Wild Rice Oryza Rufipogon Research Articles

Evaluation of Sheath Blight Resistance in Diverse Rice Varieties Under Artificial Inoculation and Field Conditions

Rice (Oryza sativa L.) a vital food crop for nearly half of the global population, facing significant threats from various biotic and abiotic stresses. Among biotic stresses, diseases pose the most common challenge. Sheath blight, caused by soil-borne fungal pathogen Rhizoctonia Solani Kühn (R. solani), is a major concern, leading to substantial damage to rice and cereal crops worldwide. This study evaluated sheath blight resistance across diverse rice varieties, including short grain, long grain, aromatic, hybrid, and wild types, under both artificial inoculation and field conditions. Ten host plant species were assessed for resistance to sheath blight caused by Rhizoctonia Solani, using physiological screening one-week post-inoculation. The highly virulent R. solani isolate (AG-1 IA anastomosis group) was cultured on PDA media, covering the entire plate 3 to 5 days. Screening of cultivated rice varieties, was conducted using field conditions and humidified chamber methods, with results confirmed through molecular characterization. Among the ten cultivated rice varieties, Arize 6444 and Dhanya 748 exhibited the lowest disease index, classifying them as moderately resistant. In contrast, Kalanamak and Pusa Basmati were highly susceptible, displaying high disease indices. Among wild rice accessions, Oryza rufipogon showed a disease index of five or less. Visual ratings indicated the highest susceptibility in Kalanamak, followed by Pusa Basmati and Swarna sub-1, while the lowest visual ratings were observed in wild rice accessions Oryza australiensis and Oryza rufipogon across all tested hosts. The findings underscore the importance of identifying resistant rice varieties to manage sheath blight effectively. The moderately resistant cultivars and wild rice accessions identified in this study offer valuable genetic resources for breeding programs aimed at enhancing sheath blight resistance in rice.

Examination of the Expression Profile of Resistance Genes in Yuanjiang Common Wild Rice (Oryza rufipogon).

The rice blight poses a significant threat to the rice industry, and the discovery of disease-resistant genes is a crucial strategy for its control. By exploring the rich genetic resources of Yuanjiang common wild rice (Oryza rufipogon) and analyzing their expression patterns, genetic resources can be provided for molecular rice breeding. The target genes' expression patterns, subcellular localization, and interaction networks were analyzed based on the annotated disease-resistant genes on the 9th and 10th chromosomes in the rice genome database using fluorescent quantitative PCR technology and bioinformatics tools. Thirty-three disease-resistant genes were identified from the database, including 20 on the 9th and 13 on the 10th. These genes were categorized into seven subfamilies of the NLR family, such as CNL and the G subfamily of the ABC family. Four genes were not expressed under the induction of the pathogen Y8, two genes were significantly down-regulated, and the majority were up-regulated. Notably, the expression levels of nine genes belonging to the ABCG, CN, and CNL classes were significantly up-regulated, yet the expression levels varied among roots, stems, and leaves; one was significantly expressed in the roots, one in the stems, and the remaining seven were primarily highly expressed in the leaves. Two interaction network diagrams were predicted based on the seven highly expressed genes in the leaves: complex networks regulated by CNL proteins and specific networks controlled by ABCG proteins. The disease-resistant genes on the 9th chromosome are actively expressed in response to the induction of rice blight, forming a critical gene pool for the resistance of Yuanjiang common wild rice (O. rufipogon) to rice blight. Meanwhile, the disease-resistant genes on the 10th chromosome not only participate in resisting the rice blight pathogen but may also be involved in the defense against other stem diseases.

