Depth of soil compaction predominantly affects rice yield reduction by reproductive-stage drought at varietal screening sites in Bangladesh, India, and Nepal.
Ontology highlight
ABSTRACT:
SUBMITTER: Singh SP
PROVIDER: S-EPMC6560918 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BackgroundThe VL elimination strategy requires cost-effective tools for case detection and management. This intervention study tests the yield, feasibility and cost of 4 different active case detection (ACD) strategies (camp, index case, incentive and blanket approach) in VL endemic districts of India, Nepal and Bangladesh.Methodology/principal findingsFirst, VL screening (fever more than 14 days, splenomegaly, rK39 test) was performed in camps. This was followed by house to house screening (blanket approach). An analysis of secondary VL cases in the neighborhood of index cases was simulated (index case approach). A second screening round was repeated 4-6 months later. In another sub-district in India and Nepal, health workers received incentives for detecting new VL cases over a 4 month period (incentive approach). This was followed by house screening for undetected cases. A total of 28 new VL cases were identified by blanket approach in the 1(st) screening round, and used as ACD gold standard. Of these, the camp approach identified 22 (sensitivity 78.6%), index case approach identified 12 (sensitivity--42.9%), and incentive approach identified 23 new VL cases out of 29 cases detected by the house screening (sensitivity--79.3%). The effort required to detect a new VL case varied (blanket approach--1092 households, incentive approach--978 households; index case approach--788 households had to be screened). The cost per new case detected varied (camp approach $21 - $661; index case approach $149 - $200; incentive based approach $50 - $543; blanket screening $112 - $629). The 2(nd) screening round yielded 20 new VL cases. Sixty and nine new PKDL cases were detected in the first and second round respectively.Conclusions/significanceACD in the VL elimination campaign has a high yield of new cases at programme costs which vary according to the screening method chosen. Countries need the right mix of approaches according to the epidemiological profile, affordability and organizational feasibility.
| S-EPMC3035672 | biostudies-literature
Project description:ObjectiveUnderstanding the causes of death is key to tackling the burden of three million annual neonatal deaths. Resource-poor settings lack effective vital registration systems for births, deaths and causes of death. We set out to describe cause-specific neonatal mortality in rural areas of Malawi, Bangladesh, Nepal and rural and urban India using verbal autopsy (VA) data.DesignWe prospectively recorded births, neonatal deaths and stillbirths in seven population surveillance sites. VAs were carried out to ascertain cause of death. We applied descriptive epidemiological techniques and the InterVA method to characterise the burden, timing and causes of neonatal mortality at each site.ResultsAnalysis included 3772 neonatal deaths and 3256 stillbirths. Between 63% and 82% of neonatal deaths occurred in the first week of life, and males were more likely to die than females. Prematurity, birth asphyxia and infections accounted for most neonatal deaths, but important subnational and regional differences were observed. More than one-third of deaths in urban India were attributed to asphyxia, making it the leading cause of death in this setting.ConclusionsPopulation-based VA methods can fill information gaps on the burden and causes of neonatal mortality in resource-poor and data-poor settings. Local data should be used to inform and monitor the implementation of interventions to improve newborn health. High rates of home births demand a particular focus on community interventions to improve hygienic delivery and essential newborn care.
| S-EPMC4552925 | biostudies-literature
Project description:BACKGROUND:The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS:The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5-20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance. CONCLUSION:The results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.
