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.     

Effect of planting date,fungicide timing and cultivar susceptibility on severity of narrow brown leaf spot and yield of rice

Narrow brown leaf spot (NBLS) of rice (Oryza sativa L.) is caused by Cercospora janseana (Racib). O. Const. (Synonyms: Cercospora oryzae Miyake, Passalora janseana Racib. U.). Experimental studies were conducted at Rice Research Station, Louisiana State University, and Agricultural Center, Crowley, to manage NBLS by fungicide application of propiconazole at different growth stages of rice cultivars having different susceptibility levels to NBLS in different planting dates. Results of these studies revealed that April (early) had less NBLS severity as compared to May (late) planting. Very susceptible cultivars, CL131 and Cheniere, had the highest and resistant cultivars, Della and Presidio, had the lowest NBLS severity at both the planting dates. Propiconazole application significantly reduced the NBLS severity in comparison to untreated. Fungicide application at panicle initiation was the most effective time to manage NBLS on the very susceptible and susceptible cultivars at both planting dates. NBLS on moderately susceptible cultivars was best managed by applying fungicide either at panicle initiation or early boot stage in early planting but panicle initiation was the best time to apply fungicide in late planting. Resistant cultivars did not need fungicide in April planting but did need in May planting. Rice yield was determined to be higher in April than May planting. Fungicide application at early boot stage protected the yield by 9.4% in April planting and 34.2% when applied at panicle initiation in May. Susceptible cultivar, Cheniere, exhibited the greatest yield and resistant cultivars had lowest yield in both the planting dates regardless of its susceptibility level to NBLS. Yield of very susceptible to susceptible cultivars was reduced in late planting but no effect was observed on yield of moderately susceptible and resistant cultivars.     

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.     

Tagging of Brown Planthopper Resistance Genes in F2s of IR50 × Ptb33 of Rice by Using Bulked Segregant Analysis

Brown planthopper(Nilaparvata lugens St?l) is one of the most damaging pests causing hopper burn in rice,and thereby reducing the productivity and also the quality of the product.The effective management strategy to control this pest is the identification and transfer of desirable genes to local rice cultivars.The most important approach for developing resistant cultivars is the identification of markers,which can help in marker-assisted selection of more durable resistant genotype.The susceptible parent IR50 and the resistant parent Ptb33,and their F2 populations were used in bulked segregant analysis for identification of resistant genes with random amplified polymorphic DNA marker(RAPD) primers.The primers OPC7 and OPAG14 showed both dominant and susceptible specific banding pattern so called co-dominant markers.Moreover,OPC7697 and OPAG14680 showed resistant specific bands and thus being in coupling phase,whereas OPC7846 and OPAG14650 showed susceptible specific genotypic bands in bulked segregant analysis.Therefore,the coupling phase markers,OPC7697 and OPAG14680,are considered to be more useful in marker-assisted selection of rice genotypes in crop improvement.     

Greenhouse techniques to identify field resistance to the brown planthopper,Nilaparvata lugens (Stål) (Homoptera: Delphacidae), in rice cultivars

Two seedbox screening techniques were compared to determine levels of resistance of rice cultivars to three brown planthopper, Nilaparvata lugens (Stål), biotypes. The commonly used standard seedbox screening test (SSST) where eight second-instar nymphs were infested on 7-day-old seedlings was compared with a modification (MSST) where four second-instar nymphs were infested on each of 20-day-old plants. In the SSST, the initial infestation killed the susceptible cultivars whereas in the MSST the F₁ progeny killed the susceptible cultivars. The cultivars ASD 11, Wagwag, Utri Rajapan, IR46 and Kencana were susceptible in the SSST but moderately resistant or resistant in the MSST, indicating an increase in the level of resistance with plant age. Feeding rate and population growth of N. lugens were the factors involved in the resistance of 30-day-old plants. The MSST provides a rapid method for identifying field-resistant cultivars in the greenhouse and can be used to identify field-resistant lines in a rice-breeding programme for stable resistance to N. lugens.     

Resistance of Oryza spp. to thrips, Stenchaetothrips biformis (Bagnall) (Thysanoptera: Thripidae)

A method to evaluate rice cultivars for resistance to Stenchaetothrips biformis (Bagnall) in the greenhouse was developed. Eleven traditional cultivars of Oryza sativa and 12 wild rices were selected for resistance. Studies on the mechanisms of resistance indicated that resistant cultivars were non-preferred for feeding and oviposition. Larval survival was lower and adult life shorter on resistant compared with susceptible cultivars. Resistant cultivars had an adverse effect on fecundity and oviposition rate which resulted in a low population growth. Plant injury on susceptible cultivars reduced plant weight and height.     

