-type pentatricopeptide repeat protein, is the most likely candidate gene for qGSN5. Pyramiding analysis showed that the effect of qGSN5 was significantly lower in the presence of a functional GS3 gene, indicating that GS3 may be a suppressor of qGSN5. In addition, we found that qGSN5 could improve the grain shape of hybrid rice. Together, our results lay the foundation for cloning a novel QTL coordinating grain size and grain number in rice and provide a good genetic material for long-grain hybrid rice breeding.

Grain number per panicle (GNP) is a complex trait controlled by quantitative trait loci (QTL), directly determining grain yield in rice. Identifying GNP-associated QTL is desirable for increasing rice yield. A rice chromosome segment substitution line (CSSL), F771, which showed increased panicle length and GNP, was identified in a set of CSSLs derived from a cross between two indica cultivars, R498 (recipient) and WY11327 (donor). Genetic analysis showed that the panicle traits in F771 were semidominant and controlled by multiple QTL. Six QTL were consistently identified by QTL-seq analysis. Among them, the major QTL qPLN10 for panicle length and GNP was localized to a 121-kb interval between markers N802 and N909 on chromosome 10. Based on quantitative real-time PCR and sequence analysis, TAWAWA1 (TAW1), a known regulator of rice inflorescence architecture, was identified as the candidate gene for qPLN10. A near-isogenic line, NIL-TAW1, was developed to evaluate its effects. In comparison with the recurrent parent R498, NIL-TAW1 showed increased panicle length (14.0%), number of secondary branches (20.9%) and GNP (22.0%), and the final grain yield per plant of NIL-TAW1 was increased by 18.6%. Transgenic experiments showed that an appropriate expression level of TAW1 was necessary for panicle development. Haplotype analysis suggested that the favorable F771-type (Hap 13) of TAW1 was introduced from aus accessions and had great potential value in high-yield breeding both in indica and japonica varieties. Our results provide a promising genetic resource for rice grain yield improvement.

Grain shape is a crucial determinant of grain weight and quality and plays a vital role in rice breeding. Although many grain shape-related genes have been reported, the regulatory relationship between them has not been well characterized in rice. In this study, we report the isolation of a short-grain-length mutant called sg5 from the heavy-panicle-type hybrid rice elite restorer line 'ShuhuiR498' (R498) after ethyl methanesulfonate (EMS) treatment. MutMap cloning revealed that SG5 encodes a Myb-like transcription factor. A missense mutation in the first exon of SG5 was found to cause an amino acid change from leucine to proline at position 197 in the mutant SG5 protein. Gene knockout and genetic complementation experiments confirmed that the point mutation in SG5 was responsible for the sg5 mutant phenotype. SG5 is mainly expressed in young panicles and hulls. In addition, the SG5 protein is found in the nucleus and does not affect subcellular localization. Histochemical observation and gene expression analysis indicated that SG5 regulates spikelet hull development by mediating cell expansion. Moreover, the expression levels of BG1, GS2, and DEP1 were reduced in sg5 plants, and dual-luciferase (LUC) assays showed that SG5 can bind to the BG1 gene promoter. The effect of pyramiding sg5 and GS3 suggests that sg5 and GS3 regulate grain length independently. The results of our study show that the missense mutation in sg5 is essential for the molecular function of SG5 and SG5 is involved in regulating cell expansion and expression of grain-shape-related genes to regulate grain length. This work provides new data to help study and understand the molecular function of SG5.

Grain filling is a complex agronomic trait that directly determines grain weight and quality in rice (Oryza sativa). Nevertheless, key factors affecting grain filling remain poorly understood. Here, we identified a grain filling gene, OsPK3, encoding a pyruvate kinase (PK). The loss of function of OsPK3 caused reduced PK activity and Suc translocation defects from source to sink in rice, which led to compromised grain filling. OsPK3 was constitutively expressed but had relatively higher expression levels in leaf and developing caryopsis and specific expression signals in tissues involved in Suc transport and unloading, supporting its biological function in regulation of grain filling by affecting Suc translocation. Subcellular localization analysis of OsPK3 revealed its association with mitochondria, and OsPK3 physically interacted and formed heterodimers in vivo with two other PK isozymes, OsPK1 and OsPK4. Both OsPK1 and OsPK4 localized to the mitochondria and cytosol and were recruited to the mitochondria by OsPK3. Despite their high sequence similarity, OsPK1 and OsPK4 had distinct expression patterns. As observed for ospk3, disruption of OsPK1 caused pleiotropic defects, while OsPK4 loss of function led to severely chalky grains without other obvious defects. Collectively, we revealed that two mitochondria-associated pyruvate kinase complexes, OsPK3-OsPK1/OsPK4, are involved in regulation of grain filling by stage-specific fine-tuning of Suc translocation.

