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Alain Ghesquiere - One of the best experts on this subject based on the ideXlab platform.
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genome wide association study pinpoints key agronomic qtls in african rice Oryza glaberrima
Rice, 2020Co-Authors: Philippe Cubry, Christine Tranchantdubreuil, Anneceline Thuillet, Helene Adam, Harold Chrestin, Alain Ghesquiere, Helene Pidon, Maria Holzinger, Honore Kam, Olivier FrancoisAbstract:African rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species. Using a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we found several association peaks, one of which co-localised with a well described gene in the Asian rice flowering pathway, OsGi, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting genomic regions and candidate genes. Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations. Our results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.
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genome wide association study pinpoints key agronomic qtls in african rice Oryza glaberrima
bioRxiv, 2020Co-Authors: Philippe Cubry, Christine Tranchantdubreuil, Anneceline Thuillet, Helene Adam, Harold Chrestin, Alain Ghesquiere, Helene Pidon, Maria Holzinger, Honore Kam, Olivier FrancoisAbstract:Background: African rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species. Results: Using a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we demonstrated that we could successfully retrieve known genes from the rice flowering pathway, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting QTLs and candidate genes (including Rymv1 for resistance and SP1, Ghd7.1, APO1 and OsMADS1 for panicle architecture). Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations. Conclusion: Our results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.
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genetic variation and population structure of Oryza glaberrima and development of a mini core collection using dartseq
Frontiers in Plant Science, 2017Co-Authors: Marie Noelle Ndjiondjop, Kassa Semagn, Arnaud Comlan Gouda, Sedjro Bienvenu Kpeki, Daniel Dro Tia, Mounirou Sow, Alphonse Goungoulou, Moussa Sie, Xavier Perrier, Alain GhesquiereAbstract:The sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection. Here, we studied the genetic variation and population structure of 2,179 Oryza glaberrima Steud. accessions conserved at the AfricaRice genebank using 27,560 DArTseq-based SNPs. Only 14% (3,834 of 27,560) of the SNPs were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other Oryza species. Genetic distance between pairs of accessions varied from 0.005 to 0.306, with 1.5% of the pairs nearly identical, 8.0% of the pairs similar, 78.1% of the pairs moderately distant, and 12.4% of the pairs very distant. The number of redundant accessions that contribute little or no new genetic variation to the O. glaberrima collection was very low. Using the maximum length sub-tree method, we propose a subset of 1,330 and 350 accessions to represent a core and mini-core collection, respectively. The core and mini-core sets accounted for ~61 and 16%, respectively, of the whole collection, and captured 97-99% of the SNP polymorphism and nearly all allele and genotype frequencies observed in the whole O. glaberrima collection available at the AfricaRice genebank. Cluster, principal component and model-based population structure analyses all divided the 2,179 accessions into five groups, based roughly on country of origin but less so on ecology. The first, third and fourth groups consisted of accessions primarily from Liberia, Nigeria, and Mali, respectively; the second group consisted primarily of accessions from Togo and Nigeria; and the fifth and smallest group was a mixture of accessions from multiple countries. Analysis of molecular variance showed between 10.8 and 28.9% of the variation among groups with the remaining 71.1-89.2% attributable to differences within groups.
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fine mapping of rymv3 a new resistance gene to rice yellow mottle virus from Oryza glaberrima
Theoretical and Applied Genetics, 2017Co-Authors: Helene Pidon, Francois Sabot, Alain Ghesquiere, Sophie Cheron, Souley Issaka, Eugenie Hebrard, Olufisayo Kolade, D SilueAbstract:A new resistance gene against Rice yellow mottle virus was identified and mapped in a 15-kb interval. The best candidate is a CC-NBS-LRR gene. Rice yellow mottle virus (RYMV) disease is a serious constraint to the cultivation of rice in Africa and selection for resistance is considered to be the most effective management strategy. The aim of this study was to characterize the resistance of Tog5307, a highly resistant accession belonging to the African cultivated rice species (Oryza glaberrima), that has none of the previously identified resistance genes to RYMV. The specificity of Tog5307 resistance was analyzed using 18 RYMV isolates. While three of them were able to infect Tog5307 very rapidly, resistance against the others was effective despite infection events attributed to resistance-breakdown or incomplete penetrance of the resistance. Segregation of resistance in an interspecific backcross population derived from a cross between Tog5307 and the susceptible Oryza sativa variety IR64 showed that resistance is dominant and is controlled by a single gene, named RYMV3. RYMV3 was mapped in an approximately 15-kb interval in which two candidate genes, coding for a putative transmembrane protein and a CC-NBS-LRR domain-containing protein, were annotated. Sequencing revealed non-synonymous polymorphisms between Tog5307 and the O. glaberrima susceptible accession CG14 in both candidate genes. An additional resistant O. glaberrima accession, Tog5672, was found to have the Tog5307 genotype for the CC-NBS-LRR gene but not for the putative transmembrane protein gene. Analysis of the cosegregation of Tog5672 resistance with the RYMV3 locus suggests that RYMV3 is also involved in Tog5672 resistance, thereby supporting the CC-NBS-LRR gene as the best candidate for RYMV3.
