Rice Spikelet Research Articles

RNA-Seq Transcriptome Analysis and Evolution of OsEBS, a Gene Involved in Enhanced Spikelet Number per Panicle in Rice.

Spikelet number per panicle (SNP) is one of the most important yield components in rice. Rice ENHANCING BIOMASS AND SPIKELET NUMBER (OsEBS), a gene involved in improved SNP and yield, has been cloned from an accession of Dongxiang wild rice. However, the mechanism of OsEBS increasing rice SNP is poorly understood. In this study, the RNA-Seq technology was used to analyze the transcriptome of wildtype Guichao 2 and OsEBS over-expression line B102 at the heading stage, and analysis of the evolution of OsEBS was also conducted. A total of 5369 differentially expressed genes (DEGs) were identified between Guichao2 and B102, most of which were down-regulated in B102. Analysis of the expression of endogenous hormone-related genes revealed that 63 auxin-related genes were significantly down-regulated in B102. Gene Ontogeny (GO) enrichment analysis showed that the 63 DEGs were mainly enriched in eight GO terms, including auxin-activated signaling pathway, auxin polar transport, auxin transport, basipetal auxin transport, and amino acid transmembrane transport, most of which were directly or indirectly related to polar auxin transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis further verified that the down-regulated genes related to polar auxin transport had important effects on increased SNP. Analysis of the evolution of OsEBS found that OsEBS was involved in the differentiation of indica and japonica, and the differentiation of OsEBS supported the multi-origin model of rice domestication. Indica (XI) subspecies harbored higher nucleotide diversity than japonica (GJ) subspecies in the OsEBS region, and XI experienced strong balancing selection during evolution, while selection in GJ was neutral. The degree of genetic differentiation between GJ and Bas subspecies was the smallest, while it was the highest between GJ and Aus. Phylogenetic analysis of the Hsp70 family in O. sativa, Brachypodium distachyon, and Arabidopsis thaliana indicated that changes in the sequences of OsEBS were accelerated during evolution. Accelerated evolution and domain loss in OsEBS resulted in neofunctionalization. The results obtained from this study provide an important theoretical basis for high-yield rice breeding.

Pushing the boundaries of organ identity: Homology of the grass lemma

Pushing the boundaries of organ identity: Homology of the grass lemma

Optimization of rice panicle architecture by specifically suppressing ligand–receptor pairs

Rice panicle architecture determines the grain number per panicle and therefore impacts grain yield. The OsER1–OsMKKK10–OsMKK4–OsMPK6 pathway shapes panicle architecture by regulating cytokinin metabolism. However, the specific upstream ligands perceived by the OsER1 receptor are unknown. Here, we report that the EPIDERMAL PATTERNING FACTOR (EPF)/EPF-LIKE (EPFL) small secreted peptide family members OsEPFL6, OsEPFL7, OsEPFL8, and OsEPFL9 synergistically contribute to rice panicle morphogenesis by recognizing the OsER1 receptor and activating the mitogen-activated protein kinase cascade. Notably, OsEPFL6, OsEPFL7, OsEPFL8, and OsEPFL9 negatively regulate spikelet number per panicle, but OsEPFL8 also controls rice spikelet fertility. A osepfl6 osepfl7 osepfl9 triple mutant had significantly enhanced grain yield without affecting spikelet fertility, suggesting that specifically suppressing the OsEPFL6–OsER1, OsEPFL7–OsER1, and OsEPFL9–OsER1 ligand–receptor pairs can optimize rice panicle architecture. These findings provide a framework for fundamental understanding of the role of ligand–receptor signaling in rice panicle development and demonstrate a potential method to overcome the trade-off between spikelet number and fertility.

