International Rice Research Institute

Indonesia has the largest tropical peatlands in the world covered an area of 14.91 
\nmillion ha. Peatlands play an important role in global carbon sequestration. This study aimed 
\nto: a] map the peatland in Pesisir Selatan, Sumatra Barat calculate the soil carbon stock in the 
\npeatlands on various land use and peat thickness and c] identify the relationship of soil 
\ncharacteristics to the soil carbon. We investigated thirty soil samples in Pesisir Selatan. The 
\nland-use types on peatland in Pesisir Selatan consisted of forest [GH], shrub [GS], oil palm 
\nplantations [GPs], annual cropland[GLp], and bareland [GLp]. The results showed that the 
\ntotal area of peatlands inPesisir Selatan is 78,998.74 ha, while the total amount of soil carbon 
\nstocks is 244 million tonnes, and the sequence follows GPs> GS> GH> GT>GLp. The average 
\nvalue of soil carbon stock is 3,090.89 per ha, the sequence follows GH> GS> GT> GPs>GLp. 
\nHence, the average amount of soil carbon stock based on depth is 8,529 tons for peat depth
\n>600cm, 4,082 tons for peat depth 300-600 cm, and 525 tons for peat depth 0-300 cm. 
\nDifferences in average values of soil carbon stock per ha are highly influenced by the 
\ndifferences in peat thickness. The dynamics of total carbon show a higher its content in the 
\nsubsurface layer rather than in the surface layer. The soil carbon is linearly correlated with 
\nwater content and it is inversely proportional to bulk density.
\nKeywords: digital mapping, peat, satellite imagery, soil carbon stock

Significance Agricultural production is vulnerable to climate change. Understanding climate change, especially the temperature impacts, is critical if policymakers, agriculturalists, and crop breeders are to ensure global food security. Our study, by compiling extensive published results from four analytical methods, shows that independent methods consistently estimated negative temperature impacts on yields of four major crops at the global scale, generally underpinned by similar impacts at country and site scales. Multimethod analyses improved the confidence in assessments of future climate impacts on global major crops, with important implications for developing crop- and region-specific adaptation strategies to ensure future food supply of an increasing world population.

ABSTRACT A wide range of modelling algorithms is used by ecologists, conservation practitioners, and others to predict species ranges from point locality data. Unfortunately, the amount of data available is limited for many taxa and regions, making it essential to quantify the sensitivity of these algorithms to sample size. This is the first study to address this need by rigorously evaluating a broad suite of algorithms with independent presence–absence data from multiple species and regions. We evaluated predictions from 12 algorithms for 46 species (from six different regions of the world) at three sample sizes (100, 30, and 10 records). We used data from natural history collections to run the models, and evaluated the quality of model predictions with area under the receiver operating characteristic curve (AUC). With decreasing sample size, model accuracy decreased and variability increased across species and between models. Novel modelling methods that incorporate both interactions between predictor variables and complex response shapes (i.e. GBM, MARS‐INT, BRUTO) performed better than most methods at large sample sizes but not at the smallest sample sizes. Other algorithms were much less sensitive to sample size, including an algorithm based on maximum entropy (MAXENT) that had among the best predictive power across all sample sizes. Relative to other algorithms, a distance metric algorithm (DOMAIN) and a genetic algorithm (OM‐GARP) had intermediate performance at the largest sample size and among the best performance at the lowest sample size. No algorithm predicted consistently well with small sample size ( n < 30) and this should encourage highly conservative use of predictions based on small sample size and restrict their use to exploratory modelling.

The impact of projected global warming on crop yields has been evaluated by indirect methods using simulation models. Direct studies on the effects of observed climate change on crop growth and yield could provide more accurate information for assessing the impact of climate change on crop production. We analyzed weather data at the International Rice Research Institute Farm from 1979 to 2003 to examine temperature trends and the relationship between rice yield and temperature by using data from irrigated field experiments conducted at the International Rice Research Institute Farm from 1992 to 2003. Here we report that annual mean maximum and minimum temperatures have increased by 0.35 degrees C and 1.13 degrees C, respectively, for the period 1979-2003 and a close linkage between rice grain yield and mean minimum temperature during the dry cropping season (January to April). Grain yield declined by 10% for each 1 degrees C increase in growing-season minimum temperature in the dry season, whereas the effect of maximum temperature on crop yield was insignificant. This report provides a direct evidence of decreased rice yields from increased nighttime temperature associated with global warming.

