One of the less known benefits of the CGIAR is the facilitation of international agricultural research for crop improvement by providing a continuous supply of breeding materials for the development of disease resistant varieties. The Germplasm Health Units (GHUs) of the CGIAR are phytosanitary mechanisms put in place to help ensure safe (from pests and diseases) and efficient international transfer of germplasm among genebanks and breeding programs around the world. To date, there is no systematic documentation of the pathways and extent to which GHUs contribute to economic impact in recipient countries. We conducted interviews with key experts and reviewed secondary literature and data to trace the pathways through which the GHU of the International Rice Research Institute (IRRI) contributes to the impact of breeding for rice blast. We applied an ex ante economic surplus framework to the case of rice blast in Bangladesh, considering productivity maintenance and time saving factors from GHU facilitation. Data were drawn from a national panel dataset of farm households (from 2013 to 2016 with about 4490 households) and field surveys of blast incidence and severity (from 2011 to 2012 in 10 agroecological zones). We augmented our model with Monte Carlo sampling to simulate distributions of parameters. Our model predicts that, in the most probable scenario (modal values), the IRRI GHU contributed about US$ 5.9 million of the total US$ 295 million net benefits over a 20-year time frame of continuous blast resistance breeding and deployment. In the most optimistic conditions (maximum), the IRRI GHU contributed as much as US$ 62 million of the US$ 1.46 billion benefits. The modal benefit–cost ratio of the GHU in this breeding program alone was estimated at 112. The results are sensitive to the rate of yield savings, which is contingent on yield levels, timing of deployment, effectiveness of resistance, and lifespan of resistance to blast. The study reinforces the important, and often overlooked, role of the GHUs in the international agricultural research that aims to enhance genetic gains in crops through efficient and timely access to clean and healthy germplasm.

Background and Objective: Arsenic phyto-toxicity tolerance of rice is largely controlled by rice genetics.The objective of present study was to evaluate the genetic variation and diversity of arsenic contaminated rice genotypes.Materials and Methods: A total of 295 SSR markers were used to study 15 arsenic contaminated rice genotypes.The molecular weights for each amplified allele were measured by using Alpha Ease.Summary statistics were determined by using Power Marker and the NTSYS-pc was used for cluster analysis.Results: Identified 191 polymorphic SSR markers detected 552 alleles among the tested genotypes of which 322 were common and the number of rare alleles was 230.Among the rare alleles, 141 were unique (genotype-specific) those could be used for varietal characterization.Polymorphism information content values ranged from 0.12-0.80,with an average of 0.37.Cluster analysis showed distinct two groups of tested genotypes.Cluster-I was constituted by the japonica subspecies US varieties ʻJeffersonʼ and ʻPriscillaʼ which were significantly different from all other genotypes.Cluster-II was comprised of indica subspecies, which were grouped into two different sub-clusters.Conclusion: It was concluded that high number of rare and unique alleles in the studied genotypes indicated their potentiality to use as a reservoir of rare genotypes.

Cultivation with Arsenic (As) contaminated water severely affects growth of rice plants that results into reduced grain yield.This study was carried out to develop a rapid and effective method of screening rice varieties and/or segregating population against arsenic phyto-toxicity tolerance.Sodium arsenate was used as arsenic source.Ten pre-germinated seeds of each variety were grown on styro-foam placed on a tray filled with either phosphate-free nutrient solution (control) or the same nutrient solution supplemented with di-sodium hydrogen arsenate (treatment).The trays were kept at controlled environmental condition in a growth chamber at 26±1°C with 70% humidity and 3500 lux.After 7 days of growth, standard growth parameters such as shoot length, root length, root-shoot biomass were recorded and percentages reduction for shoot length, root length and root shoot biomass compared to those of control were calculated.Arsenic stress reduced the phenotypic expression of all three seedling traits but the effect of arsenic was more prominent on root length compared to the shoot length and root-shoot biomass.The dose response experiment showed that the 0.75-1.25 mgL -1 Arsenic concentrations had much promise to discriminate rice genotypes for arsenic phyto-toxicity tolerance at early growth stage.The validation experiment with the 0.75-1.25 mgL -1 Arsenic doses on a set of 20 genotypes identified 1.25 mgL -1 Arsenic could effectively and efficiently differentiate rice genotypes, particularly for tolerance in shoot length and root-shoot biomass reduction, where 1.0 mgL -1 Arsenic was found sufficient for discriminating varieties for tolerance in root length reduction.The rice variety BRRI dhan47 showed more tolerance against Arsenic contaminated water.

