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Genomics’ impact on crop production continuously expands. The number of sequenced plant and microbial species and strains representing diverse populations of individual species rapidly increases thanks to the advent of next-generation sequencing technologies. Their genomic blueprints revealed candidate genes involved in various functions and processes crucial for crop health and helped in understanding how the sequenced organisms have evolved at the genome level. Functional genomics quickly translates these blueprints into a detailed mechanistic understanding of how such functions and processes work and are regulated; this understanding guides and empowers efforts to protect crops from diverse biotic and abiotic threats. Metagenome analyses help identify candidate microbes crucial for crop health and uncover how microbial communities associated with crop production respond to environmental conditions and cultural practices, presenting opportunities to enhance crop health by judiciously configuring microbial communities. Efficient conversion of disparate types of massive genomics data into actionable knowledge requires a robust informatics infrastructure supporting data preservation, analysis, and sharing. This review starts with an overview of how genomics came about and has quickly transformed life science. We illuminate how genomics and informatics can be applied to investigate various crop health-related problems using selected studies. We end the review by noting why community empowerment via crowdsourcing is crucial to harnessing genomics to protect global food and nutrition security without continuously expanding the environmental footprint of crop production.

Heavy reliance on synthetic pesticides for crop protection has become increasingly unsustainable, calling for robust alternative strategies that do not degrade the environment and vital ecosystem services. There are numerous reports of successful disease control by various microbes used in small-scale trials. However, inconsistent efficacy has hampered their large-scale application. A better understanding of how beneficial microbes interact with plants, other microbes, and the environment and which factors affect disease control efficacy is crucial to deploy microbial agents as effective and reliable pesticide alternatives. Diverse metabolites produced by plants and microbes participate in pathogenesis and defense, regulate the growth and development of themselves and neighboring organisms, help maintain cellular homeostasis under various environmental conditions, and affect the assembly and activity of plant and soil microbiomes. However, research on the metabolites associated with plant health-related processes, except antibiotics, has not received adequate attention. This review highlights several classes of metabolites known or suspected to affect plant health, focusing on those associated with biocontrol and belowground plant–microbe and microbe–microbe interactions. The review also describes how new insights from systematic explorations of the diversity and mechanism of action of bioactive metabolites can be harnessed to develop novel crop protection strategies.

Erwinia amylovora, a causal bacterium of fire blight disease, is registered as a prohibited quarantine pathogen in Korea. To control the disease, the government should diagnose the disease, dig and bury the host trees when fire blight occurs. Fire blight was the first reported in 43 orchards of Anseong, Cheonan, and Jecheon in 2015, and 42.9 ha of host trees were eradicated. However, the disease spread to eleven cities, so that 348 orchards and 260.4 ha of host trees were eradicated until 2019. Fire blight of Asian pear occurred mainly in the southern part of Gyeonggi, and Chungnam province, on average of 29±9.2 orchards per year. And the age of the infected trees were mostly 20-30 years old. In apple trees, the disease occurred mainly in the northern part of Gyeonggi, Gangwon, and Chungbuk province, on average of 41±57.6 orchards per year, increased highly in 2018 and 2019. The age of infected apple trees were under 20 years old. Therefore, because the disease spread rapidly in young apple trees, spraying control agents to the trees in a timely manner and removing infected trees quickly are important to prevent the spread of fire blight in the orchard of immature trees.

The genome of the rice blast fungus Magnaporthe oryzae contains several types of transposable elements (TEs), and some TEs cause genetic variation that allows M. oryzae to evade host detection. We studied how five abundant TEs in rice pathogens, Pot3, Pot2, MAGGY, Line-like element (MGL) and Mg-SINE, are expressed under diverse conditions related to growth, development, and stress. Expression of Pot3 and Pot2 was activated in germinated conidia and mycelia treated with tricyclazole. Retrotransposon MAGGY was highly expressed in appressoria and tricyclazole-treated mycelia. MAGGY and Pot2 were also activated during the early and late stages of perithecia development. MGL was up-regulated in conidia and during conidial germination but not during appressorium formation. No noticeable expression of Mg-SINE was observed under most conditions. Our results should help investigate if and how condition-specific expressions of some TEs contribute to the biology and evolution of M. oryzae.

This study was conducted to evaluate usefulness of numerical weather prediction data generated by the Unified Model (UM) for plant disease forecast. Using the UM06- and UM18-predicted weather data, which were released at 0600 and 1800 Universal Time Coordinated (UTC), respectively, by the Korea Meteorological Administration (KMA), disease forecast on bacterial grain rot (BGR) of rice was examined as compared with the model output based on the automated weather stations (AWS)-observed weather data. We analyzed performance of BGRcast based on the UM-predicted and the AWS-observed daily minimum temperature and average relative humidity in 2014 and 2015 from 29 locations representing major rice growing areas in Korea using regression analysis and two-way contingency table analysis. Temporal changes in weather conduciveness at two locations in 2014 were also analyzed with regard to daily weather conduciveness (C i ) and the 20-day and 7-day moving averages of C i for the inoculum build-up phase (C inc ) prior to the panicle emergence of rice plants and the infection phase (C inf ) during the heading stage of rice plants, respectively. Based on C inc and C inf , we were able to obtain the same disease warnings at all locations regardless of the sources of weather data. In conclusion, the numerical weather prediction data from KMA could be reliable to apply as input data for plant disease forecast models. Weather prediction data would facilitate applications of weather-driven disease models for better disease management. Crop growers would have better options for disease control including both protective and curative measures when weather prediction data are used for disease warning.

An endolichenic fungus, Xylaria grammica strain EL000614, showed strong nematicidal effects against plant pathogenic nematode, Meloidogyne incognita by producing grammicin. We report genome assembly of X. grammica EL000614 comprised of 25 scaffolds with a total length of 54.73 Mb, N50 of 4.60 Mb, and 99.8% of BUSCO completeness. GC contents of this genome were 44.02%. Gene families associated with biosynthesis of secondary metabolites or regulatory proteins were identified out of 13,730 gene models predicted.

Background: Dicers were member of RNase III containing proteins family with important RNAi function in eukaryotes. In this study, we tried to address the potential distribution of all RNase III containing proteins among the fungal kingdom, as well as their possible evolution paths including canonical Dicers, non-canonical Dicers and non-canonical Dicer-like proteins.Result: RNase III containing proteins were collected from 83 species, and discussed the features and possible evolution pathways of RNase III containing protein family. In general, RNase III containing protein family could be characterized into three different groups as canonical Dicer, non-canonical Dicers and Dicer-like proteins based on their domain structures and functional annotation. Most eukaryotes obtained multiple RNase III protein of different types at the same time, including canonical Dicers and Dicer-like proteins. Phylogenetic analysis showed that the RNase III domains were different between canonical Dicers and Dicer-like proteins, for the first and second RNase III domains had different insertions in different regions with certain extent of conservation. Regardless of the types, RNA-binging domains in RNase III protein family were very similar to each other. Furthermore, short insertions were found in different positions from the first and second RNase III domains in canonical Dicers separately. RNA-binging domains from all types were quite similar to each other.Conclusion: RNase III containing proteins in general widely exist in eukaryotes with minor divergent among different types and groups. Suggested by the RNase III and RDB domains, the canonical/non-canonical Dicers Dicer-like proteins might share the same ancestor and have evolved from separate mild-types through different directions.