Significant achievements have been made in breeding programs for the heavy panicle-type (HPT) rice (Oryza sativa) in Southwest China. The HPT varieties now exhibit excellent lodging resistance, allowing them to overcome the greater pressures caused by heavy panicles. However, the genetic mechanism of this lodging resistance remains elusive. Here, we isolated a major quantitative trait locus, Panicle Neck Diameter 1 (PND1), and identified the causal gene as GRAIN NUMBER 1A/CYTOKININ OXIDASE 2 (Gn1A/OsCKX2). The null gn1a allele from rice line R498 (gn1a R498 ) improved lodging resistance through increasing the culm diameter and promoting crown root development. Loss of function of Gn1a/OsCKX2 led to cytokinin accumulation in the crown root tip and accelerated the development of adventitious roots. Gene pyramiding between the null gn1a R498 allele with two gain-of-function alleles, STRONG CULM 2 (SCM2) and SCM3, further improved lodging resistance. Moreover, Gn1a/OsCKX2 had minimal influence on overall rice quality. Our research thus highlights the distinct genetic components of lodging resistance of HPT varieties and provides a strategy for tailor-made crop improvement of both yield and lodging resistance in rice. This article is protected by copyright. All rights reserved.

A leaf-to-caryopsis abscisic acid transport mechanism ensures normal seed development in response to variable temperatures., Long-distance transport of the phytohormone abscisic acid (ABA) has been studied for ~50 years, yet its mechanistic basis and biological significance remain very poorly understood. Here, we show that leaf-derived ABA controls rice seed development in a temperature-dependent manner and is regulated by defective grain-filling 1 (DG1), a multidrug and toxic compound extrusion transporter that effluxes ABA at nodes and rachilla. Specifically, ABA is biosynthesized in both WT and dg1 leaves, but only WT caryopses accumulate leaf-derived ABA. Our demonstration that leaf-derived ABA activates starch synthesis genes explains the incompletely filled and floury seed phenotypes in dg1. Both the DG1-mediated long-distance ABA transport efficiency and grain-filling phenotypes are temperature sensitive. Moreover, we extended these mechanistic insights to other cereals by observing similar grain-filling defects in a maize DG1 ortholog mutant. Our study demonstrates that rice uses a leaf-to-caryopsis ABA transport–based mechanism to ensure normal seed development in response to variable temperatures.

Background: The mesocotyl length of rice seedling is a complex trait associated with the ability of seedling emerging and controlled by quantitative trait loci (QTLs). Genome-wide association study (GWAS) is a high-through QTLs mapping method and widely used to identify QTLs in the field of plant genetics.Results: A series of rice accessions including 290 varieties from all over the world, which harbored widely genetic background, were finished whole genome re-sequencing and investigated the mesocotyl length of rice seedlings in three different sowing depths (0cm, 4cm and 6cm). The analysis of coefficient of variation (CV) showed that the rice mesocotyl length variability in the three different treatments with 0cm, 4cm and 6cm sand culture are 114.43%, 146.65% and 152.55%, respectively. The mesocotyl length of the three groups are positively correlated with each other, indicating that the variation trend is consistent despite the differences in experimental treatment conditions, which led to the different performances of the mesocotyl lengths of the same accession. After GWAS, we found There are 922 single nucleotide polymorphism (SNP) makers associated with rice seedling mesocotyl length across 20 QTL regions and covered 1246 genes.Conclusions: In this study, we found that there are 922 SNP makers associated with rice seedling mesocotyl length across 20 QTL regions and covered 1246 genes. And we detected 23 candidate genes which maybe have effect to the mesocotyl length of rice seedling at different sowing depths

ALK is the key gene of controlling rice gelatinization temperature (GT), and at least three ALK alleles are thought to be responsible for the diversity of GT among rice cultivars. But whether the sequence polymorphism of the promoter region also associated with GT is not clearly studied. In this study, we analyzed sequence variation in the promoter region of ALK and mainly two types of promoter were identified. ALK type I promoter prevails among thousands of indica and japonica rice varieties, while ALK type II promoter predominates over varieties from Aus/boro and Basmati ecotypes. Phenotypic analysis and quality characterization of CSSLs with different alleles of ALK and promoter activity assays revealed that type II promoter downregulates the expression level of ALK and subsequently, negatively affects ASV values. ALKQ1882, owning type II promoter region and TT SNP at 4329/4330 bp of ALK gene, was identified as a rare and elite ALK allele for rice quality improvement. Transcriptional detection in hybrid triploid endosperm revealed that ALK is simultaneously expressed by gene copes from both parents, the ASV of hybrid rice varieties can be estimated through the genotypes of two parents. More importantly, a new dCAPS marker was developed to discriminate the functional SNP of TT at 4329/4330 bp, which is an efficient tool for improving the grain quality with high accuracy on low testing cost.

Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research.

Broad-spectrum resistance is highly preferred in crop breeding programmes. Previously, we have reported the identification of the broad-spectrum resistance-Digu 1 (bsr-d1) allele from rice Digu. The bsr-d1 allele prevents activation of Bsr-d1 expression by Magnaporthe oryzae infection and degradation of H2 O2 by peroxidases, leading to resistance to M. oryzae. However, it remains unknown whether defence pathways other than H2 O2 burst and peroxidases contribute to the bsr-d1-mediated immunity. Blast resistance was determined in rice leaves by spray and punch inoculations. Target genes of OsMYB30 were identified by one-hybrid assays in yeast and electrophoretic mobility shift assay. Lignin content was measured by phloroglucinol-HCl staining, and acetyl bromide and thioacidolysis methods. Here, we report the involvement of the OsMYB30 gene in bsr-d1-mediated blast resistance. Expression of OsMYB30 was induced during M. oryzae infection or when Bsr-d1 was knocked out or downregulated, as occurs in bsr-d1 plants upon infection. We further found that OsMYB30 bound to and activated the promoters of 4-coumarate:coenzyme A ligase genes (Os4CL3 and Os4CL5) resulting in accumulation of lignin subunits G and S. This action led to obvious thickening of sclerenchyma cells near the epidermis, inhibiting M. oryzae penetration at the early stage of infection. Our study revealed novel components required for bsr-d1-mediated resistance and penetration-dependent immunity, and advanced our understanding of broad-spectrum disease resistance.

