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Francois Sabot - One of the best experts on this subject based on the ideXlab platform.
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Long‐fragment targeted capture for long‐read sequencing of plastomes
Wiley, 2019Co-Authors: Kevin Bethune, Cédric Mariac, Nora Scarcelli, Sylvain Santoni, Marie Couderc, Morgane Ardisson, Rommel Montúfar, Valentin Klein, Jean‐françois Martin, Francois SabotAbstract:Premise Third‐generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities for the study of biodiversity, phylogeography, and population genetics. We developed a protocol for in‐solution enrichment hybridization capture of long DNA fragments applicable to complete plastid genomes. Methods and Results The protocol uses cost‐effective in‐house probes developed via long‐range PCR and was used in six non‐model monocot species (Poaceae: African Rice, pearl millet, fonio; and three palm species). DNA was extracted from fresh and silica gel–dried leaves. Our protocol successfully captured long‐read plastome fragments (3151 bp median on average), with an enrichment rate ranging from 15% to 98%. DNA extracted from silica gel–dried leaves led to low‐quality plastome assemblies when compared to DNA extracted from fresh tissue. Conclusions Our protocol could also be generalized to capture long sequences from specific nuclear fragments
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Long-fragment targeted capture for long-read sequencing of plastomes
Applications in Plant Sciences, 2019Co-Authors: Kevin Bethune, Cédric Mariac, Nora Scarcelli, Sylvain Santoni, Marie Couderc, Morgane Ardisson, Jean-françois Martin, Rommel Montúfar, Valentin Klein, Francois SabotAbstract:Premise Third-generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities for the study of biodiversity, phylogeography, and population genetics. We developed a protocol for in-solution enrichment hybridization capture of long DNA fragments applicable to complete plastid genomes. Methods and Results The protocol uses cost-effective in-house probes developed via long-range PCR and was used in six non-model monocot species (Poaceae: African Rice, pearl millet, fonio; and three palm species). DNA was extracted from fresh and silica gel-dried leaves. Our protocol successfully captured long-read plastome fragments (3151 bp median on average), with an enrichment rate ranging from 15% to 98%. DNA extracted from silica gel-dried leaves led to low-quality plastome assemblies when compared to DNA extracted from fresh tissue. Conclusions Our protocol could also be generalized to capture long sequences from specific nuclear fragments.
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mir2118 triggered phased sirnas are differentially expressed during the panicle development of wild and domesticated African Rice species
Rice, 2016Co-Authors: K N Ta, Francois Sabot, Yves Vigouroux, Helene Adam, Alain Ghesquiere, S De Mita, Pascal Gantet, N V Do, Stefan JouannicAbstract:Background Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various Rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African Rice Oryza glaberrima and its wild relative Oryza barthii.
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mir2118 triggered phased sirnas are differentially expressed during the panicle development of wild and domesticated African Rice species
Rice, 2016Co-Authors: Francois Sabot, Yves Vigouroux, Helene Adam, Alain Ghesquiere, S De Mita, Pascal Gantet, Stefan JouannicAbstract:Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various Rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African Rice Oryza glaberrima and its wild relative Oryza barthii. Our RNA-seq analysis revealed a dramatic difference between the two species in the 21 nucleotide small RNA population, corresponding mainly to miR2118-triggered phased siRNAs. A detailed expression profiling during the panicle development of O. glaberrima and O. barthii using qRT-PCRs and in situ hybridization, confirmed a delayed expression of the phased siRNAs as well as their lncRNA precursors and regulators (miR2118 and MEL1 gene) in O. glaberrima compared to O. barthii. We provide evidence that the 21-nt phasiRNA pathway in Rice is associated with male-gametogenesis but is initiated in spikelet meristems. Differential expression of the miR2118-triggered 21-nt phasiRNA pathway between the two African Rice species reflects differential rates of determinate fate acquisition of panicle meristems between the two species.