Effects of increased ozone on rice panicle morphology

Ground-level ozone threatens rice production, which provides staple food for more than half of the world's population. Improving the adaptability of rice crops to ozone pollution is essential to ending global hunger. Rice panicles not only affect grain yield and grain quality but also the adaptability of plants to environmental changes, but the effects of ozone on rice panicles are not well understood. Through an open top chamber experiment, we investigated the effects of long-term and short-term ozone on the traits of rice panicles, finding that both long-term and short-term ozone significantly reduced the number of panicle branches and spikelets in rice, and especially the fertility of spikelets in hybrid cultivar. The reduction in spikelet quantity and fertility because of ozone exposure is caused by changes in secondary branches and attached spikelet. These results suggest the potential for effective adaptation to ozone by altering breeding targets and developing growth stage-specific agricultural techniques.

Light intensity-mediated auxin homeostasis in spikelets links carbohydrate metabolism enzymes with grain filling rate in rice.

Low light (LL) stress during the grain-filling stage acutely impairs the quality and quantity of starch accumulation in rice grains. Here, we observed that LL-induced poor starch biosynthesis is modulated by auxin homeostasis, which regulates the activities of major carbohydrate metabolism enzymes such as starch synthase (SS) and ADP-glucose pyrophosphorylase (AGPase) in rice. Further, during the grain-filling period under LL, the starch/sucrose ratio increased in leaves but significantly decreased in the developing spikelets. This suggests poor sucrose biosynthesis in leaves and starch in the grains of the rice under LL. A lower grain starch was found to be correlated with the depleted AGPase and SS activities in the developing rice grains under LL. Further, under LL, the endogenous auxin (IAA) level in the spikelets was found to be synchronized with the expression of a heteromeric G protein gene, RGB1. Interestingly, under LL, the expression of OsYUC11 was significantly downregulated, which subsequently resulted in reduced IAA in the developing rice spikelets, followed by poor activation of grain-filling enzymes. This resulted in lowered grain starch accumulation, grain weight, panicle number, spikelet fertility, and eventually grain yield, which was notably higher in the LL-susceptible (GR4, IR8) than in the LL-tolerant (Purnendu, Swarnaprabha) rice genotypes. Therefore, we hypothesize that depletion in auxin biosynthesis under LL stress is associated with the downregulation of RBG1, which discourages the expression and activities of grain-filling enzymes, resulting in lower starch production, panicle formation, and grain yield in rice.

Development and application of recombinase polymerase amplification for rapid detection of rice false smut pathogen (Ustilaginoidea virens)

Ustilaginoidea virens (Cke.) Tak. is the causal pathogen of rice false smut, a grain disease which affects both grain quality and yield. In this study, a recombinase polymerase amplification (RPA) assay protocol was developed to detect U. virens directly from rice spikelet. Three pairs of primer were designed from the U. virens GTP binding protein beta subunit (UvG-β1) gene to function both in RPA and in polymerase chain reaction (PCR). The developed RPA assay efficiently detected U. virens from both genomic DNA and mycelial crude extract. A comparison of sensitivity of RPA with PCR and loop-mediated isothermal amplification (LAMP) revealed that the latter two methods failed to detect U. virens from crude extract. The specificity of the RPA primers was evaluated using DNA from other rice pathogens, as well as, by sequencing the RPA amplicons. For validation, the RPA assay was evaluated on 32 different U. virens isolates from eastern and north-eastern India, as well as, on field samples. The developed RPA assay was able to detect U. virens directly from crude extract prepared from infected rice spikelet. The developed RPA assay will be effective for field monitoring of U. virens.

Interplay Impact of Exogenous Application of Abscisic Acid (ABA) and Brassinosteroids (BRs) in Rice Growth, Physiology, and Resistance under Sodium Chloride Stress.

