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.

Transition Metal Single-Atom Catalysts for the Electrocatalytic Nitrate Reduction: Mechanism, Synthesis, Characterization, Application, and Prospects.

Excessive accumulation of nitrate in the environment will affect human health. To combat nitrate pollution, chemical, biological, and physical technologies have been developed recently. The researcher favors electrocatalytic reduction nitrate reaction (NO3 RR) because of the low post-treatment cost and simple treatment conditions. Single-atom catalysts (SACs) offer great activity, exceptional selectivity, and enhanced stability in the field of NO3 RR because of their high atomic usage and distinctive structural characteristics. Recently, efficient transition metal-based SACs (TM-SACs) have emerged as promising candidates for NO3 RR. However, the real active sites of TM-SACs applied to NO3 RR and the key factors controlling catalytic performance in the reaction process remain ambiguous. Further understanding of the catalytic mechanism of TM-SACs applied to NO3 RR is of practical significance for exploring the design of stable and efficient SACs. In this review, from experimental and theoretical studies, the reaction mechanism, rate-determining steps, and essential variables affecting activity and selectivity are examined. The performance of SACs in terms of NO3 RR, characterization, and synthesis is then discussed. In order to promote and comprehend NO3 RR on TM-SACs, the design of TM-SACs is finally highlighted, together with the current problems, their remedies, and the way forward.

Natural variation in Tiller Number 1 affects its interaction with TIF1 to regulate tillering in rice.

Tiller number per plant-a cardinal component of ideal plant architecture-affects grain yield potential. Thus, alleles positively affecting tillering must be mined to promote genetic improvement. Here, we report a Tiller Number 1 (TN1) protein harbouring a bromo-adjacent homology domain and RNA recognition motifs, identified through genome-wide association study of tiller numbers. Natural variation in TN1 affects its interaction with TIF1 (TN1 interaction factor 1) to affect DWARF14 expression and negatively regulate tiller number in rice. Further analysis of variations in TN1 among indica genotypes according to geographical distribution revealed that low-tillering varieties with TN1-hapL are concentrated in Southeast Asia and East Asia, whereas high-tillering varieties with TN1-hapH are concentrated in South Asia. Taken together, these results indicate that TN1 is a tillering regulatory factor whose alleles present apparent preferential utilization across geographical regions. Our findings advance the molecular understanding of tiller development.

Parallel Speciation of Wild Rice Associated with Habitat Shifts.

The occurrence of parallel speciation strongly implies the action of natural selection. However, it is unclear how general a phenomena parallel speciation is since it was only shown in a small number of animal species. In particular, the adaptive process and mechanisms underlying the process of parallel speciation remain elusive. Here, we used an integrative approach incorporating population genomics, common garden, and crossing experiments to investigate parallel speciation of the wild rice species Oryza nivara from O. rufipogon. We demonstrated that O. nivara originated multiple times from different O. rufipogon populations and revealed that different O. nivara populations have evolved similar phenotypes under divergent selection, a reflection of recurrent local adaptation of ancient O. rufipogon populations to dry habitats. Almost completed premating isolation was detected between O. nivara and O. rufipogon in the absence of any postmating barriers between and within these species. These results suggest that flowering time is a "magic" trait that contributes to both local adaptation and reproductive isolation in the origin of wild rice species. Our study thus demonstrates a convincing case of parallel ecological speciation as a consequence of adaptation to new environments.

Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice.

BACKGROUND: Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice (Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold. RESULTS: This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44-68.71 million readings were obtained, resulting in the alignment of 29,128 and 30,131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis (WGCNA) revealed Y12-4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice. CONCLUSION: Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.

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.

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.

Simulation Study of Coal Seam Gas Extraction Characteristics Based on Coal Permeability Evolution Model under Thermal Effect.

The permeability evolution law of high temperature and high stress coal seam is determined by the influence of multiphase coexistence and multifield coupling. In an environment greatly affected by disturbance and high temperature, the coal permeability model under the coupling of thermal and mechanical creep is not only a vital framework from which to examine gas migration law in multiphase and multifield coal seams but also an important theoretical foundation for gas control in coal seams. The influence of high-temperature environment on creep deformation and permeability is analyzed by several creep seepage tests under different temperature conditions.A mathematical model for the evolution of coal permeability considering the influence of temperature is established through the theory of matrix-crack interaction based on gas adsorption and desorption and thermal expansion deformation. Based on the permeability model under the coupling of thermal and mechanical creep, the numerical model of gas migration, seepage field, diffusion field, stress field, and temperature field is constructed, and the law of gas migration in coal seam under multifield coupling is explored. The influence law of thermal effect on gas extraction characteristics is analyzed, in which the time-varying mechanism of temperature field, the relationship between creep deformation and temperature and pressure, the influence of creep deformation on permeability, the dynamic distribution of gas pressure, and the change of gas extraction quantity are described in detail. It is concluded that the influence of temperature on permeability is much greater than that of creep deformation and that a high initial coal seam temperature is beneficial to gas extraction. It provides theoretical basis and technical guidance for the study of multifield coupled gas migration and coal seam gas treatment.

