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Cannabis sativa L. is one of the oldest domesticated crops. Hemp-type cultivars, which predominantly produce non-intoxicating cannabidiol (CBD), have been selected for their fast growth, seed, and fibre production, while drug-type chemovars were bred for high accumulation of tetrahydrocannabinol (THC). We investigated how the generation of CBD-dominant chemovars by introgression of hemp- into drug-type Cannabis impacted plant performance. The THC-dominant chemovar showed superior sink strength, higher flower biomass and demand-driven control of nutrient uptake. By contrast, the CBD-dominant chemovar hyperaccumulated phosphate in sink organs leading to reduced carbon and nitrogen assimilation in leaves, which limited flower biomass and cannabinoid yield. RNA-seq analyses determined organ- and chemovar-specific differences in expression of genes associated with nitrate and phosphate homeostasis as well as growth-regulating transcription factors that were correlated with measured traits. Among these were genes positively selected for during Cannabis domestication encoding an inhibitor of the phosphate starvation response SPX DOMAIN GENE3, nitrate reductase and two nitrate transporters. Altered nutrient sensing, acquisition or distribution are likely a consequence of adaption to growth on marginal, low-nutrient input lands in hemp. Our data provide evidence that such ancestral traits may become detrimental for female flower development and consequently overall CBD yield in protected cropping environments., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

Germination involves highly dynamic transcriptional programs as the cells of seeds reactivate and express the functions necessary for establishment in the environment. Individual cell types have distinct roles within the embryo, so must therefore have cell type-specific gene expression and gene regulatory networks. We can better understand how the functions of different cell types are established and contribute to the embryo by determining how cell type-specific transcription begins and changes through germination. Here we describe a temporal analysis of the germinating Arabidopsis thaliana embryo at single-cell resolution. We define the highly dynamic cell type-specific patterns of gene expression and how these relate to changing cellular function as germination progresses. Underlying these are unique gene regulatory networks and transcription factor activity. We unexpectedly discover that most embryo cells transition through the same initial transcriptional state early in germination, even though cell identity has already been established during embryogenesis. Cells later transition to cell type-specific gene expression patterns. Furthermore, our analyses support previous findings that the earliest events leading to the induction of seed germination take place in the vasculature. Overall, our study constitutes a general framework with which to characterize Arabidopsis cell transcriptional states through seed germination, allowing investigation of different genotypes and other plant species whose seed strategies may differ., (© 2024. The Author(s).)

Opium poppy is a crop of great commercial value as a source of several opium alkaloids for the pharmaceutical industries including morphine, codeine, thebaine, noscapine and papaverine. Most enzymes involved in benzylisoquinoline alkaloids (BIAs) biosynthesis in opium poppy have been functionally characterized, and opium poppy currently serves as a model system to study BIA metabolism in plants. BIA biosynthesis in opium poppy involves two biosynthetic gene clusters associated respectively with the morphine and noscapine branches. Recent reports have shown that genes in the same cluster are co-expressed, suggesting they might also be co-regulated. However, the transcriptional regulation of opium poppy BIA biosynthesis is not well studied. Opium poppy BIA biosynthesis involves three cell types associated with the phloem system: companion cells, sieve elements and laticifers. The transcripts and enzymes associated with BIA biosynthesis are distributed across cell types, requiring the translocation of key enzymes and pathway intermediates between cell types. Together, these suggest that the regulation of BIA biosynthesis in opium poppy is multilayered and complex, involving biochemical, genomic, and physiological mechanisms. In this review, we highlight recent advances in genome sequencing and single cell and spatial transcriptomics with a focus on how these efforts can improve our understanding of the genomic and cell-specific regulation of BIA biosynthesis. Such knowledge is vital for opium poppy genetic improvement and metabolic engineering efforts targeting the modulation of alkaloid yield and composition., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

Lymphatic filariasis (LF) and onchocerciasis (OV) are among the neglected tropical diseases (NTD) targeted for elimination in Ethiopia. We used a transmission assessment survey (TAS-1) to evaluate the serological status of OV in three co-endemic districts in Gambella simultaneously. During May and June 2019, blood samples were collected from 6- to 7-year-old children who were randomly selected through standard community-based TAS methodology. Children were tested for both circulating filarial antigen (CFA) for LF via filariasis test strip and for Onchocerca volvulus 16 (Ov16) antibody for OV via laboratory-based ELISA. A total of 3,377 children from 150 villages in the three districts were tested; 1,823 (54.0%) were male. All three districts had CFA results below the critical threshold for stopping LF mass drug administration (MDA). In contrast, 40 children (1.2%) were positive for Ov16 antibody, well above the WHO's OV stop MDA threshold of 0.1%. The integrated assessment indicated two programmatic decisions: stop MDA for LF and continue MDA for OV. Accordingly, albendazole MDA was discontinued in the districts but ivermectin MDA continued. This integrated assessment showed that a random sample for TAS can give important information about OV transmission status in co-endemic areas.

Background: The Ethiopian southwest drainage has been designated a huge potential for fishery and aquaculture development. However, the genetic diversity of Nile tilapia along the main water bodies has yet to be uncovered. Therefore, this study used microsatellite markers to assess the genetic structure and diversity of Nile cichlid (Oreochromis niloticus) populations., Methods: One hundred and sixty-seven fish were collected from Alwero Dam, Baro River, Gilgel Gibe I Dam and Gojeb River southwest of Ethiopia. Genomic DNA was extracted from 40 tissue samples using a Qiagen DNA tissue extraction kit and genetic polymorphism was estimated using GenAlEx6.502 software., Results: The result showed that four loci were polymorphic and produced 3-6 alleles per locus, while the number of effective alleles (Ne) and the number of distinct alleles (Na) were 1.370 and 2.063, respectively. Observed heterozygosity (Ho) and expected heterozygosity (He) were expanded between 0.100.50 and 0.115-0.265, respectively. Baro River population revealed the highest mean expected heterozygosity of 0.265, whereas the lowest expected mean heterozygosity of 0.115 was from the Alwero Dam. The genetic differentiation between populations (FST) resulted in a moderate to a very high degree of divergence between the populations. The Alwero Dam and Gojeb River populations were the most divergent populations (FST = 0.524), unlike those from the Alwero Dam and Baro River. The genetic variation among individuals within populations was 69%, whereas 31% appeared among populations and no variation within individuals to the overall variance., Conclusion: This study confirmed the presence of significant genetic variations and differentiation among populations except between Gilgel Gibe I Dam and Gojeb River. This study highlights the genetic structure and differentiation amongst wild Nile tilapia (O. niloticus) populations in south-western Ethiopia and paves the way for selective aquaculture breeding programs in the study area., (© 2023 The Authors. Veterinary Medicine and Science published by John Wiley & Sons Ltd.)

The goal of the study is to determine the effect of genotype and environment on forage yield, forage nutritive value and to determine the relation between morphology and forage yield and nutritive value of lablab. Thirteen genotypes (one local and 12 improved) were replicated 3 times in a randomized complete block trial across three locations in Ethiopian lowlands namely, Bechi, Kite and Tepi. All forage samples were analyzed for dry matter (DM), crude protein (CP), and in vitro dry matter digestibility (IVDMD) using a combination of conventional nutritional analyses and near infrared reflectance spectroscopy. There was a significant (P < 0.001) effect of genotype, location and genotype*location on forage yield of DM, forage yield of CP, forage yield of IVDMD, CP, and IVDMD. The difference between means of minimum and maximum genotypes was 12.9 t/ha of DM, 3.12 t/ha CP, 8.22 t/ha IVDMD, 57 g/kg of CP and 56 g/kg of IVDMD. The correlation between plant morphology and forage yield and nutritive value was weak (r ≤ 0.41) in all locations and the combined data. Both genotype and location should be considered by the farmers when they decide to grow lablab for forage production. Morphological traits of lablab are not suitable to evaluate forage yield and nutritive value. Enhancing the awareness of farmers about the effect genetic-environment interaction effect of forage yield and nutritive value and the relation between morphology and yield and nutritive value would improve the uptake of lablab in mixed the farming system leading to more sustainable agricultural production., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors.)

