Identification of a GDSL-motif carboxylester hydrolase from rice bran (Oryza sativa L.)

A major esterase (designated OsEST1) showing high activity using 1-naphthyl acetate as a substrate was identified from rice bran and purified approximately 239-fold to near-homogeniety. The purified enzyme migrated as a single polypeptide band on native and SDS-polyacrylamide gels and had a molecular mass of 25 kDa under denaturing conditions. Analysis of its tryptic peptides by MALDI-TOF-MS and subsequent data mining identified a corresponding cDNA OsEST1 consisting of 714 nucleotides and encoding a 238 amino acid protein. Analysis of its primary sequence indicated that OsEST1 is a GDSL-motif carboxylester hydrolase belonging to the SGNH protein subfamily in containing the putative catalytic triad of Ser¹¹, Asp¹⁸⁷, and His¹⁹⁰. OsEST1 showed the highest catalytic activity at approximately pH 8.0–8.5 and at 45 °C with K_m and V_max values for 1-naphthyl acetate of 172 μM and 63.7 μmol/min/mg protein, respectively. However, OsEST1 showed no activity with triacylglycerol. Alignment of the primary sequence of OsEST1 and other rice GDSL-motif esterases/lipases showed that OsEST1 aligns with a specific family of plant SGNH esterases involved in response to dehydration and cuticle formation. These results suggest that OsEST1 is not a lipase but an esterase activity which has some other function in rice, especially during seed development.     

QTL mapping for crude protein and protein fraction contents in rice (Oryza sativa L.)

Improvement of rice storage proteins is important in rice breeding for high nutritional quality. Seventy-one recombinant inbred lines (RIL) derived from a cross between japonica variety Asominori and indica variety IR24 were used to study the inheritance of crude protein and protein fraction contents in rice. A total of 16 QTL were identified and mapped on eight chromosomes. Several QTL affecting contents of different protein fractions were mapped in the same chromosomal region. In particular, two QTL with a significant contribution were identified to simultaneously affect prolamin and glutelin contents. One QTL denoted as qCP-12 affecting crude protein content (CP) was located in the same region as QTL qGLT-12 affecting glutelin content, in agreement with the positive correlation between glutelin level and protein content. QTL with larger genetic effects were further confirmed using two sets of chromosome segment substitution lines (CSSL), where Asominori and IR24 were used as the recurrent parents. By QTL comparative analysis, two QTL for CP, three for globulin content and one for prolamin content were located in the vicinity of CP QTL previously identified in polished rice. Application of these results in rice breeding is discussed.     

A set of near-isogenic lines for blast resistance genes with an Indica-type rainfed lowland elite rice (Oryza sativa L.) genetic background

A set of near-isogenic lines for blast resistance genes was developed by using an Indica-type elite rice variety, IR49830-7-1-2-2, suitable for the rainfed lowland conditions in the tropics, as a genetic background. Initially, we revealed that IR49830-7-1-2-2 harbors five blast resistance genes - Pia, Pib, Pik-s, Pita, and Pi11(t) - by using a differential system involving 19 selected standard blast isolates from the Philippines. Based on this result, we developed nine near-isogenic lines (NILs) targeting eight resistance genes - Pik, Pi7(t), Pi3, Pi5, Pita-2, Piz-5, Pish, and Pi9 - by recurrent backcrossing. The introgression of each resistance gene in the NILs was confirmed by reaction patterns to the blast isolates, allelism tests, and DNA marker analysis. In addition, a genome-wide DNA marker survey revealed that most of the chromosome regions in each NIL were of the IR49830-7-1-2-2 type. The agricultural characteristics of most of the developed NILs were almost the same as those of IR49830-7-1-2-2. Moreover, with one exception, they showed submergence tolerance similar to IR49830-7-1-2-2. The developed NILs could be used as a multiline variety suitable for the rainfed lowland in the tropics.     

Genomic regions associated with the degree of red coloration in pericarp of rice (Oryza sativa L.)