The extent of structural variants (SVs), in particular copy number variations (CNVs) in plant and animal genomes remains unknown, mainly due to the lack of population-scale truly high-quality genomes. Here, we de novo assembled and annotated 31 gold-standard reference genomes from varieties representing all major cultivated rice subtypes, and accurately detected 107,251 non-redundant SVs affecting 644.91Mbp. A position-resolved pan-genome comprising 66,636 genes enabled our discovery that more than 38% of protein-coding genes in cultivated rice harbor CNVs, a far greater proportion than previous estimate. Illustrating functional consequences of these variations, CNVs of Awn3-1, OsVIL1 and OsMADS18, as well as a 345kb inversion likely contributed to major events in rice evolution, domestication and environmental adaptation. Beyond fully resolving the SVs of cultivated rice and comprehensively cataloguing CNVs among protein-coding genes, our study suggests that SVs-affected genes likely contribute to many mechanisms underlying domestication and phenotypic variation in rice.

In this study, three-dimensional multi-walled carbon nanotubes@g-C3N4@Fe3O4 nanocomposites (3D MWNTs@g-C3N4@Fe3O4 nanocomposites) were prepared and used as a novel magnetic solid phase extraction (MSPE) sorbent for the analysis of 16 polycyclic aromatic hydrocarbons (PAHs). The novel nanocomposites were characterized by scanning electron microscope (SEM), transmission electron microscope (TEM), Fourier-transform infrared spectroscopy (FT-IR), X-ray powder diffraction (XRD), and vibrating sample magnetometer (VSM) methods. To achieve the best extraction efficiency, several experimental parameters, including sorbent amount, extraction time, stirring rate, ionic strength, desorption solvent, desorption volume and desorption time, were optimized. Under the optimized preparation and extraction conditions, the proposed method showed the limits of detection (LODs) for polycyclic aromatic hydrocarbons (PAHs) were found to be in the range of 0.001–0.5 μg L−1, limits of quantification (LOQs) were in the range of 0.005–0.8 μg L−1 and their relative standard deviations (RSDs) were lower than 5.0%. The proposed MSPE method was applied successfully in the analysis of PAHs in rainwater, river water and industrial wastewater samples. The recovery of the PAHs in all samples spiked with 5 g L−1 ranged from 82.4 to 116.9% with RSDs below 9.7%.

Lesion mimic mutants are powerful tools for unveiling the molecular connections between cell death and pathogen resistance. Various proteins responsible for lesion mimics have been identified; however, the mechanisms underlying lesion formation and pathogen resistance are still unknown. Here, we identify a lesion mimic mutant in rice, lesion mimic leaf 1 (lml1). The lml1 mutant exhibited abnormal cell death and resistance to both bacterial blight and rice blast. LML1 is expressed in all types of leaf cells, and encodes a novel eukaryotic release factor 1 (eRF1) protein located in the endoplasmic reticulum. Protein sequences of LML1 orthologs are conserved in yeast, animals and plants. LML1 can partially rescue the growth delay phenotype of the LML1 yeast ortholog mutant, dom34. Both lml1 and mutants of AtLML1 (the LML1 Arabidopsis ortholog) exhibited a growth delay phenotype like dom34. This indicates that LML1 and its orthologs are functionally conserved. LML1 forms a functional complex with a eukaryotic elongation factor 1A (eEF1A)-like protein, SPL33/LMM5.1, whose mutant phenotype was similar to the lml1 phenotype. This complex was conserved between rice and yeast. Our work provides new insight into understanding the mechanism of cell death and pathogen resistance, and also lays a good foundation for studying the fundamental molecular function of Pelota/DOM34 and its orthologs in plants.