Potassium phosphate induces tolerance against the Russian wheat aphid (Diuraphis noxia,Homoptera: Aphididae) in wheat

Diuraphis noxia Kurdjumov is an aphid pest that hampers the global production of wheat (Triticum aestivum L.). Infestation of wheat by D. noxia reduces crop yield and sometimes leads to the death of susceptible cultivars. To date resistant cultivars have been used to control infestations. However, the development of resistance-breaking aphid biotypes is complicating this management strategy. This study aimed to ascertain the effect that 25 mM potassium phosphate (K₃PO₄) treatment has on inducing resistance in wheat against D. noxia. The effects of potassium phosphate on induced resistance against D. noxia were determined using gene regulation and enzymatic levels of lipoxygenase (EC 1.13.11) and phenylalanine ammonia lyase (EC 4.3.1.24). The results indicated that the treatment of both susceptible (Scheepers) and resistant (Tugela DN) wheat cultivars with potassium phosphate induces genes differentially. A phenotypic study showed delayed development and less severity of symptoms with decreased numbers of aphids feeding on plants treated with potassium phosphate in comparison with untreated plants for both resistant and susceptible cultivars. The results from the gene expression and enzyme activity studies indicated that both of the induced systemic resistance-linked genes were similarly regulated after potassium phosphate treatment. The data strongly support treatment of wheat with potassium phosphate to induce tolerance against D. noxia.     

Genetic analysis for resistance to the green leafhopper, Nephotettix virescens (Distant), in some cultivars of rice, Oryza sativa L.

The genetics of resistance to green leafhopper Nephotettix virescens (Distant) was studied in 17 cultivars of rice (Oryza sativa L.). Seedlings at the one-leaf stage were infested with second- and third-instar nymphs of green leafhopper. Reactions to seedling injury were recorded 7–8 days after infestation. The reactions of F₁, F₂, and F₃ populations from the crosses of resistant varieties with susceptible parent TN1 revealed that resistance of Tilakkachray, Kalimekri 77-5, and Tilockkachari was governed by two dominant genes and resistance of IR42 was conveyed by a single recessive gene. Single dominant genes govern resistance in the remaining 13 cultivars. Allele tests revealed that a single dominant gene of Segon Perak and one of the two genes of Kalimekri 77-5 are allelic to Glh 1. The single dominant gene of Ernest, Bignou and ARC614 and one of the two genes of each of Tilakkachray, Kalimekri 77-5, and Tilockkachari are allelic to Glh 2. A single dominant gene, which is allelic to Glh 3, conditions resistance in Arai and IR30. The single recessive gene which conveys resistance in IR42 appears to be allelic to glh 4. The allelic relationships of one of the two genes of Tilakkachray and Tilockkachari and single dominant genes of Fulkari 653, Chao Pho Kha, Amoule Borome, Kabero, Aus Murali, IR28 and IR34, with each other and with Glh 5 are not known.     

Genetic analyses of heading date of Japonica rice cultivars from Northeast China

Northeast regions of China (38–55°N latitude) play an important role in Japonica rice planting. Heading dates of 10 Japonica rice cultivars native to the Northeast of China were investigated and their sensitivities to photoperiod and temperature were analyzed. The results showed that these Japonica rice cultivars were insensitive to photoperiod but strongly sensitive to temperature, i.e. a high temperature can markedly shorten the heading date. Genetic analyses were conducted on these 10 cultivars using a set of heading date tester lines. All these Japonica cultivars carried a dominant early heading gene Ef-1, and most of these cultivars carried the photoperiod insensitivity allele e₁, and two types of alleles were presented at the Se-1 locus, including recessive photoperiod insensitivity gene Se-1^e and dominant strong photoperiod-sensitivity (PS) gene Se-1ⁿ. The PS of these cultivars carrying E₁ or Se-1ⁿ can be repressed or weakened by Ef-1 and the recessive allele hd2 they carried. These results provided a reasonable explanation to the adaptability of Japonica rice to the high latitude environment of the Northeast China, and could be useful for breeding new cultivars well adapted to the high latitude regions and expanding the rice cultivation range.     