DNA markers have enormous potential to improve the efficiency and precision of conventional plant breeding via marker-assisted selection (MAS). The large number of quantitative trait loci (QTLs) mapping studies for diverse crops species have provided an abundance of DNA marker-trait associations. In this review, we present an overview of the advantages of MAS and its most widely used applications in plant breeding, providing examples from cereal crops. We also consider reasons why MAS has had only a small impact on plant breeding so far and suggest ways in which the potential of MAS can be realized. Finally, we discuss reasons why the greater adoption of MAS in the future is inevitable, although the extent of its use will depend on available resources, especially for orphan crops, and may be delayed in less-developed countries. Achieving a substantial impact on crop improvement by MAS represents the great challenge for agricultural scientists in the next few decades.

Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence-absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.

Abstract Climate envelope models (CEMs) have been used to predict the distribution of species under current, past, and future climatic conditions by inferring a species' environmental requirements from localities where it is currently known to occur. CEMs can be evaluated for their ability to predict current species distributions but it is unclear whether models that are successful in predicting current distributions are equally successful in predicting distributions under different climates (i.e. different regions or time periods). We evaluated the ability of CEMs to predict species distributions under different climates by comparing their predictions with those obtained with a mechanistic model (MM). In an MM the distribution of a species is modeled based on knowledge of a species' physiology. The potential distributions of 100 plant species were modeled with an MM for current conditions, a past climate reconstruction (21 000 years before present) and a future climate projection (double preindustrial CO 2 conditions). Point localities extracted from the currently suitable area according to the MM were used to predict current, future, and past distributions with four CEMs covering a broad range of statistical approaches: Bioclim (percentile distributions), Domain (distance metric), GAM (general additive modeling), and Maxent (maximum entropy). Domain performed very poorly, strongly underestimating range sizes for past or future conditions. Maxent and GAM performed as well under current climates as under past and future climates. Bioclim slightly underestimated range sizes but the predicted ranges overlapped more with the ranges predicted with the MM than those predicted with GAM did. Ranges predicted with Maxent overlapped most with those produced with the MMs, but compared with the ranges predicted with GAM they were more variable and sometimes much too large. Our results suggest that some CEMs can indeed be used to predict species distributions under climate change, but individual modeling approaches should be validated for this purpose, and model choice could be made dependent on the purpose of a particular study.

The complex juvenile/maturity transition during a plant's life cycle includes growth, reproduction, and senescence of its fundamental organs: leaves, flowers, and fruits. Growth and senescence of leaves, flowers, and fruits involve several genetic networks where the phytohormone ethylene plays a key role, together with other hormones, integrating different signals and allowing the onset of conditions favorable for stage progression, reproductive success and organ longevity. Changes in ethylene level, its perception, and the hormonal crosstalk directly or indirectly regulate the lifespan of plants. The present review focused on ethylene's role in the development and senescence processes in leaves, flowers and fruits, paying special attention to the complex networks of ethylene crosstalk with other hormones. Moreover, aspects with limited information have been highlighted for future research, extending our understanding on the importance of ethylene during growth and senescence and boosting future research with the aim to improve the qualitative and quantitative traits of crops.

Rodents are the most abundant and diversified order of living mammals in the world. Already since the Middle Ages we know that they can contribute to human disease, as black rats were associated with distribution of plague. However, also in modern times rodents form a threat for public health. In this review article a large number of pathogens that are directly or indirectly transmitted by rodents are described. Moreover, a simplified rodent disease model is discussed.

Bacterial blight of rice is an important disease in Asia and Africa. The pathogen, Xanthomonas oryzae pv. oryzae (Xoo), secretes one or more of six known transcription-activator-like effectors (TALes) that bind specific promoter sequences and induce, at minimum, one of the three host sucrose transporter genes SWEET11, SWEET13 and SWEET14, the expression of which is required for disease susceptibility. We used CRISPR-Cas9-mediated genome editing to introduce mutations in all three SWEET gene promoters. Editing was further informed by sequence analyses of TALe genes in 63 Xoo strains, which revealed multiple TALe variants for SWEET13 alleles. Mutations were also created in SWEET14, which is also targeted by two TALes from an African Xoo lineage. A total of five promoter mutations were simultaneously introduced into the rice line Kitaake and the elite mega varieties IR64 and Ciherang-Sub1. Paddy trials showed that genome-edited SWEET promoters endow rice lines with robust, broad-spectrum resistance.