Characterization of endophytic bacteria isolated from wild rice plants in the Mekong Delta, Vietnam

Abstract. Thi QVC, Minh NLK, Thuy NP, Tat TQ, Tran T. 2024. Characterization of endophytic bacteria isolated from wild rice plants in the Mekong Delta, Vietnam. Biodiversitas 25: 2576-2585. Endophytic bacteria bring many benefits to plants, such as stimulating plant growth and inhibiting many microbial pathogens that cause plant diseases. Hence, this investigation aimed to evaluate the association of endophytic bacteria with wild rice (Oryza rufipogon) that can fix nitrogen, solubilize phosphorus and produce indole-3-acetic acid (IAA). Twelve-five bacterial strains were recovered from wild rice stems and roots collected from Vinh Long and Tien Giang provinces of the Mekong Delta. Among these strains, six had phosphorus solubilizing and seven had nitrogen-fixing activity. Strain BR3.5 fixed the highest nitrogen, i.e. ammonia (NH4+) content of 0.109 ± 0.002 mg/L after eight-day incubation. However, the highest phosphorus solubilization was recorded in two isolates, RR3.7 and RR1.1, with clear zone diameters of 0.800 ± 0.020 mm and 0.800 ± 0.030 mm, respectively. In addition, bacterial strains could synthesize IAA, and BR2.5 produced the highest, i.e., 0.067 ± 0.002 ?g/mL, IAA after eight-day incubation. Notably, strain BR3.5 exhibited multiple activities like nitrogen fixation (0.109 ± 0.002 mg/L), phosphorus solubilization (1.02 ± 0.002 mm), and IAA synthesis (0.056 ± 0.00 ?g/mL). Strain BR3.5 was identified as Pantoea sp. based on 16S rRNA gene sequencing (92.69% similarity) together with morpho-physiological and biochemical characteristics. The findings indicate that strain BR3.5 may be used for the production of biofertilizers for rice farming.

The superior allele LEA12OR in wild rice enhances salt tolerance and yield.

Soil salinity has negative impacts on food security and sustainable agriculture. Ion homeostasis, osmotic adjustment and reactive oxygen species scavenging are the main approaches utilized by rice to resist salt stress. Breeding rice cultivars with high salt tolerance (ST) and yield is a significant challenge due to the lack of elite alleles conferring ST. Here, we report that the elite allele LEA12OR, which encodes a late embryogenesis abundant (LEA) protein from the wild rice Oryza rufipogon Griff., improves osmotic adjustment and increases yield under salt stress. Mechanistically, LEA12OR, as the early regulator of the LEA12OR-OsSAPK10-OsbZIP86-OsNCED3 functional module, maintains the kinase stability of OsSAPK10 under salt stress, thereby conferring ST by promoting abscisic acid biosynthesis and accumulation in rice. The superior allele LEA12OR provides a new avenue for improving ST and yield via the application of LEA12OR in current rice through molecular breeding and genome editing.

Exploring the mating systems of wild rice Oryza rufipogon and O. nivara: implications for population genetic variation

Exploring the mating systems of wild rice Oryza rufipogon and O. nivara: implications for population genetic variation

Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice

The abundant genetic variation harbored by wild rice (Oryza rufipogon) has provided a reservoir of useful genes for rice breeding. However, the genome of wild rice has not yet been comprehensively assessed. Here, we report the haplotype-resolved gapless genome assembly and annotation of wild rice Y476. In addition, we develop two sets of chromosome segment substitution lines (CSSLs) using Y476 as the donor parent and cultivated rice as the recurrent parents. By analyzing the gapless reference genome and CSSL population, we identify 254 QTLs associated with agronomic traits, biotic and abiotic stresses. We clone a receptor-like kinase gene associated with rice blast resistance and confirm its wild rice allele improves rice blast resistance. Collectively, our study provides a haplotype-resolved gapless reference genome and demonstrates a highly efficient platform for gene identification from wild rice.

Transcription factor encoding gene OsC1 regulates leaf sheath color through anthocyanidin metabolism in Oryza rufipogon and Oryza sativa

