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Author

Hirut Kebede

Other affiliations: Texas Tech University
Bio: Hirut Kebede is an academic researcher from Agricultural Research Service. The author has contributed to research in topics: Drought tolerance & Population. The author has an hindex of 12, co-authored 23 publications receiving 689 citations. Previous affiliations of Hirut Kebede include Texas Tech University.

Papers
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Journal ArticleDOI
TL;DR: The identification of QTLs and markers for pre-flowering drought tolerance and lodging tolerance will help plant breeders in manipulating and pyramiding those traits along with stay green to improve drought tolerance in sorghum.
Abstract: Drought is a major constraint in sorghum production worldwide. Drought-stress in sorghum has been characterized at both pre-flowering and post-flowering stages resulting in a drastic reduction in grain yield. In the case of post-flowering drought stress, lodging further aggravates the problem resulting in total loss of crop yield in mechanized agriculture. The present study was conducted to identify quantitative trait loci (QTLs) controlling post-flowering drought tolerance (stay green), pre-flowering drought tolerance and lodging tolerance in sorghum using an F7 recombinant inbred line (RIL) population derived from the cross SC56×Tx7000. The RIL lines, along with parents, were evaluated for the above traits in multiple environments. With the help of a restriction fragment length polymorphism (RFLP) map, which spans 1,355 cM and consists of 144 loci, nine QTLs, located over seven linkage groups were detected for stay green in several environments using the method of composite interval mapping. Comparison of the QTL locations with the published results indicated that three QTLs located on linkage groups A, G and J were consistent. This is considered significant since the stay green line SC56 used in our investigation is from a different source compared to B35 that was used in all the earlier investigations. Comparative mapping has shown that two stay green QTLs identified in this study corresponded to stay green QTL regions in maize. These genomic regions were also reported to be congruent with other drought-related agronomic and physiological traits in maize and rice, suggesting that these syntenic regions might be hosting a cluster of genes with pleiotropic effects implicated in several drought tolerance mechanisms in these grass species. In addition, three and four major QTLs responsible for lodging tolerance and pre-flowering drought tolerance, respectively, were detected. This investigation clearly revealed the important and consistent stay green QTLs in a different stay green source that can logically be targeted for positional cloning. The identification of QTLs and markers for pre-flowering drought tolerance and lodging tolerance will help plant breeders in manipulating and pyramiding those traits along with stay green to improve drought tolerance in sorghum.

256 citations

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TL;DR: In this article, a prototype system was developed and constructed for automating the measurement and recording of canopy, soil-, and air temperature, and soil moisture status in cropped fields, consisting of a microcontroller-based circuit with solid-state components for handling clock/calendar, sensor power, and data storage and retrieval functions.

103 citations

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TL;DR: This SDS/CTAB protocol was used to isolate high quality genomic DNA subject to restriction endonuclease digestion and AFLP analysis from both plant and fungi with minimum cost and health concerns.
Abstract: The most commonly used plant DNA isolation methods use toxic and hazardous chemicals (phenol, chloroform), which require special equipment to minimize exposure and may limit their use in certain environments. Commercial DNA extraction kits are convenient and usually safe, but their availability to certain developing countries and high cost can be limiting, especially when handing a large number of samples and considering experiments with limited financial resources. Current reports on nonphenol/ chloroform protocols have not thoroughly examined the quality and suitability of the DNA for studies that require high precision. A simple, economical and rapid method is presented to isolate high quality DNA from plant and fungal species. This method uses potassium acetate to remove proteins and polysaccharides in an SDS extraction buffer. Further DNA purification is achieved using a low salt CTAB treatment. This SDS/CTAB protocol was used to isolate high quality genomic DNA subject to restriction endonuclease digestion and AFLP analysis from both plant and fungi with minimum cost and health concerns.

