Global transcript analysis of rice leaf and seed using SAGE technology.

We have compiled two comprehensive gene expression profiles from mature leaf and immature seed tissue of rice (Oryza sativa ssp. japonica cultivar Nipponbare) using Serial Analysis of Gene Expression (SAGE) technology. Analysis revealed a total of 50 519 SAGE tags, corresponding to 15 131 unique transcripts. Of these, the large majority (approximately 70%) occur only once in both libraries. Unexpectedly, the most abundant transcript (approximately 3% of the total) in the leaf library was derived from a type 3 metallothionein gene. The overall frequency profiles of the abundant tag species from both tissues differ greatly and reveal seed tissue as exhibiting a non-typical pattern of gene expression characterized by an over abundance of a small number of transcripts coding for storage proteins. A high proportion ( approximately 80%) of the abundant tags (> or = 9) matched entries in our reference rice EST database, with many fewer matches for low abundant tags. Singleton transcripts that are common to both tissues were collated to generate a summary of low abundant transcripts that are expressed constitutively in rice tissues. Finally and most surprisingly, a significant number of tags were found to code for antisense transcripts, a finding that suggests a novel mechanism of gene regulation, and may have implications for the use of antisense constructs in transgenic technology.

Influence of foliar diseases and their control by fungicides on grain yield and quality in wheat

Twenty-eight field experiments on sandy-loam soils in the UK (1982-2003) are reviewed by relating the extension of the green area duration of the flag leaf (GLADF) by fungicides to effects on yield and quality of winter wheat. Over all experiments mean grain yield = 8.85t ha(-1) at 85% DM. With regards quality, mean values were: thousand grain weight (TGW) = 44.5 g; specific weight (SWT) = 76.9 kg hl(-1); crude protein concentration (CP (N x 5.7)) = 12.5 % DM; Hagberg falling number (HFN) = 285 s; and sodium dodecyl sulphate (SDS)-sedimentation volume = 69ml. For each day (d) that fungicides increased GLADF there were associated average increases in yield (0.144 1 ha(-1) d(-1), se 0.0049, df = 333), TGW (0.56 gd(-1), se = 0.017) and SWT (0.22 kg hl(-1) d(-1), se 0.011). Some curvature was evident in all these relationships. When GLADF was delayed beyond 700 degrees Cd after anthesis, as was possible in cool wet seasons, responses were curtailed, or less reliable. Despite this apparent terminal sink limitation, fungicide effects on sink size, eg endosperm cell numbers or maximum water mass per grain, were not prerequisites for large effects on grain yield, TGW or SWT. Fungicide effects on CP were variable. Although the average response of CP was negative (-0.029%DM/d; se = 0.00338), this depended on cultivar and disease controlled. Controlling biotrophs such as rusts, (Puccinia spp.) tended to increase CP, whereas controlling a more necrotrophic pathogen (Septoria tritici) usually reducedCP. Irrespective of pathogen controlled, delaying senescence of the flag leaf was associated with increased nitrogen yields in the grain (averaging 2.24 kg N ha-1 d(-1), se = 0.0848) due to both increased N uptake into the above ground crop, and also more efficient remobilisation of N from leaf laminas. When sulphur availability appeared to be adequate, fungicide x cultivar interactions were similar on S as for CP, although N:S ratios tended to decline (i.e. improve for bread making) when S. tritici was controlled. On average, SDS-sedimentation volume declined (-0. 18 ml/d, se = 0.027) with increased GLADF, broadly commensurate with the average effect on CP. Hagberg falling number decreased as fungicide increased GLADF (-2.73 s/d, se = 0.178), indicating an increase in alpha-amylase activity.

Logit models for identifying the factors that influence the uptake of new 'no-tillage' technologies by farmers in the rice-wheat and the cotton-wheat farming systems of Pakistan's Punjab

In the 'rice-wheat' and the 'cotton-wheat' farming systems of Pakistan's Punjab, late planting of wheat is a perennial problem due to often delayed harvesting of the previously planted and late maturing rice and cotton crops. This leaves very limited time for land preparation for 'on-time' planting of wheat. 'No-tillage' technologies that reduce the turn-round time for wheat cultivation after rice and cotton have been developed, but their uptake has not been as expected.-This paper attempts to determine the farm and farmer characteristics and other socio-economic factors that influence the adoption of 'no-tillage' technologies'. Logit models were developed for the analysis undertaken. In the 'cotton-wheat' system personal characteristics like education, tenancy status, attitude towards risk implied in the use of new technologies and contact with extension agents are the main factors that affect adoption. As regards the 'rice-wheat' system, resource endowments such as farm size, access to a 'no-tillage' drill, clayey soils and the area sown to the rice-wheat sequence along with tenancy and contact with extension agents were dominant in explaining adoption. (C) 2002 Elsevier Science Ltd. All rights reserved.