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an extensive analysis of the African Rice genetic diversity through a global genotyping
Theoretical and Applied Genetics, 2014Co-Authors: Julie Orjuela, Francois Sabot, Sophie Cheron, Yves Vigouroux, Helene Adam, Harold Chrestin, Kayode Sanni, Mathias Lorieux, Alain GhesquiereAbstract:We present here the first curated collection of wild and cultivated African Rice species. For that, we designed specific SNPs and were able to structure these very low diverse species. Oryza glaberrima, the cultivated African Rice, is endemic from Africa. This species and its direct ancestor, O. barthii, are valuable tool for improvement of Asian Rice O. sativa in terms of abiotic and biotic stress resistance. However, only a few limited studies about the genetic diversity of these species were performed. In the present paper, and for the first time at such extend, we genotyped 279 O. glaberrima, selected both for their impact in current breeding and for their geographical distribution, and 101 O. barthii, chosen based on their geographic origin, using a set of 235 SNPs specifically designed for African Rice diversity. Using those data, we were able to structure the individuals from our sample in three populations for O. barthii, related to geography, and two populations in O. glaberrima; these two last populations cannot be linked however to any currently phenotyped trait. Moreover, we were also able to identify misclassification in O. glaberrima as well as in O. barthii and identified new form of O. sativa from the set of African varieties.
M N Ukwungwu - One of the best experts on this subject based on the ideXlab platform.
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population dynamics of the African Rice gall midge orseolia oryzivora diptera cecidomyiidae and its parasitoids in the forest and southern guinea savanna zones of nigeria
International Journal of Tropical Insect Science, 2009Co-Authors: E. O. Ogah, M N Ukwungwu, A A Omoloye, F E Nwilene, Tolulope A. AgunbiadeAbstract:The African Rice gall midge (AfRGM) Orseolia oryzivora Harris and Gagne is an important insect pest of Rice in Nigeria. Studies were conducted at Ogidiga (forest zone) and Edozhigi (southern Guinea savanna) in Nigeria, under rainfed lowland conditions during the 2006 and 2007 rainy seasons, on the population dynamics of AfRGM adults using light trap and random sampling of % tiller infestation (plant damage due to AfRGM) and % parasitism by Platygaster diplosisae Risbec and Aprostocetus procerae Risbec (parasitized larvae and pupae and parasitoid species present in dissected tillers). The results obtained showed that AfRGM populations were relatively low in June and July - the beginning of the 2006 and 2007 rainy seasons, respectively - and increased abruptly from September, reaching a peak in October at both locations. The increase was attributed to the rapid build-up of the pest populations at both locations. There were strong positive correlations between adult populations from light-trap catches and % tiller infestation, and between % tiller infestation and parasitism. The peak period of parasitism by P. diplosisae and A. procerae occurred towards the end of the rainy season in October, coinciding with high level of % tiller infestation. It is concluded that conservation of the parasitoids early in the cropping season (i.e. to improve their synchronization with the host) could become an effective management strategy against AfRGM.
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reactions of differential Rice genotypes to African Rice gall midge in west africa
International Journal of Pest Management, 2002Co-Authors: F. E. Nwilene, Abdoulaye Hamadoun, Dona Dakouo, C T Williams, M N Ukwungwu, O Okhidievbie, S Nacro, S I Kamara, F J Abamu, A AdamAbstract:Considerable diversity was observed in the reactions of 20 Rice genotypes to African Rice gall midge (AfRGM) at five locations in four countries in West Africa. Of 14 Oryza sativa lines studied, TOS14519 had the lowest mean plant damage; TOG7106 had the lowest mean damage among five O. glaberrima lines in the trials. The only O. sativa 2 O. glaberrima progeny in the study, WAB450-I-B-P-181-22-1- HB, showed mean damage comparable with the resistant check NHTA 8. The levels of resistance shown by the glaberrimas were better than those of the sativas. Eight genotypes could be described as possessing both stable and acceptable levels of resistance to the pest. TOG7106 and TOS14519 were rated highly stable and highly resistant. The high genotype 2 environment interaction in the reactions of the Rice lines to AfRGM could not be attributed to agroclimatic or crop management factors, leaving us to suggest the possible existence of different biotypes of AfRGM in West Africa.