Carbohydrates, proteins, lipids, minerals and vitamins are nutrient substances commonly seen in rice grains, but anthocyanidin, with benefit for plant growth and animal health, exists mainly in the common wild rice but hardly in the cultivated rice. To screen the rice germplasm with high intensity of anthocyanidins and identify the variations, we used metabolomics technique and detected significant different accumulation of anthocyanidins in common wild rice (Oryza rufipogon, with purple leaf sheath) and cultivated rice (Oryza sativa, with green leaf sheath). In this study, we identified and characterized a well-known MYB transcription factor, OsC1, through phenotypic (leaf sheath color) and metabolic (metabolite profiling) genome-wide association studies (pGWAS and mGWAS) in 160 common wild rice (O. rufipogon) and 151 cultivated (O. sativa) rice varieties. Transgenic experiments demonstrated that biosynthesis and accumulation of cyanidin-3-Galc, cyanidin 3-O-rutinoside and cyanidin O-syringic acid, as well as purple pigmentation in leaf sheath were regulated by OsC1. A total of 25 sequence variations of OsC1 constructed 16 functional haplotypes (higher accumulation of the three anthocyanidin types within purple leaf sheath) and 9 non-functional haplotypes (less accumulation of anthocyanidins within green leaf sheath). Three haplotypes of OsC1 were newly identified in our germplasm, which have potential values in functional genomics and molecular breeding of rice. Gene-to-metabolite analysis by mGWAS and pGWAS provides a useful and efficient tool for functional gene identification and omics-based crop genetic improvement.

Different contributions of PROG1 and TAC1 to the angular kinematics of the main culm and tillers of wild rice (Oryza rufipogon).

PROG1is necessary but insufficient for the main culm inclination while TAC1partially takes part in it, and both genes promote tiller inclination in Asian wild rice. Asian wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. sativa), has a prostrate architecture, with tillers branching from near the ground. The main culm of each plant grows upward and then tilts during the vegetative stage. Genes controlling tiller angle have been reported; however, their genetic contributions to the culm movement have not been quantified. Here, we quantified their genetic contributions to angular kinematics in the main culm and tillers. For the main culm inclination, one major QTL surrounding the PROG1 region was found. In cultivated rice, tillers firstly inclined and lately rose, while it kept inclining in wild rice. It was suggested that PROG1 affected the tiller elevation angle in the later kinematics, whereas TAC1 was weakly associated with the tiller angle in the whole vegetative stage. Micro-computed tomography (micro-CT) suggested that these angular changes are produced by the bending of culm bases. Because near-isogenic lines (NILs) of wild rice-type Prog1 and Tac1 alleles in the genetic background of cultivated rice did not show the prostrate architecture, the involvement of another gene(s) for inclination of the main culm was suggested. Our findings will not only contribute to the understanding of the morphological transition during domestication but also be used in plant breeding to precisely reproduce the ideal plant architecture by combining the effects of multiple genes.

Dissecting the Genetic Relationship between Root Morphological Traits with Grain Yield of Introgression Lines (ILs) Derived from Wild Rice (Oryza rufipogon Griff) under Low Soil Phosphorous Condition

Soil phosphorous (P) deficiency is one of the limiting factors in rice production in both upland and rainfed lowland ecosystems. Since P is diffusion limited in depleted root zones, understanding the link between root morphological traits and yields is crucial for improving rice productivity. To understand this link, phenotypic screening experiment was conducted for the 38 ILs (BC1F6) derived from the wild rice (Oryza rufipogon Griff) along with the six checks in specialized low P plots and normal soil P (RDF) plot at ICAR-IIRR, Hyderabad during rice growing season Kharif-2020 by adapting augmented block design. The genotypes were screened for grain yield along with root traits such as tiller number per plant (TN), shoot length (SL), root length (RL), root volume (RV), shoot fresh weight (SFW), shoot dry weight (SDW), root fresh weight (RFW), root dry weight (RDW), root to shoot ration on wet weight basis (RSRWW), root to shoot on dry weight basis (RSRDW), SPAD chlorophyll meter reading (SCMR). The results from ANOVA revealed that, MSS due to genotypes, (checks + genotypes) were significant ((p<0.01 and p<0.05)) for most of the root architectural traits and for two different regime of P under investigation. Wide range of genetic variation was recorded for the traits such as RL, RV, SFW, SDW, RFW, RDW, RSRWW, RSRDW and GYP with high GCV and PCV and high h2 coupled with high GAM under both P gradient conditions. Strong inter-correlation among the component traits was observed for the root traits such as RV (0.43**: 0.50**), SFW(0.81**:0.60**), SDW (0.65**: 0.81**), RFW (0.87**:0.64**), RDW (0.83**: 0.87**) and RL (0.36**: 0.43**) along with GYP (0.52**) under low soil P and normal soil P. Principal component analysis with first four PCs revealed existence of 69.40 and 70.30% of total variance and clustering analysis identified the promising genotypes as IL-9-10, IL-11-2, IL-21-8, IL-19-3, IL-22-1, IL-23-2, IL-23-7, IL-31-3, IL-42-3, IL-67-2, IL-69-1, IL-75-2, Swarna and Rasi with root traits RV, RDW, RFW, RL, and GYP are effective traits for rice cultivation.

