Resistance responses of rice to rice blast fungus after seed treatment with the endophytic Achromobacter xylosoxidans AUM54 strains

In the present investigation, we studied resistance imparted by seed treatment with an endophytic strain of Achromobacter xylosoxidans, AUM54, against rice blast caused by Magnaporthe oryzae. In vitro studies showed that A. xylosoxidans AUM54 was able to inhibit mycelial growth of M. oryzae by 11% and was able to increase rice germination and seedling vigor index of rice by 31 and 114%, respectively. AUM54 also showed better survivability in the spermosphere and spermoplane and was able to move systemically through the roots and stem. Among the evaluated carriers, liquid formulation amended with 2% glycerol sustained the maximum bacterial population (7.4 log cfu ml⁻¹) after six-months-storage at room temperature. Plants treated with A. xylosoxidans AUM54 followed by inoculation with M. oryzae showed a significant increase in the activities of defense related enzymes such as polyphenol oxidase (PPO), peroxidase (POD), phenylalanine ammonia-lyase (PAL) and chitinase. A. xylosoxidans AUM54 treatment was able to reduce blast disease incidence by 39% in treated rice plants. Additionally, inoculation with A. xylosoxidans AUM54 significantly enhanced the growth (3–13% plant height), and yield (11–31%) of inoculated rice plants under no-disease and disease conditions in the greenhouse experiments.     

Detection and characterization of bismerthiazol-resistance of Xanthomonas oryzae pv. oryzae

The resistance to bismerthiazol in the Xanthomonas oryzae pv. oryzae population in China has not been clearly determined. Three bismerthiazol-resistant mutants (1-1-1, 2-1-1, 4-1-1) of X. oryzae pv. oryzae were induced on rice plants and the characteristics were compared with their parental strain ZJ173. After 10 subcultures on fresh bismerthiazol-free nutrient agar plates and after being inoculation onto and re-isolation from untreated rice plants two times, the mutants remained pathogenicity on rice plants treated with 300 μg/ml bismerthiazol, indicating that the in vivo-induced bismerthiazol resistance was stable in vivo. The in vitro characteristics of the bismerthiazol-resistant mutants and a wild-type bismerthiazol-sensitive strain (ZJ173) were also compared. The three mutants grew faster than ZJ173 during the logarithmic growth phase but at the same rate during the decline phase. Bismerthiazol had protective and curative activity against strain ZJ173 but not against the three mutants. To evaluate the current degree of bismerthiazol resistance in field populations of X. oryzae pv. oryzae in China, 781 isolates of X. oryzae pv. oryzae were obtained from 1419 leaf samples collected from Yunnan, Sichuan, Jiangsu, Anhui, Hubei, Guangdong, Hainan, and Hunan Provinces in China from 2007 to 2009. The in vivo sensitivity of 505 of the 781 isolates to bismerthiazol was determined by applying them to rice plants treated with 300 μg/ml bismerthiazol and evaluating blast severity. The tested strains were considered resistant, if they showed <70% inhibition relative to strain ZJ173. Of the 505 isolates, 62 were resistant to bismerthiazol. The resistance frequencies among field population ranged from 0 to 21.1%, differed among the provinces, and was 11.2, 20.0 and 10.4% in 2007, 2008 and 2009, respectively. Resistance determined in vivo was not related to resistance determined in vitro. The in vivo-induced bismerthiazol resistance identified in this study will serve as a base line for further studying bismerthiazol resistance in fields, and the current degree of bismerthiazol resistance in field populations of X. oryzae pv. oryzae in China determined would be useful for the rice growers for control of rice bacterial blight.     