Because pathogens use diverse infection strategies, plants cannot use one-size-fits-all defence and modulate defence responses based on the nature of pathogens and pathogenicity mechanism. Here, we report that a rice glycoside hydrolase (GH) plays contrasting roles in defence depending on whether a pathogen is hemibiotrophic or necrotrophic. The Arabidopsis thaliana MORE1 (Magnaporthe oryzae resistance 1) gene, encoding a member of the GH10 family, is needed for resistance against M. oryzae and Alternaria brassicicola, a fungal pathogen infecting A. thaliana as a necrotroph. Among 13 rice genes homologous to MORE1, 11 genes were induced during the biotrophic or necrotrophic stage of infection by M. oryzae. CRISPR/Cas9-assisted disruption of one of them (OsMORE1a) enhanced resistance against hemibiotrophic pathogens M. oryzae and Xanthomonas oryzae pv. oryzae but increased susceptibility to Cochliobolus miyabeanus, a necrotrophic fungus, suggesting that OsMORE1a acts as a double-edged sword depending on the mode of infection (hemibiotrophic vs. necrotrophic). We characterized molecular and cellular changes caused by the loss of MORE1 and OsMORE1a to understand how these genes participate in modulating defence responses. Although the underlying mechanism of action remains unknown, both genes appear to affect the expression of many defence-related genes. Expression patterns of the GH10 family genes in A. thaliana and rice suggest that other members also participate in pathogen defence.

Colletotrichum scovillei, an ascomycete phytopathogenic fungus, is the main causal agent of serious yield losses of economic crops worldwide. The fungus causes anthracnose disease on several fruits, including peppers. However, little is known regarding the underlying molecular mechanisms involved in the development of anthracnose caused by this fungus. In an initial step toward understanding the development of anthracnose on pepper fruits, we retrieved 624 transcription factors (TFs) from the whole genome of C. scovillei and comparatively analyzed the entire repertoire of TFs among phytopathogenic fungi. Evolution and proliferation of members of the homeobox-like superfamily, including homeobox (HOX) TFs that regulate the development of eukaryotic organisms, were demonstrated in the genus Colletotrichum. C. scovillei was found to contain 10 HOX TF genes (CsHOX1 to CsHOX10), which were functionally characterized using deletion mutants of each CsHOX gene. Notably, CsHOX1 was identified as a pathogenicity factor required for the suppression of host defense mechanisms, which represents a new role for HOX TFs in pathogenic fungi. CsHOX2 and CsHOX7 were found to play essential roles in conidiation and appressorium development, respectively, in a stage-specific manner in C. scovillei. Our study provides a molecular basis for understanding the mechanisms associated with the development of anthracnose on fruits caused by C. scovillei, which will aid in the development of novel approaches for disease management. IMPORTANCE The ascomycete phytopathogenic fungus, Colletotrichum scovillei, causes serious yield loss on peppers. However, little is known about molecular mechanisms involved in the development of anthracnose caused by this fungus. We analyzed whole-genome sequences of C. scovillei and isolated 624 putative TFs, revealing the existence of 10 homeobox (HOX) transcription factor (TF) genes. We found that CsHOX1 is a pathogenicity factor required for the suppression of host defense mechanism, which represents a new role for HOX TFs in pathogenic fungi. We also found that CsHOX2 and CsHOX7 play essential roles in conidiation and appressorium development, respectively, in a stage-specific manner in C. scovillei. Our study contributes to understanding the mechanisms associated with the development of anthracnose on fruits caused by C. scovillei, which will aid for initiating novel approaches for disease management.

Seeds harbor not only genetic information about plants but also microbial communities affecting plants’ vigor. Knowledge on the movement and formation of seed microbial communities during plant development remains insufficient. Here, we address this knowledge gap by investigating endophytic bacterial and fungal communities of seeds, seedlings, and adult rice plants. We found that seed coats act as microbial niches for seed bacterial and fungal communities. The presence or absence of the seed coat affected taxonomic composition and diversity of bacterial and fungal communities associated with seeds and seedlings. Ordination analysis showed that niche differentiation between above- and belowground compartments leads to compositional differences in endophytic bacterial and fungal communities originating from seeds. Longitudinal tracking of the composition of microbial communities from field-grown rice revealed that bacterial and fungal communities originating from seeds persist in the leaf, stem, and root endospheres throughout the life cycle. Our study provides ecological insights into the assembly of the initial endophytic microbial communities of plants from seeds.

Rice panicle blast occurred severely in southern provinces of Korea in 2014. The proportion of panicle blast incidence area to cultivated area of rice were 11.0% and 14.6% in Jeollanam-do and Gyeongsangnam-do, respectively. To identify the causal factors of the outbreak, we investigated weather conditions in August, amount of cultivated area of mainly grown cultivars, and nitrogen contents in plants with different disease incidences in 2014. ‘Saenuri,’ ‘Ilmibyeo,’ ‘Unkwang,’ ‘Dongjin 1 ho,’ ‘Nampyeongbyeo,’ and ‘Hwangkeumnuri’ were mainly grown cultivars. Monthly average of daily air temperature in August 2014 was 3.2°C and 3.1°C less than 2018 in Haenam and Miryang, respectively. Rainfall in August 2014 was 70.0% and 42.0% greater than 2018 in Haenam and Miryang, respectively. The numbers of blast warning days in August calculated nationwide using a forecast model for blast infection were higher in 2014 than in 2018, and they were in high level throughout the country in 2014. Nitrogen contents in plant samples from high-incidence plots were significantly higher than those from low-incidence plots. Consequently, excessive use of nitrogen fertilizers was the main factor for the disease outbreak at the level of specific farms, in addition to the collective cultivation of susceptible cultivar, low temperatures and frequent rainfalls in August.

Background Plant pathogenic isolates of Rhizoctonia solani anastomosis group 1-intraspecific group IA (AG1-IA) infect a wide range of crops causing diseases such as rice sheath blight (ShB). ShB has become a serious disease in rice production worldwide. Additional genome sequences of the rice-infecting R. solani isolates from different geographical regions will facilitate the identification of important pathogenicity-related genes in the fungus. Results Rice-infecting R. solani isolates B2 (USA), ADB (India), WGL (India), and YN-7 (China) were selected for whole-genome sequencing. Single-Molecule Real-Time (SMRT) and Illumina sequencing were used for de novo sequencing of the B2 genome. The genomes of the other three isolates were then sequenced with Illumina technology and assembled using the B2 genome as a reference. The four genomes ranged from 38.9 to 45.0 Mbp in size, contained 9715 to 11,505 protein-coding genes, and shared 5812 conserved orthogroups. The proportion of transposable elements (TEs) and average length of TE sequences in the B2 genome was nearly 3 times and 2 times greater, respectively, than those of ADB, WGL and YN-7. Although 818 to 888 putative secreted proteins were identified in the four isolates, only 30% of them were predicted to be small secreted proteins, which is a smaller proportion than what is usually found in the genomes of cereal necrotrophic fungi. Despite a lack of putative secondary metabolite biosynthesis gene clusters, the rice-infecting R. solani genomes were predicted to contain the most carbohydrate-active enzyme (CAZyme) genes among all 27 fungal genomes used in the comparative analysis. Specifically, extensive enrichment of pectin/homogalacturonan modification genes were found in all four rice-infecting R. solani genomes. Conclusion Four R. solani genomes were sequenced, annotated, and compared to other fungal genomes to identify distinctive genomic features that may contribute to the pathogenicity of rice-infecting R. solani. Our analyses provided evidence that genomic conservation of R. solani genomes among neighboring AGs was more diversified than among AG1-IA isolates and the presence of numerous predicted pectin modification genes in the rice-infecting R. solani genomes that may contribute to the wide host range and virulence of this necrotrophic fungal pathogen.

