Exogenous double-stranded RNA inhibits the infection physiology of rust fungi to reduce symptoms in planta

Rust fungi (Pucciniales) are a diverse group of plant pathogens in natural and agricultural systems. They pose ongoing threats to the diversity of native flora and cause annual crop yield losses. Agricultural rusts are predominantly managed with fungicides and breeding for resistance, but new control strategies are needed on non-agricultural plants and in fragile ecosystems. RNA interference (RNAi) induced by exogenous double-stranded RNA (dsRNA) has promise as a sustainable approach for managing plant-pathogenic fungi, including rust fungi. We investigated the mechanisms and impact of exogenous dsRNA on rust fungi through in vitro and whole-plant assays using two species as models, Austropuccinia psidii (the cause of myrtle rust) and Coleosporium plumeriae (the cause of frangipani rust). In vitro, dsRNA either associates externally or is internalized by urediniospores during the early stages of germination. The impact of dsRNA on rust infection architecture was examined on artificial leaf surfaces. dsRNA targeting predicted essential genes significantly reduced germination and inhibited development of infection structures, namely appressoria and penetration pegs. Exogenous dsRNA sprayed onto 1-year-old trees significantly reduced myrtle rust symptoms. Furthermore, we used comparative genomics to assess the wide-scale amenability of dsRNA to control rust fungi. We sequenced genomes of six species of rust fungi, including three new families (Araucariomyceaceae, Phragmidiaceae, and Skierkaceae) and identified key genes of the RNAi pathway across 15 species in eight families of Pucciniales. Together, these findings indicate that dsRNA targeting essential genes has potential for broad-use management of rust fungi across natural and agricultural systems

An assessment of irrigated rice cultivation with different crop establishment practices in Vietnam

Overuse of seed and chemical inputs is a major constraint for sustainable rice production in Vietnam. In this study, two seasons of field trials were conducted to compare different crop establishment practices for rice production in the Mekong River Delta using environmental and economic sustainability performance indicators. The indicators including energy efficiency, agronomic use efficiency, net income, and greenhouse gas emissions (GHGEs) were quantified based on four treatments including manual broadcast-seeding, blower seeding, drum seeding, and mechanized transplanting. Across the four treatments, yields ranged from 7.3–7.5 Mg ha−1 and 6.2–6.8 Mg ha−1 in the Winter-Spring (WS) and Summer-Autumn (SA) seasons, respectively. In comparison with direct seeding methods, mechanized transplanting decreased the seed rate by 40%. It also led to a 30–40% reduction in pesticide use during the main crop season (WS). Mechanized transplanting required higher inputs, including machine depreciation and fuel consumption, but its net energy balance, net income and GHGE were at a similar level as the other non-mechanized planting practices. Mechanized transplanting is a technology package that should be promoted to improve the economic and environmental sustainability of lowland rice cultivation in the Mekong River Delta of Vietnam

Improving the Sustainability of Rice Cultivation in Central Thailand with Biofertilizers and Laser Land Leveling

Rice production in the Central Plains of Thailand plays a key role in the country’s food security. However, the overuse of inputs coupled with the rising production costs are making it increasingly difficult for smallholder rice farming to remain economically and environmentally sustainable. Replicated production-scale field trials of Cost Reduction Operating Principles (CROP)—Thailand’s national package of best management practices for rice production—were established in tandem with laser land leveling (LLL), mechanical drum seeder, and the application of two biofertilizer products (i.e., PGPR II, that contains Azospirillum brasilense Sp. TS29 and Burkholderia vietnamiensis S45; and LDD #12, that contains Azotobacter tropicalis, Burkholderia unamae and Bacillus subtilis) and compared with farmer’s practices (FP). Performance indicators (PI) promoted by the Sustainable Rice Platform (SRP) were used to assess economic and environmental indicators. CROP + PGPR had significantly higher net income (79%) and nitrogen-use efficiency (57%) compared with FP. Pesticide use (28%), seed (60%), inorganic fertilizer N (41%) and total production costs (19%) were reduced in all CROP treatments compared with FP. These results demonstrate that the application of CROP, LLL, mechanical drum seeder, and biofertilizers can substantially improve the economic and environmental sustainability of rice production in the Central Plains of Thailand