This experiment was conducted to investigate the supplemental effect of rosemary leaf meal (RLM) on egg production and egg quality in Lohmann-Brown laying hens. For each treatment, six replicates were performed with four 24-week-old laying hens for a total of 96 chickens. Dried rosemary leaf meal (RLM) was present in the commercial laying hen ration at 0, 1.7, 3.5 and 5.2%, respectively. The interactions between dietary treatments, egg storage temperatures (4 °C, 21.5 °C), and egg storage durations (7, 14, 21, 28, and 35 days) were examined in factorial designs using a fully randomized design. The data were analyzed using the Statistical Analysis System (SAS, 2014, Ver. 9.3) and Tukey's multiple range tests to separate the means. The inclusion of dried RLM at a level of 5.2% (p < 0.05) significantly improved the hens' daily egg production (78.9%). Feed conversion ratio (2.25) and egg weight (56.7 g) compared to control treatment. Similarly, at 3.5% and 5.2% RLM supplementation, eggshell weight (5.876 g) and eggshell strength increased significantly (p < 0.05) (compared to control, a weight of 3.76 kg/cm2 and a shell thickness (0.37 mm) was observed. In addition, the groups fed 5.2% RLM had significantly higher albumin weight (34.9 g/L), albumin height (6.9 mm), and yolk weight (15.6 g/L). l), yolk height (15.9 mm), yolk color (5.3 points), and Hough unit (83.9 points) than the control groups. Regarding the external characteristics of stored eggs, a group of hens fed at rates of 3.5 and 5.2% RLM showed significantly greater (p < 0.05) egg weight with increases in storage temperature and duration as a control group. There was a significant interaction effect between stored eggs collected from the supplemented groups in terms of egg weight, weight loss, shell weight, shell strength, and shell thickness stored at specific temperatures and storage durations. There was a decrease in albumen level and Haugh unit (HU) with an increase in storage temperature and duration over treatment (P < 0.05). Therefore, better external quality was observed in eggs collected from a group of chickens fed 4.5 and 5.2% RLM after 35 days of storage compared to a control group. Mean albumen height, albumen weight, HU, yolk height, and yolk color of eggs stored in the refrigerator (4 °C) were an exception for yolk weight, which was higher compared to room temperature (21.5 °C). Significantly low (P < 0.05) albumen height (6.61 to 2.96 cm), Hough unit (82.49 to 47.64 points), and yolk height (14.66 to 12.35 mm) were observed at 35 days storage recorded in the control group. In conclusion, supplementation with RLM at 3.5% and 5.2% improved the performance and quality of both fresh and stored eggs., Competing Interests: The authors declare that there is no competing interest., (© 2023 Published by Elsevier Ltd.)

Background: Aeromonas hydrophila is a zoonotic bacterial pathogen that frequently causes disease and mass mortalities among cultured and feral fishes worldwide. In Ethiopia, A. hydrophila outbreak was reported in Sebeta fish ponds and in Lake Tana fishery. However, there is no to little information on the molecular, and phenotypical characteristics of A. hydrophila in Ethiopian fisheries. Therefore, a cross-sectional study was conducted from November 2020 to May 2021 in selected Ethiopian Rift valley lakes., Results: A total of 140 samples were collected aseptically from fish (Muscle, Gill, Intestine, Spleen and Kidney) from fish landing sites, market and restaurants with purposive sampling methods. Aeromonas selective media (AMB), morphological and biochemical tests were used to isolate and identify A. hydrophila. Accordingly, the pathogen was isolated from 81 (60.45%) of samples. Among the isolates 92.59% expressed virulence trait through β hemolysis on blood agar media with 5% sheep blood. Moreover, 54 strains (66.67%) were further confirmed with Real-Time PCR (qPCR) using ahaI gene specific primers and optimized protocol. The highest (68.51%) were detected from live fish, (24.07%) were from market fish and the lowest (7.4%%) were from ready-to-eat products. Antibiogram analysis was conducted on ten representative isolates. Accordingly, A. hydrophila isolates were susceptible to ciprofloxacin (100%), chloramphenicol (100%) and ceftriaxone (100%). However, all ten isolates were resistant to Amoxicillin and Penicillin., Conclusions: The study indicates A. hydrophila strains carrying virulence ahaI gene that were ß-hemolytic and resistant to antibiotics commonly used in human and veterinary medicine are circulating in the fishery. The detection of the pathogen in 140 of the sampled fish population is alarming for potential outbreaks and zoonosis. Therefore, further molecular epidemiology of the disease should be studied to establish potential inter host transmission and antibiotic resistance traits. Therefore, raising the public awareness on risk associated with consuming undercooked or raw fish meat is pertinent., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Landslides pose a significant threat to infrastructure, property, and human lives in many regions worldwide, including Chira town in Ethiopia. This study presents an integrated geotechnical and geophysical investigation aimed at identifying the contributing factors to landslides in Chira town, Ethiopia, with a focus on a recent landslide event. The methodology employed a combination of geotechnical and geophysical techniques to comprehensively analyze the landslide problem. The geotechnical investigation involved a detailed analysis of the soil characteristics in the area, including the composition of fine-grained soil and the determination of cohesion and angle of internal friction through triaxial testing. The geophysical investigation utilized electrical resistivity tomography to assess the subsurface soil profile. The findings revealed the presence of a massive basaltic tertiary volcanic rock layer underlying a very low resistivity layer of sticky clay soil. Through this study, it was established that rainfall, soil type, land use, elevation, and proximity to streams, slopes, and aspects were the main factors contributing to the landslide, accounting for 22.03%, 18.89%, 15.75%, 15.46%, 10.87%, 9.7%, and 7.5% of the overall influence, respectively. Based on these findings, the study proposes a range of interventions to enhance resilience against landslides, including surface drainage, the implementation of appropriate land use management practices, and the introduction of vetiver vegetation. The integration of geotechnical and geophysical methodologies provided a comprehensive understanding of the landslide problem in Chira town. The proposed interventions aim to inform future land use planning, infrastructure development, and disaster risk reduction efforts in the region. By expanding our knowledge of the mechanisms driving landslides, this study offers valuable insights that can be utilized in similar regions facing comparable geotechnical and geophysical conditions ., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors.)

A simple wet chemical ultrasonic-assisted synthesis method was employed to prepare visible light-driven g-C 3 N 4 -ZnO-Co 3 O 4 (GZC) heterojunction photocatalysts. X-ray diffraction (XRD), scanning electromicroscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), Brunauer-Emmett-Teller (BET), ultraviolet (UV), and electrochemical impedance spectroscopy (EIS) are used to characterize the prepared catalysts. XRD confirms the homogenous phase formation of g-C 3 N 4 , ZnO, and Co 3 O 4 , and the heterogeneous phase for the composites. The synthesized ZnO and Co 3 O 4 by using cellulose as a template show a rod-like morphology. The specific surface area of the catalytic samples increases due to the cellulose template. The measurements of the energy band gap of a g-C 3 N 4 -ZnO-Co 3 O 4 composite showed red-shifted optical absorption to the visible range. The photoluminescence (PL) intensity decreases due to the formation of heterojunction. The PL quenching and EIS result shows that the reduction of the recombination rate and interfacial resistance result in charge carrier kinetic improvement in the catalyst. The photocatalytic performance in the degradation of MB dye of the GZC-3 composite was about 8.2-, 3.3-, and 2.5-fold more than that of the g-C 3 N 4 , g-C 3 N 4 -ZnO, and g-C 3 N 4 -Co 3 O 4 samples. The Mott-Schottky plots of the flat band edge position of g-C 3 N 4 , ZnO, Co 3 O 4 , and Z-scheme g-C 3 N 4 -ZnO-Co 3 O 4 photocatalysts may be created. Based on the stability experiment, GZC-3 shows greater photocatalytic activity after four recycling cycles. As a result, the GZC composite is environmentally friendly and efficient photocatalyst and has the potential to consider in the treatment of dye-contaminated wastewater., Competing Interests: The authors declare that there are no conflicts of interest., (Copyright © 2023 Mintesinot Tamiru Mengistu et al.)