Pathogens utilize multiple types of effectors to modulate plant immunity. Although many apoplastic and cytoplasmic effectors have been reported, nuclear effectors have not been well characterized in fungal pathogens. Here, we characterize two nuclear effectors of the rice blast pathogen Magnaporthe oryzae. Both nuclear effectors are secreted via the biotrophic interfacial complex, translocated into the nuclei of initially penetrated and surrounding cells, and reprogram the expression of immunity-associated genes by binding on effector binding elements in rice. Their expression in transgenic rice causes ambivalent immunity: increased susceptibility to M. oryzae and Xanthomonas oryzae pv. oryzae, hemibiotrophic pathogens, but enhanced resistance to Cochliobolus miyabeanus, a necrotrophic pathogen. Our findings help remedy a significant knowledge deficiency in the mechanism of M. oryzae–rice interactions and underscore how effector-mediated manipulation of plant immunity by one pathogen may also affect the disease severity by other pathogens., Plant pathogens secrete various effectors to manipulate host immunity. Here, Kim et al. describe two Magnaporthe oryzae effectors that translocate into the nuclei of infected rice cells and reprogram expression of immunity-associated genes, increasing susceptibility to hemibiotrophic pathogens.

To establish an infection, fungal pathogens must recognize diverse signals from host surfaces. The rice blast fungus, Magnaporthe oryzae, is one of the best models studying host-pathogen interactions. This fungus recognizes physical or chemical signals from the host surfaces and initiates the development of an infection structure called appressorium. Here, we found that protein MoAfo1(appressorium formation, MGG_10422) was involved in sensing signal molecules such as cutin monomers and long chain primary alcohols required for appressorium formation. The knockout mutant (ΔMoafo1) formed a few abnormal appressoria on the onion and rice sheath surfaces. However, it produced normal appressoria on the surface of rice leaves. MoAfo1 localized to the membranes of the cytoplasm and vacuole-like organelles in conidia and appressoria. Additionally, the ΔMoafo1 mutant showed defects in appressorium morphology, appressorium penetration, invasive growth, and pathogenicity. These multiple defects might be partially due to failure to respond properly to oxidative stress. These findings broaden our understanding of the fungal mechanisms at play in the recognition of the host surface during rice blast infection.

The fungus Aspergillus oryzae strain BP2-1 was isolated from the traditional malted starter culture nuruk. We report here the draft whole-genome sequence of A. oryzae BP2-1, which is comprised of 14 scaffolds with a total length of 39,455,382 bp and a GC content of 47.13%.

The rice blast pathogen Magnaporthe oryzae is a global threat to rice production. Here we characterized RHO2 gene (MGG_02457) that belongs to the Rho GTPase family, using a deletion mutant. This mutant ΔMorho2 exhibited no defects in conidiation and germination but developed only 6% of appressoria in response to a hydrophobic surface when compared to the wild-type progenitor. This result indicates that MoRHO2 plays a role in appressorium development. Furthermore, exogenous cAMP treatment on the mutant led to appressoria that exhibited abnormal morphology on both hydrophobic and hydrophilic surfaces. These outcomes suggested the involvement of MoRHO2 in cAMP-mediated appressorium development. ΔMorho2 mutation also delayed the development of appressorium-like structures (ALS) at hyphal tips on hydrophobic surface, which were also abnormally shaped. These results suggested that MoRHO2 is involved in morphological development of appressoria and ALS from conidia and hyphae, respectively. As expected, ΔMorho2 mutant was defective in plant penetration, but was still able to cause lesions, albeit at a reduced rate on wounded plants. These results implied that MoRHO2 plays a role in M. oryzae virulence as well.

Acetylation of histone H3 lysine 56 (H3K56) by the fungal-specific histone acetyltransferase Rtt109 plays important roles in maintaining genome integrity and surviving DNA damage. Here, we investigated the implications of Rtt109-mediated response to DNA damage on development and pathogenesis of the rice blast fungus Magnaporthe oryzae (anamorph: Pyricularia oryzae). The ortholog of Rtt109 in M. oryzae (MoRtt109) was found via sequence homology and its functionality was confirmed by phenotypic complementation of the Saccharomyces cerevisiae Rtt109 deletion strain. Targeted deletion of MoRtt109 resulted in a significant reduction in acetylation of H3K56 and rendered the fungus defective in hyphal growth and asexual reproduction. Furthermore, the deletion mutant displayed hypersensitivity to genotoxic agents, confirming the conserved importance of Rtt109 in genome integrity maintenance and genotoxic stress tolerance. Elevated expression of DNA repair genes and the results of the comet assay were consistent with constitutive endogenous DNA damage. Although the conidia produced from the mutant were not impaired in germination and appressorium morphogenesis, the mutant was significantly less pathogenic on rice leaves. Transcriptomic analysis provided insight into the factors underlying phenotypic defects that are associated with deficiency of H3K56 acetylation. Overall, our results indicate that MoRtt109 is a conserved histone acetyltransferase that affects proliferation and asexual fecundity of M. oryzae through maintenance of genome integrity and response to DNA damage.

The rice blast fungus Pyricularia oryzae (syn. Magnaporthe oryzae, Magnaporthe grisea), a member of the order Magnaporthales in the class Sordariomycetes, is an important plant pathogen and a model species for studying pathogen infection and plant-fungal interaction. In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. Our results suggest that the Magnaporthales diverged ca. 31 millon years ago from other Sordariomycetes, with the phytopathogenic blast clade diverging ca. 21 million years ago. Little evidence of inter-phylum horizontal gene transfer (HGT) was detected in Magnaporthales. In contrast, many genes underwent positive selection in this order and the majority of these sequences are clade-specific. The blast clade genomes contain more secretome and avirulence effector genes, which likely play key roles in the interaction between Pyricularia species and their plant hosts. Finally, analysis of transposable elements (TE) showed differing proportions of TE classes among Magnaporthales genomes, suggesting that species-specific patterns may hold clues to the history of host/environmental adaptation in these fungi.

Despite the plant microbiota plays an important role in plant health, little is known about the potential interactions of the flower microbiota with pathogens. In this study, we investigated the microbial community of apple blossoms when infected with Erwinia amylovora. The long-read sequencing technology, which significantly increased the genome sequence resolution, thus enabling the characterization of fire blight-induced changes in the flower microbial community. Each sample showed a unique microbial community at the species level. Pantoea agglomerans and P. allii were the most predominant bacteria in healthy flowers, whereas E. amylovora comprised more than 90% of the microbial population in diseased flowers. Furthermore, gene function analysis revealed that glucose and xylose metabolism were enriched in diseased flowers. Overall, our results showed that the microbiome of apple blossoms is rich in specific bacteria, and the nutritional composition of flowers is important for the incidence and spread of bacterial disease.

Magnaporthe oryzae infects rice, wheat, and many grass species in the Poaceae family by secreting protein effectors. Here, we analyzed the distribution, sequence variation, and genomic context of effector candidate (EFC) genes in 31 isolates that represent five pathotypes of M. oryzae, three isolates of M. grisea, a sister species of M. oryzae, and one strain each for eight species in the family Magnaporthaceae to investigate how the host range expansion of M. oryzae has likely affected the evolution of effectors. We used the EFC genes of M. oryzae strain 70-15, whose genome has served as a reference for many comparative genomics analyses, to identify their homologs in these strains. We also analyzed the previously characterized avirulence (AVR) genes and single-copy orthologous (SCO) genes in these strains, which showed that the EFC and AVR genes evolved faster than the SCO genes. The EFC and AVR repertoires among M. oryzae pathotypes varied widely probably because adaptation to individual hosts exerted different types of selection pressure. Repetitive DNA elements appeared to have caused the variation of some EFC genes. Lastly, we analyzed expression patterns of the AVR and EFC genes to test the hypothesis that such genes are preferentially expressed during host infection. This comprehensive dataset serves as a foundation for future studies on the genetic basis of the evolution and host specialization in M. oryzae.