Novel PFA-Based Inorganic Three-Phase Foam for Inhibiting Coal Spontaneous Combustion.

Fire accidents caused by coal spontaneous combustion usually lead to a large loss of coal resources and casualties. Not only that, the greenhouse effect is polluted while the environment is polluted. At present, the commonly used fire-extinguishing materials such as water, inhibitors, and organic foams have the disadvantages of poor stability and short fire-extinguishing cycles. It is difficult to effectively suppress coal spontaneous combustion and quickly extinguish the fire for a long time. To suppress the spontaneous combustion of coal, the research team proposed an inorganic three-phase foam with a high foam expansion rate, good cohesiveness, and excellent stability. In the formulation, pulverized fly ash (PFA) is used as the matrix, sodium dodecyl benzene sulfonate (SDBS) and α-olefin sulfonate (AOS) are used as foaming agents, curdlan is used as the foam stabilizer, and sodium silicate is the binder. The compound foaming agent with the best performance is optimized, through the two-group compounding test. The composite foaming agent's optimal compound ratio is SDBS/AOS (3:2). The optimal ratio of inorganic three-phase foam (ITPF) components was obtained through the control variable method experiment. The water-cement ratio is 5:1, the composite foaming agent is 0.2%, the curdlan is 0.5%, and the sodium silicate is 1.6%. In addition, it has been determined by experiments that ITPF has the strongest foaming ability when the pH value is 9 and the temperature is 60 °C. The fire-extinguishing performance of the new material ITPF was investigated by thermogravimetry and coal spontaneous combustion tendency test. It has been observed that the new material has the effect of cooling down and isolating coal from contact with oxygen. The results show that the new material ITPF has the potential to prevent coal spontaneous combustion.

Structure-performance correlation guided cerium-based metal-organic frameworks: Superior adsorbents for fluoride removal in water.

Fluoride in the hydrosphere exceeds the standard, which could be critically hazardous to human health and the natural environment. The adsorption method is a mature and effective way to remove pollutants in water, including fluoride. In this study, we synthesized three kinds of cerium-based metal-organic frameworks (Ce-MOFs) with different structures and properties by modulating the organic ligands (i.e., trimesic acid (BTC), 1,2,4,5-benzenetetracarboxylic acid (PMA), and terephthalic acid (BDC)) via the solvothermal method. The adsorption kinetics of Ce-MOFs on fluoride well fit the pseudo second order model, and their adsorption isotherms also conform to Langmuir isothermal model. The thermodynamic study reveals that the adsorption process is a spontaneous endothermic reaction. The maximum saturated adsorption capacities of Ce-BTC, Ce-PMA, and Ce-BDC are 70.7, 159.6, and 139.5 mg g-1, respectively. Ce-MOFs have stable and excellent adsorption capacity at pH = 3-9. Coexisting anions (Cl-, SO42-, and NO3-) do not affect the performance of Ce-MOFs for fluoride removal. Moreover, Ce-MOFs also show their broad prospect as superior fluoride adsorbents because of their excellent performance and reusability in real water samples. Organic ligands have a remarkable influence on the defluoridation performance of Ce-MOFs. This work will provide a feasible idea for designing MOFs as superiors adsorbents for defluoridation.

Single atom Mn anchored on N-doped porous carbon derived from spirulina for catalyzed peroxymonosulfate to degradation of emerging organic pollutants.

Highly efficient single atom catalysts are critical to substantially promote for peroxymonosulfate (PMS) activation to organic pollutant degradation, but it remains a challenge at present. Herein, single atom Mn anchored on N-doped porous carbon (SA-Mn-NSC) was synthesized by ball milling of Mn-doped carbon nitride and spirulina biochar to dominantly activate PMS. The precursor of carbon nitride and spirulina possessed a strong coordinating capability for Mn(II), facilitating the formation of highly dispersed nitrogen-coordinated Mn sites (Mn-N4). The SA-Mn-NSC catalyst exhibited high activity and stability in the heterogeneous activation of PMS to degrade a wide range of pollutants within 10 min, showing an outstanding degradation rate constant of 0.31 min-1 in enrofloxacin (ENR) degradation. The high surface density of Mn-N4 sites and abundant interconnected meso-macro pores were highly favorable for activating PMS to produce 1O2 and high-valent manganese (Mn(IV)) for pollutant degradation. This work offers a new pathway of using a low-cost and easily accessible single-atom catalysts (SACs) and could inspire more catalytic oxidation strategies.

