Seroprevalence of cytomegalovirus and rubella among pregnant women in western Sudan

<p>Abstract</p> <p>Background</p> <p>Maternal cytomegalovirus (CMV) and rubella infections have adverse neonatal outcomes. Basic epidemiological data concerning CMV and rubella is necessary for health planners and care providers.</p> <p>Methods</p> <p>A cross sectional study was conducted at El-Rahad hospital, Sudan to investigate seroprevalence of CMV and rubella infections and associated possible risk factors among pregnant women. Structured questionnaires were used to gather socio-demographic data and ELISA was used to detect CMV and rubella infections using IgG and IgM.</p> <p>Results</p> <p>Out of 231 pregnant women, 167 (72.2%) and 151 (65.3%) were CMV-IgG and rubella-IgG positive, respectively. Only 6 (2.5%) and 8 women (3.4%) were CMV-IgM and rubella-IgM positive, respectively. While, high parity (OR = 14.7, 95%CI = 1.7 - 123.6; <it>P </it>= 0.01] and illiteracy (OR = 3.0, CI = 1.4 - 6.5; <it>P </it>= 0.004) were significantly associated with seropostive CMV-IgG in multivariate analysis, none of the other obstetrical and medical characteristics were significantly associated with CMV or rubella infections.</p> <p>Conclusion</p> <p>CMV prevalence was 72.2% and rubella susceptibility among pregnant women was 34.6%. Rubella vaccine and routine screening for rubella and CMV should be introduced for pregnant women in this setting. Further research is needed.</p

Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress

BackgroundRice and barley are both members of Poaceae (grass family) but have a marked difference in salt tolerance. The molecular mechanism underlying this difference was previously unexplored. This study employs a comparative genomics approach to identify analogous and contrasting gene expression patterns between rice and barley.ResultsA hierarchical clustering approach identified several interesting expression trajectories among rice and barley genotypes. There were no major conserved expression patterns between the two species in response to salt stress. A wheat salt-stress dataset was queried for comparison with rice and barley. Roughly one-third of the salt-stress responses of barley were conserved with wheat while overlap between wheat and rice was minimal. These results demonstrate that, at transcriptome level, rice is strikingly different compared to the more closely related barley and wheat. This apparent lack of analogous transcriptional programs in response to salt stress is further highlighted through close examination of genes associated with root growth and development.ConclusionThe analysis provides support for the hypothesis that conservation of transcriptional signatures in response to environmental cues depends on the genetic similarity among the genotypes within a species, and on the phylogenetic distance between the species

Gas film retention and underwater photosynthesis during field submergence of four contrasting rice genotypes

Floods can completely submerge some rice (Oryza sativa L.) fields. Leaves of rice have gas films that aid O(2) and CO(2) exchange under water. The present study explored the relationship between gas film persistence and underwater net photosynthesis (P(N)) as influenced by genotype and submergence duration. Four contrasting genotypes (FR13A, IR42, Swarna, and Swarna-Sub1) were submerged for 13 days in the field and leaf gas films, chlorophyll, and the capacity for underwater P(N) at near ambient and high CO(2) were assessed with time of submergence. At high CO(2) during the P(N) assay, all genotypes initially showed high rates of underwater P(N), and this rate was not affected by time of submergence in FR13A. This superior photosynthetic performance of FR13A was not evident in Swarna-Sub1 (carrying the SUB1 QTL) and the declines in underwater P(N) in both Swarna-Sub1 and Swarna were equal to that in IR42. At near ambient CO(2) concentration, underwater P(N) declined in all four genotypes and this corresponded with loss of leaf gas films with time of submergence. FR13A retained leaf gas films moderately longer than the other genotypes, but gas film retention was not linked to SUB1. Diverse rice germplasm should be screened for gas film persistence during submergence, as this trait could potentially increase carbohydrate status and internal aeration owing to increased underwater P(N), which contributes to submergence tolerance in rice

Zn uptake, translocation and grain Zn loading in rice (Oryza sativa L.) genotypes selected for Zn deficiency tolerance and high grain Zn