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assessment of host plant resistance in oryza sativa to the African Rice gall midge orseolia oryzivora harris and gagne dipt cecidomyiidae with a description of a new method for screening under artificial infestation
Journal of Applied Entomology, 2001Co-Authors: C T Williams, M N Ukwungwu, B N Singh, O OkhidievbieAbstract:A new method is described for screening Rice germplasm for resistance to the African Rice gall midge (AfRGM), Orseolia oryzivora, year-round under conditions similar to a severe natural outbreak, using an AfRGM culture to start infestation in a tunnel screenhouse over an irrigated Rice field. During 1996 and 1997, 907 test entries of Oryza sativa were screened. Eighteen entries, 17 of which were traditional African lines, had infestation levels at least 50% below those on the partially resistant check variety NHTA 8 at 63-70 days after transplanting, though none showed very strong resistance. When traditional African lines and improved lines were screened together, the latter were on average markedly more susceptible. A field trial using caged plots indicated that even under no-choice conditions the varieties NHTA 8 and Eguazankpa maintained their partial resistance relative to the susceptible variety ITA 306. A comparison of the new screenhouse screening method with one using seedlings in insect cages suggested that the latter was less suitable for detecting partial resistance. An experiment in which NHTA 8 and ITA 306 were infested with one to four neonate AfRGM larvae per seedling showed that the difference in resistance between these varieties decreased with increasing infestation pressure. The potential role of partial resistance in the management of AfRGM, and methods for detecting it, are discussed.
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the host range annual cycle and parasitoids of the African Rice gall midge orseolia oryzivora diptera cecidomyiidae in central and southeast nigeria
Bulletin of Entomological Research, 1999Co-Authors: C T Williams, O Okhidievbie, K M Harris, M N UkwungwuAbstract:Host range experiments and field sampling in Nigeria produced no evidence that African Rice gall midge, Orseolia oryzivora Harris – Gagne, can develop on plants other than Oryza species. Sampling in three outbreak areas during 1994 showed that the insect's annual cycle varied according to the agroecological zone and Rice cropping pattern. In the humid forest zone, Orseolia oryzivora persisted through the short dry season on ratoons of cultivated Rice Oryza sativa at a rainfed site and on dry season Rice crops at an irrigated one. In contrast, at rainfed sites in the moist savannah zone the pest survived the longer dry season on the perennial wild Rice O. longistaminata , while ratoons and volunteers of O. sativa provided 'bridges' between the wild host and wet season Rice crops. Early in the wet season at rainfed sites, galls of Orseolia oryzivora were not found at high density on wild Rice, ratoons or volunteers. The heavy infestations which developed by October resulted primarily from rapid multiplication on Rice crops themselves during the wet season. At all 13 sites sampled, the large majority of galls were found on fallow or cropped Rice fields, rather than in ditches, bunds or uncultivated wetland, irrespective of the time of year or the hosts involved. From gall dissections, the parasitoids Aprostocetus procerae (Risbec) and Platygaster diplosisae Risbec caused over 30% mortality at some sites by October but generally increased too late to prevent crop damage. Implications of the results for the management of Orseolia oryzivora are discussed.
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farmer managed trials in south east nigeria to evaluate the Rice variety cisadane and estimate yield losses caused by the African Rice gall midge orseolia oryzivora harris gagne
International Journal of Pest Management, 1999Co-Authors: C T Williams, M N Ukwungwu, B N Singh, O Okhidievbie, J NnaboAbstract:Farmer-managed trials of the Rice variety Cisadane were undertaken at 47 rainfed lowland sites around Abakaliki, south-east Nigeria, a major outbreak area of the African Rice gall midge (ARGM). At each site a plot of Cisadane was grown alongside a control plot of the participating farmer's usual variety. On average the Cisadane yielded 26% higher than the controls but ARGM infestation levels on it were only slightly lower, suggesting thatithad greater tolerance to the pest butlittle antixenotic or antibiotic resistance. For all of 14 evaluation criteria, most participating farmers rated Cisadane as better than their control varieties. It appears to be a useful component for an ARGM management strategy. Regression analyses of yield on alternative variables for ARGM infestation derived from data recorded at 3, 7 or 11 w.a.t. (weeks after transplanting) showed that the log-transformed percent tiller infestation at 7 w.a.t. was the best predictor of yield. Variables for site topography, water level, fertilize...