Strain differences in the drug transport capacity of intestinal glucose transporters in Sprague-Dawley versus Wistar rats, C57BL/6J versus Kunming mice.

Designing oral drug delivery systems using intestinal glucose transporters (IGTs) may be one of the strategies for improving oral bioavailability of drugs. However, little is known about the biological factors affecting the drug transport capacity of IGTs. Gastrodin is a sedative drug with a structure very similar to glucose. It is a highly water-soluble phenolic glucoside. It can hardly enter the intestine through simple diffusion but exhibits good oral bioavailability of over 80%. We confirmed that gastrodin is absorbed via the intestinal glucose transport pathway. It has the highest oral bioavailability among the reported glycosides' active ingredients through this pathway. Thus, gastrodin is the most selective drug substrate of IGTs and can be used to evaluate the drug transport capacity of IGTs. Obviously, strain is one of the main biological factors affecting drug absorption. This study firstly compared the drug transport capacity of IGTs between SD rats and Wistar rats and between C57 mice and KM mice by pharmacokinetic experiments and single-pass intestinal perfusion experiments of gastrodin. Then, the sodium-dependent glucose transporter type 1 (SGLT1) and sodium-independent glucose transporters type 2 (GLUT2) in the duodenum, jejunum, ileum and colon of these animals were quantified using RT-qPCR and Western blot. The results showed that the oral bioavailability of gastrodin in Wistar rats was significantly higher than in SD rats and significantly higher in KM mice than in C57 mice. Gastrodin absorption significantly differed among different intestinal segments in SD rats, C57 mice and KM mice, except Wistar rats. RT-qPCR and Western blot demonstrated that the intestinal expression distribution of SGLT1 and GLUT2 in SD rats and C57 mice was duodenum ≈ jejunum > ileum > colon. SGLT1 expression did not differ among different intestinal segments in KM mice, whereas the intestinal expression distribution of GLUT2 was duodenum ≈ jejunum ≈ ileum > colon. However, the expression of SGLT1 and GLUT2 did not differ among different intestinal segments in Wistar rats. It was reported that the intestinal expression distribution of SGLT1 and GLUT2 in humans is duodenum > jejunum > ileum > colon. Hence, the intestinal expression distribution of SGLT1 and GLUT2 of SD rats and C57 mice was more similar to that in humans. In conclusion, the drug transport capacity of IGTs differs in different strains of rats and mice. SD rats and C57 mice are more suitable for evaluating the pharmacokinetics of glycosides' active ingredients absorbed via the intestinal glucose transport pathway.

Influence of Mine Environmental Factors on the Liquid CO2 Pipeline Transport System with Great Altitude Difference.

To prevent coal spontaneous combustion and store CO2 in the coal mine, it is necessary to establish a fire-prevention pipeline transport system which continuously injects a large amount of liquid CO2 from the ground to the underground area directly. At present, few studies are focused on the law of liquid CO2 transport with great altitude difference. Moreover, the complex transport environment in the coal mine affects the design and application of the pipeline transport system for ground direct injection of liquid CO2. This study explores the influence of environmental factors at different depths in the coal mine on the liquid CO2 transport. Excessive altitude difference, ambient temperature and airflow velocity may lead to the boiling of liquid CO2 during pipeline transport and a sudden drop in CO2 temperature and pressure, which may cause danger in the pipeline transport system. The critical insulation thickness is determined based on the occurrence of the boiling of CO2. In addition, the influence law of adding an insulating layer of different thicknesses to the CO2 pipeline system is obtained. This study is of great significance to the establishment of a pipeline system that safely transports liquid CO2 from the ground to the underground mine.

Genomic Analysis Provides Insights Into the Plant Architecture Variations in in situ Conserved Chinese Wild Rice (Oryza rufipogon Griff.).