66 citations

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TL;DR: This study identifies species differences in anatomical, biochemical, and physiological characteristics of leaves related to leaf gas exchange and whole plant WUE, which can later be tested with the molecular markers.
Abstract: Lycopersicon pennellii (Cor.) D'Arcy possesses greater drought resistance and higher water use efficiency (WUE) than the domesticated tomato L. esculentum Mill. A previous report suggested three restriction fragment length polymorphism markers for whole plant WUE. This study identifies species differences in anatomical, biochemical, and physiological characteristics of leaves related to leaf gas exchange and whole plant WUE, which can later be tested with the molecular markers. Lycopersicon pennellii exhibited 29% lower stomatal frequency, more even distribution of stomata between the upper and the lower leaf surfaces, and a 54% thicker leaf with 31% greater air space volume relative to total leaf tissue volume than L. esculentum

47 citations


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TL;DR: A synthesis of knowledge is presented at this stage for application of this new and powerful detection method, which can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species.
Abstract: Summary Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, requires a heightened awareness and attention to quality assurance and quality control protocols. Additionally, the interpretation of eDNA data demands careful consideration of multiple factors. As eDNA methods have grown in application, diverse approaches have been implemented to address these issues. With interest in eDNA continuing to expand, supportive guidelines for undertaking eDNA studies are greatly needed. Environmental DNA researchers from around the world have collaborated to produce this set of guidelines and considerations for implementing eDNA methods to detect aquatic macroorganisms. Critical considerations for study design include preventing contamination in the field and the laboratory, choosing appropriate sample analysis methods, validating assays, testing for sample inhibition and following minimum reporting guidelines. Critical considerations for inference include temporal and spatial processes, limits of correlation of eDNA with abundance, uncertainty of positive and negative results, and potential sources of allochthonous DNA. We present a synthesis of knowledge at this stage for application of this new and powerful detection method.

634 citations

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TL;DR: An automated irrigation system developed to optimize water use for agricultural crops has the potential to be useful in water limited geographically isolated areas.
Abstract: An automated irrigation system was developed to optimize water use for agricultural crops. The system has a distributed wireless network of soil-moisture and temperature sensors placed in the root zone of the plants. In addition, a gateway unit handles sensor information, triggers actuators, and transmits data to a web application. An algorithm was developed with threshold values of temperature and soil moisture that was programmed into a microcontroller-based gateway to control water quantity. The system was powered by photovoltaic panels and had a duplex communication link based on a cellular-Internet interface that allowed for data inspection and irrigation scheduling to be programmed through a web page. The automated system was tested in a sage crop field for 136 days and water savings of up to 90% compared with traditional irrigation practices of the agricultural zone were achieved. Three replicas of the automated system have been used successfully in other places for 18 months. Because of its energy autonomy and low cost, the system has the potential to be useful in water limited geographically isolated areas.

591 citations

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TL;DR: A survey of recent IoT technologies, their current penetration in the agricultural sector, their potential value for future farmers and the challenges that IoT faces towards its propagation is presented.

524 citations

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TL;DR: The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences using the MapMan 'BIN' ontology, which is tailored for functional annotation of plant 'omics' data.
Abstract: Next-generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan ‘BIN’ ontology, which is tailored for functional annotation of plant ‘omics’ data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan-to-GO translation table to export results as GO terms. Mercator is available free of charge via http://mapman.gabipd.org/web/guest/app/Mercator.

479 citations

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TL;DR: The data demonstrate that Cd perturbs the DNA methylation status through the involvement of a specific methyltransferase, linked to nuclear chromatin reconfiguration likely to establish a new balance of expressed/repressed chromatin.
Abstract: In mammals, cadmium is widely considered as a non-genotoxic carcinogen acting through a methylation-dependent epigenetic mechanism. Here, the effects of Cd treatment on the DNA methylation patten are examined together with its effect on chromatin reconfiguration in Posidonia oceanica. DNA methylation level and pattern were analysed in actively growing organs, under short- (6 h) and long- (2 d or 4 d) term and low (10 mM) and high (50 mM) doses of Cd, through a Methylation-Sensitive Amplification Polymorphism technique and an immunocytological approach, respectively. The expression of one member of the CHROMOMETHYLASE (CMT) family, a DNA methyltransferase, was also assessed by qRT-PCR. Nuclear chromatin ultrastructure was investigated by transmission electron microscopy. Cd treatment induced a DNA hypermethylation, as well as an up-regulation of CMT, indicating that de novo methylation did indeed occur. Moreover, a high dose of Cd led to a progressive heterochromatinization of interphase nuclei and apoptotic figures were also observed after long-term treatment. The data demonstrate that Cd perturbs the DNA methylation status through the involvement of a specific methyltransferase. Such changes are linked to nuclear chromatin reconfiguration likely to establish a new balance of expressed/repressed chromatin. Overall, the data show an epigenetic basis to the mechanism underlying Cd toxicity in plants.

450 citations