Significance Crops carrying broad-spectrum resistance loci provide an effective strategy for controlling infectious disease. Despite their importance, few broad-spectrum resistance loci have been reported, and the underlying mechanisms controlling the trait remain largely unknown. This report describes the identification of a gene, called “bsr-k1,” conferring broad-spectrum resistance and demonstrates that the encoded protein regulates immunity-related genes. Loss of function of BSR-K1 in rice leads to enhanced broad-spectrum resistance to two serious rice diseases with no major penalty on yield. This report provides insights into broad-spectrum resistance and offers an efficient strategy to breeding durably resistant rice., Crops carrying broad-spectrum resistance loci provide an effective strategy for controlling infectious disease because these loci typically confer resistance to diverse races of a pathogen or even multiple species of pathogens. Despite their importance, only a few crop broad-spectrum resistance loci have been reported. Here, we report the identification and characterization of the rice bsr-k1 (broad-spectrum resistance Kitaake-1) mutant, which confers broad-spectrum resistance against Magnaporthe oryzae and Xanthomonas oryzae pv oryzae with no major penalty on key agronomic traits. Map-based cloning reveals that Bsr-k1 encodes a tetratricopeptide repeats (TPRs)-containing protein, which binds to mRNAs of multiple OsPAL (OsPAL1–7) genes and promotes their turnover. Loss of function of the Bsr-k1 gene leads to accumulation of OsPAL1–7 mRNAs in the bsr-k1 mutant. Furthermore, overexpression of OsPAL1 in wild-type rice TP309 confers resistance to M. oryzae, supporting the role of OsPAL1. Our discovery of the bsr-k1 allele constitutes a significant conceptual advancement and provides a valuable tool for breeding broad-spectrum resistant rice.

Strategies to reduce cadmium (Cd) in rice grain, below concentrations that represent serious human health concerns, require that the mechanisms of Cd distribution and accumulation within rice plants be established. Here, a comprehensive hydroponic experiment was performed to investigate the differences in the Cd uptake, chelation and compartmentalization between high (D83B) and low (D62B) Cd-accumulation cultivars contrasting in Cd accumulation in order to establish the roles of these processes in limiting Cd translocation from root to shoot. D83B showed 3-fold higher Cd accumulation in the shoots than the cultivar D62B. However, a short-term Cd uptake experiment showed more Cd uptake by D62B than by D83B. The distribution of Cd in roots and shoots differed significantly. D83B translocated 38% of total Cd taken up to the shoots, whereas D62B retained most of the Cd in the roots. D62B had higher amounts of non-protein thiols (NPTs) and glutathione (GSH) than D83B. The NPT and Cd distribution ratio (CDR) in the anionic form in the roots of D62B increased gradually as Cd concentration increased. In D83B, in contrast, levels of CDR in the cationic form increased significantly from 22.10 to 43.37%, while NPT only increased slightly. Furthermore, the percentage of Cd ions retained in thiol-rich peptides, especially in the HMW complexes, was significantly higher in D62B compared with D83B. However, D83B possessed a greater proportion of potentially mobile (cationic) Cd in the roots and showed superior Cd translocation from root to shoot. Taken as a whole, the results presented in this study revealed that Cd chelation, compartmentalization and adsorption contribute to the Cd retention in roots.

Leaves are the main organs in which photosynthates are produced. Leaf senescence facilitates the translocation of photosynthates and nutrients from source to sink, which is important for plant development and especially for crop yield. However, the molecular mechanism of leaf senescence is unknown. Here, we identified a mutant, yellow leaf and dwarf 1 (yld1), which exhibited decreased plant height and premature leaf senescence. Nitroblue tetrazolium and diamiobenzidine staining analyses revealed that the concentrations of reactive oxygen species were higher in yld1 leaves than in wild type leaves. The photosynthetic pigment contents were significantly decreased in yld1. The yld1 chloroplasts had collapsed and were filled with abnormal starch granules. Combining bulk segregant and MutMap gene mapping approaches, the mutation responsible for the yld1 phenotype was mapped to a 7.3 Mb centromeric region, and three non-synonymous single nucleotide polymorphisms located in three novel genes were identified in this region. The expression patterns of the three candidate genes indicated that LOC_Os06g29380 had the most potential for functional verification. Plant hormone measurements showed that salicylic acid was highly accumulated in yld1 leaves when compared with wild type leaves, and yld1 was more sensitive to salicylic acid than wild type. This work lays the foundation for understanding the molecular regulatory mechanism of leaf senescence, and may reveal new connections among the molecular pathways related to leaf senescence, starch metabolism and salicylic acid signaling.

Novel octahedral structured Fe3O4@SiO2@polydimethylsiloxane magnetic nanoparticles (Fe3O4@SiO2@PDMS MNPs) have been successfully synthesized for the first time. The magnetic nanoparticles (MNPs) were characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, Fourier transform infrared spectrometry and vibrating sample magnetometry. The Fe3O4@SiO2@PDMS MNPs were used as the sorbent for magnetic solid phase extraction (MSPE) to determine benzene, toluene, ethylbenzene and xylenes (BTEX) in water samples. Extraction parameters, the amount of sorbent, the extraction time, the stirring rate, the salt effect, the type of desorption solvent, the volume of desorption solvent and the desorption time were optimized. The optimal extraction conditions were amount of sorbent, 100 mg; extraction time, 15 min; stirring rate, 200 rpm; no salt; desorption solvent, dichloromethane; volume of desorption solvent, 0.5 mL; and desorption time, 1.0 min. Good linearity was observed in the calibration range from 0.05 to 20 μg L−1, and the coefficient of determination (r2) was more than 0.9980. The limits of detection (LODs) and limits of quantitation (LOQs) for BTEX were observed to be 0.002–0.005 μg L−1 and 0.008–0.017 μg L−1, respectively. The intra- and inter-batch relative standard deviations (RSDs) were less than 11.6% and 15.0%, respectively.