The degree of red coloration (DRC) in pericarp of rice depends on the content of flavonoid compounds which have beneficial health effects for humans. In this study, 182 backcross-recombinant inbred lines (BILs) derived from Koshihikari (white pericarp)/Kasalath (red pericarp)//Koshihikari were used to detect the genomic regions associated with DRC through the QTL mapping approach. As a result, a total of four genomic regions were found to associate with DRC on chromosomes 1, 7, 9 and 11, respectively. Interestingly, the two genomic regions having the largest effects corresponded to previously characterized Rc and Rd genes on chromosome 7 and 1, respectively. In addition, two novel genomic regions having minor effects on DRC and located on chromosomes 9 and 11, respectively, are reported here for the first time. These results and the identification of tightly linked molecular markers that flank the genomic regions provide an opportunity for marker-aided improvement of red coloration in pericarp of rice.     

Identification of deletion mutants with improved performance under water-limited environments in rice (Oryza sativa L.)

Rice (Oryza sativa L.) is a semi-aquatic member of the grass family that is poorly adapted to dry environments and has greater sensitivity to water-deficits than other important cereals in this family. To increase productivity in aerobic or water-limited environments rice must overcome its adaptations to flooded environments. Deletion mutants offer an alternative genetic resource for improving drought tolerance. Almost 3500 IR64 deletion mutants were screened under vegetative and reproductive stage drought stress in the field and evaluated for leaf drying and/or grain yield. Seven novel conditional mutants of rice which showed gain of function through continued growth as drought stress developed compared to the wild type were identified. Mutant recovery rate was 0.1%. Further evaluation of putative drought mutants revealed that their average shoot biomass at maturity and grain yield per plant under stress exceeded those of the wild type by two-fold. Studies under controlled conditions confirmed mutants to have continued growth of both roots and shoots as drought developed compared to the wild type, and a tendency for greater water extraction. We propose that deletions in these mutants have affected a regulator of the highly conservative growth response common to irrigated lowland rice cultivars. Our results suggest that screening deletion mutants for performance under managed drought stress in the field could be a highly effective way to identify valuable genetic resources for improved drought response and aerobic adaptation in rice.     

Molecular marker assisted selection for improvement of the eating,cooking and sensory quality of rice (Oryza sativa L.)

II-32B is a key maintainer line used for hybrid rice breeding in China. However, it is of poor quality for most Chinese consumers because of its high apparent amylose content (AAC), high gelatinization temperature (GT) and non-fragrance. It is well known that the AAC, GT and fragrance traits are largely controlled by the Wx, starch synthase IIa (SSIIa), and fragrance (fgr) genes, respectively. With the aid of functional markers, we improved the quality of II-32B by introgressing the Wx, SSIIa, and fgr genes from Yixiang B, a fragrant maintainer line that has low AAC and low GT. The microsatellite allele (CT)₁₇ of Wx, the contiguous single nucleotide polymorphism TT allele of SSIIa and the 8-bp deletion allele of fgr were transferred to II-32B by two backcrosses and three selfings. Molecular marker assisted selection was applied in the series to select for individuals carrying Wx-(CT)₁₇, SSIIa-TT, and fgr-deletion alleles. According to the marker genotypes, seventeen homozygous lines for Wx-(CT)₁₇, SSIIa-TT, and fgr gene markers were finally selected. The improved II-32B lines were fragrant with reduced AAC and GT.     

Wilt disease management and enhancement of growth and yield of Cajanus cajan (L) var. Manak by bacterial combinations amended with chemical fertilizer

Root nodulating Sinorhizobium fredii KCC5 and Pseudomonas fluorescens LPK2 were isolated from nodules of Cajanus cajan and disease suppressive soil of tomato rhizosphere, respectively. Both strains produced IAA, siderophore, solubilized insoluble phosphate, showed chitinase and β-1,3-glucanase activities, and strongly inhibited the growth of Fusarium udum. It also caused degradation and digestion of cell wall components, resulting in hyphal perforations, empty cell (halo) formation, shrinking and lysis of fungal mycelia along with significant degeneration of conidia. LPK2 produced volatile cyanogen (HCN). Combinations of S. fredii KCC5 and P. fluorescens LPK2 with half dose of chemical fertilizers showed a significant increase in seed germination (94%) while seed germination with co-inoculated strains (KCC5 + LPK2), KCC5 and LPK2 alone was 90, 84 and 82% respectively as compared to control 77%. After 120 days of sowing, per plant number of pods, nodules, shoot length, root length, shoot weight and root weight were greater for the combination with half dose of chemical fertilizers compared to the control. Combinations of S. fredii KCC5 and P. fluorescens LPK2 with half dose of chemical fertilizers resulted in an 82% increase in grain yield per hectare compared to the control. Both strains KCC5 and LPK2 led to proto-cooperation as evidenced by synergism, aggressive colonization of the roots, and enhanced growth, suggesting potential biocontrol efficacy against Fusarium wilt in C. cajan.     