Occurrence of rice blast (Magnaporthe oryzae) and identification of potential resistance sources in Uganda

Rice blast caused by Magnaporthe oryzae continues to be the most destructive disease of rice worldwide, and is a number one disease of rice in Uganda. We present the footprints of M. oryzae importance, distribution, incidence and severity in the rice growing agro-ecologies of Uganda for 2009/2010, and the potential mitigation measures. Our data show that rice blast affects more than 50% of the cultivated rice area on average, and ranks as the most important disease encountered in the field. Between and within agroecologies, both incidence and severity varied (P < 0.05) reflecting the contribution of different cropping practices on rice blast epiphytotics. The highest blast incidence and severities were recorded in Bugiri, Butaleja, Mbale and Lira farmlands, which are the ancestral rice cultivation areas in Uganda. These areas showed mean yield reductions of >30% relative to other locations, suggesting that rice production history played a significant role in rice blast outbreaks. Broadcasting and drill seeding yielded 42.4% less than transplanted rice. Growing two rice crops per year is one of the methods suggested to increase rice production in Uganda, but there was a higher disease incidence in the late season than in the early season, indicating the need for improved resistant varieties. Four blast resistance genes (Pi9, Piz-t, Pi19 and Piz-5) and the cultivar Tetep had the lowest (≤4) blast severity scores in all the test locations. It could be suggested that these genes are potential resistance sources for developing varieties, which would be more relevant for the double cropping systems.     

Evaluation of bacterial biological control agents for control of root-knot nematode disease on tomato

Among 19 bacterial strains isolated in Yunnan from rhizosphere soils and plant tissues, Bacillus methylotrophicus strain R2-2 and Lysobacter antibioticus strain 13-6 exhibited the highest antagonistic activity against the tomato root-knot nematode Meloidogyne incognita in plate and greenhouse pot experiments. The two strains, when applied as soil drenches or seed treatments in greenhouse experiments, reduced root-knot severity and incidence on tomato compared to no-bacteria controls. In tomato field trials conducted in separate years, soil drench treatment with either strain reduced root-knot disease levels and increased yields compared to the control. Levels of disease control and yield enhancement provided by the strains were higher than those using the chemicals abamectin and carbofuran. This is the first report of B. methylotrophicus being used as a biocontrol agent against a plant parasitic nematode and the first demonstration that B. methylotrophicus and L. antibioticus can suppress disease caused by root-knot nematodes in the field.     

Effects of rice-water chestnut intercropping on rice sheath blight and rice blast diseases

Both sheath blight and blast are important rice diseases worldwide. The exploration of environmentally sound practices to control these diseases will help to reduce fungicide application. Effects of rice (Oryza sativa) intercropping with water chestnut (Eleocharis dulcis) on rice sheath blight and rice blast disease as well as the extracts of different plant parts and root exudates from water chestnut on pathogens of rice sheath blight (Rhizoctonia solani) and rice blast disease (Magnaporthe oryzae) were investigated using pot experiments and bioassay tests. The results from pot tests showed that rice-water chestnut intercropping system suppressed sheath blight and blast and improved land equivalent ratio (LER). The results from bioassay tests indicated that extracts and root exudates from water chestnut had significant effects to inhibit the expansion of these pathogens. The scales of these inhibitions were time and concentration dependent. The antifungal activities of the extracts from aboveground parts and pulp of water chestnut were significantly higher than the extracts from other parts and root exudates. The water extracts of aboveground parts showed the highest antifungal activity on both pathogens according to EC₅₀ values. The antifungal activities of the same extracts from water chestnut on R. solani were significantly higher than on M. oryzae. The result suggests that water chestnut possesses bioactive substances to suppress rice sheath blight disease and rice blast disease. The rice-water chestnut intercropping system can be used as an environment-friendly method for diseases control in rice field.     