C T Williams - One of the best experts on this subject based on the ideXlab platform.
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tolerance indicators and responses of Rice cultivars to infestation by the African Rice gall midge orseolia oryzivora
The Journal of Agricultural Science, 2002Co-Authors: A A Omoloye, C T Williams, Johnson A Odebiyi, B N SinghAbstract:The mechanisms and host plant responses that are indicative of tolerance to the African Rice gall midge, Orseolia oryzivora Harris & Gagne were investigated in four promising donor Rice cultivars, Cisadane, Bw 348-1, Tox 4093-17-1 and ITA 306 (local check), in a screen house at the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. Results indicated that Cisadane was tolerant to infestations on the basis of higher (P < 0.05) percentage seedling survival, production of significantly higher number of fertile tillers, productive panicles and significantly higher grain yield per infested plant than the control. Both single infestation at one larva per plant and adult infestation once at 14 days after seeding were positively correlated to higher fertile tiller production per infested plant (at 80 days after transplanting) and higher grain yield per infested plant at maturity. The grain yield per infested plant was significantly higher (P < 0.05) in the tolerant variety (Cisadane) than in the control.
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reactions of differential Rice genotypes to African Rice gall midge in west africa
International Journal of Pest Management, 2002Co-Authors: F. E. Nwilene, Abdoulaye Hamadoun, Dona Dakouo, C T Williams, M N Ukwungwu, O Okhidievbie, S Nacro, S I Kamara, F J Abamu, A AdamAbstract:Considerable diversity was observed in the reactions of 20 Rice genotypes to African Rice gall midge (AfRGM) at five locations in four countries in West Africa. Of 14 Oryza sativa lines studied, TOS14519 had the lowest mean plant damage; TOG7106 had the lowest mean damage among five O. glaberrima lines in the trials. The only O. sativa 2 O. glaberrima progeny in the study, WAB450-I-B-P-181-22-1- HB, showed mean damage comparable with the resistant check NHTA 8. The levels of resistance shown by the glaberrimas were better than those of the sativas. Eight genotypes could be described as possessing both stable and acceptable levels of resistance to the pest. TOG7106 and TOS14519 were rated highly stable and highly resistant. The high genotype 2 environment interaction in the reactions of the Rice lines to AfRGM could not be attributed to agroclimatic or crop management factors, leaving us to suggest the possible existence of different biotypes of AfRGM in West Africa.
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assessment of host plant resistance in oryza sativa to the African Rice gall midge orseolia oryzivora harris and gagne dipt cecidomyiidae with a description of a new method for screening under artificial infestation
Journal of Applied Entomology, 2001Co-Authors: C T Williams, M N Ukwungwu, B N Singh, O OkhidievbieAbstract:A new method is described for screening Rice germplasm for resistance to the African Rice gall midge (AfRGM), Orseolia oryzivora, year-round under conditions similar to a severe natural outbreak, using an AfRGM culture to start infestation in a tunnel screenhouse over an irrigated Rice field. During 1996 and 1997, 907 test entries of Oryza sativa were screened. Eighteen entries, 17 of which were traditional African lines, had infestation levels at least 50% below those on the partially resistant check variety NHTA 8 at 63-70 days after transplanting, though none showed very strong resistance. When traditional African lines and improved lines were screened together, the latter were on average markedly more susceptible. A field trial using caged plots indicated that even under no-choice conditions the varieties NHTA 8 and Eguazankpa maintained their partial resistance relative to the susceptible variety ITA 306. A comparison of the new screenhouse screening method with one using seedlings in insect cages suggested that the latter was less suitable for detecting partial resistance. An experiment in which NHTA 8 and ITA 306 were infested with one to four neonate AfRGM larvae per seedling showed that the difference in resistance between these varieties decreased with increasing infestation pressure. The potential role of partial resistance in the management of AfRGM, and methods for detecting it, are discussed.