| S-EPMC5436998 | biostudies-literature
Project description:BACKGROUND:The sucrose non-fermenting 1-related kinases 2 (SnRK2s) play important roles in osmotic stress responses in A. thaliana and rice (Oryza sativa L.). Osmotic stress/ABA-activated protein kinase 2 (SAPK2) is a member of SnRK2s subclass II in rice, but its function in rice yield under drought stress is unclear. RESULTS:Compared with wild-type (Oryza.Sativa L.spp.japonica, WT) plants, the sapk2 rice mutant lines were shorter and produced fewer grains per panicle, smaller grains and lower grain yield under reproductive stage drought stress (RDS). Subsequent analysis suggested that SAPK2 considerably influences the nitrogen, phosphorus, and potassium contents of rice grains. The examination of rice seedling growth and development under nutrient-deprived conditions (-N, -K, and?-?P) proved that SAPK2 can significantly affect rice seedling growth and root development in hydroponic cultures lacking N and K. Moreover, the NO3- influx rate and nitrate concentration analysis indicated that SAPK2 promotes nitrate uptake and assimilation by regulating nitrate-related transporters. CONCLUSION:These results suggest that SAPK2 could enhance grain production by regulating nitrogen utilization efficiency under RDS. Our work provided insights to breeding drought tolerant rice with high nutrient uptake.
| S-EPMC7280414 | biostudies-literature
Project description:BackgroundReproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers.ResultsThe study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200?kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought.ConclusionThese results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.
| S-EPMC7410978 | biostudies-literature
Project description:QTLs for rice grain yield under reproductive stage drought stress (qDTY) identified earlier with low density markers have shown linkage drag and need to be fine mapped before their utilization in breeding programs. In this study, genotyping-by-sequencing (GBS) based high-density linkage map of rice was developed using two BC1F3 mapping populations namely Swarna*2/Dular (3929 SNPs covering 1454.68?cM) and IR11N121*2/Aus196 (1191 SNPs covering 1399.68?cM) with average marker density of 0.37?cM to 1.18?cM respectively. In total, six qDTY QTLs including three consistent effect QTLs were identified in Swarna*2/Dular while eight qDTY QTLs including two consistent effect QTLs were identified in IR11N121*2/Aus 196 mapping population. Comparative analysis revealed four stable and novel QTLs (qDTY2.4, qDTY3.3, qDTY6.3, and qDTY11.2) which explained 8.62 to 14.92% PVE. However, one of the identified stable grain yield QTL qDTY1.1 in both the populations was located nearly at the same physical position of an earlier mapped major qDTY QTL. Further, the effect of the identified qDTY1.1 was validated in a subset of lines derived from five mapping populations confirming robustness of qDTY1.1 across various genetic backgrounds/seasons. The study successfully identified stable grain yield QTLs free from undesirable linkages of tall plant height/early maturity utilizing high density linkage maps.
| S-EPMC6778106 | biostudies-literature
Project description:BackgroundDelivery of essential newborn care is key to reducing neonatal mortality rates, yet coverage of protective birth practices remains incomplete and variable, with or without skilled attendance. Evidence of changes over time in newborn care provision, disaggregated by care practice and delivery type, can be used by policymakers to review efforts to reduce mortality. We examine such trends in four areas using control arm trial data.Methods and findingsWe analysed data from the control arms of cluster randomised controlled trials in Bangladesh (27 553 births), eastern India (8 939), Dhanusha, Nepal (15 344) and Makwanpur, Nepal (6 765) over the period 2001-2011. For each trial, we calculated the observed proportion of attended births and the coverage of WHO essential newborn care practices by year, adjusted for clustering and stratification. To explore factors contributing to the observed trends, we then analysed expected trends due only to observed shifts in birth attendance, accounted for stratification, delivery type and statistically significant interaction terms, and examined disaggregated trends in care practice coverage by delivery type. Attended births increased over the study periods in all areas from very low rates, reaching a maximum of only 30% of deliveries. Newborn care practice trends showed marked heterogeneity within and between areas. Adjustment for stratification, birth attendance and interaction revealed that care practices could change in opposite directions over time and/or between delivery types - e.g. in Bangladesh hygienic cord-cutting and skin-to-skin contact fell in attended deliveries but not home deliveries, whereas in India birth attendant hand-washing rose for institutional deliveries but fell for home deliveries.ConclusionsCoverage of many essential newborn care practices is improving, albeit slowly and unevenly across sites and delivery type. Time trend analyses of birth patterns and essential newborn care practices can inform policy-makers about effective intervention strategies.