A de novo evolved gene contributes to rice grain shape difference between indica and japonica

The role of de novo evolved genes from non-coding sequences in regulating morphological differentiation between species/subspecies remains largely unknown. Here, we show that a rice de novo gene GSE9 contributes to grain shape difference between indica/xian and japonica/geng varieties. GSE9 evolves from a previous non-coding region of wild rice Oryza rufipogon through the acquisition of start codon. This gene is inherited by most japonica varieties, while the original sequence (absence of start codon, gse9) is present in majority of indica varieties. Knockout of GSE9 in japonica varieties leads to slender grains, whereas introgression to indica background results in round grains. Population evolutionary analyses reveal that gse9 and GSE9 are derived from wild rice Or-I and Or-III groups, respectively. Our findings uncover that the de novo GSE9 gene contributes to the genetic and morphological divergence between indica and japonica subspecies, and provide a target for precise manipulation of rice grain shape.

Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis.

Oryza rufipogon is the wild progenitor of cultivated rice Oryza sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress-tolerant varieties and genes that could limit future climate-changed-induced yield losses. To investigate local adaptation in O. rufipogon, we analyzed single nucleotide polymorphism (SNP) data from a panel of 286 samples located across a diverse range of climates. Environmental association analysis (EAA), a genome-wide association study (GWAS)-based method, was used and revealed 15 regions of the genome significantly associated with various climate factors. Genes within these environmentally associated regions have putative functions in abiotic stress response, phytohormone signaling, and the control of flowering time. This provides an insight into potential local adaptation in O. rufipogon and reveals possible locally adaptive genes that may provide opportunities for breeding novel rice varieties with climate change-resilient phenotypes.

Asymmetric variation in DNA methylation during domestication and de-domestication of rice.

Hundreds of plant species have been domesticated to feed human civilization, while some crops have undergone de-domestication into agricultural weeds, threatening global food security. To understand the genetic and epigenetic basis of crop domestication and de-domestication, we generated DNA methylomes from 95 accessions of wild rice (Oryza rufipogon L.), cultivated rice (Oryza sativa L.) and weedy rice (O. sativa f. spontanea). We detected a significant decrease in DNA methylation over the course of rice domestication but observed an unexpected increase in DNA methylation through de-domestication. Notably, DNA methylation changes occurred in distinct genomic regions for these 2 opposite stages. Variation in DNA methylation altered the expression of nearby and distal genes through affecting chromatin accessibility, histone modifications, transcription factor binding, and the formation of chromatin loops, which may contribute to morphological changes during domestication and de-domestication of rice. These insights into population epigenomics underlying rice domestication and de-domestication provide resources and tools for epigenetic breeding and sustainable agriculture.

A leaf-emanated signal orchestrates grain size and number in response to maternal resources.

In plants, variations in seed size and number are outcomes of different reproductive strategies. Both traits are often environmentally influenced, suggesting that a mechanism exists to coordinate these phenotypes in response to available maternal resources. Yet, how maternal resources are sensed and influence seed size and number is largely unknown. Here, we report a mechanism that senses maternal resources and coordinates grain size and number in the wild rice Oryza rufipogon, a wild progenitor of Asian cultivated rice. We showed that FT-like 9 (FTL9) regulates both grain size and number and that maternal photosynthetic assimilates induce FTL9 expression in leaves to act as a long-range signal that increases grain number and reduces size. Our findings highlight a strategy that benefits wild plants to survive in a fluctuating environment. In this strategy, when maternal resources are sufficient, wild plants increase their offspring number while preventing an increase in offspring size by the action of FTL9, which helps expand their habitats. In addition, we found that a loss-of-function allele (ftl9) is prevalent among wild and cultivated populations, offering a new scenario in the history of rice domestication.

Armadillo repeat only protein GS10 negatively regulates brassinosteroid signaling to control rice grain size.

