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Sean Mayes - One of the best experts on this subject based on the ideXlab platform.

  • crop diversification through a wider use of underutilised Crops a strategy to ensure food and nutrition security in the face of climate change
    2019
    Co-Authors: Maysoun A Mustafa, Sean Mayes, Festo Massawe
    Abstract:

    Global dependence on only a few Crops for food and non-food uses is risky due to the multifaceted challenges that crop production faces. One such challenge is climate change and its effects on food production. Emerging evidence suggests that climate change will cause shifts in crop production areas and yield loss due to more unpredictable and hostile weather patterns. The shrinking list of Crops that feed the world, has also been attributed to reported reduced agricultural biodiversity and increased genetic uniformity for yield traits in crop plants. This could lead to crop vulnerability to the dangers of pests and diseases. Part of the solution to these problems lies with crop diversification through a wider use of underutilised and Minor Crops. Underutilised, Minor or neglected crop plants are plant species that are indigenous rather than adapted introductions, which often form a complex part of the culture and diets of the people who grow them. The wider use of underutilised Crops would increase agricultural biodiversity (genetic, species and ecosystem) to buffer against crop vulnerability to climate change, pests and diseases and would provide the quality of food and diverse food sources to address both food and nutritional security.

  • integrating genetic maps in bambara groundnut vigna subterranea l verdc and their syntenic relationships among closely related legumes
    BMC Genomics, 2017
    Co-Authors: Hui Hui Chai, Sean Mayes, Festo Massawe, Presidor Kendabie, N S Ahmad, Jaeyres Jani, Andrzej Kilian
    Abstract:

    Bambara groundnut [Vigna subterranea (L) Verdc.] is an indigenous legume crop grown mainly in subsistence and small-scale agriculture in sub-Saharan Africa for its nutritious seeds and its tolerance to drought and poor soils. Given that the lack of ex ante sequence is often a bottleneck in marker-assisted crop breeding for Minor and underutilised Crops, we demonstrate the use of limited genetic information and resources developed within species, but linked to the well characterised common bean (Phaseolus vulgaris) genome sequence and the partially annotated closely related species; adzuki bean (Vigna angularis) and mung bean (Vigna radiata). From these comparisons we identify conserved synteny blocks corresponding to the Linkage Groups (LGs) in bambara groundnut genetic maps and evaluate the potential to identify genes in conserved syntenic locations in a sequenced genome that underlie a QTL position in the underutilised crop genome. Two individual intraspecific linkage maps consisting of DArTseq markers were constructed in two bambara groundnut (2n = 2x = 22) segregating populations: 1) The genetic map of Population IA was derived from F2 lines (n = 263; IITA686 x Ankpa4) and covered 1,395.2 cM across 11 linkage groups; 2) The genetic map of Population TD was derived from F3 lines (n = 71; Tiga Nicuru x DipC) and covered 1,376.7 cM across 11 linkage groups. A total of 96 DArTseq markers from an initial pool of 142 pre-selected common markers were used. These were not only polymorphic in both populations but also each marker could be located using the unique sequence tag (at selected stringency) onto the common bean, adzuki bean and mung bean genomes, thus allowing the sequenced genomes to be used as an initial ‘pseudo’ physical map for bambara groundnut. A good correspondence was observed at the macro synteny level, particularly to the common bean genome. A test using the QTL location of an agronomic trait in one of the bambara groundnut maps allowed the corresponding flanking positions to be identified in common bean, mung bean and adzuki bean, demonstrating the possibility of identifying potential candidate genes underlying traits of interest through the conserved syntenic physical location of QTL in the well annotated genomes of closely related species. The approach of adding pre-selected common markers in both populations before genetic map construction has provided a translational framework for potential identification of candidate genes underlying a QTL of trait of interest in bambara groundnut by linking the positions of known genetic effects within the underutilised species to the physical maps of other well-annotated legume species, without the need for an existing whole genome sequence of the study species. Identifying the conserved synteny between underutilised species without complete genome sequences and the genomes of major Crops and model species with genetic and trait data is an important step in the translation of resources and information from major crop and model species into the Minor crop species. Such Minor Crops will be required to play an important role in future agriculture under the effects of climate change.

Jaehan Shim - One of the best experts on this subject based on the ideXlab platform.

  • determination of spinetoram and its metabolites in amaranth and parsley using quechers based extraction and liquid chromatography tandem mass spectrometry
    Food Chemistry, 2012
    Co-Authors: Ki Hun Park, Jonghyouk Park, A Abd M Elaty, Jeongheui Choi, Bo Mi Kim, Soonkil Cho, Angel Yang, Md Musfiqur Rahman, Jaehan Shim
    Abstract:

    In this study, a simultaneous method was developed for the determination of spinetoram (XDE-175-J and XDE-175-L) and its demethyl metabolites (N-demethyl-175-J and N-demethyl-175-L) and formyl metabolites (N-formyl-175-J and N-formyl-175-L) in the Minor Crops; amaranth and parsley. The method uses quick, easy, cheap, effective, rugged, and safe (QuEChERS)-based extraction. Afterwards, the analytes were quantified and confirmed via liquid chromatography-electrospray ionisation tandem mass spectrometry (LC-ESI-MS/MS) in the positive ion mode using multiple reaction monitoring (MRM). Calibration curves were linear over the calibration ranges for all the analytes tested with r(2)>0.993. Limits of detection and quantitation were 0.01 and 0.03 mg/kg for all the tested analytes in amaranth and parsley, respectively. Recovery values, at spiking levels 0.05 and 0.25 mg/kg, ranged from 71.0% to 115.2% with relative standard deviations <15%, except for N-formyl-175-J in both amaranth and parsley. This method was applied to field-incurred samples and was shown to provide an adequate sensitivity and performance for the simultaneous determination of spinetoram and metabolites. To the best of our knowledge, this is the first time spinetoram and its metabolites were quantified using LC-MS/MS in Minor Crops.

  • residual determination of clothianidin and its metabolites in three Minor Crops via tandem mass spectrometry
    Food Chemistry, 2012
    Co-Authors: Bo Mi Kim, A Abd M Elaty, Jeongheui Choi, Joonseong Park, Jaehan Shim
    Abstract:

    A determination method for clothianidin and its metabolites (MNG, TMG, TZMU, and TZNG) in crown daisy, sedum, and amaranth grown under greenhouse conditions has been developed. The target compounds were identified and quantitatively determined using liquid chromatography coupled to tandem mass spectrometry. The matrix-matched calibration curves, used for quantification of the field-incurred analyte residues, were linear with coefficients of determination (r 2 ) exceeding 0.99. The matrix effects ranged from � 61.4 ± 3.6 to 328.3 ± 26.9 in three different Crops. The limits of detection and quantitation were in the ranges of 0.01–0.04 and 0.04–0.16 mg/kg, respectively. The mean recoveries of the analytes ranged between 71.7% and 120.3%. The validated method developed herein was successively applied for the determination of clothianidin and its four metabolites in field-incurred samples. The parent compound, clothianidin, was identified as the main residue and the metabolite residues were variable in the treated crown daisy, sedum, and amaranth samples. 2011 Elsevier Ltd. All rights reserved.

  • an extrapolation from crop classifications based on pesticide residues trial data within vegetables in Minor Crops
    The Korean Journal of Pesticide Science, 2009
    Co-Authors: Jonghyouk Park, M I R Mamun, A Abd M Elaty, Jeongheui Choi, Jaehan Shim
    Abstract:

    An extrapolation of residue data of seven commonly used pesticides namely bifenthrin, chlorothalonil, cypermethrin, diazinon, fenvalerate, phenthoate and procymidone on a total of 22 Minor Crops has been carried out in an experimental field trial. The pesticides were applied to 11 leafy-, 5 root- and 6 stem-Crops grown in the experimental green-house and the Crops and plants were randomly collected at 1, 3, 5, 7 days after application. The average recoveries of applied pesticides were ranged from 72.0 to 117.0% in leafy Crops, from 81.3 to 105.0% in stem Crops and from 70.1 to 108.1 % in the root-Crops. Limits of detection (LODs) were 0.005-0.1 ㎎/㎏ in the leafy Crops and 0.001-0.005 ㎎/㎏ in both the stem & root Crops. Based on the results of residual dissipation pattern and their morphology, all Crops were classified into high and low residual groups. The results showed that it might be possible to extrapolate residual data of stem-Crops to root-Crops within the same group. Crops that have currently no registered pesticide for use, would be possible to use the pesticides which are already been registered for the similar Crops.

Patrick Roberts - One of the best experts on this subject based on the ideXlab platform.

  • stable isotopic reconstruction of dietary changes across late antiquity and the middle ages in tuscany
    Journal of Archaeological Science: Reports, 2020
    Co-Authors: Giulia Riccomi, Simona Minozzi, Jana Zech, Federico Cantini, Valentina Giuffra, Patrick Roberts
    Abstract:

    Abstract The transition from Late Antiquity to the Medieval period is considered one of the greatest periods of social, political, and economic upheaval in Europe, and has left its mark on the historical consciousness of people in this part of the world. Nevertheless, there remains considerable debate as to the degree to which the diets and economic status of different sections of society were impacted by this transition, with these so-called ‘Dark Ages’ often being uniformly considered as static and impoverished, particularly for populations along the Mediterranean rim. Such questions are especially important in central Italy, with its position at the former core of the Roman Empire leaving it most vulnerable to the major social and political shifts of the first millennium AD. However, direct insights into the diets of individuals in this region, across this key period, have been scarce, particularly in diachronic perspective. Here, we apply stable carbon (δ13C) and nitrogen (δ15N) analysis to bone collagen (n = 76), and stable carbon (δ13C) and oxygen (δ18O) isotope analysis to tooth enamel (n = 34), to human, and associated faunal, individuals dated to Late Antiquity (3rd–5th centuries AD) and the Medieval period (mid 6th–mid 13th centuries AD) in Tuscany. δ13C measurements of both tooth enamel bioapatite and bone collagen suggest that a predominantly C3 diet during Late Antiquity was gradually supplemented by increased C4 consumption during the Medieval period. We interpret this as a shift from an agricultural focus on wheat following the Roman agrarian tradition towards the inclusion of millet as a reliable fallback food. We argue that this was part of a growing local and regional resilience amongst communities in the Medieval period, with more diverse agricultural systems and cultural preferences following a transition from the Roman classical civilization toward a Germanic tradition whose economy was based on the diverse cultivation of “Minor Crops” and close integration of pastoral husbandry livestock.