Light-emitting electrochemical cell of bithiazole-based material was fabricated by solution processing rendered high external quantum efficiency over 12.8% and luminance of 1.8 104 cd m−2.

Plants that spontaneously produce lesion mimics or spots, without any signs of obvious adversity, such as pesticide and mechanical damage, or pathogen infection, are so-called lesion mimic mutants (lmms). In rice, many lmms exhibit enhanced resistance to pathogens, which provides a unique opportunity to uncover the molecular mechanism underlying lmms. We isolated a rice light-dependent leaf lesion mimic mutant 1 (llm1). Lesion spots appeared in the leaves of the llm1 mutant at the tillering stage. Furthermore, the mutant llm1 had similar agronomic traits to wild type rice. Trypan blue and diamiobenzidine staining analyses revealed that the lesion spot formation on the llm1 mutant was due to programmed cell death and reactive oxygen species. The chloroplasts were severely damaged in the llm1 mutant, suggesting that chloroplast damage was associated with the formation of lesion spots in llm1. More importantly, llm1 exhibited enhanced resistance to bacterial blight pathogens within increased expression of pathogenesis related genes (PRs). Using a map-based cloning approach, we delimited the LLM1 locus to a 121-kb interval between two simple sequence repeat markers, RM17470 and RM17473, on chromosome 4. We sequenced the candidate genes on the interval and found that a base mutation had substituted adenine phosphate for thymine in the last exon of LOC_Os04g52130, which led to an amino acid change (Asp(388) to Val) in the llm1 mutant. Our investigation showed that the putative coproporphyrinogen III oxidase (CPOX) encoded by LOC_Os04g52130 was produced by LLM1 and that amino acid Asp(388) was essential for CPOX function. Our study provides the basis for further investigations into the mechanism underlying lesion mimic initiation associated with LLM1.

Green-revertible albino mutants are important sources for studying chloroplast structure, chloroplast development, chlorophyll biosynthesis, and plant photosynthesis. In the present study, we characterized a green-revertible albino mutant gra ( k ), which was obtained from the tissue-cultured rice Kitaake. The mutant gra ( k ) exhibited albino on its first three leaves. The leaf color started to turn green at the four-leaf stage. The chlorophyll contents were deeply reduced at the seedling stage, and the chloroplast development was delayed in gra ( k ). The green-revertible albino (gra) phenotype of the mutant gra ( k ) was temperature dependent. The main agronomic traits, including plant height, tilling number per plant, seed setting rate, and thousand-grain weight, slightly decreased in gra ( k ) comparing to those in the wild-type Kitaake. Genetic analysis showed that the gra phenotype was controlled by a single recessive nucleic gene. By using 5,168 recessive F 2 individuals derived from the cross of gra ( k ) × Jodan, the locus of the gene Gra ( k ) was delimited in a DNA region of 200 kb between the makers B-31 and P11 on chromosome 5. Sequencing analysis indicated that the three functionally annotated genes, LOC_Os05g23700, LOC_Os05g23720, and LOC_Os05g23740, were all deleted in the 200 kb region in the mutant gra ( k ). Transgenic test revealed that the gra ( k ) plants over-expressing LOC_Os05g23740CDS were restored to normal green as the wild-type Kitaake. Our results proved that the deletion of the DnaK protein gene LOC_Os05g23740 (encoding the chaperon protein OsHsp70CP1) led to the gra phenotype in the mutant gra ( k ).

Image super-resolution is typically explained as converting a low-resolution (LR) image into a high resolution (HR) output. However, previous approaches could be blurry and unrealistic, especially for regions with many details. This paper took advantage of Latent Space Exploration from PULSE and a facial liveliness detection algorithm to receive a more accurate and rational outcome. (Related code can be found on https://github.com/cisgroupb/PULSE with Anti Spoofing-Detection)

Leaf color is directly associated with plant photosynthesis. Here, we have isolated and identified a spontaneous rice mutant named yd1 that has yellowish leaves and dwarf stature. Map-based cloning reveals that YD1 encodes a previously reported kinesin protein from the kinesin-4 subfamily, BC12/GDD1. Arginine-328 is replaced by leucine in yd1, BC12328Leu. YD1 is mainly expressed in leaves and is involved in chlorophyll (Chl) synthesis. The yd1 mutant had less Chl and a reduced and disordered thylakoid ultrastructure. In yd1 plants, Chl biosynthesis and photosynthesis associated gene expression was decreased and Chl degradation gene expression was increased, thereby leading to a reduced photosynthesis rate and grain yield. In this study we reveal that the novel BC12328Leu allele of BC12 modulated plant leaf color in yd1 plants, which has not been previously reported in studies of BC12/GDD1/MTD1/SRG1. Gene knockout results indicated that YD1 regulates leaf color in the indica rice background, but not in the japonica rice background. Our study provides new insights into molecular regulation of rice growth by BC12/GDD1 in different genetic backgrounds.