In situ conserved wild rice (Oryza rufipogon Griff.) is a promising source of alleles for improving rice production worldwide. In this study, we conducted a genomic analysis of an in situ conserved wild rice population (Guiping wild rice) growing at the center of wild rice genetic diversity in South China. Differences in the plant architecture in this population were investigated. An analysis using molecular markers revealed the substantial genetic diversity in this population, which was divided into subgroups according to the plant architecture. After resequencing representative individuals, the Guiping wild rice population was compared with other O. rufipogon and Oryza sativa populations. The results indicated that this in situ conserved wild rice population has a unique genetic structure, with genes that were introgressed from aromatic and O. sativa ssp. indica and japonica populations. The QTLs associated with plant architecture in this population were detected via a pair-wise comparison analysis of the sequencing data for multiple DNA pools. The results suggested that a heading date-related gene (DHD1) might be associated with variations in plant architecture and may have originated in cultivated rice. Our findings provide researchers with useful insights for future genomic analyses of in situ conserved wild rice populations.

Unveiling the genetic architecture for lodging resistance in rice (Oryza sativa. L) by genome-wide association analyses.

Lodging is one of the major abiotic stresses, affecting the total crop yield and quality. The improved lodging resistance and its component traits potentially reduce the yield losses. The section modulus (SM), bending moment at breaking (M), pushing resistance (PR), and coefficient of lodging resistance (cLr) are the key elements to estimate the lodging resistance. Understanding the genetic architecture of lodging resistance-related traits will help to improve the culm strength and overall yield potential. In this study, a natural population of 795 globally diverse genotypes was further divided into two (indica and japonica) subpopulations and was used to evaluate the lodging resistance and culm strength-related traits. Significant diversity was observed among the studied traits. We carried out the genome-wide association evaluation of four lodging resistance traits with 3.3 million deep resolution single-nucleotide polymorphic (SNP) markers. The general linear model (GLM) and compressed mixed linear model (MLM) were used for the whole population and two subpopulation genome-wide association studies (GWAS), and a 1000-time permutation test was performed to remove the false positives. A total of 375 nonredundant QTLs were observed for four culm strength traits on 12 chromosomes of the rice genome. Then, 33 pleiotropic loci governing more than one trait were mined. A total of 4031 annotated genes were detected within the candidate genomic region of 33 pleiotropic loci. The functional annotations and metabolic pathway enrichment analysis showed cellular localization and transmembrane transport as the top gene ontological terms. The in silico and in vitro expression analyses were conducted to validate the three candidate genes in a pleiotropic QTL on chromosome 7. It validated OsFBA2 as a candidate gene to contribute to lodging resistance in rice. The haplotype analysis for the candidate gene revealed a significant functional variation in the promoter region. Validation and introgression of alleles that are beneficial to induce culm strength may be used in rice breeding for lodging resistance.

[Quantitative spectrum analysis of characteristic gases of spontaneous combustion coal].

Aimed at the characteristics of spontaneous combustion gas such as a variety of gases, lou limit of detection, and critical requirement of safety, Fourier transform infrared (FTIR) spectral analysis is presented to analyze characteristic gases of spontaneous combustion In this paper, analysis method is introduced at first by combing characteristics of absorption spectra of analyte and analysis requirement. Parameter setting method, sample preparation, feature variable abstract and analysis model building are taken into consideration. The methods of sample preparation, feature abstraction and analysis model are introduced in detail. And then, eleven kinds of gases were tested with Tensor 27 spectrometer. CH4, C2H6, C3H8, iC4H10, nC4H10, C2 H4, C3 H6, C3 H2, SF6, CO and CO2 were included. The optical path length was 10 cm while the spectra resolution was set as 1 cm(-1). The testing results show that the detection limit of all analytes is less than 2 x 10(-6). All the detection limits fit the measurement requirement of spontaneous combustion gas, which means that FTIR may be an ideal instrument and the analysis method used in this paper is competent for spontaneous combustion gas measurement on line.

A numerical study on the effect of CO2 addition for methane explosion reaction kinetics in confined space.

To explore the influence of the CO2 volume fraction on methane explosion in confined space over wide equivalent ratios, the explosion temperature, the explosion pressure, the concentration of the important free radicals, and the concentration of the catastrophic gas generated after the explosion in confined space were studied. Meanwhile, the elementary reaction steps dominating the gas explosion were identified through the sensitivity analysis. With the increase of the CO2 volume fraction, the explosion time prolongs, and the explosion pressure and temperature decrease monotonously. Moreover, the concentrations of the investigated free radicals also decrease as the increase of the CO2 volume fraction. For the catastrophic gas, the concentration of the gas product CO increases and the concentrations of CO2, NO, and NO2 decrease as the volume fraction of CO2 increases. When 7% methane is added with 10% CO2, the increase rate of CO is 76%, and the decrease rates of CO2, NO, and NO2 are 27%, 37%, and 39%, respectively. If the volume fraction of CO2 is constant, the larger the volume fraction of methane in the blend gas, the greater the mole fraction of radical H and the lower the mole fraction of radical O. For radical OH, its mole fraction first increases, and then decreases with the location of peak value of 9.5%, while the CO concentration increases with the increase of the methane concentration. For all the investigated volume fraction of methane, the addition of CO2 reduces the sensitivity coefficients of each key elementary reaction step, and the sensitivity coefficient of reaction promoting methane consumption decreases faster than that of the reaction inhibit methane consumption, which indicates that the addition of CO2 effectively suppresses the methane explosion.