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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.
Marie Noelle Ndjiondjop - One of the best experts on this subject based on the ideXlab platform.
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genetics and genomics of african rice Oryza glaberrima steud domestication
Rice, 2021Co-Authors: Peterson W Wambugu, Marie Noelle Ndjiondjop, Robert J HenryAbstract:African rice (Oryza glaberrima Steud) is one of the two independently domesticated rice species, the other one being Asian rice (Oryza sativa L.). Despite major progress being made in understanding the evolutionary and domestication history of African rice, key outstanding issues remain controversial. There appears to be an underlying difficulty in identifying the domestication centre and number of times the crop has been domesticated. Advances in genomics have provided unprecedented opportunities for understanding the genetic architecture of domestication related traits. For most of the domestication traits, the underlying genes and mutations have been identified. Comparative analysis of domestication genes between Asian and African rice has revealed that the two species went through an independent but convergent evolution process. The genetic and developmental basis of some of the domestic traits are conserved not only between Asian and African rice but also with other domesticated crop species. Analysis of genome data and its interpretation is emerging as a major challenge facing studies of domestication in African rice as key studies continue giving contradictory findings and conclusions. Insights obtained on the domestication of this species are vital for guiding crop improvement efforts.
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advances in molecular genetics and genomics of african rice Oryza glaberrima steud
Plants (Basel Switzerland), 2019Co-Authors: Peterson W Wambugu, Marie Noelle Ndjiondjop, Robert J HenryAbstract:African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue giving conflicting conclusions and theories. However, the genomic resources of African rice appear to be under-utilized as there seems to be little evidence that these vast resources are being productively exploited for example in practical rice improvement programmes. Challenges in deploying African rice genetic resources in rice improvement and the genomics efforts made in addressing them are highlighted.
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the rise and fall of african rice cultivation revealed by analysis of 246 new genomes
Current Biology, 2018Co-Authors: Philippe Cubry, Marie Noelle Ndjiondjop, Nora Scarcelli, Christine Tranchantdubreuil, Anneceline Thuillet, Cecile Monat, Karine Labadie, C Cruaud, Stefan Engelen, Benedicte RhoneAbstract:Summary African rice (Oryza glaberrima) was domesticated independently from Asian rice. The geographical origin of its domestication remains elusive. Using 246 new whole-genome sequences, we inferred the cradle of its domestication to be in the Inner Niger Delta. Domestication was preceded by a sharp decline of most wild populations that started more than 10,000 years ago. The wild population collapse occurred during the drying of the Sahara. This finding supports the hypothesis that depletion of wild resources in the Sahara triggered African rice domestication. African rice cultivation strongly expanded 2,000 years ago. During the last 5 centuries, a sharp decline of its cultivation coincided with the introduction of Asian rice in Africa. A gene, PROG1, associated with an erect plant architecture phenotype, showed convergent selection in two rice cultivated species, Oryza glaberrima from Africa and Oryza sativa from Asia. In contrast, a shattering gene, SH5, showed selection signature during African rice domestication, but not during Asian rice domestication. Overall, our genomic data revealed a complex history of African rice domestication influenced by important climatic changes in the Saharan area, by the expansion of African agricultural society, and by recent replacement by another domesticated species.
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Oryza glaberrima Steud.