Identification of novel glutelin subunits and a comparison of glutelin composition between japonica and indica rice (Oryza sativa L.)

Glutelin, a major protein in rice grains, is encoded by a multigene family. However, its protein composition is not well characterised. Here, we identified and characterised two novel glutelin subunits, GluBX and GluC. The individual glutelin subunits of japonica cv. Nipponbare and indica cv. 93-11 rice were analysed using 2-dimensional gel electrophoresis, LC–MS/MS, and Western blotting. Comparison of the glutelin profiles between three japonica and three indica cultivars indicated two distinct subunits (GluA-1 and GluA-3 isomers) and a distinction in the subunit composition (notably GluA-3 and Lys-rich GluB-1 components) of these two subspecies. Sequence alignment revealed different nutritional (Lys residues) and functional (Cys residues) characteristics between the type-A and type-B glutelin subfamilies. We also analysed amino acid and total protein contents of the grains in thirty-five cultivars, and we demonstrated that the Lys-rich glutelin composition of indica cultivars is superior to that of japonica cultivars. The Lys-rich and Cys-poor GluBX subunit is a native protein and is a high nutritional protein in grains. Our combined approaches for the identification of glutelin subunits have revealed the nutritional characteristics of individual subunits in rice, and this knowledge will provide new insights for improving grain quality during rice breeding.     

Polymorphisms in the ALS gene of weedy rice (Oryza sativa L.) accessions with differential tolerance to imazethapyr

Herbicide-resistant Clearfield™ rice technology allows the use of ALS inhibitors to control weedy rice. Weedy rice plants have differential tolerance to imazethapyr, perhaps due to ALS polymorphisms. We aimed to assess ALS polymorphisms in weedy rice accessions from Arkansas, USA, with differential tolerance to imazethapyr in seedling growth bioassays. Six base changes were identified in the ALS of 14 weedy rice accessions. Three of these nucleotide changes resulted in amino acid substitutions — Pro⁹³Thr, Glu⁶³⁰Asp, and Val⁶⁶⁹Met — in four accessions: Ark-4, Ark-9, Poi-1 and Poi-6. The GR₅₀ values and inhibition of root and shoot growth (%) of these accessions differed. The Glu⁶³⁰Asp substitution occurs in the herbicide binding domain B and Val⁶⁶⁹Met occurs at the C-terminal tail where the co-factor binds. Variability in weedy rice ALS exists, but polymorphism patterns did not relate to tolerance levels. The observed mutations presented the possibility that sustained selection pressure will eventually lead to selection of a herbicide-tolerant individual that will be the progenitor of a resistant population. Concomitantly, pollen-mediated gene flow from Clearfield™ rice to weedy rice will lead to the evolution of ALS-resistant weedy rice populations.     

Genetic analysis and validation of quantitative trait loci associated with reproductive-growth traits and grain yield under drought stress in a doubled haploid line population of rice (Oryza sativa L.)