Mechanism confirmation of organofunctional silanes modified sodium silicate/polyurethane composites for remarkably enhanced mechanical properties.

Hybrid reinforced sodium silicate/polyurethane (SS/PU) composites mainly derived from low-cost SS and polyisocyanate are produced by a one-step method based on the addition of 3-chloropropyltrimethoxysilane (CTS). The wettability of SS on PU substrate surface is much improved as CTS content increases from 0.0 to 3.5 wt%. Furthermore, with 2.5 wt% of CTS optimal addition, the fracture surface morphology and elemental composition of the resulting SS/PU composites are characterized, as well as mechanical properties, chemical structure and thermal properties. The results indicate that the CTS forms multiple physical and chemical interactions with the SS/PU composites to induce an optimized organic-inorganic hybrid network structure thus achieving simultaneous improvement of compressive strength, flexural strength, flexural modulus and fracture toughness of the SS/PU composites, with the improvement of 12.9%, 6.6%, 17.5% and 9.7%, respectively. Moreover, a reasonable mechanism explanation for CTS modified SS/PU composites is confirmed. Additionally, the high interface areas of the organic-inorganic phase and the active crosslinking effect of the CTS are the main factors to determine the curing process of the SS/PU composites.

Natural Variation in OsMKK3 Contributes to Grain Size and Chalkiness in Rice.

Rice (Oryza sativa L.) is an important staple food crop for more than half of the world's population. Enhancing the grain quality and yield of rice to meet growing demand remains a major challenge. Here, we show that OsMKK3 encode a MAP kinase kinase that controls grain size and chalkiness by affecting cell proliferation in spikelet hulls. We showed that OsSPL16, GS5, and GIF1 have a substantial effect on the OsMKK3-regulated grain size pathway. OsMKK3 has experienced strong directional selection in indica and japonica. Wild rice accessions contained four OsMKK3 haplotypes, suggesting that the OsMKK3 haplotypes present in cultivated rice likely originated from different wild rice accessions during rice domestication. OsMKK3-Hap1, gs3, and gw8 were polymerized to enhance the grain length. Polymerization of beneficial alleles, such as OsMKK3-Hap1, gs3, gw8, fgr, alk, chalk5, and wx, also improved the quality of hybrid rice. Overall, the results indicated that beneficial OsMKK3 alleles could be used for genomic-assisted breeding for rice cultivar improvement and be polymerized with other beneficial alleles.

Natural Sequence Variations and Combinations of GNP1 and NAL1 Determine the Grain Number per Panicle in Rice.

BACKGROUND: The grain number per panicle (GNP), which is one of three grain yield components, is an important trait for the genetic improvement of rice. Although the NAL1 and GNP1 genes regulating the rice GNP and grain yield have been cloned, their allelic diversity, functional differences in rice germplasms, and effects of their combination on GNP and grain yield remain unclear. RESULTS: Based on DNA sequences of these two genes in 198 cultivated rice (Oryza sativa) and 8-10 wild rice (Oryza rufipogon) germplasms, 16 and 14 haplotypes were identified for NAL1 and GNP1, respectively. The NAL1 gene had the strongest effects on GNP in indica (xian) and japonica (geng) subpopulations. In contrast, GNP1 had no significant effects in the geng subpopulation and was rare in the xian background, in which the superior GNP1 allele (GNP1-6) was detected in only 4.0% of the 198 germplasms. Compared with the transgenic lines with GNP1 or NAL1, the transgenic lines with both genes had a higher GNP (15.5%-25.4% and 11.6%-15.9% higher, respectively) and grain yield (5.7%-9.0% and 8.3%-12.3% higher, respectively) across 3 years. The two genes combined in the introgression lines in Lemont background resulted in especially favorable effects on the GNP. CONCLUSIONS: Our results indicated that the GNP1 and NAL1 exhibited obvious differentiation and their combinations can significantly increase the grain yield in geng rice cultivars. These observations provide insights into the molecular basis of the GNP and may be useful for rice breeding of high yield potential by pyramiding GNP1 and NAL1.