On-farm management of rice genetic diversity: understanding farmers' knowledge on rice ecosystems and varietal development

The paper highlights the methodological development of identifying and characterizing rice (Oryza sativa L.) ecosystems and the varietal deployment process through participatory approaches. Farmers have intricate knowledge of their rice ecosystems. Evidence from Begnas (mid-hill) and Kachorwa (plain) sites in Nepal suggests that farmers distinguish ecosystems for rice primarily on the basis of moisture and fertility of soils. Farmers also differentiate the number, relative size and specific characteristics of each ecosystem within a given geographic area. They allocate individual varieties to each ecosystem, based on the principle of ‘best fit’ between ecosystem characteristics and varietal traits, indicating that competition between varieties mainly occurs within the ecosystems. Land use and ecosystems determine rice genetic diversity, with marginal land having fewer options for varieties than more productive areas. Modern varieties are mostly confined to productive land, whereas landraces are adapted to marginal ecosystems. Researchers need to understand the ecosystems and varietal distribution within ecosystems better in order to plan and execute programmes on agrobiodiversity conservation on-farm, diversity deployment, repatriation of landraces and monitoring varietal diversity. Simple and practical ways to elicit information on rice ecosystems and associated varieties through farmers’ group discussion at village level are suggested.

Diamond mining, rice farming, and a ‘Maggi cube’: a viable survivial strategy in rural Liberia?

Since the conclusion of its 14-year civil war in 2003, Liberia has struggled economically. Jobs are in short supply and operational infrastructural services, such as electricity and running water, are virtually nonexistent. The situation has proved especially challenging for the scores of people who fled the country in the 1990s to escape the violence and who have since returned to re-enter their lives. With few economic prospects on hand, many have elected to enter the artisanal diamond mining sector, which has earned notoriety for perpetuating the country's civil war. This article critically reflects on the fate of these Liberians, many of whom, because of a lack of government support, finances, manpower and technological resources, have forged deals with hired labourers to work artisanal diamond fields. Specifically, in exchange for meals containing locally grown rice and a Maggi (soup) cube, hired hands mine diamondiferous territories, splitting the revenues accrued from the sales of recovered stones amongst themselves and the individual ‘claimholder’ who hired them. Although this cycle—referred to here as ‘diamond mining, rice farming and a Maggi cube’—helps to buffer against poverty, few of the parties involved will ever progress beyond a subsistence level

Knowledge, attitudes and practices of farmers on rodent pests and their management in the lowlands of the Sierra Madre Biodiversity Corridor, Philippines

A survey of the knowledge, attitudes and practices (KAP) of 100 rice farmers and 50 coconut farmers was conducted in the coastal lowland agro-ecosystems of the Sierra Madre Biodiversity Corridor, Luzon, Philippines to identify current rodent management practices and to understand the extent of rat damage and the attitudes of farmers to community actions for rodent management. Pests were most commonly listed as one of the three most important rice and coconut production constraints. Other major crop production constraints were typhoons and insufficient water. Farmers consider rats to be the major pest of coconut and of rice during the wet season rice crop, with average yield losses of 3.0% and 13.2%, respectively. Rice and coconut farmers practised a wide range of rodent management techniques. These included scrub clearance, hunting and trapping. Of the 42 rice farmers and 3 coconut farmers that applied rodenticides to control rodents, all used the acute rodenticide, zinc phosphide. However, only ten rice farmers (23.8%) applied rodenticides prior to the booting stage and only seven farmers (15.6%) conducted pre-baiting before applying zinc phosphide. The majority of farmers belonged to farmer organisations and believed that rat control can only be done by farmers working together. However, during the last cropping season, less than a third of rice farmers (31.2%) applied rodent management as a group. In order to reduce the impact of rodents on the farmers of the coastal lowlands of the Sierra Madre Biodiversity Corridor, integrated management strategies need to be developed that specifically target the pest rodents in a sustainable manner, and community actions for rodent management should be promoted.