Drought is a major constraint for rice production and yield stability in rainfed ecosystems, especially when it occurs during the reproductive stage. Combined genetic and physiological analysis of reproductive-growth traits and their effects on yield and yield components under drought stress is important for dissecting the biological bases of drought resistance and for rice yield improvement in water-limited environments. A subset of a doubled haploid (DH) line population of CT9993-5-10-1-M/IR62266-42-6-2 was evaluated for variation in plant water status, phenology, reproductive-growth traits, yield and yield components under reproductive-stage drought stress and irrigated (non-stress) conditions in the field. Since this DH line population was previously used in extensive quantitative trait loci (QTLs) mapping of various drought resistance component traits, we aimed at identifying QTLs for specific reproductive-growth and yield traits and also to validate the consensus QTLs identified earlier in these DH lines using meta-analysis. DH lines showed significant variation for plant water status, reproductive-growth traits, yield and yield components under drought stress. Total dry matter, number of panicles per plant, harvest index, panicle harvest index, panicle fertility, pollen fertility, spikelet fertility and hundred grain weight had significant positive correlations with grain yield under drought stress. A total of 46 QTLs were identified for the various traits under stress and non-stress conditions with phenotypic effect ranging from 9.5 to 35.6% in this study. QTLs for panicle exsertion, peduncle length and pollen fertility, identified for the first time in this study, could be useful in marker-assisted breeding (MAB) for drought resistance in rice. A total of 97 QTLs linked to plant growth, phenology, reproductive-growth traits, yield and its components under non-stress and drought stress, identified in this study as well as from earlier published information, were subjected to meta-analysis. Meta-analysis identified 23 MQTLs linked to plant phenology and production traits under stress conditions. Among them, four MQTLs viz., 1.3 for plant height, 3.1 for days to flowering, 8.1 for days to flowering or delay in flowering and 9.1 for days to flowering are true QTLs. Consensus QTLs for reproductive-growth traits and grain yield under drought stress have been identified on chromosomes 1 and 9 using meta-QTL analysis in these DH lines. These MQTLs associated with reproductive-growth, grain yield and its component traits under drought stress could be useful targets for drought resistance improvement in rice through MAB and/or map-based positional analysis of candidate genes.     

Development of elite breeding lines conferring Bph18 gene-derived resistance to brown planthopper (BPH) by marker-assisted selection and genome-wide background analysis in japonica rice (Oryza sativa L.)

Brown planthopper (BPH) is a serious threat to rice production. In this study, we have used the novel resistance gene Bph18 derived from Oryza australiensis and incorporated it into an elite japonica cultivar, Junambyeo, which is highly susceptible to BPH. The Bph18 gene was introduced by marker-assisted backcross (MAB) breeding into Junambyeo. The backcrossed progenies were evaluated for desirable agronomic and grain quality traits and the selection of improved breeding lines while simultaneously evaluating BPH resistance by bioassays in the greenhouse and foreground selection. Of the 26 advanced backcross breeding lines (ABL), four lines showed agronomic traits similar to those of the recurrent parent, with strong resistance to BPH. Molecular genotyping of the four ABL revealed the conversion of genotypes closely resembling the genotype of Junambyeo. The percentage of donor chromosome segments in ABL decreased from 12.3% in the BC₂ to 9.4%, 8.4% and 5.3% in BC₃, BC₄ and BC₅ generations, respectively. ABL retained small sizes of the donor chromosome segments on chromosomes 1, 2, 10, 11 and 12 but the genomes of ABL2, ABL3 and ABL4 were homosequential to the recurrent parent on chromosomes 3, 4, 5, 6, 7 and 9 without donor chromosome segment introgression. The ABL1 and ABL2 retained only some small segments of the donor genome on chromosomes 9 and 8, respectively. Fine structure analysis of the Bph18 flanking region between RM511 and RM1584 markers on chromosome 12 showed a progressive elimination of donor-derived chromosome segments from BC₂ to BC₅ generations. The percentage of O. australiensis derived chromosome segment substitution in the recurrent parent background decreased from 28% of the donor parent to 6.7%, 3.9%, 3.4% and 3.4% in BC₂, BC₃, BC₄ and BC₅ generations, respectively. However, it was revealed that the O. australiensis-derived chromosome segment (1320 kb) in ABL containing the Bph18 gene was consistently maintained irrespective of advances in backcross generations. BPH resistant elite breeding lines with agronomic and grain quality traits similar to those of the recurrent parent were successfully developed by foreground and background analysis in japonica background without linkage drag.     