The hormonal imbalances, including abscisic acid (ABA) and brassinosteroid (BR) levels, caused by salinity constitute a key factor in hindering spikelet development in rice and in reducing rice yield. However, the effects of ABA and BRs on spikelet development in plants subjected to salinity stress have been explored to only a limited extent. In this research, the effect of ABA and BRs on rice growth characteristics and the development of spikelets under different salinity levels were investigated. The rice seedlings were subjected to three different salt stress levels: 0.0875 dS m-1 (Control, CK), low salt stress (1.878 dS m-1, LS), and heavy salt stress (4.09 dS m-1, HS). Additionally, independent (ABA or BR) and combined (ABA+BR) exogenous treatments of ABA (at 0 and 25 μM concentration) and BR (at 0 and 5 μM concentration) onto the rice seedlings were performed. The results showed that the exogenous application of ABA, BRs, and ABA+BRs triggered changes in physiological and agronomic characteristics, including photosynthesis rate (Pn), SPAD value, pollen viability, 1000-grain weight (g), and rice grain yield per plant. In addition, spikelet sterility under different salt stress levels (CK, LS, and HS) was decreased significantly through the use of both the single phytohormone and the cocktail, as compared to the controls. The outcome of this study reveals new insights about rice spikelet development in plants subjected to salt stress and the effects on this of ABA and BR. Additionally, it provides information on the use of plant hormones to improve rice yield under salt stress and on the enhancement of effective utilization of salt-affected soils.

The Chromosome-Scale Genomes of Exserohilum rostratum and Bipolaris zeicola Pathogenic Fungi Causing Rice Spikelet Rot Disease

Rice spikelet rot disease occurs mainly in the late stages of rice growth. Pathogenicity and biological characteristics of the pathogenic fungus and the infestation site have been the primary focus of research on the disease. To learn more about the disease, we performed whole-genome sequencing of Exserohilum rostratum and Bipolaris zeicola for predicting potentially pathogenic genes. The fungus B. zeicola was only recently identified in rice.We obtained 16 and 15 scaffolds down to the chromosome level for E. rostratum LWI and B. zeicola LWII, respectively. The length of LWI strain was approximately 34.05 Mb, and the G + C content of the whole genome was 50.56%. The length of the LWII strain was approximately 32.21 Mb, and the G + C content of the whole genome was 50.66%. After the prediction and annotation of E. rostratum LWI and B. zeicola LWII, we predicted that the LWI strain and LWII strain contain 8 and 13 potential pathogenic genes, respectively, which may be related to rice infection. These results improve our understanding of the genomes of E. rostratum and B. zeicola and update the genomic databases of these two species. It benefits subsequent studies on the mechanisms of E. rostratum and B. zeicola interactions with rice and helps to develop efficient control measures against rice spikelet rot disease.

Nitrogen and potassium interactions optimized asynchronous spikelet filling and increased grain yield of japonica rice.

Poor grain filling severely reduces rice yield. Fertilizers play a vital role in regulating grain filling, especially nitrogen (N) and potassium (K). In this field study we aimed to investigate the interactive effects of N and K on the asynchronous filling properties of superior and inferior spikelets of japonica rice. We looked at grain filling under three N rates (0, 90, and 180 kg N ha-1) and three K rates (0, 60, and 120 kg K2O ha-1) during 2020 and 2021. Across two years, the results showed that the combined use of N and K on superior and inferior spikelets significantly increased their weight by 1.29 mg and 2.31 mg, their maximum grain filling rate by 0.24 mg d-1 and 0.07 mg d-1, and their average grain filling rate by 0.21 mg d-1 and 0.06 mg d-1, respectively, in comparison with the control (N0K0) treatment. Likewise, K supply increased the average contribution rate of superior and inferior spikelets to yield by 9.1% and 10.0%, respectively. Correlation analysis showed that the grain filling rate of superior and inferior spikelets was an important factor in determining the spikelet weight, whereas the grain filling time was not. We also found that the 1,000-grain weight mainly increased after increasing the spikelets' maximum grain filling rate and average grain filling rate. Collectively, these results illustrate that the combined use of N and K can optimize the asynchronous filling of superior and inferior spikelets and, in particular, enhance inferior spikelet weight with higher rice yield.