Key Message: We identified and characterized a dominant FT allele for flowering without vernalization in Brassica rapa, while demonstrating its potential for deployment in breeding to accelerate flowering in various Brassicaceae crops. Controlling the timing of flowering is key to improving yield and quality of several agricultural crops including the Brassicas. Many Brassicaceae crops possess a conserved flowering mechanism in which FLOWERING LOCUS C (FLC) represses the transcription of flowering activators such as FLOWERING LOCUS T (FT) during vernalization. Here, we employed genetic analysis based on next-generation sequencing to identify a dominant FT allele, BraA.FT.2-C, for flowering in the absence of vernalization in the Brassica rapa cultivar 'CHOY SUM EX CHINA 3'. BraA.FT.2-C harbors two large insertions upstream of its coding region and is expressed without vernalization, despite FLC expression. We show that BraA.FT.2-C offers an opportunity to introduce flowering without vernalization requirement into winter-type brassica crops, including B. napus, which have many functional FLC paralogs. Furthermore, we demonstrated the feasibility of using B. rapa harboring BraA.FT.2-C as rootstock for grafting to induce flowering in radish (Raphanus sativus), which requires vernalization for flowering. We believe that the ability of BraA.FT.2-C to overcome repression by FLC can have significant applications in brassica crops breeding to increase yields by accelerating or delaying flowering., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The use of Clostridium butyricum in crustacean aquaculture for anti-abiotic stress is yet unknown. Feeds were formulated containing 0, 125, 250, 500, and 1000 mg/kg Clostridium butyricum (2 × 10 7  CFU/g), respectively. The giant freshwater prawns (Macrobrachium rosenbergii) were fed for 8 weeks in triplicate. The results showed that C. butyricum-supplemented groups improved growth performance significantly with the optimum level at 610 mg/kg. Ammonia stress reduced hemolymph glucose, total protein, total cholesterol, and triglyceride concentrations while dietary C. butyricum significantly increased hemolymph glucose and total protein levels after the ammonia challenge. Ammonia stress increased inducible nitric oxide synthase (iNOS) and nitric oxide (NO) levels, and the treatments supplemented with C. butyricum had considerably enhanced levels of iNOS and NO after stress. Treatment with C. butyricum increased the level of superoxide dismutase (SOD), and decreased the level of malondialdehyde (MDA) and superoxide anion, with the 125 mg/kg treated groups having the extreme value. Furthermore, C. butyricum-treated groups reduced the expression of HSPs after ammonia stress while the ammonia stress induced the expression of HSP60, HSP70, and HSP90. Dietary C. butyricum elevated the expression of peroxiredoxin-5 and toll in response to ammonia stress. The results indicate that dietary supplementation with 125-500 mg/kg of C. butyricum (2 × 10 7  CFU/g) improved biochemical and antioxidant features as well as intestinal immunity of M. rosenbergii under ammonia challenge by activating the toll signal pathway., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Bovine tuberculosis (bTB) is a disease with impact on dairy productivity, as well as having the potential for zoonotic transmission. Understanding the genetic diversity of the disease agent Mycobacterium bovis is important for identifying its routes of transmission. Here we investigated the level of genetic diversity of M. bovis isolates and assessed the zoonotic potential in risk groups of people working in bTB-infected dairy farms in central Ethiopia. M. bovis was isolated and spoligotyped from tissue lesions collected from slaughtered cattle as well as from raw milk collected from bTB positive cows in dairy farms from six urban areas of central Ethiopia. From consented dairy farm workers, knowledge and practices related to zoonotic TB transmission, together with demographic and clinical information, was collected through interviews. Sputum or Fine Needle Aspirate (FNA) samples were collected from suspected TB cases. Spoligotyping of 55 M. bovis isolates that originated either from cattle tissues with tuberculous lesion or from raw milk revealed seven spoligotype patterns where SB1176 was the most prevalent type (47.3%). Most isolates (89.1%) were of the M. bovis African 2 clonal complex. All sputum and FNA samples from 41 dairy farm workers with symptoms of TB were culture negative for any mycobacteria. Among the 41 TB suspected farm workers, 61% did not know about bTB in cattle and its zoonotic potential, and over two-third of these workers practiced raw milk consumption. Our spoligotype analysis suggests a wider transmission of a single spoligotype in the study area. The results reported here may be useful in guiding future work to identify the source and direction of bTB transmission and hence design of a control strategy. Isolation of M. bovis from milk, knowledge gap on zoonotic TB and practice of consumption of raw milk in the study population showed potential risk for zoonotic transmission., Competing Interests: The authors declare that they have no conflict of interests., (© 2022 The Authors. Zoonoses and Public Health published by Wiley‐VCH GmbH.)

This study aimed to assess the available livestock feed resources in the Lalo kile district of Kellem Wollega Zone, Western Ethiopia, in terms of species biomass composition and dry matter yield of dominant forage species. The district was stratified into two agro-ecologies: mid-altitude areas and low-altitude areas. The effects of grazing intensity on dry matter yields and biomass composition were analyzed using a randomized complete block design replicated three times having two blocks differed by two agro-ecologies (three mid-altitude kebeles and three low-altitude kebeles). The present study used seventy-two pasture samples and 20 × 20 m forage trees collected randomly from the two agro-ecologies of the study area. The General Linear Model of the SAS 19.0 version was used to compare the effects of the agro-ecology and species on dry matter yield and biomass composition. The result of the study indicated that the average dry matter yield for grasses, legumes, and other herbaceous forages was 1.156 t/ha, 0.242 t/ha, and 0.182 t/ha, with an overall 1.58 t/ha in the study district, respectively. About 73.13% of grasses, 15.32% of legumes, and 11.55% of other herbaceous were the species biomass composition in the study area. The midland agroecology had the average biomass fodder yields 7.98-19.78 kg/tree and 1.06-2.41 kg/shrub while lowland agroecology had 9.87-178.06 kg/tree and 1.34-3.87 kg/shrub. There was an estimate of 74.36-100 kg/ha fodder shrubs and 500-800 kg/ha fodder trees on cultivated and uncultivated land in the study area. The herbage yield of natural pasture is 1.733 t DMha -1 in the mid and 1.427 t DMha -1 in the low altitudes of the study area, with a mean herbage yield of 1.58 t DMha -1 during vegetation cover. The grazing capacity of the study area was 0.23 TLU/ha/year in the mid and 0.19 TLU/ha/year in the low altitudes of the study area, with a mean value of 0.21 TLU ha/year. The presence of limited grazing land in the study area led to overgrazing, which in turn resulted occurrence of land degradation associated with poor biomass yield, low quality and variable supply of feeds between the season. Therefore, this study suggests setting up land-use regulation policy to allocate separate land for feed production and commonly use for livestock feeding to improve livestock productivity and contribute to food security and poverty alleviation of small holder farmers in the study area., Competing Interests: The authors declare no conflict of interest., (© 2022 The Author(s).)

Opium poppy (Papaver somniferum) is one of the world's oldest medicinal plants and a versatile model system to study secondary metabolism. However, our knowledge of its genetic diversity is limited, restricting utilization of the available germplasm for research and crop improvement. We used genotyping-by-sequencing to investigate the extent of genetic diversity and population structure in a collection of poppy germplasm consisting of 91 accessions originating in 30 countries of Europe, North Africa, America, and Asia. We identified five genetically distinct subpopulations using discriminate analysis of principal components and STRUCTURE analysis. Most accessions obtained from the same country were grouped together within subpopulations, likely a consequence of the restriction on movement of poppy germplasm. Alkaloid profiles of accessions were highly diverse, with morphine being dominant. Phylogenetic analysis identified genetic groups that were largely consistent with the subpopulations detected and that could be differentiated broadly based on traits such as number of branches and seed weight. These accessions and the associated genotypic data are valuable resources for further genetic diversity analysis, which could include definition of poppy core sets to facilitate genebank management and use of the diversity for genetic improvement of this valuable crop., (© 2022. The Author(s).)