Compendium of Plant Genomes, 2018Co-Authors: Marie Noelle Ndjiondjop, Peterson W Wambugu, Jean Rodrigue Sangare, Bienvenu Kpeki, Karlin GnikouaAbstract:Oryza glaberrima is the African cultivated rice species, domesticated from its wild ancestor by farmers living in Inland Delta of Niger River. Several studies indicated that it has extremely narrow genetic diversity compared to both its wild progenitor, Oryza barthii and the Asian rice, Oryza sativa which can mainly be attributed to a severe domestication bottleneck. Despite its scarcity in farmer’s field due to its low yield potential, high shattering and lodging susceptibility, O. glaberrima is of great value not only to Africa but also globally. Perhaps its greatest contribution to regional and global food security is as a source of genes, as it possesses resistance/tolerance to various biotic and abiotic stresses. It also has unique starch-related traits which give it good cooking and eating properties. Advances in DNA sequencing have provided useful genomic resources for African rice, key among them being whole genome sequences. Genomic tools are enabling greater understanding of the useful functional diversity found in this species. These advances have potential of addressing some of the undesirable attributes found in this species which have led to its continued replacement by Asian rice. Development of new generation of rice varieties for African farmers will therefore require the adoption of advanced molecular breeding tools as these will allow efficient utilization of the wealth and resilience found in African rice in rice improvement.
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genetic variation and population structure of Oryza glaberrima and development of a mini core collection using dartseq
Frontiers in Plant Science, 2017Co-Authors: Marie Noelle Ndjiondjop, Kassa Semagn, Arnaud Comlan Gouda, Sedjro Bienvenu Kpeki, Daniel Dro Tia, Mounirou Sow, Alphonse Goungoulou, Moussa Sie, Xavier Perrier, Alain GhesquiereAbstract:The sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection. Here, we studied the genetic variation and population structure of 2,179 Oryza glaberrima Steud. accessions conserved at the AfricaRice genebank using 27,560 DArTseq-based SNPs. Only 14% (3,834 of 27,560) of the SNPs were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other Oryza species. Genetic distance between pairs of accessions varied from 0.005 to 0.306, with 1.5% of the pairs nearly identical, 8.0% of the pairs similar, 78.1% of the pairs moderately distant, and 12.4% of the pairs very distant. The number of redundant accessions that contribute little or no new genetic variation to the O. glaberrima collection was very low. Using the maximum length sub-tree method, we propose a subset of 1,330 and 350 accessions to represent a core and mini-core collection, respectively. The core and mini-core sets accounted for ~61 and 16%, respectively, of the whole collection, and captured 97-99% of the SNP polymorphism and nearly all allele and genotype frequencies observed in the whole O. glaberrima collection available at the AfricaRice genebank. Cluster, principal component and model-based population structure analyses all divided the 2,179 accessions into five groups, based roughly on country of origin but less so on ecology. The first, third and fourth groups consisted of accessions primarily from Liberia, Nigeria, and Mali, respectively; the second group consisted primarily of accessions from Togo and Nigeria; and the fifth and smallest group was a mixture of accessions from multiple countries. Analysis of molecular variance showed between 10.8 and 28.9% of the variation among groups with the remaining 71.1-89.2% attributable to differences within groups.
Stanley Lutts - One of the best experts on this subject based on the ideXlab platform.
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discriminating the impact of na and cl in the deleterious effects of salt stress on the african rice species Oryza glaberrima steud
Plant Growth Regulation, 2021Co-Authors: Willy Irakoze, Hermann Prodjinoto, Christophe Gandonou, Gilles Lepoint, Stanley LuttsAbstract:Salinity resistance of the African rice species (Oryza glaberrima) is poorly documented and the specific responses of the plant to Na+ and Cl− toxic ions remain unknown. Cultivars TOG5307 and TOG5949 were maintained for 15 days on iso-osmotic nutrient solutions containing 50 mM NaCl, or a combination of Cl− salts (Cl−-dominant) or Na+ salts (Na+-dominant). Plant water status, ion accumulation, gas exchange, fluorescence related parameters, carbon (δ13C) and nitrogen (δ15N) isotope ratios were analyzed. TOG5307 accumulated lower amounts of Na+ and Cl− in the shoot (1.63 and 1.49 µmol g−1 DW, respectively) than TOG 5949 (2.5 and 2.2 µmol g−1 DW). At 50 mM NaCl, TOG5307 also exhibited a higher net carbon assimilation rate (2.51 µmol CO2 m−2 s−1) than TOG5949 (1.51 µmol m−2 s−1) and a higher water use efficiency. Most recorded physiological parameters were affected by both Na+ and Cl−. The pattern of modification induced by both types of toxicities was similar in the two studied cultivars which thus mainly differ for the quantitative aspects of the response rather than for the qualitative nature of the response. NaCl was the most detrimental treatment, followed by Na+-dominant treatment while Cl−-treatment had the lowest effect. The two considered cultivars mainly differ for their response to the ionic component of salt stress but not for their osmotic behaviour. The impact of Na+ and Cl− on considered parameters are additive, except for mineral nutrition where synergistic interactions were recorded for Na+ and S accumulation.