Zn deficiency is a widespread problem in rice (Oryza sativa L.) grown under flooded conditions, limiting growth and grain Zn accumulation. Genotypes with Zn deficiency tolerance or high grain Zn have been identified in breeding programmes, but little is known about the physiological mechanisms conferring these traits. A protocol was developed for growing rice to maturity in agar nutrient solution (ANS), with optimum Zn-sufficient growth achieved at 1.5 μM ZnSO4.7H2O. The redox potential in ANS showed a decrease from +350 mV to −200 mV, mimicking the reduced conditions of flooded paddy soils. In subsequent experiments, rice genotypes contrasting for Zn deficiency tolerance and grain Zn were grown in ANS with sufficient and deficient Zn to assess differences in root uptake of Zn, root-to-shoot Zn translocation, and in the predominant sources of Zn accumulation in the grain. Zn efficiency of a genotype was highly influenced by root-to-shoot translocation of Zn and total Zn uptake. Translocation of Zn from root to shoot was more limiting at later growth stages than at the vegetative stage. Under Zn-sufficient conditions, continued root uptake during the grain-filling stage was the predominant source of grain Zn loading in rice, whereas, under Zn-deficient conditions, some genotypes demonstrated remobilization of Zn from shoot and root to grain in addition to root uptake. Understanding the mechanisms of grain Zn loading in rice is crucial in selecting high grain Zn donors for target-specific breeding and also to establish fertilizer and water management strategies for achieving high grain Z

Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise

BACKGROUND: Golden Promise is a salt-tolerant spring barley closely related to Maythorpe. Salt tolerance in Golden Promise has been attributed to a single mutation at the Ari-e locus (on 5H) resulting from irradiation of Maythorpe. Golden Promise accumulates lower shoot Na(+ )compared to Maythorpe when growing under saline conditions. This study focused on elucidating the genetic basis and mechanisms involved in this difference. RESULTS: The level of polymorphism between the two genotypes was explored using the Barley1 GeneChip for single feature polymorphisms (SFPs) and an oligonucleotide pool assay for single nucleotide polymorphisms (SNPs). Polymorphism analyses revealed three haplotype blocks spanning 6.4 cM on chromosome 1H, 23.7 cM on chromosome 4H and 3.0 cM on 5H. The Barley1 GeneChip was used to examine transcript abundance in different tissues and stages during development. Several genes within the polymorphic haplotype blocks were differentially regulated. Additionally, a more global difference in the jasmonic acid pathway regulation was detected between the two genotypes. CONCLUSION: The results confirm that Golden Promise and Maythorpe are genetically very closely related but establish that they are not isogenic, as previously reported, due to three polymorphic haplotype blocks. Transcriptome analysis indicates that the response of the two genotypes to salinity stress is quite different. Additionally, the response to salinity stress in the roots and shoot tissue is strikingly different

Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array

<p>Abstract</p> <p>Background</p> <p>A large number of genetic variations have been identified in rice. Such variations must in many cases control phenotypic differences in abiotic stress tolerance and other traits. A single feature polymorphism (SFP) is an oligonucleotide array-based polymorphism which can be used for identification of SNPs or insertion/deletions (INDELs) for high throughput genotyping and high density mapping. Here we applied SFP markers to a lingering question about the source of salt tolerance in a particular rice recombinant inbred line (RIL) derived from a salt tolerant and salt sensitive parent.</p> <p>Results</p> <p>Expression data obtained by hybridizing RNA to an oligonucleotide array were analyzed using a statistical method called robustified projection pursuit (RPP). By applying the RPP method, a total of 1208 SFP probes were detected between two presumed parental genotypes (Pokkali and IR29) of a RIL population segregating for salt tolerance. We focused on the <it>Saltol </it>region, a major salt tolerance QTL. Analysis of FL478, a salt tolerant RIL, revealed a small (< 1 Mb) region carrying alleles from the presumed salt tolerant parent, flanked by alleles matching the salt sensitive parent IR29. Sequencing of putative SFP-containing amplicons from this region and other positions in the genome yielded a validation rate more than 95%.</p> <p>Conclusion</p> <p>Recombinant inbred line FL478 contains a small (< 1 Mb) segment from the salt tolerant parent in the <it>Saltol </it>region. The Affymetrix rice genome array provides a satisfactory platform for high resolution mapping in rice using RNA hybridization and the RPP method of SFP analysis.</p