Two Bacillus amyloliquefaciens strains isolated using the competitive tomato root enrichment method and their effects on suppressing Ralstonia solanacearum and promoting tomato plant growth

Two tomato root colonizing strains, Bacillus amyloliquefacien CM-2 and T-5, were isolated after the enrichment procedure on the roots of tomato seedlings, and evaluated for their antagonistic activities against pathogenic Ralstonia solanacearum (RS) in vitro. Three inoculation methods were used to test their biocontrol efficacy and growth promotion effects in greenhouse based on their colonization ability in rhizosphere soil. Both CM-2 and T-5 strains showed strong biocontrol and growth promotion effects on tomato seedlings. The best biocontrol efficacy was obtained by treating both seedlings and soils with the biocontrol agents. In comparison to the control, the disease incidence was reduced by 70.1 and 79.4% for CM-2 and T-5, respectively. The numbers of colony-forming units of RS in rhizosphere soil were significantly (P < 0.05) decreased as compared to the control. The density of both strains in the rhizosphere soils remained at a high level (≥10⁷ CFU/g) during a five-week period. Both strains were recovered from the interior of the stems and roots of plants. They showed positive reactions for ammoina, indole acetic acid and siderophores production, and phosphate solubilizing activity. Our data proved the potential of isolated strains for the biocontrol of tomato bacterial wilt.     

Population dynamics of Xanthomonas campestris pv. vitians on different plant species and management of bacterial leaf spot of lettuce under greenhouse conditions

The population dynamics of Xanthomonas campestris pv. vitians (Xcv) was studied both externally and internally in lettuce, tomato and pepper plants. In addition, the application of bactericides during transplant production period was carried out for the management of bacterial leaf spot of lettuce under greenhouse conditions. Epiphytic populations of Xcv were recovered on leaves of lettuce plants (10⁵ CFU/g) 5 weeks after sprayed than the other plant species when inoculated with 10⁸ CFU/ml of Xcv. When plants of each crop species infiltrated with the bacterium at 10⁵ CFU/ml, the highest populations were developed in lettuce (10⁸ CFU/cm²) followed by pepper with 10⁶ CFU/cm² and tomato with 10⁵ CFU/cm² 10-days after infiltration. Application of a mixture of Maneb and Kocide or Kocide alone as a foliar spray on lettuce significantly reduced the incidence and disease severity of bacterial leaf spot by 29 and 27% respectively. Spread of the bacterium and development of the disease may partly be managed by avoiding intercropping of these plants commonly grown in close proximity to lettuce. For the management of leaf-associated populations of Xcv in lettuce, use of a mixture of Maneb and Kocide is advocated to minimize the effect of attacks.     

Improvements in the qualities of gluten-free bread after using a protease obtained from Aspergillus oryzae

From a nutritional perspective, rice flour is one of the most valuable flours and it is suitable for preparing food for people suffering from wheat allergy. However, bread made from rice flour is very difficult to bake because it lacks gluten. We found that pre-fermenting of rice flour using Aspergillus oryzae facilitated a better formulation of gluten-free rice bread. Bread swelling was remarkably improved with a longer pre-fermenting period at 55 °C. The specific loaf volume (SLV) without polymeric thickeners after a 12 h fermentation was approximately 2.2-fold (2.98 ml/g) higher than that after 0 h (1.36 ml/g). An enzymatic assay of the batter indicated that protease activity during the pre-fermentation period increased from 0.38 to 1.44 U/ml and this activity correlated with bread swelling. Furthermore, a commercial protease from A. oryzae also produced similar results with an adequate SLV of 3.03 ml/g. Rheological analysis showed that batter treated with protease had an increased batter viscosity and decreased flour settling behavior because of the aggregation of flour particle after partial cleavage of storage proteins. These results indicated that the improved SLV was mainly because of an A. oryzae protease, which affected the batter rheology thereby improving gas retention before baking.     

Rhizosphere Bacteria for Biocontrol of Bacterial Blight and Growth Promotion of Rice