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Discriminating the impact of Na^+ and Cl^− in the deleterious effects of salt stress on the African rice species (Oryza glaberrima Steud.)
Plant Growth Regulation, 2021Co-Authors: Hermann Prodjinoto, Willy Irakoze, Christophe Gandonou, Gilles Lepoint, Stanley LuttsAbstract:Salinity resistance of the African rice species ( Oryza glaberrima ) is poorly documented and the specific responses of the plant to Na^+ and Cl^− toxic ions remain unknown. Cultivars TOG5307 and TOG5949 were maintained for 15 days on iso-osmotic nutrient solutions containing 50 mM NaCl, or a combination of Cl^− salts (Cl^−-dominant) or Na^+ salts (Na^+-dominant). Plant water status, ion accumulation, gas exchange, fluorescence related parameters, carbon (δ^13C) and nitrogen (δ^15N) isotope ratios were analyzed. TOG5307 accumulated lower amounts of Na^+ and Cl^− in the shoot (1.63 and 1.49 µmol g^−1 DW, respectively) than TOG 5949 (2.5 and 2.2 µmol g^−1 DW). At 50 mM NaCl, TOG5307 also exhibited a higher net carbon assimilation rate (2.51 µmol CO_2 m^−2 s^−1) than TOG5949 (1.51 µmol m^−2 s^−1) and a higher water use efficiency. Most recorded physiological parameters were affected by both Na^+ and Cl^−. The pattern of modification induced by both types of toxicities was similar in the two studied cultivars which thus mainly differ for the quantitative aspects of the response rather than for the qualitative nature of the response. NaCl was the most detrimental treatment, followed by Na^+-dominant treatment while Cl^−-treatment had the lowest effect. The two considered cultivars mainly differ for their response to the ionic component of salt stress but not for their osmotic behaviour. The impact of Na^+ and Cl^− on considered parameters are additive, except for mineral nutrition where synergistic interactions were recorded for Na^+ and S accumulation.
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abscisic acid and oxidative stress implications in overall ferritin synthesis by african rice Oryza glaberrima steud seedlings exposed to short term iron toxicity
Plant and Soil, 2009Co-Authors: Valerie Majerus, Pierre Bertin, Stanley LuttsAbstract:Iron toxicity occurs under flooded conditions such as those prevailing in lowland rice fields and is due to an excess of ferrous ions. Ferritin is a multimeric protein responsible for Fe sequestration and storage, playing a key role in Fe homeostasis. Our aim was to study the modalities of overall ferritin synthesis in different organs of young seedlings from the African rice species (Oryza glaberrima) in relation to the putative involvement of abscisic acid (ABA) and oxidative stress in signalling processes. Seedlings from a moderately resistant to iron toxicity cultivar were grown in hydroponic culture for 2 weeks and treated with 500 mg l−1 Fe2+ in the presence or in the absence of 200 µM ABA, 50 µM methylviologen or 50 µM fluridone. Iron treatment increased iron and malondialdehyde concentration in all organs as well as ABA in roots and laminae. Although ferritin protein was detected in controls plants, iron treatment strongly reinforced its accumulation in sheaths and laminae after 24 h and 72 h. Ferritin mRNA was induced as early as 24 h after the beginning of the Fe-treatment in sheaths and, to a higher extent, in laminae. In the absence of iron treatment, exogenous ABA increased ferritin mRNA in laminae only but did not lead to further ferritin accumulation. Unexpectedly, it decreased ferritin mRNA levels in the sheaths of iron-treated plants and may thus have a dual influence depending on the considered organ. The inhibitor of ABA synthesis fluridone reduced endogenous ABA but did not compromise ferritin gene expression or ferritin synthesis, whatever the iron dose. Methyviologen application induced obvious oxidative damages but reduced ferritin synthesis. It is suggested that the signalling pathway leading to ferritin synthesis in the semi-aquatic African rice species may involve other components than those reported for typical terrestrial plants.