| S-EPMC4503724 | biostudies-literature
Project description:We evaluated the yields of Oryza sativa L. 'Nipponbare' rice lines expressing a gene encoding an A20/AN1 domain stress-associated protein, AlSAP, from the halophyte grass Aeluropus littoralis under the control of different promoters. Three independent field trials were conducted, with drought imposed at the reproductive stage. In all trials, the two transgenic lines, RN5 and RN6, consistently out-performed non-transgenic (NT) and wild-type (WT) controls, providing 50-90% increases in grain yield (GY). Enhancement of tillering and panicle fertility contributed to this improved GY under drought. In contrast with physiological records collected during previous greenhouse dry-down experiments, where drought was imposed at the early tillering stage, we did not observe significant differences in photosynthetic parameters, leaf water potential, or accumulation of antioxidants in flag leaves of AlSAP-lines subjected to drought at flowering. However, AlSAP expression alleviated leaf rolling and leaf drying induced by drought, resulting in increased accumulation of green biomass. Therefore, the observed enhanced performance of the AlSAP-lines subjected to drought at the reproductive stage can be tentatively ascribed to a primed status of the transgenic plants, resulting from a higher accumulation of biomass during vegetative growth, allowing reserve remobilization and maintenance of productive tillering and grain filling. Under irrigated conditions, the overall performance of AlSAP-lines was comparable with, or even significantly better than, the NT and WT controls. Thus, AlSAP expression inflicted no penalty on rice yields under optimal growth conditions. Our results support the use of AlSAP transgenics to reduce rice GY losses under drought conditions.
| S-EPMC5466986 | biostudies-literature
Project description:To understand the genetic diversity and indica-japonica differentiation in Bangladesh rice varieties, a total of 151 accessions of rice varieties mostly Bangladesh traditional varieties including Aus, Boro, broadcast Aman, transplant Aman and Rayada varietal groups were genotyped using 47 rice nuclear SSRs. As a result, three distinct groups were detected by cluster analysis, corresponding to indica, Aus and japonica rice. Among deepwater rice varieties analyzed some having particular morphological features that mainly corresponded to the japonica varietal group. Some small seeded and aromatic varieties from Bangladesh also corresponded to the japonica varietal group. This research for the first time establishes that the japonica varietal group is a prominent component of traditional varieties in Bangladesh, particularly in deepwater areas.
| S-EPMC3688385 | biostudies-literature
Project description:Tropospheric aerosol optical depth (AOD) over India was simulated by Goddard Earth Observing System (GEOS)-Chem, a global 3-D chemical-transport model, using SMOG (Speciated Multi-pOllutant Generator from Indian Institute of Technology Bombay) and GEOS-Chem (GC) (current inventories used in the GEOS-Chem model) inventories for 2012. The simulated AODs were ~80% (SMOG) and 60% (GC) of those measured by the satellites (Moderate Resolution Imaging Spectroradiometer and Multi-angle Imaging SpectroRadiometer). There is no strong seasonal variation in AOD over India. The peak AOD values are observed/simulated during summer. The simulated AOD using SMOG inventory has particulate black and organic carbon AOD higher by a factor ~5 and 3, respectively, compared to GC inventory. The model underpredicted coarse-mode AOD but agreed for fine-mode AOD with Aerosol Robotic Network data. It captured dust only over Western India, which is a desert, and not elsewhere, probably due to inaccurate dust transport and/or noninclusion of other dust sources. The calculated AOD, after dust correction, showed the general features in its observed spatial variation. Highest AOD values were observed over the Indo-Gangetic Plain followed by Central and Southern India with lowest values in Northern India. Transport of aerosols from Indo-Gangetic Plain and Central India into Eastern India, where emissions are low, is significant. The major contributors to total AOD over India are inorganic aerosol (41-64%), organic carbon (14-26%), and dust (7-32%). AOD over most regions of India is a factor of 5 or higher than over the United States.
| S-EPMC7894385 | biostudies-literature