Several bacterial strains were isolated from different rhizospheres. Among these, strain PDY7 exhibited strong antibacterial activity against the rice bacterial blight (BB) pathogen Xanthomonas oryzae pv. oryzae (Xoo) by the laboratory dual plate assays. The antibacterial property of the strain PDY7 was further investigated for the production of 2,4-diacetylphloroglucinol (DAPG), which amplified a characteristic of 629-bp DNA fragment by PCR-based screening method using phlD primers. The application of phlD positive strains was carefully evaluated for disease control and growth promotion of rice plants under field conditions. The selected strain PDY7 suppressed the rice BB by 58.83% and 51.88% under glass house and field conditions, respectively. In addition, the strain PDY7 showed significant two-fold increase in root length (18.08 cm), shoot length (29.81 cm), and grain yield (96.07 g). Strain PDY7 promoted the growth of rice plants by production of indole-3-acetic acid (IAA), which was determined by high performance liquid chromatography (HPLC) analysis. Our findings suggest that PDY7 belongs to the P. fluorescens group and can serve as potential biocontrol of BB as well as biofertilizer agent for growth promotion of rice.     

Maximizing yields in rice–groundnut cropping sequence through integrated nutrient management

Integrated use of organic and inorganic fertilizers can improve crop productivity and sustain soil health and fertility. The present research was conducted to study the effects of application of green manures [sesbania (Sesbania aculeate Poiret) and crotalaria (Crotalaria juncea L.)] and farmyard manure on productivity of rice (Oryza sativa L.) and its residual effects on subsequent groundnut (Arachis hypogaea L.) crop. Rice and groundnut crops were grown in sequence during rainy and post-rainy seasons with and without green manure in combination with different fertilizer and spacing treatments under irrigated conditions. The results showed that application of green manures sesbania and crotalaria at 10 t ha⁻¹ to rice compared to no green manure application significantly increased grain yield of rice by 1.6 and 1.1 t ha⁻¹, and pod yields of groundnut crop succeeding rice by 0.25 and 0.16 t ha⁻¹, respectively. There was no significant difference between the application of crotalaria or farmyard manure at 10 t ha⁻¹ on grain yields of rice, but pod yields of subsequent groundnut crop were greater with application of green manure. There was no significant effect of different spacing 20×15,15×15,15×10 cm² (333 000; 444 000; 666 000 plant ha⁻¹, respectively) on grain yield of rice. Pod yields of groundnut were significantly greater with closer spacing 15×15 cm² (444 000 plants ha⁻¹) as compared to spacing of 30×10 cm² (333 000 plants ha⁻¹). Maximum grain of rice was obtained by application of 120:26:37 kg NPK ha⁻¹ in combination with green manures, whereas maximum pod yield of groundnut was obtained by residual effect of green manure applied to rice and application of 30:26:33 kg NPK ha⁻¹ in combination with gypsum applied to groundnut crop.     

Insecticidal activity influence of beta-cypermethrin on the pathogenicity of Beauveria bassiana against Aleurodicus disperses

The bioactivities of entomopathogen, Beauveria bassiana and a chemical beta-cypermethrin against Aleurodicus disperses were tested during these studies. The LC₅₀ values of B. bassiana were 2.74 × 10¹⁰, 1.03 × 10⁸conidia/ml after 5 and 10 days of fungal treatment. Beta-cypermethrin gave an apparent increase in adjusted larval mortality in a dose dependent manner whereas no influence of beta-cypermethrin (10 ppm) was observed on percent germination and mycelial growth of B. bassiana. Furthermore, the synergism between B. bassiana and beta-cypermethrin was also studied under laboratory and field conditions. Percent accumulated adjusted mortality of A. disperses after the application of different concentration of beta-cypermethrin and B. bassiana showed that the mortalities were directly related to the concentration of beta-cypermethrin in the mixtures and their accumulative effect was retained for an extended period.     

Field evaluation of Lymantria obfuscata multiple nucleopolyhedrovirus for the management of Indian gypsy moth in Jammu & Kashmir,India