The release of silicon from amorphous silica and rice straw in Sri Lankan soils

Silicon release from rice straw and amorphous silica when shaken in solution with five Sri Lankan soils was studied indirectly using sorption isotherms and changes in concentration and directly using straw in dialysis bags examined using electron microscopy. The aim was to further our understanding of the processes and factors affecting the release of straw-Si in soils and its availability to rice. The soils (alfisols and ultisols) shaken with 0.1 M NaCl (5 g per 125 mL for 250 days) produced concentrations of 1 - 4 mg L-1 of monosilicic acid-Si. Amorphous silica added to these suspensions (36.5 mg, containing 17 mg Si) raised the concentrations to 20 - 40 mg L-1, and added rice straw (0.5 g, containing 17 mg Si) gave 10 - 25 mg L-1. Sorption isotherms (7 days equilibrations) were used to calculate from the concentrations the amounts of Si released ( 24 - 38% and 8 - 21%, respectively). Both materials gave about 40 mg L-1 of monosilicic acid-Si plus 30 mg L-1 of disilicic acid-Si when shaken in solution alone (5 g per 125 mL). Straw in dialysis bags ( 0.5 g per 25 mL in 0.1 M NaCl) was shaken in soil suspension ( 5 g per 100 mL) for 60 days. Similar concentrations and releases were measured to those obtained above. About one fifth of the mass of straw was lost by decomposition in the first 15 days. A chloroform treatment prevented decomposition, but Si release was unaffected. Disintegration continued throughout the experiments, with phytoliths being exposed and dissolved. Compared to the rate of release from straw into solution without soil, the release of Si into soil suspensions was increased during the first 20 days by adsorption on the soil, but was then reduced probably through the effect of Fe and Al on the phytolith surfaces. The extent of this blocking effect varied between soils and was not simply related to soil pH.

The release of silicon from amorphous silica and rice straw in Sri Lankan soils

Silicon release from rice straw and amorphous silica when shaken in solution with five Sri Lankan soils was studied indirectly using sorption isotherms and changes in concentration and directly using straw in dialysis bags examined using electron microscopy. The aim was to further our understanding of the processes and factors affecting the release of straw-Si in soils and its availability to rice. The soils (alfisols and ultisols) shaken with 0.1 M NaCl (5 g per 125 mL for 250 days) produced concentrations of 1 - 4 mg L-1 of monosilicic acid-Si. Amorphous silica added to these suspensions (36.5 mg, containing 17 mg Si) raised the concentrations to 20 - 40 mg L-1, and added rice straw (0.5 g, containing 17 mg Si) gave 10 - 25 mg L-1. Sorption isotherms (7 days equilibrations) were used to calculate from the concentrations the amounts of Si released ( 24 - 38% and 8 - 21%, respectively). Both materials gave about 40 mg L-1 of monosilicic acid-Si plus 30 mg L-1 of disilicic acid-Si when shaken in solution alone (5 g per 125 mL). Straw in dialysis bags ( 0.5 g per 25 mL in 0.1 M NaCl) was shaken in soil suspension ( 5 g per 100 mL) for 60 days. Similar concentrations and releases were measured to those obtained above. About one fifth of the mass of straw was lost by decomposition in the first 15 days. A chloroform treatment prevented decomposition, but Si release was unaffected. Disintegration continued throughout the experiments, with phytoliths being exposed and dissolved. Compared to the rate of release from straw into solution without soil, the release of Si into soil suspensions was increased during the first 20 days by adsorption on the soil, but was then reduced probably through the effect of Fe and Al on the phytolith surfaces. The extent of this blocking effect varied between soils and was not simply related to soil pH.

The survival advantage of milk and dairy consumption: An overview of evidence from cohort studies of vascular diseases, diabetes and cancer

Objectives: To conduct it detailed evaluation, with meta-analyses, of the published evidence on milk and dairy consumption and the incidence of vascular diseases and diabetes. Also to summarise the evidence on milk and dairy consumption and cancer reported by the World Cancer Research Fund and then to consider the relevance of milk and dairy consumption to survival in the UK, a typical Western community. Finally, published evidence on relationships with whole milk and fat-reduced milks was examined. Methods: Prospective cohort studies of vascular disease and diabetes with baseline data on milk or dairy consumption and a relevant disease outcome were identified by searching MEDLINE, and reference lists in the relevant published reports. Meta-analyses of relationships in these reports were conducted. The likely effect of milk and dairy consumption on survival was then considered, taking into account the results of published overviews of relationships of these foods with cancer. Results: From meta-analysis of 15 studies the relative risk of stroke and/or heart disease in subjects with high milk or dairy consumption was 0.84 (95% CI 0.76, 0,93) and 0.79 (0.75, 0.82) respectively, relative to the risk in those with low consumption. Four studies reported incident diabetes as an outcome, and the relative risk in the Subjects with the highest intake of milk or diary foods was 0.92 (0.86, 0.97). Conclusions: Set against the proportion of total deaths attributable to the life-threatening diseases in the UK, vascular disease, diabetes and cancer, the results of meta-analyses provide evidence of an overall survival advantage from the consumption of milk and dairy foods.