Rice blast disease caused by Pyricularia oryzae is a major disease in Bangladesh. In the search of resistant source against P. oryzae, resistant gene (R-gene) was assessed by (i) host-pathogen interaction and (ii) PCR-based screening at the laboratory of Bangladesh Rice Research Institute. One hundred and forty four plant materials were classified into 10 cultivar groups (CG) based on their reaction patterns to four distinct blast isolates (SDBI; standard differential blast isolate) H-11-64, H-1-8, H-1-1 and H-11-67. The reaction patterns of plant materials to these four standard blast isolates indicated presence of Pish, Pi9, Pita2 and Pita genes and their combination in the genetic background of tested plant materials. Gene specific primer 195R-1/195F-1, Pita440 (YL153)/Pita440 (YL154), OSM89 and AOL45/AOL48 were used to identify and confirm the presence of Pi9, Pita, Pita2 and Pish genes in plant materials, respectively through PCR-based assay. Plant materials, H13, H23, H25, H35, H47, H49, H136, H138 harbored all three genes, Pita, Pita2 and Pish in their genetic background. The Pi9 gene together with Pita2 was detected in local rice cultivar H100 and H129, which were confirmed by DNA analysis in PCR assay. These materials could be used in gene pyramiding in promising high yielding cultivar for durable blast resistance.

Summary Upon pathogen attack, the plant defence response is mediated by a set of connected signal transduction pathways, guided by several classes of plant hormones. In this study, experiments were conducted to observe the role of the plant hormone gibberellic acid in the response of rice to infection by the migratory root-rot nematode Hirschmanniella oryzae. Foliar treatments with gibberellic acid showed a negative effect on H. oryzae infection in the roots. Analyses of mutant rice lines impaired in the production or signalling of gibberellic acid confirmed the effect of the plant hormone on H. oryzae infection. Taken together, the results clearly indicate that gibberellic acid has a positive effect on the capability of the rice plant to fend off an infection by the migratory nematode H. oryzae.

Incidence and severity of blast disease of rice was recorded in ten agro-ecological zones (AEZs) of Bangladesh during Boro (November to May; irrigated ecosystem) and Transplanted Aman (July to December; rain fed ecosystem) seasons. Disease incidence and severity was higher in irrigated ecosystem (Boro season) (21.19%) than in rain fed ecosystem (Transplanted Aman season) (11.98%) regardless of locations (AEZs). It was as high as 68.7% in Jhalak hybrid rice variety followed by high yielding rice cultivar BRRI dhan47 (58.2%), BRRI dhan29 (39.8%), BRRI dhan28 (20.3%) during Boro and in BRRI dhan34 (59.8%) during T. Aman season. Maximum yield loss was noted in AEZ9 for both the seasons. Percent yield loss was higher in all the locations for Boro season (irrigated ecosystem) compared to T. Aman season (rain fed ecosystem). In the crop sequence1 (CS-1= Crop cycle with one rice followed by fallow/other crops) disease incidence was 16.7% and in crop sequence2 (CS-2= Crop cycle with two rice followed by fallow/other crops) it was 31.9%. Most popularly adopted Boro rice was BRRI dhan28 (29.6%) followed by BRRI dhan29 (25.9%) and T. Aman rice was BRRI dhan34 (22.9%).

Upon pathogen attack, the plant defence response is mediated by a set of connected signal transduction pathways. Experiments were conducted to observe the role of plant hormone, in particular gibberellin (GA), in the response of rice to infection by the migratory internal tissue infecting (endoparasitic) root-rot nematode Hirschmanniella oryzae . Exogenous application of GA was done several times on Nipponbare, and there was significant effect of GA in reducing infection in Nipponbare against H. oryzae . A significantly higher number of H. oryzae per plant was found in GA-deficient mutant waitoC compared to WT and a lower number in GA-insensitive mutant gid1-3 plants. Both the number of nematodes/plant and the number of nematodes/g of root were significantly higher in waitoC than gid1-3. The results indicated that low levels of GA (naturally present) were needed for successful infection in rice plant by H. oryzae , but high levels were inhibitory.

Experiments were conducted to know the genetic diversity of Rhizoctoniaoryzae-sativae. Aggregate sheath spot infected disease samples were collected from four locations viz. Bogra, Comilla, Gazipur and Rajshahi districts of Bangladesh. Sixty AFLP and nineteen SSR markers were screened in PCRbased analysis to generate polymorphisms in R. oryzae-sativae. Out of 60 AFLP primer combinations only 6 combinations viz. EcoR1CT & Mse1-CG, EcoR1-GA & Mse1-CC, EcoR1-GT & Mse1-CG, EcoR1-TA & Mse1CC, EcoR1-TC & Mse1-CG and EcoR1-TG & Mse1-CG were found better for generating polymorphisms. On the other hand, out of 19 SSR primers only 8 primers viz. ACA5, GCAGA3, GCAG4, GACG4, CAC5, GAC5, GCA5 and MR produced more polymorphisms in R. oryzae-sativae of which GACG4 was better as comparable with others. A dendogram, resulted from SSR-PCR using GACG4 primer, was constructed where 68 isolates of R. oryzae-sativae grouped into nine different fingerprinting types (FPTs) or cluster groups at 90% similarity level. Diverse populations of R. oryzaesativae were suggested to use in screening for resistant genes and for selecting effective fungicide to manage aggregate sheath spot disease.