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the host range annual cycle and parasitoids of the African Rice gall midge orseolia oryzivora diptera cecidomyiidae in central and southeast nigeria
Bulletin of Entomological Research, 1999Co-Authors: C T Williams, O Okhidievbie, K M Harris, M N UkwungwuAbstract:Host range experiments and field sampling in Nigeria produced no evidence that African Rice gall midge, Orseolia oryzivora Harris – Gagne, can develop on plants other than Oryza species. Sampling in three outbreak areas during 1994 showed that the insect's annual cycle varied according to the agroecological zone and Rice cropping pattern. In the humid forest zone, Orseolia oryzivora persisted through the short dry season on ratoons of cultivated Rice Oryza sativa at a rainfed site and on dry season Rice crops at an irrigated one. In contrast, at rainfed sites in the moist savannah zone the pest survived the longer dry season on the perennial wild Rice O. longistaminata , while ratoons and volunteers of O. sativa provided 'bridges' between the wild host and wet season Rice crops. Early in the wet season at rainfed sites, galls of Orseolia oryzivora were not found at high density on wild Rice, ratoons or volunteers. The heavy infestations which developed by October resulted primarily from rapid multiplication on Rice crops themselves during the wet season. At all 13 sites sampled, the large majority of galls were found on fallow or cropped Rice fields, rather than in ditches, bunds or uncultivated wetland, irrespective of the time of year or the hosts involved. From gall dissections, the parasitoids Aprostocetus procerae (Risbec) and Platygaster diplosisae Risbec caused over 30% mortality at some sites by October but generally increased too late to prevent crop damage. Implications of the results for the management of Orseolia oryzivora are discussed.
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farmer managed trials in south east nigeria to evaluate the Rice variety cisadane and estimate yield losses caused by the African Rice gall midge orseolia oryzivora harris gagne
International Journal of Pest Management, 1999Co-Authors: C T Williams, M N Ukwungwu, B N Singh, O Okhidievbie, J NnaboAbstract:Farmer-managed trials of the Rice variety Cisadane were undertaken at 47 rainfed lowland sites around Abakaliki, south-east Nigeria, a major outbreak area of the African Rice gall midge (ARGM). At each site a plot of Cisadane was grown alongside a control plot of the participating farmer's usual variety. On average the Cisadane yielded 26% higher than the controls but ARGM infestation levels on it were only slightly lower, suggesting thatithad greater tolerance to the pest butlittle antixenotic or antibiotic resistance. For all of 14 evaluation criteria, most participating farmers rated Cisadane as better than their control varieties. It appears to be a useful component for an ARGM management strategy. Regression analyses of yield on alternative variables for ARGM infestation derived from data recorded at 3, 7 or 11 w.a.t. (weeks after transplanting) showed that the log-transformed percent tiller infestation at 7 w.a.t. was the best predictor of yield. Variables for site topography, water level, fertilize...
Matty Demont - One of the best experts on this subject based on the ideXlab platform.