Quantification of rice spikelet rot disease severity at organ scale with proximal imaging spectroscopy

Quantification of rice spikelet rot disease severity at organ scale with proximal imaging spectroscopy

Analysis of co-expression and gene regulatory networks associated with sterile lemma development in rice

BackgroundThe sterile lemma is a unique organ of the rice (Oryza sativa L.) spikelet. However, the characteristics and origin of the rice sterile lemma have not been determined unequivocally, so it is important to elucidate the molecular mechanism of the development of the sterile lemma.ResultsIn the paper, we outline the regulatory mechanism of sterile lemma development by LONG STERILE LEMMA1 (G1), which has been identified as the gene controlling sterile lemma development. Based on the comprehensive analyses of transcriptome dynamics during sterile lemma development with G1 alleles between wild-type (WT) and mutant (MT) in rice, we obtained co-expression data and regulatory networks related to sterile lemma development. Co-transfection assays of rice protoplasts confirmed that G1 affects the expression of various phytohormone-related genes by regulating a number of critical transcription factors, such as OsLBD37 and OSH1. The hormone levels in sterile lemmas from WT and MT of rice supports the hypotheses that lower auxin, lower gibberellin, and higher cytokinin concentrations are required to maintain a normal phenotype of sterile lemmas.ConclusionThe regulatory networks have considerable reference value, and some of the regulatory relationships exhibiting strong correlations are worthy of further study. Taken together, these work provided a detailed guide for further studies into the molecular mechanism of sterile lemma development.

Effect of sterile rice spikelets derived biochar amendment on nutrient leaching and availability in paddy soil under continuous standing water

ABSTRACT Undisturbed soil columns were used to study the effect of sterile rice spikelets-derived biochar (SRSB) on NH4 +-N, available P, and available K leaching and nutrients availability in a paddy soil under continuous standing water (CSW) condition. The experiment was conducted for two crop cycles and comprised of three treatments: recommended dose of sole chemical fertilizers (CF), CF+SRSB (2 t ha−1), and control. In both crop cycles, incorporation of SRSB reduced the leachate NH4 +-N and available K concentrations, while increased the available P concentration compared to sole CF. The SRSB amendment reduced the cumulative losses of NH4 +-N by 35–38% and available K by 23–25% than CF only. However, there was no significant variation in cumulative available P loss between SRSB and CF only. The reduced leaching loss of NH4 +-N and available K could be attributed to the better nutrient adsorption capacity of SRSB. After completion of two crop cycles, the soil pH, soil organic carbon, soil total N, available P, and available K increased with SRSB amended soils than sole CF. This study showed positive effects of SRSB on retaining nutrients and increasing their availability in the soil which could benefit efficient fertilizer management in paddy soil under CSW.

Characterization of the chemical fungicides-responsive and bacterial pathogen-preventing Bacillus licheniformis in rice spikelet

Abstract Seed-borne bacterial pathogens cause severe yield loss and biotoxin contamination in rice, leading to increasing concern on the global food supply and environmental safety. Plant native microbes play an important role in defending against diseases, but their actions are often influenced by the chemical fungicides applied in the field. Here, Bacillus licheniformis mmj was isolated from rice spikelet, which uniquely showed not only fungicide-responsiveness but also broad-spectrum antimicrobial activity against major rice bacterial pathogens including Xanthomonas oryzae pv. oryzae, Burkholderia plantarii and Burkholderia glumae. To understand the hallmark underlying the environmental adaptation and antimicrobial activity of B. licheniformis mmj, the genome sequence was determined by SMRT and subjected to bioinformatics analysis. Genome sequence analysis enabled the identification of a set of antimicrobial-resistance and antibacterial activity genes together with an array of harsh environment-adaptive genes. Moreover, B. licheniformis mmj metabolites were analyzed with gas chromatography coupled to triple quadrupole mass spectrometry, and the volatile components that were linked with the antimicrobial activity were preliminarily profiled. Collectively, the present findings reveal the genomic and metabolic landscapes underlying fungicide-responsive B. licheniformis, which offers a new opportunity to design harsh environment-adaptive biopesticides to cope with prevalent bacterial phytopathogens.