Background: Precancerous cervical lesion is an abnormality in the cells of the cervix that could eventually develop into cervical cancer. Cervical cancer is a public health problem that contributes to the death of women worldwide. In line with the high burden of the issue, the Ethiopian government had attempted to expand cervical cancer screening centers and recommendation of services to age-eligible as well as high-risk groups of women. Therefore, the study aimed to assess the prevalence of precancerous lesions of cervix cancer among women aged 30-49 years and associated factors in West Wollega., Method: Facility-based analytic cross-sectional study design was conducted in selected hospitals of West Wollega from January 1- February 20, 2022, among 339 women. A face-to-face interview was conducted and the presence or absence of precancerous cervical lesion was tested by visual inspection with acetic acid. Data were analyzed by SPSS version 25. Variable with P -value <.25 in the bi-variable analysis were entered into multivariable logistic regression. Results with a P -value ≤ .05 at 95% confidence level were considered for statistical significance., Result: The prevalence of precancerous cervical lesions was 27.4% (95% CI: 22.7%32.1%). The mean standard deviation of participants was 35.22 +6.32 years. More than half (63.4%) and 67.6% of them were regarded as having good knowledge and a favorable attitude towards precancerous cervical lesions respectively. History of menstrual irregularity had two folds higher odds of being diagnosed with the precancerous cervical lesion when compared with counterparts at, [AOR = 2.29(95% CI:1.29-4.04]. Women with a history of STI had 3.5 times higher odds of developing precancerous cervical lesion compared to women with no history of STI [AOR)=3.46(95% CI:1.94-6.18)], history of bleeding after sexual intercourse was 2.88 times more likely to have precancerous cervical lesion compared to those without it at [AOR=2.88(95% CI:1.43-5.78)]. Parity greater than or equal to five had 2.4 times higher odds of developing precancerous cervical lesions compared to women with parity less than five at [AOR=2.41(95% CI: 1.23-4.75)]. History of steroid use had 3.5 times higher odds of developing precancerous cervical lesion compared with opponents at [AOR=3.5(95% CI: 1.32-9.34) and women with an Unfavorable attitude towards screening for Cervical cancer screening, prevention, and control methods had 2.2 times higher odds of developing precancerous cervical lesion compared their counterpart at [AOR=2.15(95% CI: 1.21-3.83)]., Conclusion: The precancerous cervical lesions continue to be a significant public health concern in Ethiopia. It will remain a significant cause of death of women unless effective screening methods like VIA and vaccination against HPV are scaled up. Furthermore, having a history of menstrual irregularities, STI, bleeding after coitus, parity greater than ≥5, steroid use, and having an unfavorable attitude towards screening factors are significantly associated with the occurrence of the precancerous lesion. Therefore, effective prevention approaches have to consider these factors for the control of cervical cancer in the early phase of the lesion.

The purpose of this research was to determine the impact of seasonality on feed balance in the Lalo kile district of the Kellem Wollega Zone of Western Ethiopia. The district was divided into two agro-ecological zones: mid and low altitude. A total of 127 respondents were chosen to be interviewed. To collect the required data in the study areas, a cross-sectional survey was used. To analyses the qualitative data, descriptive statistics were performed, while the General Linear Model (GLM) method was used to assess the impacts of seasonal feed availability and agro-ecology on dry matter yield and production constraints. The result showed that there has been seasonal fluctuation in the feed availability and the feed is generally abundant from June to September. The feed supply in terms of DM, ME, and DCP per household per year was 118.7 kg, 74,781 MJ/kg, and 118.61kg, respectively. The feed balance was negatively associated and substantially different all across the studied areas (P < 0.01). With a year's approach, the annual total feed supply exceeds only 66.13, 25.81, and 87.24 percent of the DM, DCP, and ME demands per household, respectively. As a result, total dry matter production, digestible crude protein, and metabolizable energy supply were only fulfilled for 9, 3.5, and 12 months in the research area's mid-altitude and 7, 3 and 9 months in the study area's low land altitude, respectively. The main limitations in both agro-ecologies of the research area include low production and reproduction, poor use of existing feedstuffs, and poor adoption of improved forage production. As a result, for successful livestock development in the study area, the adoption of better fodder and supplementation of productive animals should be considered., Competing Interests: The authors declare no conflict of interest., (© 2021 The Author(s).)

In the search for alternative feed resources for laying hens, papaya pomace is available as industrial by-product but information on its nutritive value is lacking. Dried papaya pomace was included in a common laying hen diet at 0%, 2.5%, 5% and 7.5% to evaluate its effect on egg production performance, egg quality and general health parameters in Bovan brown layers. For every inclusion level, three cages with ten 20-week-old layers were used, making a total of 120 hens. The effect of dried papaya pomace inclusion on egg production, egg quality and general health parameters was evaluated. Dried papaya pomace inclusion improved egg production and laying by 6.15% and 17% respectively, while it significantly decreased feed conversion ratio by 7.5%. Eggshell weight, thickness and strength of PP5 were higher than the control by 0.3 g, 0.8 mm and 0.43 kg/cm 2 , respectively. There was a significant improvement in albumin weight (by 1.5 g/L), albumin height (2.1 mm), yolk weight (0.4 g/L), yolk height (0.4 mm), yolk colour (4.4 points) and Haugh unit (8 points) due to PP5 treatment. Inclusion of papaya pomace at a level of 7.5% of layers diet had negative effect on Egg production, feed conversion ratio and interior and exterior egg quality traits. Inclusion of papaya pomace affected significantly serum total cholesterol, serum triglyceride, serum low density lipoprotein, serum high density lipoprotein, aspartate aminotransferase, alanine aminotransferase and white blood cell count. However, all blood traits of the experimental animals were within the normal ranges reported for layers. Inclusion of papaya pomace in 5% of layers commercial diets improves egg production and quality without negative impact on health while decreasing feeding cost., (© 2021 The Authors Veterinary Medicine and Science Published by John Wiley & Sons Ltd.)

Advances in next generation sequencing (NGS)-based methodologies have accelerated the identifications of simple genetic variants such as point mutations and small insertions/deletions (InDels). Structural variants (SVs) including large InDels and rearrangements provide vital sources of genetic diversity for plant breeding. However, their analysis remains a challenge due to their complex nature. Consequently, novel NGS-based approaches are needed to rapidly and accurately identify SVs. Here, we present an NGS-based bulked-segregant analysis (BSA) technique called Sat-BSA (SVs associated with traits) for identifying SVs controlling traits of interest in crops. Sat-BSA targets allele frequencies at all SNP positions to first identify candidate genomic regions associated with a trait, which is then reconstructed by long reads-based local de novo assembly. Finally, the association between SVs, RNA-seq-based gene expression patterns and trait is evaluated for multiple cultivars to narrow down the candidate genes. We applied Sat-BSA to segregating F 2 progeny obtained from crosses between turnip cultivars with different tuber colors and successfully isolated two genes harboring SVs that are responsible for tuber phenotypes. The current study demonstrates the utility of Sat-BSA for the identification of SVs associated with traits of interest in species with large and heterozygous genomes., (Copyright © 2021 by JAPANESE SOCIETY OF BREEDING.)

Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is Mycobacterium bovis , which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole-genome sequencing to examine the population structure of M. bovis in Ethiopia. A total of 134 M . bovis isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of M. bovis , based on spoligotyping and demonstrated that the population is dominated by the clonal complexes African 2 (Af2) and European 3 (Eu3). A range of within-host diversity was observed amongst the isolates and evidence was found for both short- and long-distance transmission. Detailed analysis of available genomes from the Eu3 clonal complex combined with previously published genomes revealed two distinct introductions of this clonal complex into Ethiopia between 1950 and 1987, likely from Europe. This work is important to help better understand bTB transmission in cattle in Ethiopia and can potentially inform national strategies for bTB control in Ethiopia and beyond.

Background: Neglected Tropical Diseases (NTDs) are a group of several communicable and non-communicable diseases prevalent in tropical and subtropical areas. The co-endemicity of these diseases, the similarity of their clinical signs, and the need to maximize limited financial and human resources suggest the importance of adoptingan integratedapproach to their prevention and treatment., Aims: This study describes the development of a comprehensive package of physical, mental health and psychosocial care for people with lower-limb lymphoedema caused bypodoconiosis, lymphatic filariasis (LF)or leprosy as part of the EnDPoINT program in Ethiopia., Method: The care package was developed using a mixed-methods approach, consisting of a literature review, situational analysis, Theory of Change (ToC) workshops, qualitative research, and additional workshops to fine-tune the draft care package. The care package was developed between March 2018 and January 2020 in Addis Ababa and the implementation research site, Awi zone in the North-West of Ethiopia., Results: The holistic care package includes components implemented at three levels of the health care system:health organization, facility, and community. Sections of the care package are directed at strengthening capacity building, program management, community engagement, awareness-raising, stigma-reduction, morbidity management, disability prevention, follow-up visits, referral linkage, community-based rehabilitation, and monitoring and evaluation., Conclusions: The study developed a holistic integrated care package for lower limb disorder and co-morbid mental health problems caused by podoconiosis, LF or leprosy. The approach has the potential to significantly reduce lower limb disorder-associated morbidity, disability, and psychosocial problems. It also standardizes a scalable approach appropriate for the Ethiopian setting and, most likely, other countries where these NTDs are present., Competing Interests: The authors have declared that no competing interests exist.