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how can west African Rice compete in urban markets a demand perspective for policymakers
EuroChoices, 2018Co-Authors: Rose Fiamohe, Matty Demont, Kazuki Saito, Harold Roymacauley, Eric TollensAbstract:In West Africa, Rice produced locally falls short of meeting the demand and preferences of urban consumers. We analyzed the challenges facing local Rice in urban markets and identified policies that can be implemented to improve the competitiveness of the regional Rice sector. We argue that without addressing the demand side of the value chain, efforts on the supply side might fall short in reducing import dependency. Evidence suggests that while imported Rice has easy access to urban markets, local Rice faces more challenges in reaching urban consumers. The low market share of local Rice in urban markets is in part due to consumers’ dislike of local Rice as it is perceived as being of inferior quality relative to imported Rice. Local Rice also tends to fetch lower pRices. The experimental studies reviewed suggest, however, that urban consumers are willing to pay pRice premiums for local Rice if its quality is upgraded. We propose a two‐stage policy sequence: (i) encouraging investment in quality upgrading; (ii) gradually increasing the Common External Tariff (CET) from 10 to 35 per cent to increase cost‐competitiveness of West African Rice relative to imported Rice. To stabilise and finance the sector, we further advocate the establishment of a flat‐rate levy on the value of Rice imports. En Afrique de l'Ouest, le riz produit localement ne repond pas a la demande et aux preferences des consommateurs urbains. Nous avons analyse les defis auxquels fait face le riz local sur les marches urbains et identifie les politiques qui peuvent etre mises en œuvre pour ameliorer la competitivite du secteur rizicole regional. Nous soutenons que, sans aborder les questions de demande dans la chaine de valeur, les efforts du cote de l'offre pourraient ne pas aboutir a une reduction de la dependance vis‐a‐vis des importations. Les donnees suggerent que si le riz importe accede facilement aux marches urbains, le riz local a plus de difficultes a atteindre les consommateurs urbains. La faible part de marche du riz local sur les marches urbains est en partie due au fait qu'il deplait aux consommateurs car il est percu comme etant de qualite inferieure a celle du riz importe. Le riz local tend egalement a etre moins cher. Les etudes experimentales examinees suggerent cependant que les consommateurs urbains sont prets a payer des prix superieurs pour le riz local si sa qualite est amelioree. Nous proposons des politiques mises en œuvre en deux etapes : (i) encourager l'investissement dans l'amelioration de la qualite; (ii) augmenter progressivement le tarif exterieur commun (TEC) de 10 a 35 pour cent pour accroitre la competitivite‐cout du riz ouest‐africain par rapport au riz importe. Pour stabiliser et financer le secteur, nous preconisons en outre l’etablissement d'un prelevement forfaitaire sur la valeur des importations de riz. In Westafrika deckt der lokal produzierte Reis weder die Nachfrage noch die Vorlieben der stadtischen Konsumenten. Wir untersuchen die Grunde hierfur und identifizieren mogliche Politiken, die zu einer Verbesserung der Wettbewerbsfahigkeit des heimischen Reissektors beitragen konnen. Unserer Einschatzung nach sind alle Anstrengungen auf der Angebotsseite zur Reduzierung von Importabhangigkeiten umsonst, sofern die Nachfrageseite der Wertschopfungskette nicht berucksichtigt wird. Es gibt Anhaltspunkte dafur, dass importierter Reis im Vergleich zu lokal produziertem Reis einen einfachen Zugang zu stadtischen Markten hat. Der derart niedrige Marktanteil des lokal produzierten Reises auf stadtischen Markten ist zum Teil darauf zuruckzufuhren, dass die Konsumenten mit diesem eine schlechtere Qualitat verbinden. Zudem sind die erzielten Preise fur heimischen Reis geringer. Experimentelle Studien zeigen jedoch, dass stadtische Konsumenten bereit waren, hohere Preise fur lokal produzierten Reis zu zahlen, sofern dieser eine bessere Qualitat hatte. Wir schlagen eine zweistufige Abfolge von politischen Masnahmen vor: (1) Forderung von Investitionen in die Verbesserung der Qualitat. (2) Eine schrittweise Erhohung des gemeinsamen Ausenzolltarifs von 10 auf 35%, um die Kostenwettbewerbsfahigkeit von westafrikanischem Reis gegenuber importiertem Reis zu verbessern. Des Weiteren pladieren wir zur Stabilisierung und Finanzierung des Sektors fur die Erhebung einer pauschalen Abgabe auf den Wert von Reisimporten.