Grain yield and grain quality are major determinants in modern breeding controlled by many quantitative traits loci (QTLs) in rice (Oryza sativa). However, the mechanisms underlying grain shape and quality are poorly understood. Here, we characterize a QTL for grain size and grain quality via map-based cloning from wild rice (W1943), GS10 (Grain Size on Chromosome 10), which encodes a protein with 6 tandem armadillo repeats. The null mutant gs10 shows slender and narrow grains with altered cell size, which has a pleiotropic effect on other agronomical traits. Functional analysis reveals that GS10 interacts with TUD1 (Taihu Dwarf1) and is epistatic to OsGSK2 (glycogen synthase kinase 2) through regulating grain shape and lamina joint inclination, indicating it is negatively involved in brassinosteroid (BR) signaling. Pyramiding gs10 and the grain size gene GW5 into cultivar GLA4 substantially improved grain shape and appearance quality. Natural variation analysis revealed that gs10 from the wild rice Oryza rufipogon W1943 is a rare allele across the rice population. Collectively, these findings advance our understanding of the underlying mechanism of grain shape and provide the beneficial allele of gs10 for future rice breeding and genetic improvement.

QTL Mapping of Mineral Element Contents in Rice Using Introgression Lines Derived from an Interspecific Cross

Developing rice varieties with increased mineral element content is the most cost-effective and efficient approach for alleviating human malnutrition and nutrient deficiencies. In this study, quantitative trait loci (QTLs) were mapped for mineral element content in 96 introgression lines derived from a cross between the elite Korean Oryza sativa japonica cultivar “Hwaseong” and the wild rice Oryza rufipogon (IRGC105491). The population was grown in two locations, and Fe, Zn, Mn, and Ca contents of the brown rice were measured. Six QTLs were identified on chromosomes 6, 8, and 10, and all O. rufipogon alleles increased trait values. The positions of qFe10 and qZn10 were further defined; higher Fe and Zn contents are related to the 375-kb O. rufipogon segment between the markers RM1873 and RM25612. The combined analysis of the whole-genome sequencing data, spatiotemporal expression profile, and gene expression suggested that a transcription factor gene, namely the rice homeobox gene 9 (LOC_Os10g33960) marks as the high potential candidate associated with Fe and/or Zn regulation. This study provides valuable information on candidate genes qFe10 and qZn10 from O. rufipogon, which may be vital in developing rice varieties with increased Fe and/or Zn content without any penalty in traits of agronomic importance.

Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome

BackgroundThe assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the core microbiome after long-term cultivation. We sampled three natural reserve populations of wild rice (i.e., in situ) and three populations of transplanted in situ wild rice grown ex situ for more than 40 years to determine the core wild rice rhizomicrobiome.ResultsGeneralized joint attribute modeling (GJAM) identified a total of 44 amplicon sequence variants (ASVs) composing the core wild rice rhizomicrobiome, including 35 bacterial ASVs belonging to the phyla Actinobacteria, Chloroflexi, Firmicutes, and Nitrospirae and 9 fungal ASVs belonging to the phyla Ascomycota, Basidiomycota, and Rozellomycota. Nine core bacterial ASVs belonging to the genera Haliangium, Anaeromyxobacter, Bradyrhizobium, and Bacillus were more abundant in the rhizosphere of ex situ wild rice than in the rhizosphere of in situ wild rice. The main ecological functions of the core microbiome were nitrogen fixation, manganese oxidation, aerobic chemoheterotrophy, chemoheterotrophy, and iron respiration, suggesting roles of the core rhizomicrobiome in improving nutrient resource acquisition for rice growth. The function of the core rhizosphere bacterial community was significantly (p < 0.05) shaped by electrical conductivity, total nitrogen, and available phosphorus present in the soil adhering to the roots.ConclusionWe discovered that nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the core rhizomicrobiome of the wild rice Oryza rufipogon. Our findings suggest that further potential utilization of the core rhizomicrobiome should consider the effects of soil properties on the abundances of different genera.92mDw1vveJ8f3-hG51Jkn-Video

Chromosome-level genome assembly of Dongxiang wild rice (Oryza rufipogon) provides insights into resistance to disease and freezing.