Improvement of bacterial blight resistance of hybrid rice in China using the Xa23 gene derived from wild rice (Oryza rufipogon)

A novel bacterial blight (BB) resistance gene, Xa23, identified from Oryza rufipogon was introgressed into three popular restorer lines (Minghui63, YR293 and Y1671) for wild abortive cytoplasmic male sterility by marker-assisted backcross breeding approach in combination with artificial inoculation and stringent phenotypic selections. The three derived BB resistant restorer lines (Minghui63-Xa23, YR293-Xa23 and Y1671-Xa23) and their hybrid combinations with Zhenshan97A (Shanyou63-Xa23), NongfengA (Fengyou293-Xa23) and Zhong9A (Zhongyou1671-Xa23) demonstrated similar BB resistance spectrum as the donor parent, CBB23 (B). The newly developed BB resistant restorers and their derived hybrids were identical to their respective original versions for agronomic traits especially under disease free condition. However, under severe disease condition, the three BB resistant restorer lines exhibited significantly higher grain weight and spikelet fertility as compared to the respective original restorer lines thus further resulting in BB resistant hybrids with significantly higher grain yields than their respective popular original hybrids. The results indicated that the Xa23 gene could completely express its dominant broad spectrum resistance in different backgrounds of both restorer and male sterile lines across different growth stages, suggesting its immense breeding value in BB resistance improvement for hybrid rice. Moreover, a reasonable utilization and deployment of Xa23 gene for efficient control of BB disease in hybrid rice production was recommended.     

Potential of Waxy gene microsatellite and single-nucleotide polymorphisms to develop japonica varieties with desired amylose levels in rice (Oryza sativa L.)

The Waxy (Wx) gene is responsible for the synthesis of amylose, a key determinant of the cooking and processing qualities of rice. Polymorphisms of CT-microsatellite and G–T single-nucleotide polymorphism (SNP) in the Wx gene and their relationship to amylose content (Ac) were explored using 178 non-waxy rice genotypes. Nine Wx microsatellite alleles, namely (CT)10 and 11, and (CT)14–20 were identified and 11 haplotypes were recognised by different combinations of CT-microsatellite and G–T SNP. Amylose content analysed in a random set of 39 genotypes was correlated with different microsatellite alleles/haplotypes. The highest Ac levels (>30%) correlated with (CT)10 and 16, high (26–30%) with (CT)11, 15 and 20, and intermediate (21–25%) with (CT)14, in all cases with G at the G–T SNP. The CT-classes (CT)17 and 18 (mean Ac value of 21%), could be subdivided into low amylose haplotypes (16–20%) for 17T and 18T and intermediate amylose haplotypes (21–25%) for 17G and 18G. The use of haplotypes proved to discriminate between intermediate and low amylose accessions within the same microsatellite class. Analyses of a segregating population of a cross between low and high Ac parents showed that CT-microsatellite may help to classify breeding lines and identify pollen contamination. We suggest that CT-microsatellite together with G–T SNP may be used as molecular marker by breeders to develop varieties with desired amylose levels.     

Effect of salinity on yield and 2-acetyl-1-pyrroline content in the grains of three fragrant rice cultivars (Oryza sativa L.) in Camargue (France)

Aromatic quality of rice grains is known to vary greatly with environmental factors and cultivation methods. Among the environmental factors, soil salinity is thought to have a positive impact on the content of 2-acetyl-1-pyrroline (2AP) in grains, the key volatile compound of rice aroma. This study compared 2AP content in grains of three improved fragrant rice (Oryza sativa L.) varieties grown in two fields, differing mainly in their soil salinity level. The impact of salinity on yield and main yield components was also investigated to understand the relationship between aromatic quality and yield build-up. Soil salinity was monitored by measuring the electrical conductivity (EC) of soil solution samples extracted every week. 2AP content in grains was determined by a newly developed stable isotope dilution method involving solid-phase microextraction (SPME) and GC MS/MS analysis. The results showed an increase of 2AP content in grains with salinity for the three varieties. The relationship between 2AP and mean EC of the crop fitted a single model for the three varieties (R² = 0.728). In contrast, the impact of salinity on yield and yield components differed greatly between the three varieties. One variety appeared to be very sensitive to salt stress, with significant yield loss up to 40%, while the two other varieties proved to be resistant to the salinity levels experienced by the plants, with no significant yield loss or even higher yields in saline conditions. Nevertheless, the three varieties presented a significant negative correlation between 1000 grain weight (TGW) and the mean EC of the crop, and between TGW and 2AP content. It was concluded that the increase of 2AP content with salinity resulted partially from a 2AP concentration mechanism in smaller size grains. The direct effect of salinity on 2AP synthesis through stimulation of the proline metabolism is further discussed.     