The Indian gypsy moth (Lymantria obfuscata) is a pest of national significance, which attacks a wide range of forest and fruit crops in India. The outbreaks of this pest over the past few years spurred interest towards sustainable biointensive approaches for quality fruit production of apple and walnut for agricultural export in Jammu & Kashmir (J & K). The exploratory survey's were conducted for the isolation of native strains of L. obfuscata multiple nucleopolyhedrovirus (LyobMNPV) and field evaluation was conducted to determine the most promising strain as a potential biological control agent of this pest. The virus was recovered from different locations of J&K with its natural incidence varying from 0.77 to 7.43 percent. This is the first report from the Indian sub-continent and worldwide of the occurrence of NPVs in natural larval populations of L. obfuscata. The in vivo mass production was optimised by inoculating per os late 3rd instar L. obfuscata larvae with an inoculum dose of 1.44 × 10⁵ OBs/larva and followed by a 10 day incubation period. To prevent the disintegration of larval cuticle and microbial contamination, moribund larvae were harvested with an average yield of 1.42 × 10⁸ OBs/larva. The field application of LyobMNPV against the host populations on apple and willow with the pre-standardised dosage of 2.5 × 10¹² OBs/ha reduced the larval population density by 25–63%. In the year following application, the larval population density in the treated blocks was 19–28% lower as compared to controls on both apple and willow. This suggests that the virus has considerable potential as a biocontrol agent and the timely application with LyobMNPV on non-fruit trees such as willow which are the preferred hosts for egg laying may help to initiate viral epizootics to keep population outbreaks under check.     

An SNP downstream of the OsBEIIb gene is significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.)

Allele mining in starch synthesis-related genes (SSRGs) has facilitated the discovery of desired natural sequence variations for eating quality in rice. This study investigated the sequence variations from 10 SSRGs, and further evaluated their relationship with the amylose content (AC) and rapid viscosity analysis profiles in a global collection of rice accessions by association mapping (AM). In total, 83 sequence variations were found in 10 sequenced amplicons, including 73 single nucleotide polymorphisms (SNPs), eight insertion-deletions (InDels) and two polymorphic simple sequence repeats (SSRs). Four subpopulations were identified by population structure analysis based on 170 genome-wide SSR genotypes. AM revealed 11 significant associations between three phenotypic indices and three sequence variations. One SNP with a g/c transversion at the 63rd nucleotide downstream of the OsBEIIb gene termination codon on rice chromosome 2 was significantly associated with multiple trait indices in both the general linear and mixed linear models (GLM and MLM), including the final viscosity (p < 0.001, R² = 23.87%) in both 2009 and 2010, and AC (p < 0.01, R² = 11.25%) and trough viscosity (p < 0.01, R² = 20.43) in 2010. This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.     

Physical and chemical parameters,Fusarium verticillioides growth and fumonisin production in kernels of nine maize genotypes

Fusarium verticilloides synthesizes fumonisins (FBs) in the field and during faulty storage of maize. FBs are worrisome because of their toxicological effects. Nine maize genotypes differing in physical grain properties, phytochemical profiles, and chemical compositions were evaluated. Kernels were tempered to 18% moisture and purposely contaminated with F. verticilloides to assess differences in mold growth and FBs. The genotype significantly influenced counts with mean values ranging from 12.9 CFU/mLx10⁴ for the highly susceptible Blue Don Goyo to only 1.0 CFU/mLx10⁴ for the Pob84C3 genotype. The concentrations of FBs in these two genotypes were 6.85 and 0.3 ppm, respectively. Popcorn kernels showed a relatively high level of Fusarium counts (7.0 CFU/mLx10⁴) but low concentrations of FBs (1.4 ppm). The large-sized Cacahuacintle and Don Goyo kernels, which had the lowest test weights and highest 1000 kernel weight (TKW) showed the highest occurrence of CFU likely due to their low proportion of pericarp, bound phenolics (coumaric), diferulic acids and bound antioxidants. Correlations indicated that mold counts did not correlate (r² = 0.6, P = 0.08) with FBs. However, grain thickness, hardness, TKW and bound phenolics were related to Fusarium counts. This research demonstrated that contrasting maize genotypes showed different susceptibilities to Fusarium growth and FBs contamination.     

