Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes

[EN] Brinjal (Solanum melongena), scarlet (S. aethiopicum) and gboma (S. macrocarpon) eggplants are three Old World domesticates. The genomic DNA of a collection of accessions belonging to the three cultivated species, along with a representation of various wild relatives, was characterized for the presence of single nucleotide polymorphisms (SNPs) using a genotype-by-sequencing approach. A total of 210 million useful reads were produced and were successfully aligned to the reference eggplant genome sequence. Out of the 75,399 polymorphic sites identified among the 76 entries in study, 12,859 were associated with coding sequence. A genetic relationships analysis, supported by the output of the FastSTRUCTURE software, identified four major sub-groups as present in the germplasm panel. The first of these clustered S. aethiopicum with its wild ancestor S. anguivi; the second, S. melongena, its wild progenitor S. insanum, and its relatives S. incanum, S. lichtensteinii and S. linneanum; the third, S. macrocarpon and its wild ancestor S. dasyphyllum; and the fourth, the New World species S. sisymbriifolium, S. torvum and S. elaeagnifolium. By applying a hierarchical FastSTRUCTURE analysis on partitioned data, it was also possible to resolve the ambiguous membership of the accessions of S. campylacanthum, S. violaceum, S. lidii, S. vespertilio and S. tomentsum, as well as to genetically differentiate the three species of New World Origin. A principal coordinates analysis performed both on the entire germplasm panel and also separately on the entries belonging to sub-groups revealed a clear separation among species, although not between each of the domesticates and their respective wild ancestors. There was no clear differentiation between either distinct cultivar groups or different geographical provenance. Adopting various approaches to analyze SNP variation provided support for interpretation of results. The genotyping-by-sequencing approach showed to be highly efficient for both quantifying genetic diversity and establishing genetic relationships among and within cultivated eggplants and their wild relatives. The relevance of these results to the evolution of eggplants, as well as to their genetic improvement, is discussed.This work has been funded in part by European Unions Horizon 2020 Research and Innovation Programme under grant agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and by Spanish Ministerio de Economia, Industria y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL2015-64755-R from MINECO/FEDER). Funding has also been received from the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives", which is supported by the Government of Norway. This last project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew and implemented in partnership with national and international gene banks and plant breeding institutes around the world. For further information see the project website:http://www.cwrdiversity.org/. Pietro Gramazio is grateful to Universitat Politecnica de Valencia for a pre-doctoral (Programa FPI de la UPV-Subprograma 1/2013 call) contract. Mariola Plazas is grateful to Spanish Ministerio de Economia, Industria y Competitividad for a post-doctoral grant within the Santiago Grisolia Programme (FCJI-2015-24835). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Acquadro, A.; Barchi, L.; Gramazio, P.; Portis, E.; Vilanova Navarro, S.; Comino, C.; Plazas Ávila, MDLO.... (2017). Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes. PLoS ONE. 12(7). https://doi.org/10.1371/journal.pone.0180774Se018077412

Prevalence and potential for aflatoxin contamination in groundnuts and peanut butter from farmers and traders in Nairobi and Nyanza provinces of Kenya

Objective: Most of the peanut butter marketed in Nairobi is processed in cottage industry and its aflatoxin contamination status has not been documented. This study was therefore conducted to determine the status of aflatoxin contamination in groundnuts and peanut butter in Nairobi and Nyanza. Methodology and results: Eighty two fresh samples comprising raw and roasted groundnuts and peanut butter were obtained from market outlets and cottage processors in Nairobi and Nyanza regions. The marketers and processors were asked for information on the source of groundnuts. The incidence of Aspergillus section Flavi was determined using standard laboratory methods. Defective nuts in raw groundnuts were determined by manual sorting. Aflatoxin analysis was done using competitive ELISA technique. Groundnuts in Nairobi were imported from Malawi while those Nyanza were grown in the region. The fungal species isolated from the samples were: Aspergillus flavus (L and S strains), A. parasiticus, A. niger, A. tamari, A. alliaceus, A. caeletus and Penicillium spp. The percentage of defective nuts among all unsorted groundnuts ranged from 0.0% to 26.3%. The mean percent defective nuts was higher for Nairobi samples than Nyanza. Aflatoxin levels in all samples ranged from 0 to 2377.1 μg/kg. The mean aflatoxin level was higher for raw samples from Nairobi than Nyanza. The source of groundnuts and defective nuts were positively associated with aflatoxin levels. Conclusions and application of findings: The source of groundnuts and presence of defective nuts were identified as the main factors influencing increased aflatoxin contamination in the cottage industry. Mechanisms for inspection and certification of imported groundnuts should be put in place accompanied by effective monitoring for compliance to set aflatoxins standards. All the market players should sort their groundnuts before selling or processing in order to reduce aflatoxin contamination of peanut butter. Key words: Aflatoxin, cottage industry, groundnut, peanut butter. J. Appl. Biosci. 201

Science, coloniality and “the great rationality divide” : How practices, places and persons are culturally attached to one another in science education

This article aims to analyze how science is discursively attached to certain parts of the world and certain "kinds of people," i.e., how scientific knowledge is culturally con- nected to the West and to whiteness. In focus is how the power technology of coloniality organizes scientific content in textbooks as well as how science students are met in the classroom. The empirical data consist of Swedish science textbooks. The analysis is guided by three questions: (1) if and how the colonial history of science is described in Swedish textbooks; (2) how history of science is described; (3) how the global South is represented. The analysis focuses on both what is said and what is unsaid, recurrent narratives, and cultural silences. To discuss how coloniality is organizing the idea of science eduation in terms of the science learner, previous studies are considered. The concepts of power/knowledge, epistemic violence, and coloniality are used to analyze how notions of scientific rationality and modernity are deeply entangled with a colonial way of seeing the world. The analysis shows that the colonial legacy of science and technology is not present in the textbooks. More evident is the talk about science as development. I claim that discourses on scientific development block out stories problematizing the violence done in the name of science. Furthermore, drawing on earlier classroom studies, I examine how the power of coloniality organize how students of color are met and taught, e.g., they are seen as in need of moral fostering rather than as scientific literate persons