Variation in root system architecture and drought response in rice (Oryza sativa): Phenotyping of the OryzaSNP panel in rainfed lowland fields

Root growth at soil depths below 30 cm may provide access to critical soil water reserves during drought in rainfed lowland rice. In this study, the OryzaSNP panel, a set of 20 lines representing genetic diversity in rice used for the discovery of DNA sequence polymorphisms, was evaluated for root characteristics in the field over three seasons varying in drought severity. Root length density (RLD) at a depth of 30–45 cm varied up to 74–92% among genotypes under drought stress (2008–2009 dry seasons), ranging from 0.024 to 0.23 cm cm⁻³ in 2008 and from 0.19 to 0.81 cm cm⁻³ in 2009. Real-time monitoring of soil moisture profiles revealed significant differences among genotypes, and these differences were correlated with RLD at those soil depths. Among the lines evaluated, the Aus isozyme group, particularly the genotype Dular, showed greater drought resistance associated with deep root growth and the highest drought response index (less reduction in yield by drought stress). Since the set of genotypes used in this study has been completely sequenced for SNP markers, the phenotypic information on root growth and drought avoidance responses presented here could be used in initial analysis of the genetic basis of dehydration avoidance traits and in facilitating improvement in drought resistance in rice.     

Management of the root-knot nematode Meloidogyne incognita on tomato with combinations of different biocontrol organisms

The nematicidal effect of Pseudomonas fluorescens, Paecilomyces lilacinus, Pichia guilliermondii and Calothrix parietina singly or in combination was tested against root-knot nematode, Meloidogyne incognita. Treatments with P. fluorescens and P. lilacinus caused mortality of M. incognita as 45% and 30% of juveniles after 48 h of exposures, respectively compared to water control in vitro. Under greenhouse conditions, all treatments reduced the disease severity and enhanced plant growth compared to untreated control. Application of P. fluorescens, P. lilacinus and P. guilliermondii Moh 10 was more effective compared to C. parietina. There was a negative interaction between C. parietina and either P. lilacinus or P. guilliermondii. Fresh and dry weight of shoots and roots of plants were significantly reduced as a result of infection with M. incognita, however application of biocontrol agents singly or in mix recovered this reduction. Moreover, they enhanced the growth parameters compared with the control. Our results proved that application of different biocontrol agents (P. fluorescens, P. lilacinus and P. guilliermondii) not only has a lethal effect on nematode, but also enhances the plant growth, supplying many nutritional elements and induction the systemic resistance in plants. Presence of C. parietina as a soil inhabitant cyanobacterium could antagonize biocontrol agents leading to the reduction of their practical efficiency in soil.     

Diversity of weedy red rice (Oryza sativa L.) in Arkansas,U.S.A. in relation to weed management

Weedy rice, specifically red rice (Oryza sativa L.), is a major weed in rice which causes up to 80% yield loss and reduction of grain quality. Red rice accessions from Arkansas, U.S.A., were characterized to classify red rice accessions into certain phenotypic groups relevant to weedy rice management. The red rice accessions were 70% strawhull, 22% blackhull, 7% brownhull and <1% goldhull. Generally, blackhull red rice was the tallest (139 cm) and strawhull the shortest (133 cm) among all accessions. Blackhull red rice had more tillers (102/plant), smaller flag leaves (13 cm wide, 34 cm long), and flowered later (1225 heat units) than strawhull red rice which had 85 tillers/plant, 15 cm-wide and 34 cm-long flag leaves, and flowered after accumulating 1195 heat units. Morphological differences between accessions within each hull type were highly significant, showing great diversity within a hull color group as indicated by large ranges in traits. For example, blackhulls were 75–190 cm tall with 18–69 cm long flag leaves, 21–188 tillers and produced 40–949 g seed. Strawhulls were 46–189 cm tall with 18–66 cm flag leaf length, 16–172 tillers and produced 100–608 g seed. Some traits, such as seed production, differed widely between accessions within each hull color group such that the average seed production/accession for blackhull did not differ from that of strawhull weedy rice (196 vs. 192 g/plant). The onset of flowering among all accessions ranged from 56 to 126 d after planting. Red rice accessions formed six phenotypic clusters generally segregated by plant size or flowering time. Each morphotype would have different competitive abilities; thus, weedy rice management could be geared toward plant types. Highly competitive plant types would require intensive control measures to minimize yield losses and reduce the soil seed bank. Flowering dates impact stewardship strategies for herbicide-resistant or any genetically modified rice.     