Magnaporthe oryzae infects rice, wheat, and many grass species in the Poaceae family by secreting protein effectors. Here, we analyzed the distribution, sequence variation, and genomic context of effector candidate (EFC) genes in 31 isolates that represent five pathotypes of M. oryzae, three isolates of M. grisea, a sister species of M. oryzae, and one strain each for eight species in the family Magnaporthaceae to investigate how the host range expansion of M. oryzae has likely affected the evolution of effectors. We used the EFC genes of M. oryzae strain 70-15, whose genome has served as a reference for many comparative genomics analyses, to identify their homologs in these strains. We also analyzed the previously characterized avirulence (AVR) genes and single-copy orthologous (SCO) genes in these strains, which showed that the EFC and AVR genes evolved faster than the SCO genes. The EFC and AVR repertoires among M. oryzae pathotypes varied widely probably because adaptation to individual hosts exerted different types of selection pressure. Repetitive DNA elements appeared to have caused the variation of some EFC genes. Lastly, we analyzed expression patterns of the AVR and EFC genes to test the hypothesis that such genes are preferentially expressed during host infection. This comprehensive dataset serves as a foundation for future studies on the genetic basis of the evolution and host specialization in M. oryzae.

The fungal genus Cochliobolus describes necrotrophic pathogens that give rise to significant losses on rice, wheat, and maize. Revealing plant mechanisms of non-host resistance (NHR) against Cochliobolus will help to uncover strategies that can be exploited in engineered cereals. Therefore, we developed a heterogeneous pathosystem and studied the ability of Cochliobolus to infect dicotyledons. We report here that C. miyabeanus and C. heterostrophus infect Arabidopsis accessions and produce functional conidia, thereby demonstrating the ability to accept Brassica spp. as host plants. Some ecotypes exhibited a high susceptibility, whereas others hindered the necrotrophic disease progression of the Cochliobolus strains. Natural variation in NHR among the tested Arabidopsis accessions can advance the identification of genetic loci that prime the plant's defence repertoire. We found that applied phytotoxin-containing conidial fluid extracts of C. miyabeanus caused necrotic lesions on rice leaves but provoked only minor irritations on Arabidopsis. This result implies that C. miyabeanus phytotoxins are insufficiently adapted to promote dicot colonization, which corresponds to a retarded infection progression. Previous studies on rice demonstrated that ethylene (ET) promotes C. miyabeanus infection, whereas salicylic acid (SA) and jasmonic acid (JA) exert a minor function. However, in Arabidopsis, we revealed that the genetic disruption of the ET and JA signalling pathways compromises basal resistance against Cochliobolus, whereas SA biosynthesis mutants showed a reduced susceptibility. Our results refer to the synergistic action of ET/JA and indicate distinct defence systems between Arabidopsis and rice to confine Cochliobolus propagation. Moreover, this heterogeneous pathosystem may help to reveal mechanisms of NHR and associated defensive genes against Cochliobolus infection.

Isolates of Colletotrichum graminicola were obtained from barnyard grass showing anthracnose symptoms and the fungus was evaluated as a potential biocontrol agent. C. graminicola KA001 was highly pathogenic to two varieties of barnyard grass in a wide range of growth stages, with the most damage at the three- to four-leaf stages. Disease severity of barnyard grass increased with the increase of the inoculum density from 1 × 104 to 1 × 105 conidia/ml, but inoculum density above 1 × 106 conidia/ml did not increase disease severity. A total of 13 rice cultivars tested showed no disease symptoms when inoculated with this fungus. Appressoria were formed on both barnyard grass and rice leaves, but infection hyphae were only found in the cells of barnyard grass. The fungus grew and sporulated in a wide range of temperature regimes, with optimal temperature at 27 to 30°C. These data suggest that C. graminicola KA001 has potential as a mycoherbicide to control barnyard grass with a safe selectivity in rice fields.

This study was conducted to determine phytotoxicity of domestic rice varieties and characteristic of sensitive gene involved in herbicide reaction of 4-HPPD (4-hydroxy phenylpyruvate dioxygenase) inhibiting herbicides. The five rice varieties were grown for 2 to 3 leaf stage on seedling trays and then transplanted into plastic pot: 4-Japonica type (Sangjubyeo, Sambaekbyeo, Sanduljinmi and Kumyoung) varieties and 1-Indica type variety (IR8). We trialled standard (14 g a.i. 10 a −1 ) and double fold (28 g a.i. 10 a −1 ) dose of benzobicyclon treatment at 10 days after transplanting in order to investigate phytoxicity. The Japonica-type Sangjubyeo showed no rice injury but Indica-type IR8 show 4-5 (standard) and 5-6 (double fold) phytoxicity levels. In spite of Japonica-type, Sanduljinmi and kumyoung showed 3-4 and 4-5 levels. Target resistant gene, Hydroxyphenylpyruvate dioxygenase inhibitor sensitive gene No.1 (HIS1) have been isolated from five domestic rice cultivars (Sangjubyeo, Sambaekbyeo, Sanduljinmi, Kumyoung and IR8). Results of the sequence through PCR, all five tested rice cultivars had HIS1 gene regardless to rice cultivars. And the difference between rice varieties from sequence of HIS1 were identified some variation in genes.

Because molecular oxygen functions as the final acceptor of electrons during aerobic respiration and a substrate for diverse enzymatic reactions, eukaryotes employ various mechanisms to maintain cellular homeostasis under varying oxygen concentration. Human fungal pathogens change the expression of genes involved in virulence and oxygen-required metabolisms such as ergosterol (ERG) synthesis when they encounter oxygen limitation (hypoxia) during infection. The oxygen level in plant tissues also fluctuates, potentially creating hypoxic stress to pathogens during infection. However, little is known about how in planta oxygen dynamics impact pathogenesis. In this study, we investigated oxygen dynamics in rice during infection by Magnaporthe oryzae via two approaches. First, rice leaves infected by M. oryzae were noninvasively probed using a microscopic oxygen sensor. Second, an immunofluorescence assay based on a chemical probe, pimonidazole, was used. Both methods showed that oxygen concentration in rice decreased after fungal penetration. We also functionally characterized five hypoxia-responsive genes participating in ERG biosynthesis for their role in pathogenesis. Resulting insights and tools will help study the nature of in planta oxygen dynamics in other pathosystems.

Colletotrichum has a broad host range and causes major yield losses of crops. The fungus Colletotrichum gloeosporioides is associated with anthracnose on Chinese fir. In this study, we present a high-quality draft genome sequence of C. gloeosporioides sensu stricto SMCG1#C, providing a reference genomic data for further research on anthracnose of Chinese fir and other hosts.

Hot pepper (Capsicum annuum) is one of the most consumed vegetable crops in the world and useful to human as it has many nutritional and medicinal values. Genomic resources of pepper are publically available since the pepper genomes have been completed and massive data such as transcriptomes have been deposited. Nevertheless, global transcriptome profiling is needed to identify molecular mechanisms related to agronomic traits in pepper, but limited analyses are published. Here, we report the comprehensive analysis of pepper transcriptomes during fruit ripening and pathogen infection. For the ripening, transcriptome data were obtained from placenta and pericarp at seven developmental stages. To reveal global transcriptomic landscapes during infection, leaves at six time points post-infection by one of three pathogens (Phytophthora infestans, Pepper mottle virus, and Tobacco mosaic virus P0 strain) were profiled. The massive parallel transcriptome profiling in this study will serve as a valuable resource for detection of molecular networks of fruit development and disease resistance in Capsicum annuum.