Cannabis (Cannabis sativa L.) is one of the oldest cultivated plants purported to have unique medicinal properties. However, scientific research of cannabis has been restricted by the Single Convention on Narcotic Drugs of 1961, an international treaty that prohibits the production and supply of narcotic drugs except under license. Legislation governing cannabis cultivation for research, medicinal and even recreational purposes has been relaxed recently in certain jurisdictions. As a result, there is now potential to accelerate cultivar development of this multi-use and potentially medically useful plant species by application of modern genomics technologies. Whilst genomics has been pivotal to our understanding of the basic biology and molecular mechanisms controlling key traits in several crop species, much work is needed for cannabis. In this review we provide a comprehensive summary of key cannabis genomics resources and their applications. We also discuss prospective applications of existing and emerging genomics technologies for accelerating the genetic improvement of cannabis., (© 2020 The Authors New Phytologist © 2020 New Phytologist Foundation.)

Lymphedema causes disability and exacerbates poverty in many countries. The management of lymphatic filariasis (LF) and podoconiosis-related lymphedema involves daily hygiene to reduce secondary infections, but self-massage and deep-breathing, which have proven beneficial in cancer-related lymphedema, are not included. A cluster randomized trial in northern Ethiopia investigated the effects of lymphatic stimulation for people affected by moderate to severe lymphedema. Participants were allocated to either standard (control n = 59) or enhanced (intervention n = 67) self-care groups. Primary outcomes were lymphedema stage, mid-calf circumference, and tissue compressibility. Secondary outcomes were the frequency and duration of acute attacks. After 24 weeks, fewer patients were assessed as severe (control -37.8%, intervention -42.4%, p = 0.15) and there were clinically relevant changes in mid-calf tissue compressibility but not circumference. There was a significant between-group difference in patients who reported any acute attacks over the study period (control n = 22 (38%), intervention n = 7 (12%), p = 0.014). Daily lymphedema self-care resulted in meaningful benefits for all participants with a greater reduction in acute episodes among people performing lymphatic stimulation. Observations of a change in lymphedema status support earlier findings in Bangladesh and extend the demonstrated benefits of enhanced self-care to people affected by podoconiosis.

White Guinea yam ( Dioscorea rotundata ) is an important staple tuber crop in West Africa. However, its origin remains unclear. In this study, we resequenced 336 accessions of white Guinea yam and compared them with the sequences of wild Dioscorea species using an improved reference genome sequence of D. rotundata In contrast to a previous study suggesting that D. rotundata originated from a subgroup of Dioscorea praehensilis , our results suggest a hybrid origin of white Guinea yam from crosses between the wild rainforest species D. praehensilis and the savannah-adapted species Dioscorea abyssinica We identified a greater genomic contribution from D. abyssinica in the sex chromosome of Guinea yam and extensive introgression around the SWEETIE gene. Our findings point to a complex domestication scenario for Guinea yam and highlight the importance of wild species as gene donors for improving this crop through molecular breeding., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)

Bovine tuberculosis (bTB) is endemic in Ethiopia with higher prevalence in cattle, particularly in the central parts. Spread of Mycobacterium bovis (M. bovis) to wider regions is inevitable in uncontrolled conditions. This study was conducted to explore the pathology, characterize M. bovis strains, and describe genotypic diversity to demonstrate possible epidemiological links in emerging dairy areas of Ethiopia, namely, Mekelle and Gondar. Twenty-seven bTB positive cattle identified by the Single Intradermal Comparative Cervical Tuberculin (SICCT) test were subjected to post-mortem inspection to determine lesion distribution and pathological score. Samples from tissues with visible tuberculous or suspected non-visible lesions were processed and cultured following a standard protocol. Isolates identified as M. bovis by Region of Difference (RD)-based Polymerase Chain Reaction (PCR) were also spoligotyped to determine their spoligotype patterns. Post-mortem inspection of visceral organs indicated bTB suggestive lesions in 41% of the animals, with 25% being in the lungs. Lymph nodes from 77% of the animals had lesions. Fifty-five isolates identified from 24 of the slaughtered animals were confirmed as M. bovis . No other mycobacterial species were isolated. Spoligotyping classified strains from 21 of these animals into seven spoligotype patterns: SB0133, SB0134, SB1176, SB2233, SB2290, SB2467, and SB2520. More than one spoligotype were identified from five of these animals, and none of the last four spoligotypes had been reported in Ethiopia before. SB0134 was the most predominant type (47%) followed by SB0133 (25.5%). SB0133, SB2290, SB2467, and SB1176 are spoligotypes lacking spacers 3-7, characteristics of M. bovis strains of the African 2 (Af2) clonal complex, while SB0134, SB2233, and SB2520 do not belong to any of the established clonal complexes and likely to have a different evolutionary history. Despite a small sample size, the present study showed strain diversity with multiple genotypes identified in a single herd and even within a single animal, and the genotypes showed no sign of geographical localization, which could be a consequence of significant movement of bTB diseased cattle around the country, spreading the disease. Therefore, any future control programme of bTB in Ethiopia needs to address the risks of cattle movement., (Copyright © 2020 Mekonnen, Mihret, Tamiru, Hailu, Olani, Aliy, Sombo, Lakew, Gumi, Ameni, Wood and Berg.)

Background: Lymphoedema caused by lymphatic filariasis (LF) or podoconiosis can result in physical disability and social exclusion, which is exacerbated by painful acute dermatolymphangioadenitis (ADLA) episodes. These conditions have a significant impact on patients, however, little is known about the indirect effects on their caregivers. This study, therefore, aimed to determine the impact on caregivers for patients with leg lymphoedema in a co-endemic district of Ethiopia., Methodology/principal Findings: A cross-sectional survey of lymphoedema patients and their caregivers was conducted using semi-structured questionnaires in the Southern Nation Nationalities Peoples Region (SNNPR) of Ethiopia. Lymphoedema patient information on clinical severity (mild, moderate, severe), frequency of ADLAs, their socio-demographic characteristics and the identity of main caregiver(s) was collected. Caregiver information on socio-demographic characteristics, types of care provided, their quality of life (QoL) measured across nine domains, and productivity was collected, with key indicators compared in the presence and absence of patients' ADLAs. A total of 73 patients and 76 caregivers were included. Patients were grouped by mild/moderate (n = 42, 57.5%) or severe (n = 31, 42.5%) lymphoedema, and reported an average of 6.1 (CI± 2.18) and 9.8 (CI± 3.17) ADLAs respectively in the last six months. A total of 48 (65.8%) female and 25 (34.2%) male patients were interviewed. Caregivers were predominately male (n = 45, 59.2%), and spouses formed the largest caregiving group for both female and male patients. In the absence of an ADLA, most caregivers (n = 42, 55.2%) did not provide care, but only one caregiver did not provide care during an ADLA. In the absence of an ADLA, the average time (hour:minute) spent by mild/moderate (00:17, CI: ± 00:08) and severe (00:10, CI: ± 00:07) patient caregiver per task was minimal. The time mild/moderate (00:47, CI: ± 00:11) and severe (00:51, CI: ± 00:16) patient caregivers spent per task significantly increased in the presence of an ADLA. In addition, caregivers' QoL was negatively impacted when patients experienced an ALDA, and they had to forfeit an average of 6 to 7 work/school days per month., Conclusion/significance: Lymphoedema and ADLAs impact negatively on patients' and their caregivers' lives. This emphasises the importance of increasing access to effective morbidity management and disability prevention services to reduce the burden and help to address the Sustainable Development Goal (SDG) 5, target 5.4, which seeks to recognise and value unpaid care and domestic work., Competing Interests: The authors have declared that no competing interests exist.