Development of a formulation of Trichoderma asperellum to control black rot disease on pineapple caused by (Thielaviopsis paradoxa)

A local isolate of Trichoderma asperellum was tested for its antagonistic activity against Thielaviopsis paradoxa (telemorph = Ceratocyctis paradoxa). The highest antagonistic activity was achieved when the concentration of T. asperellum conidia was 1 × 10⁷ conidia/mL. The highest biomass and number of colony forming unit/mL of the T. asperellum peaked at 144 h after incubation in yeast waste residue medium. The minimum inhibition concentration value of the formulation was observed as 1% on growth of Th. paradoxa incubated at 28 ± 2 °C for 10 d. In the soil fungicide-screening test, the effect of concentrations 100-1600 μg/mL on mycelia growth was not significant (P < 0.05). Complete mycelial growth inhibition occurred at concentration above 52,600 μg/mL. Results of the fruit application tests clearly showed that all treated fruits were free of disease at the end of the incubation period. No significant differences (P > 0.05) in pH, total soluble solids and titratable acidity were observed between fruits treated with formulation of T. asperellum and the control formulation treated pineapples.     

Influence of the soil physical environment on rice (Oryza sativa L.) response to drought stress and its implications for drought research

Plant performance under drought stress is not solely defined by an inadequate water supply but by an interaction among many factors, including climatic, edaphic, and biological factors. An important interacting factor affecting root growth, and therefore the ability of a plant to access and take up water, is the soil physical environment. Soil penetration resistance can restrict, or even halt, root system growth. For rice, a soil penetration resistance of 1.4 MPa is sufficient to inhibit root system expansion. This review describes the effects of the soil physical environment on root growth and its interaction with drought stress. A large variation in soil penetration resistance exists among rainfed rice-growing areas of South and Southeast Asia and within experimental stations used for managed-drought field phenotyping. This variability may influence genotypic performance across experimental sites/countries and the response of crop genotypes to drought stress. A case study is presented in which differences in the soil physical environment may partially elucidate differences in experimental results between two field studies conducted at different locations. These results highlight the need for increased knowledge of environmental interactions to allow the outputs of genomics to increase drought tolerance at the field level.     

Use of field-integrated information in GIS-based maps to evaluate Moko disease (Ralstonia solanacearum) in banana growing farms in Colombia

Ralstonia solanacearum (formerly Pseudomonas solanacearum) causes large losses in more than 200 different cultivated plant species. Banana and plantain “Moko” disease is caused by R. solanacearum race 2. Moko disease may cause 100% loss if prompt control measures are not applied. Although a number of investigations have been carried out, many ecological and epidemiological aspects of R. solanacearum race 2 are still unknown, particularly in the tropics. Bacteria dispersion occurs by infested tools, soil, water, insects, domestic animals and agricultural labourers. Alternative hosts have been described which may contribute to inoculum availability in crop fields. In banana crops, cable-ways are routinely used to transport fruit and materials inside plantations. In most humid tropical areas, drainage channels are made to evacuate excess soil water. It is thought that agricultural activities associated with drainage channels and cable-ways may play a role in bacteria dispersion but individual contributions have not yet been quantified. In this work we have used field-integrated information in geographical information systems (GIS)-based maps to evaluate Moko presence in the Urabá region of Colombia, during three different time periods. A previously described risk index (RI) and losses throughout the three periods were quantified. A regression model was developed to quantify the relationship between infested area and distance from every Moko focus to the nearest cable-way and drainage channels. Farms were grouped into four different profiles according to the RI. Parameters calculated using the regression model showed that 76% of Moko foci detected during the three time periods were associated with cable-ways used for transport of fruit and consumables. This finding has important implications for disease management since bacteria spread in these ways may be prevented by simple measures taken inside plantations.