Seed pre-treatment in rice reduces damage, enhances carbohydrate mobilization and improves emergence and seedling establishment under flooded conditions

Priming rice seeds (soaking followed by drying) or soaking just before sowing improved emergence from flooded soil, reduced membrane damage from ROS and hastened carbohydrate mobilization. Most benefit was to lines with a superior ability to germinate in flooded soil even when untreated

Participatory evaluation guides the development and selection of farmers’ preferred rice varieties for salt- and flood-affected coastal deltas of South and Southeast Asia

Rice is the staple food and provides livelihood for smallholder farmers in the coastal delta regions of South and Southeast Asia. However, its productivity is often low because of several abiotic stresses including high soil salinity and waterlogging during the wet (monsoon) season and high soil and water salinity during the dry season. Development and dissemination of suitable rice varieties tolerant of these multiple stresses encountered in coastal zones are of prime importance for increasing and stabilizing rice productivity, however adoption of new varieties has been slow in this region. Here we implemented participatory varietal selection (PVS) processes to identify and understand smallholder farmers’ criteria for selection and adoption of new rice varieties in coastal zones. New breeding lines together with released rice varieties were evaluated in on-station and on-farm trials (researcher-managed) during the wet and dry seasons of 2008–2014 in the Indian Sundarbans region. Significant correlations between preferences of male and female farmers in most trials indicated that both groups have similar criteria for selection of rice varieties. However, farmers’ preference criteria were different from researchers’ criteria. Grain yield was important, but not the sole reason for variety selection by farmers. Several other factors also governed preferences and were strikingly different when compared across wet and dry seasons. For the wet season, farmers preferred tall (140–170cm), long duration (160–170 d), lodging resistant and high yielding rice varieties because these traits are required in lowlands where water stagnates in the field for about four months (July to October). For the dry season, farmers’ preferences were for high yielding, salt tolerant, early maturing (115–130 d) varieties with long slender grains and good quality for better market value. Pest and disease resistance was important in both seasons but did not rank high. When farmers ranked the two most preferred varieties, the ranking order was sometimes variable between locations and years, but when the top four varieties that consistently ranked high were considered, the variability was low. This indicates that at least 3–4 of the best-performing entries should be considered in succeeding multi-location and multi-year trials, thereby increasing the chances that the most stable varieties are selected. These findings will help improve breeding programs by providing information on critical traits. Selected varieties through PVS are also more likely to be adopted by farmers and will ensure higher and more stable productivity in the salt- and flood-affected coastal deltas of South and Southeast Asia

Characterizing the Saltol quantitative trait locus for salinity tolerance in rice

This study characterized Pokkali-derived quantitative trait loci (QTLs) for seedling stage salinity tolerance in preparation for use in marker-assisted breeding. An analysis of 100 SSR markers on 140 IR29/Pokkali recombinant inbred lines (RILs) confirmed the location of the Saltol QTL on chromosome 1 and identified additional QTLs associated with tolerance. Analysis of a series of backcross lines and near-isogenic lines (NILs) developed to better characterize the effect of the Saltol locus revealed that Saltol mainly acted to control shoot Na +/K + homeostasis. Multiple QTLs were required to acquire a high level of tolerance. Unexpectedly, multiple Pokkali alleles at Saltol were detected within the RIL population and between backcross lines, and representative lines were compared with seven Pokkali accessions to better characterize this allelic variation. Thus, while the Saltol locus presents a complex scenario, it provides an opportunity for markerassisted backcrossing to improve salt tolerance of popular varieties followed by targeting multiple loci through QTL pyramiding for areas with higher salt stress