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effects of iron toxicity on osmotic potential osmolytes and polyamines concentrations in the african rice Oryza glaberrima steud
Plant Science, 2007Co-Authors: Valerie Majerus, Pierre Bertin, Stanley LuttsAbstract:The African rice species Oryza glaberrima is well adapted to iron toxicity frequently occurring under flooded conditions. Seedlings belonging to two cultivars differing in their level of resistance to iron stress (TOG 7105: resistant and IRGC 104047: sensitive) were grown in hydroponic culture for 2 weeks and treated with 0,250 and 500 mg 1(-1) Fe2+. Iron concentration in roots was higher in the resistant cv. TOG 7105 than in the sensitive cv. IRGC 104047, while an opposite trend was recorded in laminae, thus suggesting that iron exclusion could be an efficient mechanism of iron resistance. Osmotic potential in laminae decreased to a higher extent in cv. IRGC 104047 than in cv. TOG 7105. Proline and soluble sugars concentrations increased in the iron-sensitive cv. IRGC 104047 only and remained unaffected in the resistant one. Polyamine concentrations were always higher in cv. TOG 7105 than in cv. IRGC 104047, whatever the organ and the duration of treatment. Iron treatment stimulated ethylene biosynthesis to a higher extent in TOG 7105 than in IRGC 104047. These results are discussed in relation to the physiological strategies involved in iron stress resistance in African rice. (c) 2007 Elsevier Ireland Ltd. All rights reserved.
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organ dependent responses of the african rice to short term iron toxicity ferritin regulation and antioxidative responses
Biologia Plantarum, 2007Co-Authors: Valerie Majerus, Pierre Bertin, V Swenden, A Fortemps, S Lobreaux, Stanley LuttsAbstract:Hydroponically grown African rice (Oryza glaberrima) was exposed for 72 h to a high Fe2+ concentration (500 mg dm(-3)) to identify the first steps of iron toxicity response in various organs. Iron accumulated in all plant parts analysed and had only a limited impact on absorption and translocation of other nutrients. The content of the iron-storage protein ferritin increased as a consequence of transcription stimulation or increase in mRNA stability and culminated after 48 h of treatment in laminae and to a lesser extent in sheaths but was not detected in roots. Although endogenous iron concentrations were similar in sheaths and laminae, superoxide dismutase activity was stimulated only in sheaths while ascorbate peroxidase activity increased mainly in laminae. It is concluded that both ferritin synthesis and antioxidative response may play a key role in the resistance of Oryza glaberrima to iron toxicity but that their relative importance are not the same in all organs.
Paul Richards - One of the best experts on this subject based on the ideXlab platform.
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Evidence for the Emergence of New Rice Types of Interspecific Hybrid Origin in West African Farmers’
2016Co-Authors: Farmers Fields, Edwin Nuijten, Robbert Van Treuren, Bela Teeken, Paul Richards, Paul C. Struik, Louis Bolk Instituut, See ProfileAbstract:In West Africa two rice species (Oryza glaberrima Steud. and Oryza sativa L.) co-exist. Although originally it was thought that interspecific hybridization is impossible without biotechnological methods, progenies of hybridization appear to occur in farmer fields. AFLP analysis was used to assess genetic diversity in West Africa (including the countries The Gambia
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robustness and strategies of adaptation among farmer varieties of african rice Oryza glaberrima and asian rice Oryza sativa across west africa
PLOS ONE, 2013Co-Authors: Alfred Mokuwa, Edwin Nuijten, Florent Okry, Bela Teeken, Paul Richards, Harro Maat, P C StruikAbstract:This study offers evidence of the robustness of farmer rice varieties (Oryza glaberrima and O. sativa) in West Africa. Our experiments in five West African countries showed that farmer varieties were tolerant of sub-optimal conditions, but employed a range of strategies to cope with stress. Varieties belonging to the species Oryza glaberrima – solely the product of farmer agency – were the most successful in adapting to a range of adverse conditions. Some of the farmer selections from within the indica and japonica subspecies of O. sativa also performed well in a range of conditions, but other farmer selections from within these two subspecies were mainly limited to more specific niches. The results contradict the rather common belief that farmer varieties are only of local value. Farmer varieties should be considered by breeding programmes and used (alongside improved varieties) in dissemination projects for rural food security.