The rice blast pathogen Magnaporthe oryzae is a global threat to rice production. Here we characterized RHO2 gene (MGG_02457) that belongs to the Rho GTPase family, using a deletion mutant. This mutant ΔMorho2 exhibited no defects in conidiation and germination but developed only 6% of appressoria in response to a hydrophobic surface when compared to the wild-type progenitor. This result indicates that MoRHO2 plays a role in appressorium development. Furthermore, exogenous cAMP treatment on the mutant led to appressoria that exhibited abnormal morphology on both hydrophobic and hydrophilic surfaces. These outcomes suggested the involvement of MoRHO2 in cAMP-mediated appressorium development. ΔMorho2 mutation also delayed the development of appressorium-like structures (ALS) at hyphal tips on hydrophobic surface, which were also abnormally shaped. These results suggested that MoRHO2 is involved in morphological development of appressoria and ALS from conidia and hyphae, respectively. As expected, ΔMorho2 mutant was defective in plant penetration, but was still able to cause lesions, albeit at a reduced rate on wounded plants. These results implied that MoRHO2 plays a role in M. oryzae virulence as well.

This research was performed to establish economic threshold (ET) for rice sheath blight disease with the cultivar Odeabyeo. Total yield and yield components, such as the panicle number per hill, the spikelet per panicle, the percent ripened grain and the thousand grain weight were evaluated depending on the disease severity of sheath blight on rice, respectively. Significant negative correlation between the percent of diseased hill (PDH) and total yield was observed (r = -0.93). Moreover, negative correlation coefficients were found between PDH and spikelet per panicle, and percent ripened grain (r = -0.66 and -0.77, respectively). There were no correlations between PDH and the panical number per hill, and a thousand grain weight, respectively. In this study, economic threshold level on sheath blight disease on rice was established on 7.8% of PDH.

A disease forecast model for bacterial grain rot (BGR) of rice, which is caused by Burkholderia glumae, was developed in this study. The model, which was named 'BGRcast', determined daily conduciveness of weather conditions to epidemic development of BGR and forecasted risk of BGR development. All data that were used to develop and validate the BGRcast model were collected from field observations on disease incidence at Naju, Korea during 1998-2004 and 2010. In this study, we have proposed the environmental conduciveness as a measure of conduciveness of weather conditions for population growth of B. glumae and panicle infection in the field. The BGRcast calculated daily environmental conduciveness, Ci , based on daily minimum temperature and daily average relative humidity. With regard to the developmental stages of rice plants, the epidemic development of BGR was divided into three phases, i.e., lag, inoculum build-up and infection phases. Daily average of Ci was calculated for the inoculum build-up phase (Cinf ) and the infection phase (Cinc ). The Cinc and Cinf were considered environmental conduciveness for the periods of inoculum build-up in association with rice plants and panicle infection during the heading stage, respectively. The BGRcast model was able to forecast actual occurrence of BGR at the probability of 71.4% and its false alarm ratio was 47.6%. With the thresholds of Cinc = 0.3 and Cinf = 0.5, the model was able to provide advisories that could be used to make decisions on whether to spray bactericide at the pre- and post-heading stage.

Conidiation and appressorium differentiation are key processes for polycyclic dissemination and infection in many pathogens. Our previous study using DNA microarray led to the discovery of the MoYAK1 gene in Magnaporthe oryzae that is orthologous to YAK1 in Saccharomyces cerevisiae. Although the mechanistic roles of YAK1 in S. cerevisiae have been described, roles of MoYAK1 in M. oryzae, a phytopathogenic fungus responsible for rice blast, remain uncharacterized. Targeted disruption of MoYAK1 results in pleiotropic defects in M. oryzae development and pathogenicity. The ΔMoyak1 mutant exhibits a severe reduction in aerial hyphal formation and conidiation. Conidia in the ΔMoyak1 are delayed in germination and demonstrate decreased glycogen content in a conidial age-dependent manner. The expression of hydrophobin-coding genes is dramatically changed in the ΔMoyak1 mutant, leading to a loss of surface hydrophobicity. Unlike the complete inability of the ΔMoyak1 mutant to develop appressoria on an inductive surface, the mutant forms appressoria of abnormal morphology in response to exogenous cyclic adenosine-5'-monophosphate and host-driven signals, which are all defective in penetrating host tissues due to abnormalities in glycogen and lipid metabolism, turgor generation and cell wall integrity. These data indicate that MoYAK1 is a protein kinase important for the development and pathogenicity of M. oryzae.

Rice diseases, responsible for about 8% of annual yield losses of rice production in South Korea, are likely to be affected by meteorological changes resulting from global climate change. No critical evaluation has yet been made of the potential impacts of climate change on rice diseases in South Korea. This study involved a quantitative analysis of two rice diseases that result in the greatest damages, leaf blast and sheath blight, using the generic epidemiological model, EPIRICE. The goals of the study were to evaluate the EPIRICE model using historical rice disease incidence data and fine-scale weather data for 2002–2010 in South Korea, and then to assess likely changes in national disease probabilities under climate change scenarios to allow for more robust planning. EPIRICE was calibrated and validated against observed disease incidence data for leaf blast and sheath blight. Observed and simulated epidemics for both diseases were compared using disease progress curves and the area under the disease progress curve. Statistical equivalence and quantitative envelope of acceptance tests were applied on the deviations of the model outputs to evaluate whether EPIRICE was sufficiently accurate for its intended purpose. The level of agreement between the observed and simulated epidemics was high and the model was found to be valid according to the performance criteria. Predicted daily climate data based on the Intergovernmental Panel on Climate Change (IPCC) Representative Concentration Pathways (RCP) 8.5 and 4.5 scenarios were used as inputs into the EPIRICE model. Outputs from the model runs were displayed using geographic information systems (GIS) to show future changes in potential epidemics for both rice diseases. Overall, the incidence of epidemics for both diseases was simulated to gradually decrease toward 2100. These results can be used to interpret the likely magnitude of changes in disease risk in regions of South Korea and to estimate climate change impacts on disease losses and disease control.

Background Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants. Results We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific. Conclusions Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1341-9) contains supplementary material, which is available to authorized users.

SummaryTransposable elements (TEs) provide major evolutionary forces leading to new genome structure and species diversification. However, the role of TEs in the expansion of disease resistance gene families has been unexplored in plants. Here, we report high-quality de novo genomes for two peppers (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum). Dynamic genome rearrangements involving translocations among chromosome 3, 5 and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs exhibited great abundance across the angiosperms, with most cases lineage-specific and thus recent events. Our study revealed that retroduplication has played key roles in the emergence of new disease-resistance genes in plants.

Genomes contain a large number of unique genes which have not been found in other species. Although the origin of such “orphan” genes remains unclear, they are thought to be involved in species-specific adaptive pro cesses. Here, we analyzed seven orphan genes (MoSPC1 to MoSPC7) prioritized based on in planta expressed sequence tag data in the rice blast fungus, Magnaporthe oryzae. Expression analysis using qRT-PCR confirmed the expression of four genes (MoSPC1, MoSPC2, MoSPC3 and MoSPC7) during plant infection. However, individual deletion mutants of these four genes did not differ from the wild-type strain for all phenotypes examined, including pathogenicity. The length, GC contents, codon adaptation index and expression during mycelial growth of the four genes suggest that these genes formed during the evolutionary history of M. oryzae. Synteny analyses using closely related fungal species corroborated the notion that these genes evolved de novo in the M. oryzae genome. In this report, we discuss our inability to detect phenotypic changes in the four deletion mutants. Based on these results, the four orphan genes may be products of de novo gene birth processes, and their adaptive potential is in the course of being tested for retention or extinction through natural selection.