Redox imbalance disrupts spikelet fertility in rice: A study under stage-specific and multi-stage drought in eastern Indo-Gangetic plain

To support the increasing food demand of the drought-prone eastern Indo-Gangetic plain (EIGP), we assessed the effects of natural drought stress on the individual (seedling stage drought; SSD, vegetative stage drought; VSD, reproductive stage drought; RSD) as well as the multiple growth stages (multi-stage drought; MSD) of twenty-four rice genotypes (n = 24) under field conditions for two consecutive rice growing seasons (2019-2020). High temperature and low rainfall during both the trial years exerted moderate to severe drought stress to the rice genotypes leading to average grain yield reduction of 43.5, 28.9, 59.3, and 69.9% under SSD, VSD, RSD, and MSD conditions, respectively. The present study also revealed that drought stress caused enhanced accumulation of reactive oxygen species (ROS) in the spikelets of rice genotypes thereby, impeding the spikelet fertility. The promising rice genotypes showed an average decrease of 3.18, 4.83, 13.9, and 13.06% in spikelet fertility under SSD, VSD, RSD, and MSD conditions, respectively. Identified promising rice genotypes, IR83929-B-B-291-2-1-1-2, IR93827-29-1-1-2 and IR84899-B-183-20-1-1-1 showed extreme drought tolerance and better maintained photosynthetic rate, stomatal conductance, relative water content, membrane stability index, and total chlorophyll content under drought conditions irrespective of growth stages. Following the study, drought tolerance in the tolerant rice genotypes was associated with increased antioxidant enzyme mediated efficacious ROS detoxification, which contributed in maintaining pollen viability and spikelet fertility. Overall, the study identified drought tolerant rice genotypes for EIGP and established a comprehensive understanding of the complexity and plasticity of the rice genotypes under stage-specific and cumulative drought stress. • Identification of stage-specific and cumulative drought tolerant rice genotypes for eastern Indo-Gangetic plain • Drought during seedling and reproductive stages are more deleterious for sustainable grain yield in rice • ROS build up in flag-leaf leads to cellular membrane damage and lower photosynthetic rate • Increased antioxidant enzyme activities facilitates in flag-leaf sustain membrane integrity and P N by successful ROS scavenging • ROS accumulation in rice spikelets under drought leads to loss of pollen viability and spikelet infertility

The ABC of Flower Development in Monocots: The Model of Rice Spikelet.

The initial seminal studies of flower developmental genetics were made from observations in several eudicot model species, particularly Arabidopsis and Antirrhinum. However, an increasing amount of research in monocot model and crop species is finally giving the credit that monocots deserve for their position in the evolutionary history of Angiosperms, their astonishing diversification and adaptation, their diversified floral structures, their pivotal function in most ecosystems on Earth and, finally, their importance in agriculture and farming, economy, landscaping and feeding mankind. Rice is a staple crop and the major monocot model to study the reproductive phase and flower evolution. Inspired by this, this chapter reviews a story of highly conserved functions related to the ABC model of flower development. Nevertheless, this model is complicated in rice by cases of gene neofunctionalization, like the recruitment of MADS-box genes for the development of the unique organs known as lemma and palea, subfunctionalization, and rewiring of conserved molecular pathways.

Thermo-Sensitive Spikelet Defects 1 acclimatizes rice spikelet initiation and development to high temperature.