Introgression of Gene for Non-Pollen Type Thermo-Sensitive Genic Male Sterility to Thai Rice Cultivars

For the two-line hybrid rice system, pol en sterility is regulated by recessive gene that responds to temperature. The recessive gene controlling thermo-sensitive genetic male sterility （TGMS） is expressed when the plants are grown in conditions with higher or lower critical temperatures. To transfer tgms gene（s） control ing TGMS to Thai rice cultivars by backcross breeding method, a male sterile line was used as a donor parent while Thai rice cultivars ChaiNat 1, PathumThani 1, and SuphanBuri 1 were used as recurrent parents. The BC2F2 lines were developed from backcrossing and selfing. Moreover, the simple sequence repeat （SSR） markers were developed for identifying tgms gene and the linked marker was used for assisting selection in backcrossing. The identification lines were confirmed by pol en observation. The results showed the success of introgression of the tgms gene into Thai rice cultivars. These lines will be tested for combining ability and used as female parent in hybrid rice production in Thailand.     

Molecular Scree ning of Blast Resistance Genes in Rice Germplasms Resistant to Magnaporthe oryzae

Molecular screening of major rice blast resistance genes was determined with molecular markers, which showed close-set linkage to 11 major rice blast resistance genes (Pi-d2, Pi-z, Piz-t, Pi-9, Pi-36, Pi-37, Pi5, Pi-b, Pik-p, Pik-h and Pi-ta²), in a collection of 32 accessions resistant to Magnaporthe oryzae. Out of the 32 accessions, the Pi-d2 and Pi-z appeared to be omnipresent and gave positive express. As the second dominant, Pi-b and Piz-t gene frequencies were 96.9% and 87.5%. And Pik-h and Pik-p gene frequencies were 43.8% and 28.1%, respectively. The molecular marker linkage to Pi-ta² produced positive bands in eleven accessions, while the molecular marker linkage to Pi-36 and Pi-37 in only three and four accessions, respectively. The natural field evaluation analysis showed that 30 of the 32 accessions were resistant, one was moderately resistant and one was susceptible. Infection types were negatively correlated with the genotype scores of Pi-9, Pi5, Pi-b, Pi-ta² and Pik-p, although the correlation coefficients were very little. These results are useful in identification and incorporation of functional resistance genes from these germplasms into elite cultivars through marker-assisted selection for improved blast resistance in China and worldwide.     

Marker-Assisted Selection of Xa21 Conferring Resistance to Bacterial Leaf Blight in indica Rice Cultivar LT2

Bacterial leaf blight of rice (BLB), caused by Xanthomonas oryzae pv. oryzae, is one of the most destructive diseases in Asian rice fields. A high-quality rice variety, LT2, was used as the recipient parent. IRBB21, which carries the Xa21 gene, was used as the donor parent. The resistance gene Xa21 was introduced into LT2 by marker-assisted backcrossing. Three Xoo races were used to inoculate the improved lines following the clipping method. Eleven BC₃F₃ lines carrying Xa21 were obtained based on molecular markers and agronomic performance. The 11 lines were then inoculated with the three Xoo races. All the 11 improved lines showed better resistance to BLB than the recipient parent LT2. Based on the level of resistance to BLB and their agronomic performance, five lines (BC₃F₃ 5.1.5.1, BC₃F₃ 5.1.5.12, BC₃F₃ 8.5.6.44, BC₃F₃ 9.5.4.1 and BC₃F₃ 9.5.4.23) were selected as the most promising for commercial release. These improved lines could contribute to rice production in terms of food security.     

The Relationship Between Active Oxygen Metabolism and Resistance to Late Blight in Potato

The relationship between active oxygen metabolism and resistance to late blight (Phytophthora infestans) in potato (Solanum tuberosum L.) was studied for 72 h post-inoculation by comparing three resistant cultivars (low disease index) with three susceptible ones (high disease index). Activities of superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX), and the content of ascorbic acid (ASA), were higher in the resistant cultivars than in the susceptible ones. The production rate of the superoxide anion radical (O₂^?) was lower in the resistant cultivars than in the susceptible ones. These changes, which were associated with the potato plant’s response to infection with P. infestans, provide some insight into the physiological basis of resistance and may also provide a screening tool for resistance to late blight.     