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Maintaining or Abandoning African Rice: Lessons for Understanding Processes of Seed Innovation
Human Ecology, 2012Co-Authors: Bela Teeken, Edwin Nuijten, Alfred Mokuwa, Florent Okry, Marina Padrão Temudo, Paul C. Struik, Paul RichardsAbstract:Rice breeding and crop research predominantly emphasize adaptation to ecological conditions. Based on qualitative and quantitative research conducted between 2000 and 2012 we show how ecological factors, combined with socioeconomic variables, cultural norms and values, shape the use and development of local technologies related to the cultivation of African rice ( Oryza glaberrima Steud.) in seven West African countries (Ghana, Guinea, Guinea-Bissau, Senegal, Sierra Leone, The Gambia and Togo). In this region the role of African rice is diverse across ethnic groups. Findings suggest that farmers, through various pathways, are active in the development of promising new varieties based on genetic resources of Asian rice, African rice, or both, as well as in the adoption of modern varieties. These findings require further research into interactions among ecological, genetic, socioeconomic and cultural factors within farmers’ innovation systems and recognition of emergent knowledge and technologies resulting from such interactions.
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evidence for the emergence of new rice types of interspecific hybrid origin in west african farmers fields
PLOS ONE, 2009Co-Authors: Edwin Nuijten, Robbert Van Treuren, P C Struik, Alfred Mokuwa, Florent Okry, Bela Teeken, Paul RichardsAbstract:In West Africa two rice species (Oryza glaberrima Steud. and Oryza sativa L.) co-exist. Although originally it was thought that interspecific hybridization is impossible without biotechnological methods, progenies of hybridization appear to occur in farmer fields. AFLP analysis was used to assess genetic diversity in West Africa (including the countries The Gambia, Senegal, Guinea Bissau, Guinea Conakry, Sierra Leone, Ghana and Togo) using 315 rice samples morphologically classified prior to analysis. We show evidence for farmer interspecific hybrids of African and Asian rice, resulting in a group of novel genotypes, and identify possible mechanisms for in-field hybridization. Spontaneous back-crossing events play a crucial role, resulting in different groups of genetic diversity in different regions developed by natural and cultural selection, often under adverse conditions. These new groups of genotypes may have potential relevance for exploitation by plant breeders. Future advances in crop development could be achieved through co-operation between scientists and marginalized farmer groups in order to address challenges of rapid adaptation in a world of increasing socio-political and climatic uncertainty.
Edwin Nuijten - One of the best experts on this subject based on the ideXlab platform.
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Evidence for the Emergence of New Rice Types of Interspecific Hybrid Origin in West African Farmers’
2016Co-Authors: Farmers Fields, Edwin Nuijten, Robbert Van Treuren, Bela Teeken, Paul Richards, Paul C. Struik, Louis Bolk Instituut, See ProfileAbstract:In West Africa two rice species (Oryza glaberrima Steud. and Oryza sativa L.) co-exist. Although originally it was thought that interspecific hybridization is impossible without biotechnological methods, progenies of hybridization appear to occur in farmer fields. AFLP analysis was used to assess genetic diversity in West Africa (including the countries The Gambia
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aroma chemistry of african Oryza glaberrima and Oryza sativa rice and their interspecific hybrids
Journal of the Science of Food and Agriculture, 2014Co-Authors: Sungeun Cho, Edwin Nuijten, Robert L Shewfelt, Stanley J KaysAbstract:BackgroundTo increase rice production in Africa, considerable research has focused on creating interspecific hybrids between African (Oryza glaberrima Steud.) and Asian (O. sativa L.) rice in an attempt to obtain the positive attributes of each in new cultivars. Since flavor is a key criterion in consumer acceptance of rice, as an initial inquiry we characterized and compared the aroma chemistry of selected cultivars of African O. sativa ssp. japonica, O. sativa ssp. indica, O. glaberrima, and their interspecific hybrids grown in West Africa, using gas chromatography-mass spectrometry, gas chromatography-olfactometry and descriptive sensory analysis. ResultsOf 41 volatiles identified across seven representative rice cultivars grown in West Africa, 3,5,5-trimethyl-2-cyclopenten-1-one, styrene, eucalyptol, linalool, myrtenal and l--terpineol had not been previously reported in rice. Thirty-three odor-active compounds were characterized. 4-Ethylphenol and (E,E)-2,4-heptadienal were unique to O. glaberrima, and pyridine, eucalyptol and myrtenal were described only in an interspecific hybrid. Descriptive sensory analysis indicated cooked grain', barny' and earthy' attributes were statistically different among the cultivars. ConclusionThe aroma chemistry data suggest that it should be possible to separate African cultivars into distinct flavor types thereby facilitating selection of new cultivars with superior flavor in African rice breeding programs. (c) 2013 Society of Chemical Industry