Dongxiang wild rice (DXWR, Oryza rufipogon Griff.) belongs to common wild rice O. rufipogon, which is the well-known ancestral progenitor of cultivated rice, possessing important gene resources for rice breeding. However, the distribution of DXWR is decreasing rapidly, and no reference genome has been published to date. In this study, we constructed a chromosome-level reference genome of DXWR by Oxford Nanopore Technology (ONT) and High-through chromosome conformation capture (Hi-C). A total of 58.41Gb clean data from ONT were de novo assembled into 231 contigs with the total length of 413.46Mb and N50 length of 5.18Mb. These contigs were clustered and ordered into 12 pseudo-chromosomes covering about 97.39% assembly with Hi-C data, with a scaffold N50 length of 33.47Mb. Moreover, 54.10% of the genome sequences were identified as repeat sequences. 33,862 (94.21%) genes were functionally annotated from a total of predicted 35,942 protein-coding sequences. Compared with other species of Oryza genus, the genes related to disease and cold resistance in DXWR had undergone a large-scale expansion, which may be one of the reasons for the stronger disease resistance and cold resistance of DXWR. Comparative transcriptome analysis also determined a list of differentially expressed genes under normal and cold treatment, which supported DXWR as a cold-tolerant variety. The collinearity between DXWR and cultivated rice was high, but there were still some significant structural variations, including a specific inversion on chromosome 11, which may be related to the differentiation of DXWR. The high-quality chromosome-level reference genome of DXWR assembled in this study will become a valuable resource for rice molecular breeding and genetic research in the future.

First Report ofPyricularia oryzae Causing Blast onWild Rice (Oryza rufipogon) in China.

Wild rice (Oryza rufipogon) is an excellent genetic resource for rice breeding programs. In June 2019, typical symptoms of blast on the leaves of wild rice cv. 'Haihong-12' were observed in a 3.3-ha field in Zhanjiang (20.93° N, 109.79° E), China. The symptoms included fusiform lesions with yellowish halo at the age of lesion, grayish-white color at the center, brown and elongated central veins at both ends of lesion, and grayish-white mold layer formed on the back of lesion under humid weather conditions. Disease incidence was more than 10%. Thirty diseased leaves were collected, and infected tissues were cut into 2 × 2 mm pieces, surface disinfected with 75% ethanol for 30 s and 2% sodium hypochlorite for 60 s and rinsed three times with sterile water. The tissues were plated onto potato dextrose agar (PDA) medium and incubated at 28 °C in darkness for 3 days. Three single-spore isolates (Pos-1, Pos-2, and Pos-3) were obtained using the method described by Jia (Jia 2009) and were subjected to further morphological and molecular identification. Colonies on PDA were light grey, with cottony mycelium. Conidiophores were solitary, erect, straight or curved, septate, and pale brown and measured 68 to 125×3 to 4 µm. Conidiogenous cells were sympodial and denticulate. Conidia were pale brown, pyriform, and 18.2 to 42.4×5.1 to 8.5 µm (n=30) in size, with two septa. Appressoria were spherical and had the size ranging 4.3 to 6.5×4.7 to 6.5 µm (n = 20). These morphological features agreed with the previous description of Pyricularia oryzae Cavara (Klaubauf et al. 2014). For molecular identification, the colony PCR method with MightyAmp DNA Polymerase (Lu et al. 2012) was used to amplify the internal transcribed spacer (ITS), calmodulin (CAL), actin (ACT), -tubulin (TUB) loci of the isolates using primer pairs ITS1/ITS4, CL1C/CL2C, ACT-512F/ACT-783R, and T1/βt2b, respectively (O'Donnell et al. 1997; Weir et al. 2012; White et al. 1990). Analysis of ITS (acc. nos. MW042176 to MW042178), ACT (MW091444 to MW091446), CAL (MW091447 to MW091449), and TUB (MW091441 to MW091443) sequences revealed 100% identity with the corresponding ITS (MH859782), ACT (MH589787), CAL (MH589663), and TUB (MH589547) sequences of P. oryzae in GenBank. A phylogenetic tree was generated based on the ITS sequences using maximum likelihood method that clustered Isolates Pos-1, Pos-2, and Pos-3 with known P. oryzae. Thus, the isolates were identified asP. oryzae. Pathogenicity tests were performed using Isolate Pos-1 in a greenhouse at 24to 30°C with 80% relative humidity. Individual rice plants (cv. 'Haihong-12') with three leaves were grown in 10 pots, with 50 plants per pot (40 × 60 cm). Five pots were spray inoculated with a spore suspension (105 spores/ml) until runoff from leaves, and the remaining five pots were sprayed with sterile water to serve as the controls. The test was conducted three times. Disease symptoms were observed on 10% of leaves at 10 days after inoculation, but the control plants remained healthy. The fungus was re-isolated from the diseased plants and morphologically identified as P. oryzae. Thus, this is the first report of P. oryzae causing blast on O. rufipogon in China. The results provide the information that can be used by rice breeders and fungal geneticists for further studies.