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comparative advantage in demand and the development of Rice value chains in west africa
World Development, 2017Co-Authors: Matty Demont, Rose Fiamohe, Thierry A KinkpeAbstract:Summary National Rice development strategies in Africa are often supply-focused and implicitly assume that consumers will readily substitute imported for domestic Rice. However, due to increasing import dependency, urban consumer preferences for Rice have become biased toward Asian export quality standards, against which African Rice has difficulties to compete. Anecdotal evidence suggests that this import bias is higher in cities close to the port and remote from the geographical centers of cultural heritage where African Rice was domesticated more than 3,000 years ago. We purposely select a sample of five West African urban markets which are supplied by both foreign and domestic Rice value chains and which are located at varying distances from the nearest ports and centers of cultural heritage, and conduct framed field experiments based on auctions to analyze the drivers of urban demand for domestic Rice with upgraded quality characteristics. We find that West African Rice has increasing difficulties competing against imported Rice on urban markets the more consumers appreciate characteristics of imported Asian Rice, the closer to the port, and the further the geographical and genealogical distance from Rice cultural heritage. These challenges provide crucial insights into value chain upgrading in policy makers’ struggle to achieve Rice self-sufficiency in West Africa. Our findings suggest that the optimal portfolio of investment in value chain upgrading is a function of the targeted end-market and its distance from the port and Rice cultural heritage. The closer the end-market is located toward the port, the more investment is needed in lifting demand of domestic Rice through quality upgrading, branding, and promotion to enable it to compete against imported Rice. Proximity to centers of cultural heritage, on the other hand, endows Rice value chains with a “comparative advantage in demand,” requiring less investment in demand-lifting and leaving more room for supply-shifting investments.
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reversing urban bias in African Rice markets a review of 19 national Rice development strategies
Global Food Security, 2013Co-Authors: Matty DemontAbstract:Abstract Economic development in poor countries is often hampered by urban bias. Partly as a result of historical urban bias, African countries have become heavily dependent on food imports with concomitant risks for food security as witnessed during the 2008 food crisis. African governments now recognize that they should reverse urban bias by investing in agriculture in order to decrease food import dependency. However, they typically focus primarily on supply-shifting investments that may be insufficient to render domestically produced food competitive, particularly in import-biased food markets. We review the national Rice development investment strategies of 19 African countries and argue that in order to reverse urban bias in African Rice markets, more resources will need to be allocated to value-adding and demand-lifting investments.
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reversing urban bias in African Rice markets evidence from senegal
World Development, 2013Co-Authors: Matty Demont, Pieter Rutsaert, Maimouna Ndour, Wim VerbekeAbstract:Summary. — Urban bias constitutes an important institutional impediment to economic development in poor countries. Some African governments now recognize that they should invest in agricultural productivity in order to reverse urban bias, but often forget the equally important objective of investing in quality tailored to consumers so as to reverse urban bias’ footprint on food markets. We conduct framed field experiments in two major urban markets in Senegal and find that the majority of urban consumers are willing to pay quality premiums for local Rice suggesting that investment in post-harvest Rice quality is a priority in the reversal of urban bias. 2012 Elsevier Ltd. All rights reserved.
Stefan Jouannic - One of the best experts on this subject based on the ideXlab platform.