Pre-harvest glyphosate application effects on properties of β-glucan from oat groats

Pre-harvest glyphosate is applied to cereal grains to control weed growth. However, it has been claimed that oat (Avena sativa L.) composition is affected by pre-harvest glyphosate application. The research was conducted to evaluate differences in properties of β-glucan in grains of pre-harvest glyphosate treated versus untreated oat plants. Two oat cultivars (Rockford and Souris) were grown at Minot and Prosper, ND, in 2015, and glyphosate was sprayed during the soft dough stage, hard dough stage, or not applied. β-glucan viscosity was not significantly (p > 0.05) affected by treatment at soft dough (1082 cP) or mature (1166 cP) stages compared with untreated (1150 cP) controls. Applying glyphosate at the soft dough stage significantly (p < 0.05) reduced the content and solubility of the β-glucan versus untreated samples. β-glucan content and solubility in oat treated at soft dough were 4.35% and 52.1%, respectively, while in untreated samples were 4.65% and 60.6%, respectively. Treatment at soft dough and hard dough stages significantly (p < 0.05) increased weight average molecular weight (M_w) of the high molecular weight fraction of soluble β-glucan (4.4 × 10⁶ and 3.8 × 10⁶, respectively), compared with untreated controls (3.5 × 10⁶). The M_w of the low molecular weight fraction of soluble β-glucan fraction significantly (p < 0.05) increased at soft and hard dough treatments (5.5 × 10⁵ and 3.3 × 10⁵, respectively), versus untreated samples (3.0 × 10⁵). Therefore, glyphosate can be applied when the grain has reached physiological maturity or thereafter.     

Improving Rice Blast Resistance by Mining Broad-Spectrum Resistance Genes at Pik Locus

Magnaporthe oryzae is known for its genetic diversity and pathogenic variability, leading to rapid breakdown of resistance in rice. Incorporating multiple broad-spectrum blast resistance genes into rice cultivars would extend disease resistance longevity. Effective resistance breeding in rice therefore requires continual enrichment of the reservoir of resistance genes and alleles. We conducted a large-scale screen of rice blast resistance in about 2 000 rice accessions. Among them, 247 accessions showed at least medium resistance to the natural infection of rice blast and 7 novel Pik alleles were identified from them. Variations in gene sequences were then correlated with the phenotypic trait to enable the identification of favorable alleles. Among the seven novel Pik alleles, the resistant rate of Pik-R0/ME/7017 donors was greater than 80%, and the disease score was less than 3. Through molecular marker-assisted backcross breeding, we successfully transferred the three Pik alleles, Pik-R0/ME/7017, into an elite cultivated line Kongyu 131 to obtain BC₃F₂ lines, which showed enhanced resistance to rice blast compared with the recurrent parent. Assessment of these near-isogenic lines in the greenhouse using 31 isolates of M. oryzae from Heilongjiang Province of China revealed that the resistant levels of the BC₃F₂ lines with Pik-R0/ME/7017 were significantly higher than those of the established cloned resistance genes Pik-m and Pi1. Exploring such alleles will enrich our gene library for resistance to rice blast.     

Control of postharvest radish decay using a Cryptococcus albidus yeast coating formulation

An antagonist yeast strain, WY-1, was identified using 18S and internal transcribed spacer (ITS) 1-5.8S-ITS2 rDNA region sequences. The 18S and ITS1-5.8S-ITS2 rDNA sequences of this yeast strain were amplified and sequenced using the universal primer pairs NS1/NS8 and ITS4/ITS5. The ITS1-5.8S-ITS2 rDNA sequence and 18S neighbor-joining tree showed that WY-1 was a strain of Cryptococcus albidus. The biocontrol activity of C. albidus WY-1 on postharvest decay of radishes caused by Alternaria spp. and Fusarium spp. was investigated. In vitro, at 10⁸ CFU ml⁻¹ C. albidus WY-1 inhibited the mycelial weight increases of Alternaria spp. and Fusarium spp. by 45.3% and 59.6%, respectively. In vivo, infection incidence and lesion development of radish decay were suppressed by the application of C. albidus WY-1 at 10⁸ CFU ml⁻¹. After 6 days of incubation at 20 °C or 24 days at 4 °C, disease incidences were 2.8% and 1.4%, respectively; however, the disease incidences of control fruit were 98.6% and 87.5% under these incubation conditions, respectively. Application of C. albidus WY-1 and the chemical fungicide thiabendazole were statistically just as effective. Finally, C. albidus cell counts around inoculation sites remained high at 4 °C even 32 days after inoculation (6.7 × 10⁵ CFU per cm²).     