A 2275-marker genetic map of rice (Oryza sativa L.) covering 1521.6 cM in the Kosambi function has been constructed using 186 F2 plants from a single cross between the japonica variety Nipponbare and the indica variety Kasalath. The map provides the most detailed and informative genetic map of any plant. Centromere locations on 12 linkage groups were determined by dosage analysis of secondary and telotrisomics using > 130 DNA markers located on respective chromosome arms. A limited influence on meiotic recombination inhibition by the centromere in the genetic map was discussed. The main sources of the markers in this map were expressed sequence tag (EST) clones from Nipponbare callus, root, and shoot libraries. We mapped 1455 loci using ESTs; 615 of these loci showed significant similarities to known genes, including single-copy genes, family genes, and isozyme genes. The high-resolution genetic map permitted us to characterize meiotic recombinations in the whole genome. Positive interference of meiotic recombination was detected both by the distribution of recombination number per each chromosome and by the distribution of double crossover interval lengths.

The above- and below-ground parts of rice plants create specific habitats for various microorganisms. In this study, we characterized the phyllosphere and rhizosphere microbiota of rice cultivars using a metaproteogenomic approach to get insight into the physiology of the bacteria and archaea that live in association with rice. The metaproteomic datasets gave rise to a total of about 4600 identified proteins and indicated the presence of one-carbon conversion processes in the rhizosphere as well as in the phyllosphere. Proteins involved in methanogenesis and methanotrophy were found in the rhizosphere, whereas methanol-based methylotrophy linked to the genus Methylobacterium dominated within the protein repertoire of the phyllosphere microbiota. Further, physiological traits of differential importance in phyllosphere versus rhizosphere bacteria included transport processes and stress responses, which were more conspicuous in the phyllosphere samples. In contrast, dinitrogenase reductase was exclusively identified in the rhizosphere, despite the presence of nifH genes also in diverse phyllosphere bacteria.

Rice production in China has more than tripled in the past five decades mainly due to increased grain yield rather than increased planting area. This increase has come from the development of high-yielding varieties and improved crop management practices such as nitrogen fertilization and irrigation. However, yield stagnation of rice has been observed in the past ten years in China. As its population rises, China will need to produce about 20% more rice by 2030 in order to meet its domestic needs if rice consumption per capita stays at the current level. This is not an easy task because several trends and problems in the Chinese rice production system constrain the sustainable increase in total rice production. Key trends include a decline in arable land, increasing water scarcity, global climate change, labor shortages, and increasing consumer demand for high-quality rice (which often comes from low-yielding varieties). The major problems confronting rice production in China are narrow genetic background, overuse of fertilizers and pesticides, breakdown of irrigation infrastructure, oversimplified crop management, and a weak extension system. Despite these challenges, good research strategies can drive increased rice production in China. These include the development of new rice varieties with high yield potential, improvement of resistances to major diseases and insects, and to major abiotic stresses such as drought and heat, and the establishment of integrated crop management. We believe that a sustainable increase in rice production is achievable in China with the development of new technology through rice research.

BACKGROUND AND AIMS: Salinity is a widespread soil problem limiting productivity of cereal crops worldwide. Rice is particularly sensitive to salt stress during the seedling stage, with consequent poor crop establishment, as well as during reproduction where salinity can severely disrupt grain formation and yield. Tolerance at the seedling stage is weakly associated with tolerance during reproduction. Physiological responses to salinity were evaluated for contrasting genotypes, during the seedling and reproductive stages. METHODS: Three rice genotypes differing in their tolerance of salinity were evaluated in a set of greenhouse experiments under salt stress during both seedling stage and reproduction. KEY RESULTS: Photosynthetic CO2 fixation, stomatal conductance (gs) and transpiration decreased substantially because of salt stress, but with greater reduction in the sensitive cultivar IR29. The tolerant lines IR651 and IR632 had more responsive stomata that tended to close faster during the first few hours of stress, followed by partial recovery after a brief period of acclimation. However, in the sensitive line, gs continued to decrease for longer duration and with no recovery afterward. Chlorophyll fluorescence measurements revealed that non-photochemical quenching increased, whereas the electron transport rate decreased under salt stress. Salt-tolerant cultivars exhibited much lower lipid peroxidation, maintained elevated levels of reduced ascorbic acid and showed increased activities of the enzymes involved in the reactive oxygen scavenging system during both developmental stages. CONCLUSIONS: Upregulation of the anti-oxidant system appears to play a role in salt tolerance of rice, with tolerant genotypes also maintaining relatively higher photosynthetic function; during both the vegetative and reproductive stages.

Proline has been recognized as a multi-functional molecule, accumulating in high concentrations in response to a variety of abiotic stresses. It is able to protect cells from damage by acting as both an osmotic agent and a radical scavenger. Proline accumulated during a stress episode is degraded to provide a supply of energy to drive growth once the stress is relieved. Proline homeostasis is important for actively dividing cells as it helps to maintain sustainable growth under long-term stress. It also underpins the importance of the expansion of the proline sink during the transition from vegetative to reproductive growth and the initiation of seed development. Its role in the reproductive tissue is to stabilize seed set and productivity. Thus, to cope with abiotic stress, it is important to develop strategies to increase the proline sink in the reproductive tissue. We give a holistic account of proline homeostasis, taking into account the regulation of proline synthesis, its catabolism, and intra- and intercellular transport, all of which are vital components of growth and development in plants challenged by stress.