Crop reproductive development is vulnerable to heat stress, and the genetic modulation of thermotolerance during the reproductive phase, especially the early stage, remains poorly understood. We isolated a Poaceae-specific FAR-RED ELONGATED HYPOCOTYLS3 (FHY3)/FAR-RED IMPAIRED RESPONSE1 (FAR1)family transcription factor, Thermo-sensitive Spikelet Defects 1 (TSD1), derived from transposase in rice (Oryza sativa) TSD1 was highly expressed in spikelets, induced by heat, and specifically enhanced the thermotolerance of spikelet morphogenesis. Disrupting TSD1 did not affect vegetative growth but markedly retarded spikelet initiation and development, as well as caused varying degrees of spikelet degeneration, depending on the temperature. Most tsd1 spikelets were normal at low temperature but gradually degenerated as temperature increased, and all disappeared at high temperature, leading to naked branches. TSD1 directly promoted the transcription of YABBY1 and YABBY3 and could physically interact with YABBY1 and three TOB proteins, YABBY5, YABBY4, and YABBY3. These YABBY proteins can form either homodimers or heterodimers and play an important role in spikelet morphogenesis, similar to TSD1. Notably, the knockout mutant yab5-ko and double mutant tsd1 yab5-ko resembled tsd1 in spikelet appearance and response to temperature, indicating that these genes likely participate in spikelet development through the cooperative TSD1-YABBY module. These findings reveal a distinctive function of FHY3/FAR1 family genes and a unique TSD1-YABBY complex to acclimate spikelet development to high temperature in rice, providing insight into the regulating pathway of enhancing thermotolerance in plant reproductive development.

Genomic footprints related with adaptation and fumonisins production in Fusarium proliferatum.

Fusarium proliferatum is the principal etiological agent of rice spikelet rot disease (RSRD) in China, causing yield losses and fumonisins contamination in rice. The intraspecific variability and evolution pattern of the pathogen is poorly understood. Here, we performed whole-genome resequencing of 67 F. proliferatum strains collected from major rice-growing regions in China. Population structure indicated that eastern population of F. proliferatum located in Yangtze River with the high genetic diversity and recombinant mode that was predicted as the putative center of origin. Southern population and northeast population were likely been introduced into local populations through gene flow, and genetic differentiation between them might be shaped by rice-driven domestication. A total of 121 distinct genomic loci implicated 85 candidate genes were suggestively associated with variation of fumonisin B1 (FB1) production by genome-wide association study (GWAS). We subsequently tested the function of five candidate genes (gabap, chsD, palA, hxk1, and isw2) mapped in our association study by FB1 quantification of deletion strains, and mutants showed the impact on FB1 production as compared to the wide-type strain. Together, this is the first study to provide insights into the evolution and adaptation in natural populations of F. proliferatum on rice, as well as the complex genetic architecture for fumonisins biosynthesis.

The Adaptor Protein UvSte50 Governs Fungal Pathogenicity of Ustilaginoidea virens via the MAPK Signaling Pathway.

The mitogen-activated protein kinase (MAPK) signaling pathways regulate diverse cellular processes and have been partially characterized in the rice false smut fungus Ustilaginoidea virens. UvSte50 has been identified as a homolog to Saccharomyces cerevisiae Ste50, which is known to be an adaptor protein for MAPK cascades. ΔUvste50 was found to be defective in conidiation, sensitive to hyperosmotic and oxidative stresses, and non-pathogenic. The mycelial expansion of ΔUvste50 inside spikelets of rice terminated at stamen filaments, eventually resulting in a lack of formation of false smut balls on spikelets. We determined that UvSte50 directly interacts with both UvSte7 (MAPK kinase; MEK) and UvSte11 (MAPK kinase kinase; MEKK), where the Ras-association (RA) domain of UvSte50 is indispensable for its interaction with UvSte7. UvSte50 also interacts with UvHog1, a MAP kinase of the Hog1-MAPK pathway, which is known to have important roles in hyphal growth and stress responses in U. virens. In addition, affinity capture–mass spectrometry analysis and yeast two-hybrid assay were conducted, through which we identified the interactions of UvSte50 with UvRas2, UvAc1 (adenylate cyclase), and UvCap1 (cyclase-associated protein), key components of the Ras/cAMP signaling pathway in U. virens. Together, UvSte50 functions as an adaptor protein interacting with multiple components of the MAPK and Ras/cAMP signaling pathways, thus playing critical role in plant infection by U. virens.