Genome-wide association mapping for identification of sheath blight resistance loci from wild rice Oryza rufipogon

Sheath blight (ShB) caused by Rhizoctonia solani is one of the serious constraints that hamper global rice production. It causes severe yield loss of up to 69% under favorable environmental conditions. The application of chemical fungicides remains the primary approach for the management of this disease. But, overuse of chemical fungicides causes potential health and environmental risk. The use of host plant resistance is a very effective, economic, and sustainable strategy to control sheath blight disease in rice. In this report, we have evaluated 405 accessions of Oryza rufipogon for four ShB-related traits i.e. lesion height (LH), plant height (PH), relative lesion length (RLH), and disease score (DS) during the years 2015, 2016, and 2017. A total of 44,109 high-quality SNP markers on 301 accessions were employed to identify significant marker-trait associations using a genome-wide association study (GWAS). The GWAS analysis revealed a total of 22 significant SNPs associated with the ShB-related traits distributed on all the rice chromosomes except 10 and 12. Among them, eleven were associated with RLH, seven with PH, and one each with LH and DS. The SNPs on chromosomes 3 and 9 were associated with multiple traits. Furthermore, seven ShB resistance loci were also found to be co-localized with previously reported ShB resistance genes/QTLs. These findings provide valuable information to identify key SNPs associated with ShB resistance. Significantly associated SNPs could be used for introgression of ShB resistance traits into rice cultivars using marker-assisted selection.

Mapping QTLs for yield and photosynthesis-related traits in three consecutive backcross populations of Oryza sativa cultivar Cottondora Sannalu (MTU1010) and Oryza rufipogon.

Identification of trait enhancing QTLs for yield and photosynthesis-related traits in rice using interspecific mapping population and chromosome segment substitution lines derived from a cross between Oryza sativa and Oryza rufipogon. Wild rice contains novel genes which can help in improving rice yield. Common wild rice Oryza rufipogon is a known source for enhanced photosynthesis and yield-related traits. We developed BC2F2:3:4 mapping populations using O. rufipogon IC309814 with high photosynthetic rate as donor, and elite cultivar MTU1010 as recurrent parent. Evaluation of 238 BC2F2 families for 13 yield-related traits and 208 BC2F2 families for seven photosynthesis-related physiological traits resulted in identification of significantly different lines which performed better than MTU1010 for various yield contributing traits. 49 QTLs were identified for 13 yield traits and 7 QTLs for photosynthesis-related traits in BC2F2. In addition, 34 QTLs in BC2F3 and 26 QTLs in BC2F4 were also detected for yield traits.11 common QTLs were identified in three consecutive generations and their trait-increasing alleles were derived from O. rufipogon. Significantly, one major effect common QTL qTGW3.1 for thousand grain weight with average phenotypic variance 8.1% and one novel QTL qBM7.1 for biomass were identified. Photosynthesis-related QTLs qPN9.1, qPN12.1, qPN12.2 qSPAD1.1 and qSPAD6.1 showed additive effect from O. rufipogon. A set of 145 CSSLs were identified in BC2F2 which together represented 87% of O. rufipogon genome. In addition, 87 of the 145 CSSLs were significantly different than MTU1010 for at least one trait. The major effect QTLs can be fine mapped for gene discovery. CSSLs developed in this study are a good source of novel alleles from O. rufipogon in the background of Cottondora Sannalu for rapid improvement of any trait in rice.