Appearance quality is an important determinant of rice quality. Many genes that affect grain appearance quality have been identified, but the regulatory mechanisms that contribute to this trait remain unclear. Here, two grains with chalkiness (gwc1) mutants, gwc1-1 and gwc1-2, were identified from an EMS-mutagenized population of indica rice cultivar Shuhui498 (R498). The gwc1 mutants had poor grain appearance quality consistent with the measured values for the percentage of grains with chalkiness, square of chalky endosperm, the total starch, amylose and sucrose contents. Milling quality and grain size were also affected in the gwc1 mutants. The gwc1-1 and gwc1-2 were found to be loss-of-function allelic mutants. GWC1 was mapped to the long arm of rice chromosome 8 using the MutMap strategy and incorrectly annotated in the reference genome for Nipponbare (MSU). The GWC1 gene corresponds to the WTG1/OsOTUB1 gene, which encodes an otubain-like protease with deubiquitinating activity that is homologous to human OTUB1. GWC1 transcripts accumulated to high levels in early endosperm after fertilization and developing inflorescences, and GWC1-green fluorescent protein (GFP) signal was detected in the nucleus and cytoplasm. GWC1 is likely to regulate grain appearance quality through genes involved in sucrose metabolism and starch biosynthesis. Overall, the present findings reveal that GWC1 is important for grain quality and yield due to its effects on grain chalkiness and size.

Retraction of ‘Facile preparation of bithiazole-based material for inkjet printed light-emitting electrochemical cell’ by Jingpei Huo et al., RSC Adv., 2019, 9, 6163–6168.

Grain weight and grain number are two important traits directly determining grain yield in rice. To date, a lot of genes related to grain weight and grain number have been identified; however, the regulatory mechanism underlying these genes remains largely unknown. In this study, we studied the biological function of OsSPL18 during grain and panicle development in rice. Knockout (KO) mutants of OsSPL18 exhibited reduced grain width and thickness, panicle length and grain number, but increased tiller number. Cytological analysis showed that OsSPL18 regulates the development of spikelet hulls by affecting cell proliferation. qRT-PCR and GUS staining analyses showed that OsSPL18 was highly expressed in developing young panicles and young spikelet hulls, in agreement with its function in regulating grain and panicle development. Transcriptional activation experiments indicated that OsSPL18 is a functional transcription factor with activation domains in both the N-terminus and C-terminus, and both activation domains are indispensable for its biological functions. Quantitative expression analysis showed that DEP1, a major grain number regulator, was significantly down-regulated in OsSPL18 KO lines. Both yeast one-hybrid and dual-luciferase (LUC) assays showed that OsSPL18 could bind to the DEP1 promoter, suggesting that OsSPL18 regulates panicle development by positively regulating the expression of DEP1. Sequence analysis showed that OsSPL18 contains the OsmiR156k complementary sequence in the third exon; 5' RLM-RACE experiments indicated that OsSPL18 could be cleaved by OsmiR156k. Taken together, our results uncovered a new OsmiR156k-OsSPL18-DEP1 pathway regulating grain number in rice.

Autophagy is essential for appressorium-mediated plant infection by Magnaporthe oryzae, the causal agent of rice blast disease and a major threat to global food security. The regulatory mechanism of pathogenicity-associated autophagy, however, remains largely unknown. Here, we report the identification and functional characterization of a plausible ortholog of yeast SNT2 in M. oryzae, which we term MoSNT2. Deletion mutants of MoSNT2 are compromised in autophagy homeostasis and display severe defects in autophagy-dependent fungal cell death and pathogenicity. These mutants are also impaired in infection structure development, conidiation, oxidative stress tolerance and cell wall integrity. MoSnt2 recognizes histone H3 acetylation through its PHD1 domain and thereby recruits the histone deacetylase complex, resulting in deacetylation of H3. MoSnt2 binds to promoters of autophagy genes MoATG6, 15, 16, and 22 to regulate their expression. In addition, MoTor controls MoSNT2 expression to regulate MoTor signaling which leads to autophagy and rice infection. Our study provides evidence of a direct link between MoSnt2 and MoTor signaling and defines a novel epigenetic mechanism by which MoSNT2 regulates infection-associated autophagy and plant infection by the rice blast fungus. Abbreviations: M. oryzae: Magnaporthe oryzae; S. cerevisiae: Saccharomyces cerevisiae; F. oxysporum: Fusarium oxysporum; U. maydis: Ustilago maydis; Compl.: complemented strains of ΔMosnt2 expressing MoSNT2-GFP; ATG: autophagy-related; HDAC: histone deacetylase complex; Tor: target of rapamycin kinase; MTOR: mechanistic target of rapamycin kinase in mammals; MoSnt2: DNA binding SaNT domain protein in M. oryzae; MoTor: target of rapamycin kinase in M. oryzae; MoAtg8: autophagy-related protein 8 in M. oryzae; MoHos2: hda one similar protein in M. oryzae; MoeIf4G: eukaryotic translation initiation factor 4 G in M. oryzae; MoRs2: ribosomal protein S2 in M. oryzae; MoRs3: ribosomal protein S3 in M. oryzae; MoIcl1: isocitrate lyase in M. oryzae; MoSet1: histone H3K4 methyltransferase in M. oryzae; Asd4: ascus development 4; Abl1: AMP-activated protein kinase β subunit-like protein; Tig1: TBL1-like gene required for invasive growth; Rpd3: reduced potassium dependency; KAT8: lysine (K) acetyltransferase 8; PHD: plant homeodomain; ELM2: Egl-27 and MTA1 homology 2; GFP: green fluorescent protein; YFP: yellow fluorescent protein; YFP(CTF): C-terminal fragment of YFP; YFP(NTF): N-terminal fragment of YFP; GST: glutathione S-transferase; bp: base pairs; DEGs: differentially expressed genes; CM: complete medium; MM-N: minimum medium minus nitrogen; CFW: calcofluor white; CR: congo red; DAPI: 4ʹ, 6-diamidino-2-phenylindole; BiFC: bimolecular fluorescence complementation; RT: reverse transcription; PCR: polymerase chain reaction; qPCR: quantitative polymerase chain reaction; RNAi: RNA interference; ChIP: chromatin immunoprecipitation