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robustness and strategies of adaptation among farmer varieties of african rice Oryza glaberrima and asian rice Oryza sativa across west africa
PLOS ONE, 2013Co-Authors: Alfred Mokuwa, Edwin Nuijten, Florent Okry, Bela Teeken, Paul Richards, Harro Maat, P C StruikAbstract:This study offers evidence of the robustness of farmer rice varieties (Oryza glaberrima and O. sativa) in West Africa. Our experiments in five West African countries showed that farmer varieties were tolerant of sub-optimal conditions, but employed a range of strategies to cope with stress. Varieties belonging to the species Oryza glaberrima – solely the product of farmer agency – were the most successful in adapting to a range of adverse conditions. Some of the farmer selections from within the indica and japonica subspecies of O. sativa also performed well in a range of conditions, but other farmer selections from within these two subspecies were mainly limited to more specific niches. The results contradict the rather common belief that farmer varieties are only of local value. Farmer varieties should be considered by breeding programmes and used (alongside improved varieties) in dissemination projects for rural food security.
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Maintaining or Abandoning African Rice: Lessons for Understanding Processes of Seed Innovation
Human Ecology, 2012Co-Authors: Bela Teeken, Edwin Nuijten, Alfred Mokuwa, Florent Okry, Marina Padrão Temudo, Paul C. Struik, Paul RichardsAbstract:Rice breeding and crop research predominantly emphasize adaptation to ecological conditions. Based on qualitative and quantitative research conducted between 2000 and 2012 we show how ecological factors, combined with socioeconomic variables, cultural norms and values, shape the use and development of local technologies related to the cultivation of African rice ( Oryza glaberrima Steud.) in seven West African countries (Ghana, Guinea, Guinea-Bissau, Senegal, Sierra Leone, The Gambia and Togo). In this region the role of African rice is diverse across ethnic groups. Findings suggest that farmers, through various pathways, are active in the development of promising new varieties based on genetic resources of Asian rice, African rice, or both, as well as in the adoption of modern varieties. These findings require further research into interactions among ecological, genetic, socioeconomic and cultural factors within farmers’ innovation systems and recognition of emergent knowledge and technologies resulting from such interactions.
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evidence for the emergence of new rice types of interspecific hybrid origin in west african farmers fields
PLOS ONE, 2009Co-Authors: Edwin Nuijten, Robbert Van Treuren, P C Struik, Alfred Mokuwa, Florent Okry, Bela Teeken, Paul RichardsAbstract:In West Africa two rice species (Oryza glaberrima Steud. and Oryza sativa L.) co-exist. Although originally it was thought that interspecific hybridization is impossible without biotechnological methods, progenies of hybridization appear to occur in farmer fields. AFLP analysis was used to assess genetic diversity in West Africa (including the countries The Gambia, Senegal, Guinea Bissau, Guinea Conakry, Sierra Leone, Ghana and Togo) using 315 rice samples morphologically classified prior to analysis. We show evidence for farmer interspecific hybrids of African and Asian rice, resulting in a group of novel genotypes, and identify possible mechanisms for in-field hybridization. Spontaneous back-crossing events play a crucial role, resulting in different groups of genetic diversity in different regions developed by natural and cultural selection, often under adverse conditions. These new groups of genotypes may have potential relevance for exploitation by plant breeders. Future advances in crop development could be achieved through co-operation between scientists and marginalized farmer groups in order to address challenges of rapid adaptation in a world of increasing socio-political and climatic uncertainty.