Morphological and molecular based experiments were conducted to identify the presence of Rhizoctonia solani, R. oryzae and R. oryzae-sativae which were the causal agents of sheath blight and sheath blight-like symptoms associated with sheath disease complex of rice.Disease survey was conducted at Bogra, Comilla, Gazipur and Rajshahi Districts in Bangladesh.The data collected revealed that sheath blight was the most important disease (19.8%) followed by aggregated sheath spot (2.4%), and sheath spot (2.3%).Three pathogens of the disease complex were identified morphologically by their spot size, general appearance of spot, number of spot, position in plant, sclerotium visibility and sclerotial size on infected plant.Those three species of Rhizoctonia of rice sheath disease complex were confirmed by diagnostic-PCR with their corresponding reference isolates by using specific primers GMRS-3, GMRO-3, GMROS-2 to Rhizoctonia solani, R. oryzae and R. oryzae-sativae, respectively.Molecular approaches might overcome the limitations of morphological characterization particularly when huge samples were needed to distinguish.

Experiments were conducted to observe the role of gibberellin (GA) in the response of rice to infection by rice root-knot nematode, Meloidogyne graminicola. Gibberellin might have a negative effect on defence in Nipponbare against M. graminicola. On the other hand, an inhibitory effect to M. graminicola in Taichung 65 (wild type) was found when GA was applied exogenously. Galling was significantly and reproducibly lower in mutants, whether it was GA insensitive or GA deficient, than in Taichung 65. There were even significantly lower galls in these GA deficient mutants after GA treatment than in non-treated mutant plants. The expression of GA signaling gene Osgid1-7 was significantly higher only in whole root at 2 dpi (days post inoculation) but not in leaves or root tips. Even this gene was not differentially expressed in root and leaf tissues at later stage (6 dpi days post inoculation) of infection. The nematode inhibited biosynthesis of OsGA20ox in leaves at 2 dpi and, in both of leaves and roots at 6 dpi. The GA response gene AK073385 was also less expressed in root tip at 6 dpi (days post inoculation). These might help M. graminicola to continue their infection in Taichung 65.

Three experiments were conducted to find out the feeding type and age structure of nematodes in different soil habitats; to know the efficiency of different extraction techniques of nematodes and to observe the hatching behavior of Meloidogyne juvenile in a Baermann device.Bacterivore, Omnivore, Predator, Fungivore and Plant Parasitic nematodes were recorded in the soil of flower, vegetable, moss, grass, and corn and compost habitats.Bacterivore was the highest feeder (67.5%) in the soil habitats.In comparison of nematode extraction methods, Seinhorst method extracted more cysts (188), but less juvenile (34) and eggs (18) from cysts than stirring (145, 87 and 50, respectively) while AZC was found superior (936) over Cobb method (204) in extracting nematodes.The AZC method also extracted huge juvenile number from roots which was higher than Baermann funnel method.In Baermann funnel, juvenile hatched more in favorable condition than unfavorable condition which led to an increasing and decreasing pattern of hatching.

In this study, host-specific forms of the blast pathogen Magnaporthe oryzae in sub-Saharan Africa (SSA) were characterised from distinct cropping locations using a combination of molecular and biological assays. Finger millet blast populations in East Africa revealed a continuous genetic variation pattern and lack of clonal lineages, with a wide range of haplotypes. M. oryzae populations lacked the grasshopper ( grh ) element (96%) and appeared distinct to those in Asia. An overall near equal distribution (47–53%) of the mating types MAT1 - 1 and MAT1 - 2 , high fertility status (84–89%) and the dominance of hermaphrodites (64%) suggest a strong sexual reproductive potential. Differences in pathogen aggressiveness and lack of cultivar incompatibility suggest the importance of quantitative resistance. Rice blast populations in West Africa showed a typical lineage-based structure. Among the nine lineages identified, three comprised ~90% of the isolates. Skewed distribution of the mating types MAT1 - 1 (29%) and MAT1 - 2 (71%) was accompanied by low fertility. Clear differences in cultivar compatibility within and between lineages suggest R gene-mediated interactions. Distinctive patterns of genetic diversity, sexual reproductive potential and pathogenicity suggest adaptive divergence of host-specific forms of M. oryzae populations linked to crop domestication and agricultural intensification.