Receptor-like cytoplasmic kinases (RLCKs) belong to a large subgroup of kinases that play pivotal roles in plant development and in protecting plants from various stresses. Here, we report the isolation and characterization of rice OsRLCK102, from the OsRLCK VII subgroup. Silencing of OsRLCK102 compromised receptor kinase XA21-mediated resistance to Xanthomonas oryzae pv. oryzae (Xoo) but did not affect plant basal resistance to Xoo or Magnaporthe oryzae (M. oryzae). Plants with silenced OsRLCK102 exhibit architecture alterations, including reduced plant height, enlarged angle of the lamina joint, decreased rates of seed setting and enhanced sensitivity to hormone brassinolide (BR). Collectively, our study reveals that OsRLCK102 positively regulates XA21-mediated immunity and negatively regulates rice development through BR signaling in rice.

Summary Rice blast caused by the fungal pathogen Magnaporthe oryzae is one of the most destructive diseases worldwide. Although the rice–M. oryzae interaction has been studied extensively, the early molecular events that occur in rice before full maturation of the appressorium during M. oryzae invasion are unknown. Here, we report a comparative transcriptomics analysis of the durably resistant rice variety Digu and the susceptible rice variety Lijiangxintuanheigu (LTH) in response to infection by M. oryzae (5, 10 and 20 h post-inoculation, prior to full development of the appressorium). We found that the transcriptional responses differed significantly between these two rice varieties. Gene ontology and pathway analyses revealed that many biological processes, including extracellular recognition and biosynthesis of antioxidants, terpenes and hormones, were specifically activated in Digu shortly after infection. Forty-eight genes encoding receptor kinases (RKs) were significantly differentially regulated by M. oryzae infection in Digu. One of these genes, LOC_Os08g10300, encoding a leucine-rich repeat RK from the LRR VIII-2 subfamily, conferred enhanced resistance to M. oryzae when overexpressed in rice. Our study reveals that a multitude of molecular events occur in the durably resistant rice Digu before the full maturation of the appressorium after M. oryzae infection and that membrane-associated RKs play important roles in the early response.

Morphology of wild type (R498) and sg2 mutant. Figure S2. Identification of the causal SNP of the small grain (sg2) mutant using MutMap approach. Figure S3. Linkage analysis of 08sg2. Figure S4. The 08sg2 mutant exhibited slightly shorter plant height because of the reduced panicle and the uppermost internode. Figure S5. Effect of 08SG2 on endosperm size and grain filling. Figure S6. Comparisons of transcripts of genes determining panicle branching in R498 and 08sg2. Figure S7. Comparisons of transcripts of genes determining grain size in R498 and 08sg2. Figure S8. Comparisons of phenotypes of wild type (WT, Nipponbare) and knock out (KO) mutants at reproductive stage. Figure S9. Data statistics of the other agronomic traits in R498 and 08sg2, the wild type (WT) and knock-out (KO) mutants. Figure S10. The expression pattern of 08SG2/OsBAK1 in different tissues. Figure S11. Sequence alignment of 08SG2/OsBAK1 and its orthologs in plants. Figure S12. Phylogenetic and protein similarity analysis of 08SG2/OsBAK1 orthologs in plants. Figure S13. The donor parent of GS3 has significantly smaller grain size than R498. Figure S14. 08SG2 and GS3 donâ t interact at transcriptional level. Table S1. Agronomic traits of R498 and sg2. Table S2. A cluster of three SNPs with SNP index of 1 on chromosome 8 (PPTX 2792Â kb)

Correction for ‘Facile preparation of bithiazole-based material for inkjet printed light-emitting electrochemical cell’ by Jingpei Huo et al., RSC Adv., 2019, 9, 6163–6168.