Key Message: An improved protocol of QTL-seq, an NGS-based method for bulked segregant analysis we previously developed in rice, allowed successful mapping of QTLs of interest in the highly heterozygous genome of B. rapa, demonstrating the power of this elegant method for genetic analyses in heterozygous species of economic importance. Recent advances in next-generation sequencing (NGS) and the various NGS-based methods developed for rapidly identifying candidate genes of interest have accelerated genetic analysis mainly in the model plants rice and Arabidopsis. Brassica rapa includes several economically important crops such as Chinese cabbage, turnip and various leafy vegetables. The application of NGS-based approaches for the analysis of B. rapa has been limited mainly due to its highly heterozygous genome and poor quality of the reference genome sequence currently available for this species. In this study, we have improved QTL-seq, a method for NGS-based bulked segregant analysis we previously developed in rice, extending its applicability for accelerating the genetic analysis and molecular breeding of B. rapa. Addition of new filters to the original QTL-seq pipeline allowed removal of spurious single-nucleotide polymorphisms caused by alignment/sequencing errors and variability between parents, significantly improving accuracy of the analysis. As proof of principle, we successfully applied the new approach to identify candidate genomic regions controlling flowering and trichome formation using segregating F2 progeny obtained from crosses made between cultivars of B. rapa showing contrasting phenotypes for these traits. We strongly believe that the improved QTL-seq method reported here will extend the applicability of NGS-based genetic analysis not only to B. rapa but also to other plant species of economic importance with heterozygous genomes.

Dioecy (distinct male and female individuals) and scarce to non-flowering are common features of cultivated yam (Dioscorea spp.). However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are largely unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify flowering and sex-related genes in white Guinea yam (D. rotundata), generating 20,236 unique tags. Of these, 13,901 were represented by a minimum of 10 tags. A total 88 tags were significantly differentially expressed in male, female and monoecious plants, of which 18 corresponded to genes previously implicated in flower development and sex determination in multiple plant species. We validated the SuperSAGE data with quantitative real-time PCR (qRT-PCR)-based analysis of the expression of three candidate genes. We further investigated the flowering patterns of 1938 D. rotundata accessions representing diverse geographical origins over two consecutive years. Over 85% of accessions were either male or non-flowering, less than 15% were female, while monoecious plants were rare. Intensity of flowering varied between male and female plants, with the former flowering more abundantly than the latter. Candidate genes identified in this study can be targeted for further validation and to induce regular flowering in poor to non-flowering cultivars. Findings of the study provide important inputs for further studies aiming to overcome the challenge of flowering in yams and to improve efficiency of yam breeding., Competing Interests: The authors have declared that no competing interests exist.

The perception mechanism for the strigolactone (SL) class of plant hormones has been a subject of debate because their receptor, DWARF14 (D14), is an α/β-hydrolase that can cleave SLs. Here we show via time-course analyses of SL binding and hydrolysis by Arabidopsis thaliana D14, that the level of uncleaved SL strongly correlates with the induction of the active signaling state. In addition, we show that an AtD14 D218A catalytic mutant that lacks enzymatic activity is still able to complement the atd14 mutant phenotype in an SL-dependent manner. We conclude that the intact SL molecules trigger the D14 active signaling state, and we also describe that D14 deactivates bioactive SLs by the hydrolytic degradation after signal transmission. Together, these results reveal that D14 is a dual-functional receptor, responsible for both the perception and deactivation of bioactive SLs.

Background: Ethiopia is currently facing new challenges related to food insecurity among the urban poor. Pensioners are segments of the population with reduced income and working capacity because of advancement of age and other related problems. There is no empirical evidence on Jimma Town pensioner's household food insecurity and coping strategies., Methods: A cross-sectional study was conducted among households in Jimma Town living on an income obtained from a pension from March 01-28, 2017. Data were collected from 399 randomly selected participants. Data were entered into EPi-Data version 3.1 and analyzed using SPSS Version 20.0. Variables with p ≤ 0.25 in the bivariate analyses were entered into a multivariable regression model to control for confounding variables., Results: Nearly, 83.5% of households were food insecure. The odds of food insecurity among households with heads attending secondary school and above was 78% lower when compared to that of households with uneducated household heads (AOR = 0.22, 95% CI: 0.97 to 0.49). The odds of food insecurity among households headed by merchants was 91% lower when compared to that of households headed by guards (AOR = 0.09, 95% CI: 0.03, 0.29). Food insecure households were using coping strategies such as changing consumption patterns (44%), eating inexpensive foods (72.4%), reducing meal frequency (62.4%) and selling household assets, such as household food utensils (30.8%). The odds of food insecurity among households having large family size (≥ 7) was 3.74 times higher when compared to that of households with family size less than three (AOR = 3.74(1.27 , 10.99)., Conclusions: Household food insecurity was associated with having households headed by uneducated, widowed and guard household heads and having large family size. Food insecure households used both consumption and asset-based coping strategies such as eating less preferred, lower quality or less expensive foods and receiving donation from relatives or friends. Government policies should consider revising the current social protection scheme for pensioners. Special attention should be given to widow pensioners and pensioners with low educational status and with large family sizes.

Background: The genome-wide expression profile of genes in different tissues/cell types and developmental stages is a vital component of many functional genomic studies. Transcriptome data obtained by RNA-sequencing (RNA-Seq) is often deposited in public databases that are made available via data portals. Data visualization is one of the first steps in assessment and hypothesis generation. However, these databases do not typically include visualization tools and establishing one is not trivial for users who are not computational experts. This, as well as the various formats in which data is commonly deposited, makes the processes of data access, sharing and utility more difficult. Our goal was to provide a simple and user-friendly repository that meets these needs for data-sets from major agricultural crops., Description: AgriSeqDB ( https://expression.latrobe.edu.au/agriseqdb ) is a database for viewing, analysing and interpreting developmental and tissue/cell-specific transcriptome data from several species, including major agricultural crops such as wheat, rice, maize, barley and tomato. The disparate manner in which public transcriptome data is often warehoused and the challenge of visualizing raw data are both major hurdles to data reuse. The popular eFP browser does an excellent job of presenting transcriptome data in an easily interpretable view, but previous implementation has been mostly on a case-by-case basis. Here we present an integrated visualisation database of transcriptome data-sets from six species that did not previously have public-facing visualisations. We combine the eFP browser, for gene-by-gene investigation, with the Degust browser, which enables visualisation of all transcripts across multiple samples. The two visualisation interfaces launch from the same point, enabling users to easily switch between analysis modes. The tools allow users, even those without bioinformatics expertise, to mine into data-sets and understand the behaviour of transcripts of interest across samples and time. We have also incorporated an additional graphic download option to simplify incorporation into presentations or publications., Conclusion: Powered by eFP and Degust browsers, AgriSeqDB is a quick and easy-to-use platform for data analysis and visualization in five crops and Arabidopsis. Furthermore, it provides a tool that makes it easy for researchers to share their data-sets, promoting research collaborations and data-set reuse.

Contents Summary 540 I. Introduction 540 II. There are different types of sRNA mobility 541 III. Mechanisms of sRNA movement 541 IV. Long-distance, shoot-root, mobile siRNAs influence DNA methylation in recipient tissues 541 V. Classes of interactions between shoot-root mobile siRNAs and DNA methylation 542 VI. Loci targeted directly and indirectly by shoot-root mobile siRNAs are associated with different histone modifications 543 VII. Is mobile siRNA-regulated DNA methylation important in specific tissues or under specific conditions? 543 VIII. Mobile sRNAs can be used to modify plant traits 544 IX. Conclusions 544 Acknowledgements 544 References 544 SUMMARY: RNA-directed DNA methylation (RdDM) at cytosine residues regulates gene expression, silences transposable elements and influences genome stability. The mechanisms responsible for RdDM are guided to target loci by small RNAs (sRNAs) that can move within plants cell to cell and long distance. Here we discuss recent advances in the understanding of interactions between mobile sRNAs and DNA methylation. We describe the mechanisms of sRNA movement, the differences between known classes of mobile sRNA-DNA methylation interactions and the limits of current knowledge. Finally, we discuss potential applications of mobile sRNAs in modifying plant traits., (© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.)