Rice blast disease caused by Magnaporthe oryzae is one of the most serious diseases of cultivated rice (Oryza sativa L.) in most rice-growing regions of the world. In order to investigate early response genes in rice, we utilized the transcriptome analysis approach using a 300 K tilling microarray to rice leaves infected with compatible and incompatible M. oryzae strains. Prior to the microarray experiment, total RNA was validated by measuring the differential expression of rice defense-related marker genes (chitinase 2, barwin, PBZ1, and PR-10) by RT-PCR, and phytoalexins (sakuranetin and momilactone A) with HPLC. Microarray analysis revealed that 231 genes were up-regulated (>2 fold change, p < 0.05) in the incompatible interaction compared to the compatible one. Highly expressed genes were functionally characterized into metabolic processes and oxidation-reduction categories. The oxidative stress response was induced in both early and later infection stages. Biotic stress overview from MapMan analysis revealed that the phytohormone ethylene as well as signaling molecules jasmonic acid and salicylic acid is important for defense gene regulation. WRKY and Myb transcription factors were also involved in signal transduction processes. Additionally, receptor-like kinases were more likely associated with the defense response, and their expression patterns were validated by RT-PCR. Our results suggest that candidate genes, including receptor-like protein kinases, may play a key role in disease resistance against M. oryzae attack.

Although multiple transcription factors (TFs) have been characterized via mutagenesis to understand their roles in controlling pathogenicity and infection-related development in Magnaporthe oryzae, the causal agent of rice blast, if and how forkhead-box (FOX) TFs contribute to these processes remain to be characterized. Four putative FOX TF genes were identified in the genome of M. oryzae, and phylogenetic analysis suggested that two of them (MoFKH1 and MoHCM1) correspond to Ascomycota-specific members of the FOX TF family while the others (MoFOX1 and MoFOX2) are Pezizomycotina-specific members. Deletion of MoFKH1 (ΔMofkh1) resulted in reduced mycelial growth and conidial germination, abnormal septation and stress response, and reduced virulence. Similarly, ΔMohcm1 exhibited reduced mycelial growth and conidial germination. Conidia of ΔMofkh1 and ΔMohcm1 were more sensitive to one or both of the cell cycle inhibitors hydroxyurea and benomyl, suggesting their role in cell cycle control. On the other hand, loss of MoFOX1 (ΔMofox1) did not show any noticeable changes in development, pathogenicity, and stress response. Deletion of MoFOX2 was not successful even after repeated attempts. Taken together, these results suggested that MoFKH1 and Mo-HCM1 are important in fungal development and that MoFKH1 is further implicated in pathogenicity and stress response in M. oryzae.

Center for Fungal Genetic Resources, PlantGenomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151 -921, Korea(Received on April 30, 2013; Revised on May 25; Accepted on May 25, 2013)Rice blast fungus, Magnaporthe oryzae, inflicts seriousdamage to global rice production. Due to high vari-ability of this fungal pathogen, resistance of newly-released rice cultivars is easily broken down. To under-stand the population structure of M. oryzae, we analyz-ed the genetic diversity of the Korean population usingmultilocus microsatellite typing. Eleven microsatellitemarkers were applied to the population of 190 riceisolates which had been collected in Korea for twodecades since the 1980’s. Average values of gene diver-sity and allele frequency were 0.412 and 6.5, respective-ly. Comparative analysis of the digitized allele informationrevealed that the Korean population exhibited a similarlevel of allele diversity to the integrated diversity of theworld populations, suggesting a particularly high diver-sity of the Korean population. Therefore, these micro-satellite markers and the comprehensive collection offield isolates will be useful genetic resources to identifythe genetic diversity of M. oryzae population.Keywords : gene diversity, Magnaporthe oryzae, simplesequence repeat Rice is a major staple food for over a half of the world’spopulation in charge of more than 20% of their daily calorieintake (Seck et al., 2012; Skamnioti and Gurr, 2009). Itsstable production is socioeconomically important in inter-national food security. Rice blast disease caused by theascomycete Magnaporthe oryzae occurs in every rice-growing region worldwide, resulting in serious damage torice production (Kato, 2001; Ou, 1985). High variability ofthis fungal population often leads to break down ofresistance in newly-released rice cultivars in the fieldsbecause new races which overcome the resistance are fre-quently emerged out of the mixed population of M. oryzae(Ou, 1980; Valent and Chumley, 1991; Zhu et al., 2000).Understanding the structure and the dynamics of the patho-gen population is essential for development of sustainablestrategies for disease management of rice blast (Meung etal., 2003). One of the popular markers for characterizing populationof M. oryzae is restriction fragment-length polymorphism(RFLP) analysis using repetitive DNA sequences calledMGR (Magnaporthe grisea repeat) (Borromeo et al., 1993;Hamer et al., 1989). Since MGRs are characteristically ab-undant in the genome of the rice-infecting isolates (Dean etal., 2005), the numbers of bands in Southern hybridizationassay can distinguish between the rice-infecting and theweed-infecting isolates (Hamer et al., 1989). Furthermore,MGR-RFLP has been employed to characterize populationdynamics of rice-infecting isolates in different populationsover the world (Levy et al., 1991; Levy et al., 1993; Park etal., 2003; Xia et al., 1993; Zeigler et al., 1995). AlthoughMGR-RFLP has limitations in correlating genotypes withpathotypes within the rice-infecting populations, it is still auseful marker in understanding the genetic diversity offungal populations. However, MGR-RFLP is time-consum-ing, labor-intensive and is not based on one-locus alleleswhich are used in measuring classical population para-meters (Adreit et al., 2007; Brondani et al., 2000). Microsatellites, also known as Simple Sequence Repeats(SSR), are tandemly repeated sequences of short lengthDNA (usually 2−6 bp) found in all prokaryotic andeukaryotic genomes (Zane et al., 2002). They show varia-tion in the number of repeats at a specific locus and strandslippage replication is generally considered to contribute tosuch variation (Levinson and Gutman, 1987; Tautz, 1989).Due to their prevalence and abundance in the genome, easydetection by PCR, and length polymorphism at a givenlocus, they have become a popular and powerful molecularmarker for genetic and physical mapping, forensic DNAstudies, and population genetics (Jarne and Lagoda, 1996;Tautz, 1989). Since the genome sequence information of M. oryzaebecame publicly available (Dean et al., 2005), the computa

This study was carried out to investigate yield loss due to soybean leaf spot disease caused by Cercospora sojina Hara and to determine the economic threshold level. The investigations revealed highly significant correlations between disease severity (diseased leaf area) and yield components (pod number per plant, total grain number per plant, total grain weight per plant, percent of ripened grain, weight of hundred seed, and yield). The correlation coefficients between leaf spot severity and each component were �0.90, �0.90, �0.92, �0.99, �0.90 and �0.94, respectively. The yield was inversely proportional to the diseased leaf area increased. The regression equation, yield prediction model, between disease severity (x) and yield (y) was obtained as y= �3.7213x + 354.99 (R 2 = 0.9047). Based on the yield prediction model, economic injury level and economic threshold level could be set as 3.3% and 2.6% of diseased leaf area of soybean.

Seed coat of hairy vetch is very thick and hard, and difficult to absorb water during germination. It requires much time that cotyledon comes out from seed coat. Therefore this experiment was carried out to increase the germination rate by enhancing water absorption through water-soaking of seed, chemical scarification by sulfuric acid, and mechanical scarification on seed coat. Water-soaking for 5 hours seemed to be highly effective in enhancing germination rate. Although not significant, water-soaking resulted in increase of germination rate by 9%. Effect of soaking temperature was not significant, but early germination rate was increased to be 5.0%, 31.7% and 48.3% at , and , respectively. Mechanical scarification of seed coat led to a germination rate of 97% whereas intact seed showed that of 65%. Chemical scarification by sulfuric acid for 10min, 20min and 30min resulted in a germination rate of 76.7%, 74.7% and 96.0% respectively. It is clear that scarification increased germination rate.