Background: Organ size is determined by the number and size of cells, which are controlled by cell proliferation and cell expansion. Organ size in rice plays a crucial role in determination of rice yield. Cadmium (Cd), one of the major environmental pollutants, is harmful to human health. Cd-polluted rice grains have been a major source of human Cd-intake, thus reducing Cd-uptake into rice grains isimportant. Strigolactone (SL), a hormone, has been well-studied in terms of regulating plant architecture and in its signal perception, but its biological roles in cell proliferation, cell expansion and Cd-uptake have not been uncovered.Methods: We comprehensively investigated agronomic traits and cell size between WT and so1 . We treated WT and so1 with Cd, and analyzed Cd content in rice grain using inductively coupled plasma massspectrometry (ICP-MS). We used bulk segregation analysis for SO1 mapping, and analyzed sequences surrounding SO1 in rufipogo , indica, japonica and intermedia varieties of rice. Results: We identified a spontaneous rice mutant, small organs 1 ( so1) , which exhibited small organs,such as small leaves, panicles and grains. Cytological analysis indicated that the small organs of so1 were due to both impaired cell proliferation and expansion. We found that so1 grains highly accumulated Cd after Cd treatment. In the so1 mutant, an 8bp insertion resulting in a premature stop codon was identified in LOC_Os04g46470 ( High-Tillering Dwarf1 ) which is involved in Strigolactone (SL) synthesis. Because both htd1 and so1 mutants exhibited dwarf and excessive tillers, the 8bp insertion was responsible for the so1 phenotype. SO1/HTD1 was ubiquitously expressed, most highly in stem and sheath. Very few SNP polymorphisms surrounding SO1/HTD1 were identified in japonica group, whereas SNPs were abundant in the rufipogon, indica and intermedia groups.Discussion: Our work showed the novel biological roles of SO1/HTD1 in controlling rice organ size and Cd-uptake, and indicated that the SL signaling pathway is involved in cell proliferation, cell expansion, and Cd-uptake, a role completely different from the previously reported role of HTD1. Therefore, our study is helpful for understanding the molecular functions of SO1/HTD1 and SL during rice development.

Normal uptake, transportation and assimilation of primary nutrients are essential to plant growth. Tracheary elements (TEs) are tissues responsible for the transport of water and minerals and characterized by patterned secondary cell wall (SCW) thickening. Exocysts are involved in the regulation of SCW deposition by mediating the targeted transport of materials and enzymes to specific membrane areas. EXO70s are highly duplicated in plants and provide exocysts with functional specificity. In this study, we report the isolation of a rice mutant rapid leaf senescence2 (rls2) that exhibits dwarfism, ferruginous spotted necrotic leaves, decreased hydraulic transport and disordered primary nutrient assimilation. Histological analysis of rls2-1 mutants has indicated impaired cell expansion, collapsed vascular tissues and irregular SCW deposition. Map-based cloning has revealed that RLS2 encodes OsEXO70A1, which is one of the 47 members of EXO70s in rice. RLS2 was widely expressed and spatially restricted in vascular bundles. Subcellular localization analysis demonstrated that RLS2 was present on both membrane and nuclear regions. Expression analysis revealed that mutations in rls2 triggers transcriptional fluctuation of orthologous EXO70 genes and affects genes involved in primary nutrient absorption and transport. In brief, our study revealed that RLS2 is required for normal vascular bundle differentiation and primary nutrient assimilation.

Electric field modeling of nodular defects is performed to investigate the interaction between defective multilayer coatings and Gaussian profile laser beam. Light-intensity is significantly enhanced as large as six times in areas adjacent to the defect boundary as well as within the defects. Different geometry of defects irradiated by a range of 0–45° incident laser is analyzed. Nodules with large but shallow seed or in the case of 45° oblique incidence tend to have the greatest enhancement effect.

Summary Rice blast caused by the fungal pathogen M agnaporthe oryzae is one of the most destructive diseases worldwide. Although the rice–M . oryzae interaction has been studied extensively, the early molecular events that occur in rice before full maturation of the appressorium during M . oryzae invasion are unknown. Here, we report a comparative transcriptomics analysis of the durably resistant rice variety Digu and the susceptible rice variety Lijiangxintuanheigu (LTH) in response to infection by M . oryzae (5, 10 and 20 h post‐inoculation, prior to full development of the appressorium). We found that the transcriptional responses differed significantly between these two rice varieties. Gene ontology and pathway analyses revealed that many biological processes, including extracellular recognition and biosynthesis of antioxidants, terpenes and hormones, were specifically activated in Digu shortly after infection. Forty‐eight genes encoding receptor kinases (RKs) were significantly differentially regulated by M . oryzae infection in Digu. One of these genes, LOC _Os08g10300, encoding a leucine‐rich repeat RK from the LRR VIII‐2 subfamily, conferred enhanced resistance to M . oryzae when overexpressed in rice. Our study reveals that a multitude of molecular events occur in the durably resistant rice Digu before the full maturation of the appressorium after M . oryzae infection and that membrane‐associated RKs play important roles in the early response.

Summary Rice feeds half the world's population, and rice blast is often a destructive disease that results in significant crop loss. Non-race-specific resistance has been more effective in controlling crop diseases than race-specific resistance because of its broad spectrum and durability. Through a genome-wide association study, we report the identification of a natural allele of a C 2 H 2 -type transcription factor in rice that confers non-race-specific resistance to blast. A survey of 3,000 sequenced rice genomes reveals that this allele exists in 10% of rice, suggesting that this favorable trait has been selected through breeding. This allele causes a single nucleotide change in the promoter of the bsr-d1 gene, which results in reduced expression of the gene through the binding of the repressive MYB transcription factor and, consequently, an inhibition of H 2 O 2 degradation and enhanced disease resistance. Our discovery highlights this novel allele as a strategy for breeding durable resistance in rice.