Background: Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected "orphan" crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop., Results: To accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage., Conclusions: Guinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture.

Problem: Lymphatic filariasis and podoconiosis are the major causes of tropical lymphoedema in Ethiopia. The diseases require a similar provision of care, but until recently the Ethiopian health system did not integrate the morbidity management., Approach: To establish health-care services for integrated lymphoedema morbidity management, the health ministry and partners used existing governmental structures. Integrated disease mapping was done in 659 out of the 817 districts, to identify endemic districts. To inform resource allocation, trained health extension workers carried out integrated disease burden assessments in 56 districts with a high clinical burden. To ensure standard provision of care, the health ministry developed an integrated lymphatic filariasis and podoconiosis morbidity management guideline, containing a treatment algorithm and a defined package of care. Experienced professionals on lymphoedema management trained government-employed health workers on integrated morbidity management. To monitor the integration, an indicator on the number of lymphoedema-treated patients was included in the national health management information system., Local Setting: In 2014, only 24% (87) of the 363 health facilities surveyed provided lymphatic filariasis services, while 12% (44) provided podoconiosis services., Relevant Changes: To date, 542 health workers from 53 health centres in 24 districts have been trained on integrated morbidity management. Between July 2013 and June 2016, the national health management information system has recorded 46 487 treated patients from 189 districts., Lessons Learnt: In Ethiopia, an integrated approach for lymphatic filariasis and podoconiosis morbidity management was feasible. The processes used could be applicable in other settings where these diseases are co-endemic.

Podoconiosis is a geochemical disease occurring in individuals exposed to red clay soil of volcanic origin. This Neglected Tropical Disease (NTD) is highly prevalent in Ethiopia. According to the nationwide mapping in 2013, the disease is endemic in 345 districts, where an estimated 35 million people live. The government of Ethiopia prioritized podoconiosis as one of eight priority NTDs and included it in the national integrated master plan for NTDs. An integrated lymphoedema management guideline has been developed. Service expansion has continued in the last few years and lymphoedema management services have been expanded to over one hundred endemic districts. The last few years have been critical in generating evidence about the distribution, burden and effective interventions for podoconiosis in Ethiopia. Although the extent of the problem within Ethiopia is considerable, the country is well positioned to now scale-up elimination efforts. Given the extraordinary progress of the past ten years and the current commitment of government, private and third sectors, Ethiopia seems to be on course for the elimination of podoconiosis in our lifetime. We need continued strong partner commitment, evidence-building, and scale-up of activities to accomplish this.

Introduction: Neglected tropical diseases (NTDs) are important public health problems in Ethiopia. In 2013, the Federal Ministry of Health (FMOH) has launched a national NTD master plan to eliminate major NTDs of public health importance by 2020. Benchmarking the current status of NTDs in the country is important to monitor and evaluate the progress in the implementation of interventions and their impacts. Therefore, this study aims to assess the trends of mortality and Disability-adjusted Life-Years (DALY) for the priority NTDs over the last 25 years., Methods: We used the Global Burden of Disease (GBD) 2015 estimates for this study. The GBD 2015 data source for cause of death and DALY estimation included verbal autopsy (VA), Demographic and Health Surveys (DHS), and other disease specific surveys, Ministry of Health reports submitted to United Nations (UN) agencies and published scientific articles. Cause of Death Ensemble modeling (CODEm) and/or natural history models were used to estimate NTDs mortality rates. DALY were estimated as the sum of Years of Life Lost (YLL) due to premature mortality and Years Lived with Disability (YLD)., Results: All NTDs caused an estimated of 6,293 deaths (95% uncertainty interval (UI): 3699-10,080) in 1990 and 3,593 deaths (95% UI: 2051 - 6178) in 2015, a 43% reduction over the 25 years. Age-standardized mortality rates due to schistosomiasis, STH and leshmaniasis have declined by 91.3%, 73.5% and 21.6% respectively between 1990 to 2015. The number of DALYs due to all NTDs has declined from 814.4 thousand (95% UI: 548 thousand-1.2million) in 1990 to 579.5 thousand (95%UI: 309.4 thousand-1.3 million) in 2015. Age-standardized DALY rates due to all NTDs declined by 30.7%, from 17.6 per 1000(95%UI: 12.5-26.5) in 1990 to 12.2 per 1000(95%UI: 6.5 - 27.4) in 2015. Age-standardized DALY rate for trachoma declined from 92.7 per 100,000(95% UI: 63.2 - 128.4) in 1990 to 41.2 per 100,000(95%UI: 27.4-59.2) in 2015, a 55.6% reduction between 1990 and 2015. Age-standardized DALY rates for onchocerciasis, schistosomiasis and lymphiaticfilariasis decreased by 66.2%, 29.4% and 12.5% respectively between 1990 and 2015. DALY rate for ascariasis fell by 56.8% over the past 25 years., Conclusions: Ethiopia has made a remarkable progress in reducing the DALY rates for most of the NTDs over the last 25 years. The rapid scale of interventions and broader system strengthening may have a lasting impact on achieving the 2020 goal of elimination of most of NTDs. Ethiopia should strengthen the coverage of integrated interventions of NTD through proper coordination with other health programs and sectors and community participation to eliminate NTDs by 2020.

Lymphatic filariasis (LF) is one of the most debilitating and disfiguring diseases common in Ethiopia and is caused by Wuchereria bancrofti. Mapping for LF has shown that 70 woredas (districts) are endemic and 5.9 million people are estimated to be at risk. The national government's LF elimination programme commenced in 2009 in 5 districts integrated with the onchocerciasis programme. The programme developed gradually and has shown significant progress over the past 6 years, reaching 100% geographical coverage for mass drug administration (MDA) by 2016. To comply with the global LF elimination goals an integrated morbidity management and disability prevention (MMDP) guideline and a burden assessment programme has also been developed; MMDP protocols and a hydrocoele surgical handbook produced for country-wide use. In Ethiopia, almost all LF endemic districts are co-endemic with malaria and vector control aspects of the activities are conducted in the context of malaria programme as the vectors for both diseases are mosquitoes. In order to monitor the elimination, 11 sentinel and spot-check sites have been established and baseline information has been collected. Although significant achievements have been achieved in the scale up of the LF elimination programme, there is still a need to strengthen operational research to generate programme-relevant evidence, to increase access to morbidity management services, and to improve monitoring and evaluation of the LF programme. However, the current status of implementation of the LF national programme indicates that Ethiopia is poised to achieve the 2020 goal of elimination of LF. Nevertheless, to achieve this goal, high and sustained treatment coverage and strong monitoring and evaluation of the programme are essential.

Understanding how plants allocate their resources to growth or defence is of long-term importance to the development of new and improved varieties of different crops. Using molecular genetics, plant physiology, hormone analysis and Next-Generation Sequencing (NGS)-based transcript profiling, we have isolated and characterized the rice (Oryza sativa) LESION AND LAMINA BENDING (LLB) gene that encodes a chloroplast-targeted putative leucine carboxyl methyltransferase. Loss of LLB function results in reduced growth and yield, hypersensitive response (HR)-like lesions, accumulation of the antimicrobial compounds momilactones and phytocassanes, and constitutive expression of pathogenesis-related genes. Consistent with these defence-associated responses, llb shows enhanced resistance to rice blast (Magnaporthe oryzae) and bacterial blight (Xanthomonas oryzae pv. oryzae). The lesion and resistance phenotypes are likely to be caused by the over-accumulation of jasmonates (JAs) in the llb mutant including the JA precursor 12-oxo-phytodienoic acid. Additionally, llb shows an increased lamina inclination and enhanced early seedling growth due to elevated brassinosteroid (BR) synthesis and/or signalling. These findings show that LLB functions in the chloroplast to either directly or indirectly repress both JA- and BR-mediated responses, revealing a possible mechanism for controlling how plants allocate resources for defence and growth., (© 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.)

