Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Identification of Insertion/Deletion Markers for Photoperiod Sensitivity in Rice (<i>Oryza sativa</i> L.)

The current study aims to identify candidate insertion/deletion (INDEL) markers associated with photoperiod sensitivity (PS) in rice landraces from the Vietnamese Mekong Delta. The whole-genome sequencing of 20 accessions was conducted to analyze INDEL variations between two photoperiod-sensitivity groups. A total of 2240 INDELs were identified between the two photoperiod-sensitivity groups. The selection criteria included INDELs with insertions or deletions of at least 20 base pairs within the improved rice group. Six INDELs were discovered on chromosomes 01 (5 INDELs) and 6 (1 INDEL), and two genes were identified: LOC_Os01g23780 and LOC_Os01g36500. The gene LOC_Os01g23780, which may be involved in rice flowering, was identified in a 20 bp deletion on chromosome 01 from the improved rice accession group. A marker was devised for this gene, indicating a polymorphism rate of 20%. Remarkably, 20% of the materials comprised improved rice accessions. This INDEL marker could explain 100% of the observed distinctions. Further analysis of the mapping population demonstrated that an INDEL marker associated with the MADS-box gene on chromosome 01 was linked to photoperiod sensitivity. The F1 population displayed two bands across all hybrid individuals. The marker demonstrates efficacy in distinguishing improved rice accessions within the indica accessions. This study underscores the potential applicability of the INDEL marker in breeding strategies

Effects of social learning on rural farmers? adaptive capacity: Empirical insights from the Vietnamese Mekong Delta

10.1080/08941920.2019.1693677Society & Natural Resources3391053-107

Effects of Social Learning on Rural Farmers' Adaptive Capacity: Empirical Insights from the Vietnamese Mekong Delta

Environmental challenges in the Vietnamese Mekong Delta characterized by adverse impacts of climate change, upstream hydropower development and localized dyke expansion present imperatives for rural farmers to 'learn to adapt.' However, little is known about how learning contributes to improving their capacity in adapting to these 'wicked' problems. This study investigates potential effects of farmers' learning on their adaptive capacity, utilizing nine focus group discussions, 33 interviews, and a structured survey of 300 farmers. The exploratory factor analysis produced two factors for social learning: (1) learning through social interactions and (2) self-reflection, and one factor for adaptive capacity. The regression results show that the social learning factors have significantly positive effects on adaptive capacity. Farmers with a higher level of social learning are likely to demonstrate higher adaptive capacity. The findings call for policy considerations to promote learning in a broader context of the delta to enhance local capacity.This work was part of the doctoral research of the first author under the ALA/AusAID sponsorship at the Australian National University. It was also partially benefited from the support of a Singapore Ministry of Education’s Social Science Research Council (SSRC) grant entitled “Sustainable Governance of the Transboundary Environmental Commons in Southeast Asia” [MOE2016-SSRTG-068]

Modelling adoption of rice-fish systems with fuzzy logic

Most current models analyzing technology adoption are based on a function that assumes farmers make decisions upon utility maximization but ignores cultural or social factors. The traditional production systems of the Mekong Delta were based on floating rice varieties and fish harvested both from rivers and rice fields. Since 1980 the presence of fish in the rice fields decreased and research developed the socalled concurrent rice–fish system to capture the advantages of the synergy. Whether this is a feasible option depends on the farmers’ drives and motives for taking-up the technology. In 2000 we made an inventory among 60 farmers who adopted the rice–fish system in four districts to describe their resources and motivations. In 2006 we repeated this survey among 94 farmers including potential adopters, in order to evaluate the take-up potential of the rice–fish system in the Mekong Delta. Income/person and income/ha of the farm households with a rice–fish system were close to double, while their land area (2.5ha) was not significantly larger than those farms without a rice–fish system (1.95ha). Usually farmers integrating also pigs and fish had the smallest land area. The farmers’ non-adoption of the rice–fish system was mainly due to low availability of capital and land, and to inappropriate location of the field in relation to the homestead, water availability, and agro-ecological conditions. To create space for more upland crops was an important argument for the construction of a rice–fish system. Modeling confirmed that under appropriate agro-ecological conditions the take-up of rice–fish systems can be stimulated by increasing know-how on fish and on system component integration. The sensitivity of the fuzzy logic simulation did not confirm the importance of land size and wealth ranking for the take-up

Assessment of a Farmer Base Network in Promoting an Integrated Farming System at the Mekong Delta in Vietnam