ABSTRACT Since the release of IR8 in 1966, 42 additional indica rice ( Oryza sativa L.) cultivars developed by the International Rice Research Institute (IRRI) for the irrigated and favorable rainfed lowlands have been released in the Philippines. The maximum yield of IR8 has been reduced by about 2 Mg ha −1 during the past 30 yr. Empirical breeding for population improvement within the indica germplasm has resulted in the maintenance of rice yield potential in the tropics of about 10 Mg ha −1 . To break the yield barrier, several approaches are being explored. These include development of a new plant type (NPT) with low tillering capacity and large panicles from tropical japonica germplasm and exploitation of heterosis through intervarietal and intersubspecific hybrids. Hybrid rice between indicas increased yield potential by about 9% under the tropical conditions. The higher yield potential of indica/indica hybrids compared with indica inbred cultivars was attributed to the greater biomass production rather than harvest index. New plant type breeding has not yet improved yield potential due to poor grain filling and low biomass production. Factors that cause poor grain filling and low biomass production of the NPT lines have been identified. Selecting parents with good grain filling traits, introduction of indica genes into NPT's tropical japonica background, and a refinement of the original NPT design are expected to improve the performance of the NPT lines. Further enhancement in yield potential may be possible from use of intersubspecific heterosis between indica and NPT lines.

Climate change will have far-reaching impacts on crop, livestock and fisheries production, and will change the prevalence of crop pests. Many of these impacts are already measurable. Climate impact studies are dominated by those on crop yields despite the limitations of climate-crop modelling, with very little attention paid to more systems components of cropping, let alone other dimensions of food security. Given the serious threats to food security, attention should shift to an action-oriented research agenda, where we see four key challenges: (a) changing the culture of research; (b) deriving stakeholder-driven portfolios of options for farmers, communities and countries; (c) ensuring that adaptation actions are relevant to those most vulnerable to climate change; (d) combining adaptation and mitigation.

Rice, the primary source of dietary calories for half of humanity, is the first crop plant for which a high-quality reference genome sequence from a single variety was produced. We used resequencing microarrays to interrogate 100 Mb of the unique fraction of the reference genome for 20 diverse varieties and landraces that capture the impressive genotypic and phenotypic diversity of domesticated rice. Here, we report the distribution of 160,000 nonredundant SNPs. Introgression patterns of shared SNPs revealed the breeding history and relationships among the 20 varieties; some introgressed regions are associated with agronomic traits that mark major milestones in rice improvement. These comprehensive SNP data provide a foundation for deep exploration of rice diversity and gene-trait relationships and their use for future rice improvement.

Data from farmer-managed fields have not been used previously to disentangle the impacts of daily minimum and maximum temperatures and solar radiation on rice yields in tropical/subtropical Asia. We used a multiple regression model to analyze data from 227 intensively managed irrigated rice farms in six important rice-producing countries. The farm-level detail, observed over multiple growing seasons, enabled us to construct farm-specific weather variables, control for unobserved factors that either were unique to each farm but did not vary over time or were common to all farms at a given site but varied by season and year, and obtain more precise estimates by including farm- and site-specific economic variables. Temperature and radiation had statistically significant impacts during both the vegetative and ripening phases of the rice plant. Higher minimum temperature reduced yield, whereas higher maximum temperature raised it; radiation impact varied by growth phase. Combined, these effects imply that yield at most sites would have grown more rapidly during the high-yielding season but less rapidly during the low-yielding season if observed temperature and radiation trends at the end of the 20th century had not occurred, with temperature trends being more influential. Looking ahead, they imply a net negative impact on yield from moderate warming in coming decades. Beyond that, the impact would likely become more negative, because prior research indicates that the impact of maximum temperature becomes negative at higher levels. Diurnal temperature variation must be considered when investigating the impacts of climate change on irrigated rice in Asia.

Summary A protein isolate was prepared from mung bean flour by extraction with 0.001 NNaOH, precipitation at pH4.5, neutralization of the dispersed precipitate to pH6.8–7.0, and subsequent freeze drying. the isolate's amino acid composition was determined and found to be similar to that of mung bean flour except for cystine which was destroyed during isolate preparation. the following properties of the protein isolate were investigated: nitrogen solubility, buffer capacity, foamability, gelation. Except for buffer capacity, the isolate demonstrated good functional abilities in simple systems under laboratory conditions.