Hui Hui Chai - One of the best experts on this subject based on the ideXlab platform.

  • integrating genetic maps in bambara groundnut vigna subterranea l verdc and their syntenic relationships among closely related legumes
    BMC Genomics, 2017
    Co-Authors: Hui Hui Chai, Sean Mayes, Festo Massawe, Presidor Kendabie, N S Ahmad, Jaeyres Jani, Andrzej Kilian
    Abstract:

    Bambara groundnut [Vigna subterranea (L) Verdc.] is an indigenous legume crop grown mainly in subsistence and small-scale agriculture in sub-Saharan Africa for its nutritious seeds and its tolerance to drought and poor soils. Given that the lack of ex ante sequence is often a bottleneck in marker-assisted crop breeding for Minor and underutilised Crops, we demonstrate the use of limited genetic information and resources developed within species, but linked to the well characterised common bean (Phaseolus vulgaris) genome sequence and the partially annotated closely related species; adzuki bean (Vigna angularis) and mung bean (Vigna radiata). From these comparisons we identify conserved synteny blocks corresponding to the Linkage Groups (LGs) in bambara groundnut genetic maps and evaluate the potential to identify genes in conserved syntenic locations in a sequenced genome that underlie a QTL position in the underutilised crop genome. Two individual intraspecific linkage maps consisting of DArTseq markers were constructed in two bambara groundnut (2n = 2x = 22) segregating populations: 1) The genetic map of Population IA was derived from F2 lines (n = 263; IITA686 x Ankpa4) and covered 1,395.2 cM across 11 linkage groups; 2) The genetic map of Population TD was derived from F3 lines (n = 71; Tiga Nicuru x DipC) and covered 1,376.7 cM across 11 linkage groups. A total of 96 DArTseq markers from an initial pool of 142 pre-selected common markers were used. These were not only polymorphic in both populations but also each marker could be located using the unique sequence tag (at selected stringency) onto the common bean, adzuki bean and mung bean genomes, thus allowing the sequenced genomes to be used as an initial ‘pseudo’ physical map for bambara groundnut. A good correspondence was observed at the macro synteny level, particularly to the common bean genome. A test using the QTL location of an agronomic trait in one of the bambara groundnut maps allowed the corresponding flanking positions to be identified in common bean, mung bean and adzuki bean, demonstrating the possibility of identifying potential candidate genes underlying traits of interest through the conserved syntenic physical location of QTL in the well annotated genomes of closely related species. The approach of adding pre-selected common markers in both populations before genetic map construction has provided a translational framework for potential identification of candidate genes underlying a QTL of trait of interest in bambara groundnut by linking the positions of known genetic effects within the underutilised species to the physical maps of other well-annotated legume species, without the need for an existing whole genome sequence of the study species. Identifying the conserved synteny between underutilised species without complete genome sequences and the genomes of major Crops and model species with genetic and trait data is an important step in the translation of resources and information from major crop and model species into the Minor crop species. Such Minor Crops will be required to play an important role in future agriculture under the effects of climate change.

Ryo Matsumoto - One of the best experts on this subject based on the ideXlab platform.

  • Non-destructive shoot biomass evaluation using a handheld NDVI sensor for field-grown staking Yam (Dioscorea rotundata Poir.)
    Taylor & Francis Group, 2019
    Co-Authors: Kohtaro Iseki, Ryo Matsumoto
    Abstract:

    Crop phenotyping is a key process used to accelerate breeding programs in the era of high-throughput genotyping. However, most rapid phenotyping methods developed to date have focused on major cereals or legumes, and their application to Minor Crops has been delayed. In this study, we developed a non-destructive method to predict shoot biomass by measuring spectral reflectance in staking yam (Dioscorea rotundata). The normalized difference vegetation index (NDVI) was evaluated using a handheld sensor that was vertically scanned from the top to the bottom of a plant alongside the stake. A linear regression model was constructed to predict shoot biomass through Bayesian analysis using NDVI as a parameter. The model well predicted the observed values of shoot biomass, irrespective of the growth stage and genotypes. Conversely, the model tended to underestimate the shoot biomass when the actual shoot biomass exceeded 150 g plant−1; this was compensated for when the parameter green area, calculated from plant image, was included in the model. This method reduced the time, cost, effort, and field space needed for shoot biomass evaluation compared with that needed for the sampling method, enabling shoot biomass phenotyping for a large population of plants. A total of 210 cross-populated plants were evaluated, and a correlation analysis was performed between the predicted shoot biomass and tuber yield. In addition to the prediction of tuber yield, this method could also be applied for the evaluation of crop models and stress tolerance, as well as for genetic analyses