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crispr mediated accelerated domestication of African Rice landraces
PLOS ONE, 2020Co-Authors: Elia Lacchini, Helene Adam, Stefan Jouannic, Edward Kiegle, Marco Castellani, Veronica Gregis, Martin M KaterAbstract:African Oryza glaberrima and Oryza sativa landraces are considered valuable resources for breeding traits due to their adaptation to local environmental and soil conditions. They often possess superior resistance to endemic pests and tolerance to drought and nutrient deficiencies when compared to the "imported" high production Asian Rice varieties. In contrast, "domestication traits" such as seed shattering, lodging, and seed yield are not well established in these African landraces. Therefore, the use of these African varieties for high production agriculture is limited by unpredictable yield and grain quality. We are addressing this shortcoming by developing protocols for genetically transforming African landraces to allow the use of CRISPR-Cas mediated breeding approaches. Here we use as proof of concept the cultivated African landrace Kabre to target selected known "domestication loci" and improve the agronomic potential of Kabre Rice. Stable genetic transformation with CRISPR-Cas9-based vectors generated single and simultaneous multiple gene knockouts. Plants with reduced stature to diminish lodging were generated by disrupting the HTD1 gene. Furthermore, three loci shown to control seed size and/or yield (GS3, GW2 and GN1A) were targeted using a multiplex CRISPR-Cas9 construct. This resulted in mutants with significantly improved seed yield. Our study provides an example of how new breeding technologies can accelerate the development of highly productive African landrace Rice varieties, an important advancement considering that Africa is a hotspot for worldwide population growth and therefore prone to food shortage.
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differences in meristem size and expression of branching genes are associated with variation in panicle phenotype in wild and domesticated African Rice
Evodevo, 2017Co-Authors: Helene Adam, Alain Ghesquiere, Pascal Gantet, Yannick M Staedler, Jurg Schonenberger, Thomas W R Harrop, James Tregear, Stefan JouannicAbstract:The African Rice Oryza glaberrima was domesticated from its wild relative Oryza barthii about 3000 years ago. During the domestication process, panicle complexity changed from a panicle with low complexity in O. barthii, to a highly branched panicle carrying more seeds in O. glaberrima. To understand the basis of this differential panicle development between the two species, we conducted morphological and molecular analyses of early panicle development. Using X-ray tomography, we analyzed the morphological basis of early developmental stages of panicle development. We uncovered evidence for a wider rachis meristem in O. glaberrima than in O. barthii. At the molecular level, spatial and temporal expression profiles of orthologs of O. sativa genes related to meristem activity and meristem fate control were obtained using in situ hybridization and qRT-PCR. Despite highly conserved spatial expression patterns between O. glaberrima and O. barthii, differences in the expression levels of these early acting genes were detected. The higher complexity of the O. glaberrima panicle compared to that of its wild relative O. barthii is associated with a wider rachis meristem and a modification of expression of branching-related genes. Our study indicates that the expression of genes in the miR156/miR529/SPL and TAW1 pathways, along with that of their target genes, is altered from the unbranched stage of development. This suggests that differences in panicle complexity between the two African Rice species result from early alterations to gene expression during reproductive development.
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mir2118 triggered phased sirnas are differentially expressed during the panicle development of wild and domesticated African Rice species
Rice, 2016Co-Authors: K N Ta, Francois Sabot, Yves Vigouroux, Helene Adam, Alain Ghesquiere, S De Mita, Pascal Gantet, N V Do, Stefan JouannicAbstract:Background Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various Rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African Rice Oryza glaberrima and its wild relative Oryza barthii.
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mir2118 triggered phased sirnas are differentially expressed during the panicle development of wild and domesticated African Rice species
Rice, 2016Co-Authors: Francois Sabot, Yves Vigouroux, Helene Adam, Alain Ghesquiere, S De Mita, Pascal Gantet, Stefan JouannicAbstract:Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various Rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African Rice Oryza glaberrima and its wild relative Oryza barthii. Our RNA-seq analysis revealed a dramatic difference between the two species in the 21 nucleotide small RNA population, corresponding mainly to miR2118-triggered phased siRNAs. A detailed expression profiling during the panicle development of O. glaberrima and O. barthii using qRT-PCRs and in situ hybridization, confirmed a delayed expression of the phased siRNAs as well as their lncRNA precursors and regulators (miR2118 and MEL1 gene) in O. glaberrima compared to O. barthii. We provide evidence that the 21-nt phasiRNA pathway in Rice is associated with male-gametogenesis but is initiated in spikelet meristems. Differential expression of the miR2118-triggered 21-nt phasiRNA pathway between the two African Rice species reflects differential rates of determinate fate acquisition of panicle meristems between the two species.