The dual inoculation response of soybean with rhizobium and mycorrhiza was examined in pot vermiculite and field soils. In order to select a symbiotically compatible mycorrhiza with Bradyrhizobium japonicum, a highly germinating spore among 60 strains from 32 upland soils in southern part of Korea was obtained in Acaulospora sp., Gigaspora sp. and Glomus sp., respectively. As a result of dual inoculation of Glycin max cv. Dajangkong and Eunhakong both with cells of B. japonicum YCK 213 and 10 spores of each mycorrhiza in vermiculite pot, only Glomus sp. treatment together with the rhizobium showed significant increase () both in shoot dry wt and nodule mass of not Eunhakong but Dajangkong. In red-yellow soils with pH 5.2() and 203 mg of Lancaster P per kg of soil, in which cells of B. japonicum and spores of mycorrhizae per gram of soil were naturalized, grain yield of G. max cv. Dajangkong was increased to 3.9% by dual inoculation both of cells of B. japonicum and 10 spores of mycorrhizae per two seeds under condition applied with 30 kg and 34 kg per hectare compared to conventionally fertilized plot (2.75 MT ) added with 30 kg N . However, there was not significant.

SUMMARYAlthough plant genome sizes are extremely diverse, the mechanism underlying the expansion of hugegenomes that did not experience whole-genome duplication has not been elucidated. The pepper, Capsicumannuum,isanexcellentmodelforstudiesofgenomeexpansionduetoitslargegenomesize(2700 Mb)andtheabsence of whole genome duplication. As most of the pepper genome structure has been identified asconstitutiveheterochromatin,weinvestigatedtheevolutionofthisregionindetail.Ourfindingsshowthattheconstitutive heterochromatin in pepper was actively expanded 20.0–7.5 million years ago through a massiveaccumulation of single-type Ty3/Gypsy-like elements that belong to the Del subgroup. Interestingly,derivatives of the Del elements, such as non-autonomous long terminal repeat retrotransposons and long-unit tandem repeats, played important roles in the expansion of constitutive heterochromatic regions. Thisexpansion occurred not only in the existing heterochromatic regions but also into the euchromatic regions.Furthermore, our results revealed a repeat of unit length 18–24 kb. This repeat was found not only in thepepper genome but also in the other solanaceous species, such as potato and tomato. These results representa characteristic mechanism for large genome evolution in plants.Keywords: genome expansion, heterochromatin, LTR retrotransposon, Capsicum annuum, tandem repeat.INTRODUCTIONHeterochromatin is the tightly condensed chromosomeregion that is visualized by staining of pachytene chro-mosomes during interphase of cell division. Heterochro-matin can be divided into two types, constitutive andfacultative heterochromatin, according to the sequencecomponents in the heterochromatic region (Grewal andJia, 2007). Constitutive heterochromatin mainly consists ofdense repeat elements and is observed at flanking regionsof centromeres and also near telomere or knob regions. Incontrast, facultative heterochromatin can be found in gene-rich regions and the chromatin state can be changed inresponse to cellular signals and gene activity. Constitutiveheterochromatin maintains a condensed structure through-out the cell cycle and comprises large parts of eukaryoticgenomes.Formation of constitutive heterochromatin structureoccurs by epigenetic control via RNA interference of repet-itivesequences(Volpeet al.,2002;Lippmanet al.,2004).Therepeat elements in the constitutive heterochromatin arelargely divided into two types: class I retrotransposons thatuse an RNA transcript as an intermediate and class IItransposons that use DNA as an intermediate (Wicker et al.,2007). In plant genomes, the class I retrotransposons,particularly the long terminal repeat (LTR) retrotransposons,are major factors that constitute the heterochromatinsequence(CSHL/WUGSC/PEBArabidopsisSequencingCon-sortium., 2000; Mao et al., 2000; Meyers et al., 2001; Wanget al., 2006).In general, heterochromatic regions are considered lessimportant than euchromatic regions due to the extremely

Rice bakanae disease, caused by the fungus Fusarium fujikuroi, is one of the most important rice diseases anddistributed widely in Asia. Resistance screening system in rice field had been established. However, theevaluation results of the system vary according to the environmental conditions when the test is conducted. Todevelop precise and rapid evaluation method of disease resistance of rice to bakanae disease, in vitro screeningsystem was attempted in this study. The six cultivars namely, ‘Nampyeongbyeo’, ‘Junambyeo’,‘Chucheongbyeo’, ‘Samcheonbyeo’, ‘Odaebyeo’ and ‘Hwasinbyeo’ were tested. They were planted onto MSagar medium (10 ml) in test tube (450 mm × φ30 mm) and incubated at 25oC and 28oC in growth chamberunder 12 hr light condition. Symptoms of over growth appeared a few days after seeding and then seedlingwere withered 2−3 weeks after over growth. The disease symptoms such as leaf dryness on top of rice wereappeared in the ‘Nampyeongbyeo’ from 28 days at the concentration of 105 spores/ml culturing at 28oC andthen withered completely 35 days after seeding. Whereas the other varieties withered entirely 19−23 daysafter seeding. Using the in vitro seedling screening method, 72 rice varieties were investigated to selectresistant cultivar. Finally, two resistant cultivars (‘Nampyeongbyeo’ and ‘Inwolbyeo’) and seven moderatelyresistant cultivars (‘Hwadongbyeo’, ‘Seokjeongbyeo’, ‘Samgwangbyeo’, ‘Sampyeongbyeo’, ‘Nonghobyeo’,‘Heukjinjubyeo’ and, ‘Joanbyeo’) were selected. If in vitro seedling screening method was used for evaluationof bakanae disease resistance, it would be completed within 35 days after sowing of rice seed.

Rice blast, caused by the pathogen Magnaporthe oryzae, is a serious hindrance to rice production and has emerged as an important model for the characterization of molecular mechanisms relevant to pathogenic development in plants. Similar to other pathogenic fungi, conidiation plays a central role in initiation of M. oryzae infection and spread over a large area. However, relatively little is known regarding the molecular mechanisms that underlie conidiation in M. oryzae. To better characterize these mechanisms, we identified a conidiation-defective mutant, ATMT0225B6 (MoCDC15T-DNA), in which a T-DNA insertion disrupted a gene that encodes a homolog of fission yeast cdc15, and generated a second strain containing a disruption in the same allele (ΔMoCDC15T-DNA). The cdc15 gene has been shown to act as a coordinator of the cell cycle in yeast. Functional analysis of the MoCDC15T-DNA and ΔMoCDC15T-DNA mutants revealed that MoCDC15 is required for conidiation, preinfection development and pathogenicity in M. oryzae. Conidia from these mutants were viable, but failed to adhere to hydrophobic surface, a crucial step required for subsequent pathogenic development. All phenotypic defects observed in mutants were rescued in a strain complemented with wild type MoCDC15. Together, these data indicate that MoCDC15 functions as a coordinator of several biological processes important for pathogenic development in M. oryzae.