Arthropod diversity and community structure in relation to land use in the mekong delta, vietnam

Declining biodiversity in agro-ecosystems, caused by intensification of production or expansion of monocultures, is associated with the emergence of agricultural pests. Understanding how land-use and management control crop-associated biodiversity is, therefore, one of the key steps towards the prediction and maintenance of natural pest-control. Here we report on relationships between land-use variables and arthropod community attributes (for example, species diversity, abundance and guild structure) across a diversification gradient in a rice-dominated landscape in the Mekong delta, Vietnam. We show that rice habitats contained the most diverse arthropod communities, compared with other uncultivated and cultivated land-use types. In addition, arthropod species density and Simpson's diversity in flower, vegetable and fruit habitats was positively related to rice cover in the local landscape. However, across the landscape as a whole, reduction in heterogeneity and the amount of uncultivated cover was associated, generally, with a loss of diversity. Furthermore, arthropod species density in tillering and flowering stages of rice was positively related to crop and vegetation richness, respectively, in the local landscape. Differential effects on feeding guilds were also observed in rice-associated communities with the proportional abundance of predators increasing and the proportional abundance of detritivores decreasing with increased landscape rice cover. Thus, we identify a range of rather complex, sometimes contradictory patterns concerning the impact of rice cover and landscape heterogeneity on arthropod community attributes. Importantly, we conclude that that land-use change associated with expansion of monoculture rice need not automatically impact diversity and functioning of the arthropod community.

The rodent species of the Ifugao Rice Terraces, Philippines - Target or non-target species for management?

We investigated the species diversity and habitat use of rodents in the Ifugao Rice Terraces (IRT), Luzon, Philippines, as a first step in their assessment either as pest species of rice or as potential non-target species of rodent control practice. Trapping was carried out in caneland and forest habitats adjacent to rice cropland using trap lines of 10 - 15 cage-traps. Four trapping rounds, each consisting of 5 nights trapping, were replicated at two sites during the months of May and June. A diverse rodent fauna was recorded, including the non-native pest species, Rattus tanezumi, and the native species, Rattus everetti and Chrotomys mindorensis. Results from trapping and spool-and-line tracking suggested that these native species do not contribute to rice damage and that several may actually be beneficial in the ricefield ecosystem as vermivores that feed on invertebrate pests. Control should therefore be directed at the pest species, R. tanezumi, minimising non-target effects on the non-pest rodent species.

Reaping the benefits: science and the sustainable intensification of global agriculture