More accurate, rapid, and easy phenotyping tools are required to match the recent advances in high-throughput genotyping for accelerating breeding and genetic analysis. The conventional data recording in field notebooks and then inputting data to computers for further analysis is inefficient, time-consuming, laborious, and prone to human error. Here, we report WIPPER (for Wireless Plant Phenotyper), a new phenotyping platform that combines field phenotyping and data recording with the aid of Bluetooth communication, thus saving time and labor not only for field data recoding but also for inputting data to computers. Additionally, it eliminates the risk of human error associated with phenotyping and inputting data. We applied WIPPER to 100 individuals of a rice recombinant inbred line (RIL) for measuring leaf width and relative chlorophyll content (SPAD value), and were able to record an accurate data in a significantly reduced time compared with the conventional method of data collection. We are currently using WIPPER for routine management of rice germplasm including recording and documenting information on phenotypic data, seeds, and DNA for their accelerated utilization in crop breeding.

Cytochrome P450s are among the largest protein coding gene families in plant genomes. However, majority of the genes remain uncharacterized. Here, we report the characterization of dss1, a rice mutant showing dwarfism and reduced grain size. The dss1 phenotype is caused by a non-synonymous point mutation we identified in DSS1, which is member of a P450 gene cluster located on rice chromosome 3 and corresponds to the previously reported CYP96B4/SD37 gene. Phenotypes of several dwarf mutants characterized in rice are associated with defects in the biosynthesis or perception of the phytohormones gibberellins (GAs) and brassinosteroids (BRs). However, both GA and BR failed to rescue the dss1 phenotype. Hormone profiling revealed the accumulation of abscisic acid (ABA) and ABA metabolites, as well as significant reductions in GA19 and GA53 levels, precursors of the bioactive GA1, in the mutant. The dss1 contents of cytokinin and auxins were not significantly different from wild-type plants. Consistent with the accumulation of ABA and metabolites, germination and early growth was delayed in dss1, which also exhibited an enhanced tolerance to drought. Additionally, expressions of members of the DSS1/CYP96B gene cluster were regulated by drought stress and exogenous ABA. RNA-seq-based transcriptome profiling revealed, among others, that cell wall-related genes and genes involved in lipid metabolism were up- and down-regulated in dss1, respectively. Taken together, these findings suggest that DSS1 mediates growth and stress responses in rice by fine-tuning GA-to-ABA balance, and might as well play a role in lipid metabolism.

Lesion mimic mutants (LMMs) provide a useful tool to study defense-related programmed cell death (PCD) in plants. Although a number of LMMs have been identified in multiple species, most of the candidate genes are yet to be isolated. Here, we report the identification and characterization of a novel rice (Oryza sativa L.) lesion mimic resembling (lmr) mutant, and cloning of the corresponding LMR gene. The LMR locus was initially delineated to 1.2 Mb region on chromosome 6, which was further narrowed down to 155-kb using insertions/deletions (INDELs) and cleavage amplified polymorphic sequence markers developed in this study. We sequenced the open reading frames predicted within the candidate genomic region, and identified a G-A base substitution causing a premature translation termination in a gene that encodes an ATPase associated with various cellular activities type (AAA-type) protein. RNA interference transgenic lines with reduced LMR transcripts exhibited the lesion mimic phenotype similar to that of lmr plants. Furthermore, expression of the wild-type LMR in the mutant background complemented the lesion phenotype, confirming that the mutation identified in LMR is responsible for the mutant phenotype. The pathogenesis-related (PR) genes PBZ1 and PR1 were induced in lmr, which also showed enhanced resistance to rice blast (Magnaporthe oryzae) and bacterial blight (Xanthomonas oryzae pv. oryzae), suggesting LMR is a negative regulator of cell death in rice. The identification of lmr and cloning of the corresponding LMR gene provide an additional resource for the study of PCD in plants.

The significance of plastid terminal oxidase (PTOX) in phytoene desaturation and chloroplast function has been demonstrated using PTOX-deficient mutants, particularly in Arabidopsis. However, studies on its role in monocots are lacking. Here, we report cloning and characterization of the rice (Oryza sativa) PTOX1 gene. Using Ecotype Targeting Induced Local Lesions IN Genomes (EcoTILLING) and TILLING as forward genetic tools, we identified the causative mutation of an EMS mutant characterized by excessive tillering, semi-dwarfism and leaf variegation that corresponded to the PTOX1 gene. The tillering and semi-dwarf phenotypes of the ptox1 mutant are similar to phenotypes of known strigolactone (SL)-related rice mutants, and both phenotypic traits could be rescued by application of the synthetic SL GR24. The ptox1 mutant accumulated phytoene in white leaf sectors with a corresponding deficiency in β-carotene, consistent with the expected function of PTOX1 in promoting phytoene desaturase activity. There was also no accumulation of the carotenoid-derived SL ent-2'-epi-5-deoxystrigol in root exudates. Elevated concentrations of auxin were detected in the mutant, supporting previous observations that SL interaction with auxin is important in shoot branching control. Our results demonstrate that PTOX1 is required for both carotenoid and SL synthesis resulting in SL-deficient phenotypes in rice., (© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.)

We describe a protocol for transient gene expression in rice protoplasts and its application to the study of Magnaporthe oryzae avirulence (AVR) gene function. In this assay the gene encoding the firefly luciferase protein is transfected into rice protoplasts by electroporation together with the candidate AVR genes. The luminescence can then be used to assess the viability of rice protoplasts. The hypersensitive response (HR) caused by the interaction between M. oryzae AVR and rice R genes can subsequently be monitored by recording the decrease in luminescence from the transfected cells.

Next-generation sequencing allows the identification of mutations responsible for mutant phenotypes by whole-genome resequencing and alignment to a reference genome. However, when the resequenced cultivar/line displays significant structural variation from the reference genome, mutations in the genome regions missing from the reference (gaps) cannot be identified by simple alignment. Here we report on a method called 'MutMap-Gap', which involves delineating a candidate region harboring a mutation of interest using the recently reported MutMap method, followed by de novo assembly, alignment, and identification of the mutation within genome gaps. We applied MutMap-Gap to isolate the blast resistant gene Pii from the rice cv Hitomebore using mutant lines that have lost Pii function. MutMap-Gap should prove useful for cloning genes that exhibit significant structural variations such as disease resistance genes of the nucleotide-binding site-leucine rich repeat (NBS-LRR) class., (© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.)

Advances in genome sequencing technologies have enabled researchers and breeders to rapidly associate phenotypic variation to genome sequence differences. We recently took advantage of next-generation sequencing technology to develop MutMap, a method that allows rapid identification of causal nucleotide changes of rice mutants by whole genome resequencing of pooled DNA of mutant F2 progeny derived from crosses made between candidate mutants and the parental line. Here we describe MutMap+, a versatile extension of MutMap, that identifies causal mutations by comparing SNP frequencies of bulked DNA of mutant and wild-type progeny of M3 generation derived from selfing of an M2 heterozygous individual. Notably, MutMap+ does not necessitate artificial crossing between mutants and the wild-type parental line. This method is therefore suitable for identifying mutations that cause early development lethality, sterility, or generally hamper crossing. Furthermore, MutMap+ is potentially useful for gene isolation in crops that are recalcitrant to artificial crosses.

The majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). Mapping and isolation of QTLs is important for efficient crop breeding by marker-assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. However, since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been time-consuming and labor-intensive. Here we report the rapid identification of plant QTLs by whole-genome resequencing of DNAs from two populations each composed of 20-50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL-seq as applied to plant species. We applied QTL-seq to rice recombinant inbred lines and F2 populations and successfully identified QTLs for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL-seq is able to detect QTLs over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps., (© 2013 The Authors The Plant Journal © 2013 Blackwell Publishing Ltd.)

The majority of agronomic traits are controlled by multiple genes that cause minor phenotypic effects, making the identification of these genes difficult. Here we introduce MutMap, a method based on whole-genome resequencing of pooled DNA from a segregating population of plants that show a useful phenotype. In MutMap, a mutant is crossed directly to the original wild-type line and then selfed, allowing unequivocal segregation in second filial generation (F(2)) progeny of subtle phenotypic differences. This approach is particularly amenable to crop species because it minimizes the number of genetic crosses (n = 1 or 0) and mutant F(2) progeny that are required. We applied MutMap to seven mutants of a Japanese elite rice cultivar and identified the unique genomic positions most probable to harbor mutations causing pale green leaves and semidwarfism, an agronomically relevant trait. These results show that MutMap can accelerate the genetic improvement of rice and other crop plants.