Yield gaps in rice-based farming systems: Insights from local studies and prospects for future analysis

The important contribution of rice to global food security requires an understanding of yield gaps in rice-based farming systems. However, estimates of yield gaps are often compromised by a failure to recognize the components that determine them at a local scale. It is essential to define yield gaps by the biological limitations of the genotype and the environment. There exist a number of methods for estimating rice yield gaps, including the use of crop growth simulation models, field experiments and farmer yields. We reviewed the existing literature to (i) assess the methods used to estimate rice yield gaps at a local scale and to summarize the yield gaps estimated in those studies, (ii) identify practical methods of analysis that provides realistic estimates of exploitable rice yield gaps, and (iii) provide recommendations for future studies on rice yield gaps that will allow accurate interpretation of available data at a local level. Rice yield gap analysis can be simplified without sacrificing precision and context specificity. This review identifies the comparison of the attainable farm yield (the mean of the top decile) with the population mean, as a practical and robust approach to estimate an exploitable yield gap that is highly relevant at the local level, taking into account what is achievable given the local socio-economic conditions. With this method we identified exploitable yield gaps ranging from 23 to 42% for one particular season in four different rice growing areas in Southeast Asia. To enable accurate estimation and interpretation of yield gaps in rice production systems, we propose a minimum dataset needed for rice yield gap assessment. Future studies on rice yield gaps should consider the region, season and crop ecosystem (e.g. upland rainfed, lowland irrigated) as a minimum to facilitate decisions at a local level. In addition, we recommend taking into account the cultivar, soil type, planting date, crop establishment method and nitrogen application rates, as well as field topography and toposequence for rainfed systems. A good understanding of rice yield gaps and the factors leading to yield gaps will allow better targeting of agricultural research and development priorities for livelihood improvement and sustainable rice production.</p

Revisiting yield gaps and the scope for sustainable intensification for irrigated lowland rice in Southeast Asia

CONTEXT: Recent studies on yield gap analysis for rice in Southeast Asia revealed different levels of intensification across the main ‘rice bowls’ in the region. Identifying the key crop management and biophysical drivers of rice yield gaps across different ‘rice bowls’ provides opportunities for comparative analyses, which are crucial to better understand the scope to narrow yield gaps and increase resource-use efficiencies across the region. OBJECTIVE: The objective of this study was to decompose rice yield gaps into their efficiency, resource, and technology components and to map the scope to sustainably increase rice production across four lowland irrigated rice areas in Southeast Asia through improved crop management. METHODS: A novel framework for yield gap decomposition accounting for the main genotype, management, and environmental factors explaining crop yield in intensive rice irrigated systems was developed. A combination of crop simulation modelling at field-level and stochastic frontier analysis was applied to household survey data to identify the drivers of yield variability and to disentangle efficiency, resource, and technology yield gaps, including decomposing the latter into its sowing date and genotype components. RESULTS AND CONCLUSION: The yield gap was greatest in Bago, Myanmar (75% of Yp), intermediate in Yogyakarta, Indonesia (57% of Yp) and in Nakhon Sawan, Thailand (47% of Yp), and lowest in Can Tho, Vietnam (44% of Yp). The yield gap in Myanmar was largely attributed to the resource yield gap, reflecting a large scope to sustainably intensify rice production through increases in fertilizer use and proper weed control (i.e., more output with more inputs). In Vietnam, the yield gap was mostly attributed to the technology yield gap and to resource and efficiency yield gaps in the dry season and wet season, respectively. Yet, sustainability aspects associated with inefficient use of fertilizer and low profitability from high input levels should also be considered alongside precision agriculture technologies for site-specific management (i.e., more output with the same or less inputs). The same is true in Thailand, where the yield gap was equally explained by the technology, resource, and efficiency yield gaps. The yield gap in Indonesia was mostly attributed to efficiency and technology yield gaps and yield response curves to N based on farmer field data in this site suggest it is possible to reduce its use while increasing rice yield (i.e., more output with less inputs). SIGNIFICANCE: This study provides a novel approach to decomposing rice yield gaps in Southeast Asia's main rice producing areas. By breaking down the yield gap into different components, context-specific opportunities to narrow yield gaps were identified to target sustainable intensification of rice production in the region

Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility

INTRODUCTION: Multiple sclerosis (MS) is an inflammatory and degenerative disease of the central nervous system (CNS) that often presents in young adults. Over the past decade, certain elements of the genetic architecture of susceptibility have gradually emerged, but most of the genetic risk for MS remained unknown. RATIONALE: Earlier versions of the MS genetic map had highlighted the role of the adaptive arm of the immune system, implicating multiple different T cell subsets. We expanded our knowledge of MS susceptibility by performing a genetic association study in MS that leveraged genotype data from 47,429 MS cases and 68,374 control subjects. We enhanced this analysis with an in-depth and comprehensive evaluation of the functional impact of the susceptibility variants that we uncovered. RESULTS: We identified 233 statistically independent associations with MS susceptibility that are genome-wide significant. The major histocompatibility complex (MHC) contains 32 of these associations, and one, the first MS locus on a sex chromosome, is found in chromosome X. The remaining 200 associations are found in the autosomal non-MHC genome. Our genome-wide partitioning approach and large-scale replication effort allowed the evaluation of other variants that did not meet our strict threshold of significance, such as 416 variants that had evidence of statistical replication but did not reach the level of genome-wide statistical significance. Many of these loci are likely to be true susceptibility loci. The genome-wide and suggestive effects jointly explain ~48% of the estimated heritability for MS. Using atlases of gene expression patterns and epigenomic features, we documented that enrichment for MS susceptibility loci was apparent in many different immune cell types and tissues, whereas there was an absence of enrichment in tissue-level brain profiles. We extended the annotation analyses by analyzing new data generated from human induced pluripotent stem cell–derived neurons as well as from purified primary human astrocytes and microglia, observing that enrichment for MS genes is seen in human microglia, the resident immune cells of the brain, but not in astrocytes or neurons. Further, we have characterized the functional consequences of many MS susceptibility variants by identifying those that influence the expression of nearby genes in immune cells or brain. Last, we applied an ensemble of methods to prioritize 551 putative MS susceptibility genes that may be the target of the MS variants that meet a threshold of genome-wide significance. This extensive list of MS susceptibility genes expands our knowledge more than twofold and highlights processes relating to the development, maturation, and terminal differentiation of B, T, natural killer, and myeloid cells that may contribute to the onset of MS. These analyses focus our attention on a number of different cells in which the function of MS variants should be further investigated. Using reference protein-protein interaction maps, these MS genes can also be assembled into 13 communities of genes encoding proteins that interact with one another; this higher-order architecture begins to assemble groups of susceptibility variants whose functional consequences may converge on certain protein complexes that can be prioritized for further evaluation as targets for MS prevention strategies. CONCLUSION: We report a detailed genetic and genomic map of MS susceptibility, one that explains almost half of this disease’s heritability. We highlight the importance of several cells of the peripheral and brain resident immune systems—implicating both the adaptive and innate arms—in the translation of MS genetic risk into an auto-immune inflammatory process that targets the CNS and triggers a neurodegenerative cascade. In particular, the myeloid component highlights a possible role for microglia that requires further investigation, and the B cell component connects to the narrative of effective B cell–directed therapies in MS. These insights set the stage for a new generation of functional studies to uncover the sequence of molecular events that lead to disease onset. This perspective on the trajectory of disease onset will lay the foundation for developing primary prevention strategies that mitigate the risk of developing MS