Virulence Types of Magnaporthe oryzae to Hybrid Rice in Sichuan,China

A total of 638 isolates of rice blast(Magnaporthe oryzae) were isolated in 2002-2009 from different rice varieties in different regions of Sichuan,China and inoculated onto seven rice varieties(Lijiangxintuanheigu,IR24,Minghui 63,Duohui 1,Chenghui 448,Neihui 99-14 and RHR-1) to differentiate the virulence types of the fungus and trace the changes.The virulence to the seven varieties was respectively scored at 1,2,4,8,16,32 and 64.The total scores of individual M.grisea isolates which were the sum of scores infecting differential varieties could,in turn,be used for the nomenclature of the virulence types due to their accordance to the special virulence patterns.The 638 tested isolates were then differentiated into 56 different virulence types.Type 15 virulent to Lijiangxintuanheigu,IR24 and Minghui 63,and Type 127 virulent to all of the seven varieties were the most dominant virulence types respectively with the occurrence frequencies of 15.99% and 15.83%.Type 19 and other seven virulence types were not monitored during 2002-2009.Type 15 was the predominant virulence type in 2002,2003,2004 and 2007,whereas Type 127 had been the most dominant virulence type after 2005 except for the year 2007 when the province underwent severe drought.Five hundred and seven out of the 638 tested isolates were virulent to Minghui 63,and 89.58% of the 384 isolates virulent to either Duohui 1,Chenghui 448 or Neihui 99-14 were virulent to Minghui 63,which indicated the impact of the extensive plantation of hybrid rice Minghui 63 as the restorer line on the virulence evolution of M.oryzae in Sichuan.The virulence pattern of the dominant virulence types suggested that the acquiring of virulence to all the major resistant restorer lines was the main routes of the evolution in virulence of M.oryzae to hybrid rice in Sichuan.The virulence frequencies of the 638 tested isolates to IR24,Minghui 63,Duohui 1,Chenghui 448,Neihui 99-14 and RHR-1 were respectively 74.6%,79.5%,73.8%,37.0%,39.0% and 40.4%.The analysis for the sources of the different virulence type isolates indicated the pathogen on the newly released resistant varieties were stronger than conventional rice varieties which had become susceptible in the field since 1980s.     

Damage Potential,Effect on Germination,and Development of Sitophilus oryzae (Coleoptera: Curculionidae) on Wheat Grains in Northwestern Himalayas

The present investigation was carried out to study the biological parameters and orientation of Sitophilus oryzae (L.) toward wheat cultivar HPW-236 and mixed grains of different cultivars (HPW-155, HPW-236, HPW-249, HPW-349, HPW-360, HS-490, and VL-892). The incubation period, larval period, pupal period, and total life cycle period of S. oryzae was longer when fed on mixed grains as compared to HPW-236. Also, the weevils were more oriented toward HPW-236 and lower germination rates were observed from HPW-236 than mixed cultivars when exposed to S. oryzae. We also evaluated quantitative losses caused by S. oryzae in different cultivars of wheat recommended in the northwestern Himalayas under free-choice conditions. The weevil inflicted greater damage and weight loss in grains of HPW-236 while it was negligible in the case of HPW-360 and HPW-249. HPW-236 which is the most cultivated variety of wheat in northwestern Himalayas proved to be highly susceptible to the weevil and provided a more suitable environment for weevil’s development. Therefore, this particular cultivar can be avoided for prolong storage and the farmers should prefer cultivars such as HPW-360 and HPW-249, which proved to be least affected the weevil.     

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.     

Proteomic analysis of a disease-resistance-enhanced lesion mimic mutant spotted leaf 5 in rice

Background

Rice is a major source of dietary intake of arsenic (As) for the populations that consume rice as a staple food. Therefore, it is necessary to reduce the As concentration in rice to avoid the potential risk to human health. In this study, the genetic diversity in As accumulation and As speciation in rice grains was investigated using a world rice core collection (WRC) comprising 69 accessions grown over a 3-year period. Moreover, quantitative trait locus (QTL) analysis was conducted to identify QTLs controlling the dimethylarsinic acid (DMA) content of rice grains.

Results

There was a 3-fold difference in the grain As concentration of WRC. Concentrations of total-As, inorganic As, and DMA were significantly affected by genotype, year, and genotype-year interaction effects. Among the WRC accessions, Local Basmati and Tima (indica type) were identified as cultivars with the lowest stable total-As and inorganic As concentrations. Using an F₂ population derived from Padi Perak (a high-DMA accession) and Koshihikari (a low-DMA cultivar), we identified two QTLs on chromosome 6 (qDMAs6.1 and qDMAs6.2) and one QTL on chromosome 8 (qDMAs8) that were responsible for variations in the grain DMA concentration. Approximately 73% of total phenotypic variance in DMA was explained by the three QTLs.

Conclusions

Based on the results provided, one strategy for developing rice cultivars with a low level of toxic As would be to change the proportion of organic As on the basis of a low level of total As content.