To use barley as a green manure crop, this study has been conducted in Suwon, Gyeonggi-do to establish the barley green manure (BGM)-rice cropping system with emphasis on soil incorporation date and BGM density. The nitrogen (N) contents of rye and barley, grass green manure crops, were 1.4~2.4% at early growth stage and decreased rapidly to 0.6~1.0% at late growth stage. The biomass of barley was 449 kg/l0a at heading stage (HS) and increased to 421 kg/10a at 10 days after heading stage (DAH), 473 kg/10a at 20 DAH. C/N ratio of BGM was the lowest 26.3 at HS. The N contents of BGM was in the range of 0.9~1.5%, the highest at HS and gradually decreased, and the output of N were 4.3-6.3 kg/10a. The total amount of nitrogen, phosphorous and potassium of BGM showed the highest level at 10 DAH. Culm length of rice was relatively longer as the BGM application time was delayed. The application of BGM into soil increased plant height of rice by 7.2~7.7 em as compared to the plants treated with commercial fertilizer at recommended rate. but panicle length of rice showed a similar tendency in both the soil-applied of BGM and commercial fertilizer. N contents of unhulled rice was the highest at HS of BGM and followed by 10 DAH of BGM and 20 DAH of BGM. This trend could also be seen in rice straw. The yield of rice in the soil-applied of BGM was 10~15% lower than in the soil-applied of commercial fertilizer. Based on this study, application of BGM made it possible to save 30~50% of application amount of nitrogen fertilizer for following crops.

Bakanae disease symptom were observed in barnyard grass in paddy field in Heanam, Jeonnam. The infected plants were blighted and white mass of spore were formed on the stem. Fusarium species were isolated from infected stem and the isolates were identified as Fusarium fujikuroi based on their morphological and molecular characteristics. The isolates of F. fujikuroi were assigned to reference of F. fujikuroi among related Fusarium species based on the translation elongation factor 1-alpha gene sequence. Pathogenicity of the fungal isolates was confirmed on seedlings of rice and barnyard grass by artificial inoculation. The results indicated that barnyard grass can be inoculum source of Bakanae disease on rice. Thus, effective weed management is necessary to Bakanae disease control and healthy seed production.

Soft rot caused by Rhizopus oryzae occurred on unshiu orange (Citrus unshiu Marc.) sampled from commercial markets in Jinju, Korea, 2010. The first symptom of soft rot on orange is a water-soaked appearance of the affected tissue. The infected parts later disintegrated into a mushy mass of disorganized cells followed by rapid softening of the diseased tissue. The lesion on orange was rapidly softened and rotted, then became brown or dark brown. Optimum temperature for mycelial growth of the causal fungus on potato dextrose agar was 30℃ and growth was still apparent at 37℃. Sporangiophores were 6~20 μm in diameter. Sporangia were globose and 40~200 μm in size. The color of sporangia was brownish-grey to blackish-grey at maturity. Sporangiospores were sub-globose, brownish- black streaked and 4~10 μm in size. Columella were globose to sub-globose and 85~120 μm in size. On the basis of mycological characteristics, pathogenicity test, and the ITS sequence analysis, the causal fungus was identified as Rhizopus oryzae. To our knowledge, this is the first report of soft rot caused by R. oryzae on unshiu orange in Korea.

Department of Plant Pathology, The Pennsylvania State University, University Park 16802, USA(Received on September 27, 2010; Accepted on November 2, 2010)Genetic instability of the rice blast fungus Magnaportheoryzae has been suggested as a major factor underlyingthe rapid breakdown of host resistance in the field.However, little information is available on the mech-anism of genetic instability. In this study, we assessedthe stability of repetitive DNA elements and several keyphenotypic traits important for pathogenesis afterserially transferring two isolates though rice plants andan artificial medium. Using isolate 70-15, we obtained atotal of 176 single-spore isolates from 10 successiverounds of culturing on artificial medium. Another 20isolates were obtained from germ tubes formed at thebasal and apical cells of 10 three-celled conidia. Addi-tionally, 60 isolates were obtained from isolate KJ201after serial transfers through rice plants and an arti-ficial medium. No apparent differences in phenotypes,including mycelial growth, conidial morphologies, coni-diation, conidial germination, appressorium formation,and virulence, or in DNA fingerprints using MGR586,MAGGY, Pot2, LINE, MG-SINE and PWL2 as probeswere observed among isolates from the same parent iso-late. Southern hybridization and sequence analysis oftwo avirulence genes, AVR-Pita1 and AVR-Pikm, show-ed that both genes were also maintained stably during10 successive generations on medium and plants. How-ever, one reversible loss of restriction fragments wasfound in the telomere-linked helicase gene ( TLH1) family,suggesting some telomere regions may be more unstablethan the rest of the genome. Taken together, our resultssuggest that phenotype and genotype of M. oryzae iso-lates do not noticeably change, at least up to 10 successivegenerations on a cultural medium and in host plants.Keywords :genetic stability, genotypes, Magnaporthe grisea,phenotypes, repeat sequencesMagnaporthe oryzae is a heterothallic ascomycete fungusthat causes rice blast, one of the most devastating diseasesin rice throughout the world. Since there is no evidence forsexual reproduction in the field in most parts of the world,asexual spores (conidia) are the most important source ofinoculum. Through the production of conidia, M. oryzaenormally undergoes 8-11 disease cycles in rice plants underfield conditions during one growing season (Han et al.,1997). Although asexual reproduction is expected to pro-duce genetically identical clones, the high rate of appear-ance of new races with the ability to infect previouslyresistant varieties of rice, suggests that M. oryzae may havehigh mutation rates in avirulence genes, which determinerace (also called pathotype in M. oryzae) (Kang et al., 2001;Kang and Lee, 2000; Zhou et al., 2007).Although the most effective control strategy for rice blastis cultivating resistant varieties, it has often achieved onlyshort-term success due to frequent breakdown of newlyintroduced resistance. This resistance breakdown has beenattributed to genetic variability in M. oryzae (Bonman et al.,1986; Correa-Victoria and Zeigler, 1993; Correa-Victoriaand Zeigler, 1993). Various mechanisms have been sug-gested to explain the frequent generation of race variants,including heterokaryosis, parasexuality, and mutations(Genovesi and Magill, 1976; Wu and Magill, 1995; Xia andCorrell, 1995; Zeigler et al., 1997). Parasexual recombina-tion of genetic markers, resulting new genetic variants, hasbeen demonstrated in the laboratory for M. oryzae, sug-gesting the potential for parasexual recombination togenerate new races (Noguchi et al., 2006; Zeigler et al.,1997). However, no evidence for parasexuality has beenfound in nature for M. oryzae. The activity of transposableDNA elements is another possible mechanism that has beensuggested (Kang et al., 2001; Nishimura et al., 2000; Zhouet al., 2007). For example, mobilization of Pot2, Pot3, andLINE elements has been shown to cause variation by insert-ing into promoter region or coding sequences of avirulence

The purpose of this study was to evaluate the antioxidant compounds and their activities of the methanolic extracts from milling fractions of sorghum. To determine the antioxidant compounds in the methanolic extract from the milling fractions, the content of polyphenol, flavonoids, tannin, anthocyanins and proanthocyanidin were measured by spectrophotometric methods. These were evaluated for antioxidative activities by ABTS and DPPH radical scavenging assays. The extraction yield of hull, bran and grain of sorghum were 9.95, 19.05 and 2.94%, respectively. The methanolic extracts from sorghum bran showed generally higher antioxidant activities than the extracts from hull and grain of sorghum. In addition, antioxidant compounds distributed much higher contents in sorghum bran extract than in the extracts from hull and grain of sorghum. A significant correlation was also noted between free radical scavenging activity and polyphenolic compounds. The results of this study show that notable antioxidant activity in sorghum bran is considered to have significant health benefits.

During the period from 1999 to 2008, we surveyed the major diseases incidence of rice in Korea. Leaf blast showed 0.85% of the diseased leaf area in 2000 and then consistently decreased to 0.02% by 2008. However, panicle blast irregularly appeared by the years depending on weather conditions for disease development from heading to milk stage of rice. Diseased lesion height of sheath blight had the lowest (10.1%) incidence in 2001 and the highest (21.4%) incidence in 2007. A negative corelation ($r