Food security is one of this century’s key global challenges. By 2050 the world will require increased crop production in order to feed its predicted 9 billion people. This must be done in the face of changing consumption patterns, the impacts of climate change and the growing scarcity of water and land. Crop production methods will also have to sustain the environment, preserve natural resources and support livelihoods of farmers and rural populations around the world. There is a pressing need for the ‘sustainable intensifi cation’ of global agriculture in which yields are increased without adverse environmental impact and without the cultivation of more land. Addressing the need to secure a food supply for the whole world requires an urgent international effort with a clear sense of long-term challenges and possibilities. Biological science, especially publicly funded science, must play a vital role in the sustainable intensifi cation of food crop production. The UK has a responsibility and the capacity to take a leading role in providing a range of scientifi c solutions to mitigate potential food shortages. This will require signifi cant funding of cross-disciplinary science for food security. The constraints on food crop production are well understood, but differ widely across regions. The availability of water and good soils are major limiting factors. Signifi cant losses in crop yields occur due to pests, diseases and weed competition. The effects of climate change will further exacerbate the stresses on crop plants, potentially leading to dramatic yield reductions. Maintaining and enhancing the diversity of crop genetic resources is vital to facilitate crop breeding and thereby enhance the resilience of food crop production. Addressing these constraints requires technologies and approaches that are underpinned by good science. Some of these technologies build on existing knowledge, while others are completely radical approaches, drawing on genomics and high-throughput analysis. Novel research methods have the potential to contribute to food crop production through both genetic improvement of crops and new crop and soil management practices. Genetic improvements to crops can occur through breeding or genetic modifi cation to introduce a range of desirable traits. The application of genetic methods has the potential to refi ne existing crops and provide incremental improvements. These methods also have the potential to introduce radical and highly signifi cant improvements to crops by increasing photosynthetic effi ciency, reducing the need for nitrogen or other fertilisers and unlocking some of the unrealised potential of crop genomes. The science of crop management and agricultural practice also needs to be given particular emphasis as part of a food security grand challenge. These approaches can address key constraints in existing crop varieties and can be applied widely. Current approaches to maximising production within agricultural systems are unsustainable; new methodologies that utilise all elements of the agricultural system are needed, including better soil management and enhancement and exploitation of populations of benefi cial soil microbes. Agronomy, soil science and agroecology—the relevant sciences—have been neglected in recent years. Past debates about the use of new technologies for agriculture have tended to adopt an either/or approach, emphasising the merits of particular agricultural systems or technological approaches and the downsides of others. This has been seen most obviously with respect to genetically modifi ed (GM) crops, the use of pesticides and the arguments for and against organic modes of production. These debates have failed to acknowledge that there is no technological panacea for the global challenge of sustainable and secure global food production. There will always be trade-offs and local complexities. This report considers both new crop varieties and appropriate agroecological crop and soil management practices and adopts an inclusive approach. No techniques or technologies should be ruled out. Global agriculture demands a diversity of approaches, specific to crops, localities, cultures and other circumstances. Such diversity demands that the breadth of relevant scientific enquiry is equally diverse, and that science needs to be combined with social, economic and political perspectives. In addition to supporting high-quality science, the UK needs to maintain and build its capacity to innovate, in collaboration with international and national research centres. UK scientists and agronomists have in the past played a leading role in disciplines relevant to agriculture, but training in agricultural sciences and related topics has recently suffered from a lack of policy attention and support. Agricultural extension services, connecting farmers with new innovations, have been similarly neglected in the UK and elsewhere. There is a major need to review the support for and provision of extension services, particularly in developing countries. The governance of innovation for agriculture needs to maximise opportunities for increasing production, while at the same time protecting societies, economies and the environment from negative side effects. Regulatory systems need to improve their assessment of benefits. Horizon scanning will ensure proactive consideration of technological options by governments. Assessment of benefi ts, risks and uncertainties should be seen broadly, and should include the wider impacts of new technologies and practices on economies and societies. Public and stakeholder dialogue—with NGOs, scientists and farmers in particular—needs to be a part of all governance frameworks.

Not all sigmodontine rodents in the sugarcane fields in costal Veracruz, Mexico, are pests

Rats and mice have traditionally been considered one of the most important pests of sugarcane. However, "control" campaigns are rarely specific to the target species, and can have an effect on local wildlife, in particular non-pest rodent species. The objective of this study was to distinguish between rodent species that are pests and those that are not, and to identify patterns of food utilization by the rodents in the sugarcane crop complex. Within the crop complex, subsistence crops like maize, sorghum, rice, and bananas, which are grown alongside the sugarcane, are also subject to rodent damage. Six native rodent species were trapped in the Papaloapan River Basin of the State of Veracruz; the cotton rat (Sigmodon hispidus), the rice rat (Oryzomys couesi), the small rice rat (O. chapmani), the white footed mouse (Peromyscus leucopus), the golden mouse (Reithrodontomys sumichrasti), and the pigmy mouse (Baiomys musculus). In a stomach content analysis, the major food components for the cotton rat, the rice rat and the small rice rat were sugarcane (4.9 to 30.1 %), seed (2.7 to 22.9%), and vegetation (0.9 to 29.8%); while for the golden mouse and the pigmy mouse the stomach content was almost exclusively seed (98 to 100%). The authors consider the first three species to be pests of the sugarcane crop complex, while the last two species are not.

Integrating pests and pathogens into the climate change/food security debate

While many studies have demonstrated the sensitivities of plants and of crop yield to a changing climate, a major challenge for the agricultural research community is to relate these findings to the broader societal concern with food security. This paper reviews the direct effects of climate on both crop growth and yield and on plant pests and pathogens and the interactions that may occur between crops, pests, and pathogens under changed climate. Finally, we consider the contribution that better understanding of the roles of pests and pathogens in crop production systems might make to enhanced food security. Evidence for the measured climate change on crops and their associated pests and pathogens is starting to be documented. Globally atmospheric [CO(2)] has increased, and in northern latitudes mean temperature at many locations has increased by about 1.0-1.4 degrees C with accompanying changes in pest and pathogen incidence and to farming practices. Many pests and pathogens exhibit considerable capacity for generating, recombining, and selecting fit combinations of variants in key pathogenicity, fitness, and aggressiveness traits that there is little doubt that any new opportunities resulting from climate change will be exploited by them. However, the interactions between crops and pests and pathogens are complex and poorly understood in the context of climate change. More mechanistic inclusion of pests and pathogen effects in crop models would lead to more realistic predictions of crop production on a regional scale and thereby assist in the development of more robust regional food security policies.