Insecticidal efficacy of two pirimiphos-methyl formulations for the control of three stored-product beetle species: Effect of commodity

Laboratory bioassays were conducted to evaluate the insecticidal effect of two pirimiphos-methyl formulations, an emulsifiable concentrate (EC) and a capsule suspension (CS) against adults of Sitophilus oryzae, Rhyzopertha dominica and Tribolium confusum in wheat, maize and rice. Pirimiphos-methyl was applied at two dose rates, 2 and 4 ppm, and adult mortality was measured after 2, 7, 14 and 21 days of exposure in the treated commodity. Progeny production was assessed 65 d after the removal of the parental adults. S. oryzae adult survival was significantly higher in rice than in wheat and maize, whereas T. confusum mortality was significantly higher in maize than in the other grains. From the species tested, the most susceptible species was S. oryzae, for which mortality reached 100% after 7 days of exposure in treated wheat and maize, followed by T. confusum and R. dominica. Progeny production was significantly suppressed by pirimiphos-methyl in the case of S. oryzae, but not in the case of R. dominica. In general, only few differences in performance between the EC and the CS formulation were detected. We conclude that the type of grain commodity significantly affects mortality after the application of the two pirimiphos-methyl formulations tested, but this effect is species-dependent.     

Phylogenomic Relationships of Rice Oxalate Oxidases to the Cupin Superfamily and Their Association with Disease Resistance QTL

Rice oxalate oxidase genes (OXO) may play a role in resistance to Magnaporthe oryzae. Genome analyses showed four tandemly duplicated OXO genes, OsOXO1–OsOXO4, which mapped to a blast resistance QTL in chromosome 3. These genes have >90% nucleotide and amino acid identity, but they have unique gene structures, conserved motifs, and phylogeny compared to the 70 other members of the cupin superfamily in the Nipponbare genome, which were divided into several classes. In resistant and susceptible Vandana/Moroberekan advanced backcross lines, only OsOXO4 was expressed during rice–M. oryzae interactions, and its expression increased earlier in resistant than susceptible lines. The earlier expression of OsOXO4 in resistant lines correlated with a 26-bp promoter insertion containing an additional copy of the bacterial responsive nodulation cis-element. Our results showed that OsOXO1–4 are in a separate class of rice cupin genes and supports a role for the promoter variant of OsOXO4 in resistance to M. oryzae.     

An SNP downstream of the OsBEIIb gene is significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.)

Allele mining in starch synthesis-related genes (SSRGs) has facilitated the discovery of desired natural sequence variations for eating quality in rice. This study investigated the sequence variations from 10 SSRGs, and further evaluated their relationship with the amylose content (AC) and rapid viscosity analysis profiles in a global collection of rice accessions by association mapping (AM). In total, 83 sequence variations were found in 10 sequenced amplicons, including 73 single nucleotide polymorphisms (SNPs), eight insertion-deletions (InDels) and two polymorphic simple sequence repeats (SSRs). Four subpopulations were identified by population structure analysis based on 170 genome-wide SSR genotypes. AM revealed 11 significant associations between three phenotypic indices and three sequence variations. One SNP with a g/c transversion at the 63rd nucleotide downstream of the OsBEIIb gene termination codon on rice chromosome 2 was significantly associated with multiple trait indices in both the general linear and mixed linear models (GLM and MLM), including the final viscosity (p < 0.001, R² = 23.87%) in both 2009 and 2010, and AC (p < 0.01, R² = 11.25%) and trough viscosity (p < 0.01, R² = 20.43) in 2010. This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.