Mapping and Validation of qHD7b: Major Heading-Date QTL Functions Mainly under Long-Day Conditions.

Heading date (HD) is one of the agronomic traits that influence maturity, regional adaptability, and grain yield. The present study was a follow-up of a previous quantitative trait loci (QTL) mapping study conducted on three populations, which uncovered a total of 62 QTLs associated with 10 agronomic traits. Two of the QTLs for HD on chromosome 7 (qHD7a and qHD7b) had a common flanking marker (RM3670) that may be due to tight linkage, and/or weakness of the statistical method. The objectives of the present study were to map QTLs associated with HD in a set of 76 chromosome segment substitution lines (CSSLs), fine map and validate one of the QTLs (qHD7b) using 2997 BC5F2:3 plants, and identify candidate genes using sequencing and expression analysis. Using the CSSLs genotyped with 120 markers and evaluated under two short-day and two long-day growing conditions, we uncovered a total of fourteen QTLs (qHD2a, qHD4a, qHD4b, qHD5a, qHD6a, qHD6b, qHD7b, qHD7c, qHD8a, qHD10a, qHD10b, qHD11a, qHD12a, and qHD12b). However, only qHD6a and qHD7b were consistently detected in all four environments. The phenotypic variance explained by qHD6a and qHD7b varied from 10.1% to 36.1% (mean 23.1%) and from 8.1% to 32.8% (mean 20.5%), respectively. One of the CSSL lines (CSSL52), which harbored a segment from the early heading XieqingzaoB (XQZB) parent at the qHD7b locus, was then used to develop a BC5F2:3 population for fine mapping and validation. Using a backcross population evaluated for four seasons under different day lengths and temperatures, the qHD7b interval was delimited to a 912.7-kb region, which is located between RM5436 and RM5499. Sequencing and expression analysis revealed a total of 29 candidate genes, of which Ghd7 (Os07g0261200) is a well-known gene that affects heading date, plant height, and grain yield in rice. The ghd7 mutants generated through CRISPR/Cas9 gene editing exhibited early heading. Taken together, the results from both the previous and present study revealed a consistent QTL for heading date on chromosome 7, which coincided not only with the physical position of a known gene, but also with two major effect QTLs that controlled the stigma exertion rate and the number of spikelets in rice. The results provide contributions to the broader adaptability of marker-assisted breeding to develop high-yield rice varieties.

Genome-Wide Characterization Reveals Variation Potentially Involved in Pathogenicity and Mycotoxins Biosynthesis of Fusarium proliferatum Causing Spikelet Rot Disease in Rice.

Fusarium proliferatum is the primary cause of spikelet rot disease in rice (Oryza sativa L.) in China. The pathogen not only infects a wide range of cereals, causing severe yield losses but also contaminates grains by producing various mycotoxins that are hazardous to humans and animals. Here, we firstly reported the whole-genome sequence of F. proliferatum strain Fp9 isolated from the rice spikelet. The genome was approximately 43.9 Mb with an average GC content of 48.28%, and it was assembled into 12 scaffolds with an N50 length of 4,402,342 bp. There is a close phylogenetic relationship between F. proliferatum and Fusarium fujikuroi, the causal agent of the bakanae disease of rice. The expansion of genes encoding cell wall-degrading enzymes and major facilitator superfamily (MFS) transporters was observed in F. proliferatum relative to other fungi with different nutritional lifestyles. Species-specific genes responsible for mycotoxins biosynthesis were identified among F. proliferatum and other Fusarium species. The expanded and unique genes were supposed to promote F. proliferatum adaptation and the rapid response to the host’s infection. The high-quality genome of F. proliferatum strain Fp9 provides a valuable resource for deciphering the mechanisms of pathogenicity and secondary metabolism, and therefore shed light on development of the disease management strategies and detoxification of mycotoxins contamination for spikelet rot disease in rice.