This study analyzed forces driving the emergence of farmer networks in Vietnam and quantified the benefits of an integrated farming system (IFS) and the role of a farmer network in promoting IFS in the Mekong Delta. This case study applied a combination of literature review, participatory community assessment, and household survey approaches. The case study was undertaken in the My An commune, Cho Moi districtW of An Giang province. Findings from the study show that both networking and non-networking household groups recognize the important advantages of farmer networks, and that practicing IFS gives farming households economic, environmental, and social benefits and food security. Networking and practicing IFS are synergistic. By networking, farmers can gain better access to agricultural extension and credit services as well as improve their social networking, and hence adopt and practice IFS efficiently and contribute to rural poverty reduction. These benefits of networking and IFS practices should be considered at the community and regional levels rather than only at the level of individual households. Positive linkages and synergism should go beyond network or farm boundary (i.e., between specific networks or farms). Further development of farmer networks and IFS needs more effective policies and support from the government

From Rice Bowl to Rural Development: Challenges and Opportunities Facing Vietnam’s Mekong Delta Region

The Mekong Delta has long been a major producing area for Vietnamese rice. It now accounts for more than half of national production and accounted for most of the growth in that production over the past decade. While this has given the Mekong Delta the reputation as Vietnam’s ‘rice bowl’—critical for national food security—virtually all of its incremental production (and now 70% of its output) has been channeled into exports. With Vietnam’s rice export trade mostly servicing the low price market segment, and with shortcomings in efficiency and coordination within the export supply chain, the surging export trade has not translated into wealth among Mekong Delta farmers. The paper examines the evolving dynamics in rice production and economics in the Mekong Delta, pertinent features of the structure and performance of the rice value chain, and the challenges and opportunities associated both with improving efficiencies and profitability for rice and with promoting a more balanced pattern of rural development within the region

Financial Capacity of Rice-based Farming Households in the Mekong Delta, Vietnam

This study examines financial capacity of various types of rice farming households in the Mekong Delta. Household financial capacity was elicited and quantified through interviews with 449 households practicing rice-based farming systems in four agro-ecological zones of the Mekong Delta. Household net income, long-standing debt, and savings represent the three key parameters of household financial capacity. Analysis of farm size classes revealed that financial capacity was weak, especially among households with farms that were less than one hectare. Agricultural production was the primary component of household net income. The level of diversity of non-rice crops did not contribute significantly to increased household income. Net household income was positively correlated with farm size, land use circle (i.e., number of crops in a field), and non-farm activities. Mean household savings accounted for 27 percent of total net household income, and mean long-term debt was 11 percent of household savings. The low financial capacity of rice-based farming households introduces substantial challenges for Mekong Delta farmers to recover production costs caused by irregular weather patterns associated with climate change

Evolutionary social and biogeophysical changes in the Amazon, Ganges–Brahmaputra–Meghna and Mekong deltas

Policy-making in social-ecological systems increasingly looks to iterative, evolutionary approaches that can address the inherent complexity of interactions between human wellbeing, provision of goods, and the maintenance of ecosystem services. Here, we show how the analysis of available time-series in tropical delta regions over past decades can provide important insight into the social-ecological system dynamics in deltaic regions. The paper provides an exploratory analysis of the recent changes that have occurred in the major elements of three tropical deltaic social-ecological systems, such as demography, economy, health, climate, food, and water. Time-series data from official statistics, monitoring programmes, and Earth observation data are analysed to explore possible trends, slow and fast variables, and observed drivers of change in the Amazon, Ganges–Brahmaputra–Meghna and Mekong deltas. In the Ganges–Brahmaputra–Meghna delta zone, increasing gross domestic product and per capita income levels since the 1980s mirror rising levels of food and inland fish production. In contrast, non-food ecosystem services, such as water availability, water quality, and land stability appear to be deteriorating. In the Amazon delta, natural and anthropogenic perturbations are continuously degrading key ecosystem services, such as carbon storage in biomass and soils, the regulation of water balance, and the modulation of regional climate patterns. In the Mekong delta, rapid economic development, changing land-use practices, and salinity intrusion are progressively putting more pressure on the delivery of important provisioning services, such as rice and inland aquaculture production, which are key sources of staple food, farm incomes, and export revenue. Observed changes in many key indicators of ecosystem services point to a changing dynamic state and increased probability of systemic threshold transformations in the near future