Morpho-agronomic and molecular characterisation of Oryza glaberrima germplasm from Mali

In order to exploit the important agronomic traits that make Oryza glaberrima Steud suitable for harsh growing conditions, 79 Riz Africain du Mali (RAM) including four checks of known cultivated rice species (Oryza sativa and O. glaberrima) were used for both field evaluation over two seasons (2007 and 2008) and assessment of molecular diversity. The molecular characterization showed all the 37 SSR markers used amplified and were polymorphic. The average heterozygosity of the accessions were relatively higher (0.18) than some earlier studies. The population from Mopti and Gao had a higher genetic diversity than other populations. Clustering of individuals showed no clear pattern of grouping based on either location or growing condition; this is due to the higher gene flow (Nm = 7.83) that may occur between different growing condition within location. Moreover, populations from different locations were highly differentiated (fst = 0.06) as compared to populations from different growing conditions (fst = 0.03). The dendrogram based on populations from different growing conditions revealed more similarity among populations with relatively similar growing conditions. Accessions such as, RAM116, RAM100 and RAM122, performed better under drought with a grain weight advantage of 40, 16 and 6.7% respectively over the best performing check.Key words: Genetic diversity, SSR markers, drought tolerance, Oryza glaberrima

Molecular basis of African yam domestication: Analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes

Background: After cereals, root and tuber crops are the main source of starch in the human diet. Starch biosynthesis was certainly a significant target for selection during the domestication of these crops. But domestication of these root and tubers crops is also associated with gigantism of storage organs and changes of habitat. Results: We studied here, the molecular basis of domestication in African yam, Dioscorea rotundata. The genomic diversity in the cultivated species is roughly 30% less important than its wild relatives. Two percent of all the genes studied showed evidences of selection. Two genes associated with the earliest stages of starch biosynthesis and storage, the sucrose synthase 4 and the sucrose-phosphate synthase 1 showed evidence of selection. An adventitious root development gene, a SCARECROW-LIKE gene was also selected during yam domestication. Significant selection for genes associated with photosynthesis and phototropism were associated with wild to cultivated change of habitat. If the wild species grow as vines in the shade of their tree tutors, cultivated yam grows in full light in open fields. Conclusions: Major rewiring of aerial development and adaptation for efficient photosynthesis in full light characterized yam domestication. (Résumé d'auteur

Identification of novel major and minor QTLs associated with Xanthomonas oryzae pv. oryzae (African strains) resistance in rice (Oryza sativa L.)

Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of Bacterial Leaf Blight (BB), an emerging disease in rice in West-Africa which can induce up to 50 % of yield losses. So far, no specific resistance gene or QTL to African Xoo were mapped. The objectives of this study were to identify and map novels and specific resistance QTLs to African Xoo strains. The reference recombinant inbred lines (RIL) mapping population derived from the cross between IR64 and Azucena was used to investigate Xoo resistance. Resistance to African and Philippine Xoo strains representing different races was assessed on the RIL population under greenhouse conditions. Five major quantitative trait loci (QTL) for resistance against African Xoo were located on different chromosomes. Loci on chromosomes 1, 7, 9, 10 and 11 explained as much as 13 %, 37 %, 13 %, 11 % and 15 % of resistance variation, respectively. A major novel QTL located on chromosome 7 explained 37 % of the phenotypic variance to the African Xoo corresponding to race A3 whereas that on chromosome 11 is effective to all African races tested. Together with genes and QTLs for resistance to bacterial blight previously described, the QTLs described here were mapped onto the reference O. sativa subs japonica (var. Nipponbare) physical map. We characterized new resistance QTLs. While some co-localize with known resistance genes/QTLs to Asian strains, others are specific to African strains. We result with new information on genes and QTLs for resistance to bacterial blight that will be useful for controlling the disease

Assessment of genetic diversity among cultivated Pearl millet (Pennisetum glaucum, Poaceae) accessions from Benin, West Africa

UMR AGAP : équipe GE2popSimple sequence repeat (SSR) molecular markers were used for genetic diversity analysis and population structure of the cultivated Pearl millet in Benin, West Africa. In order to assess the level of genetic diversity, 14 polymorphic SSR markers were used to screen 114 accessions from different agro-ecological zones in Benin. SSR markers were found to reveal a total of 57 alleles with an average of 4.071 allele per locus. Genetic diversity index varied from 0.099 to 0.633 with an average of 0.405. The average observed heterozygosity was found to reach 0.425. The analysis of molecular variance showed no real differentiation between regions. Only 5% of genetic variation was observed between samples collected from north-eastern and north-western region. A high level of variation (95%) was observed among accessions. Moreover, both principal component analysis (PCA) and the dendrogram obtained from the genetic distance among accessions revealed the absence of any specific structuration of accessions from each region under study. Our results confirmed diversity among cultivated Pearl millet in Benin and such diversity is not clustering according to geographical patterns

Ecological origins of the African cultivated yam Dioscorea rotundata: a study from Benin in West Africa

Ecological origins of the African cultivated yam Dioscorea rotundata: a study from Benin in West Africa. PhD Days Université Paris-Su

Evidence of genomic regions under adaptive selection in Yam (Dioscorea spp)

Prix du meilleur poster Jeunes Chercheurs décerné par la Société Française de GénétiqueEvidence of genomic regions under adaptive selection in Yam (Dioscorea spp). DynaGeV 201

African yam domestication: analyses of selection pinpoint to starch, root and photosynthesis related genes

African yam domestication: analyses of selection pinpoint to starch, root and photosynthesis related genes. PhD days Université Paris-Sacla

Rice pests in the Republic of Benin: farmers’ perceptions, knowledge and management practices

International audienceBACKGROUND: Rice (Oryza spp) is one of the most consumed cereals in the Republic of Benin. However, rice production is threatened by various pests, which lead to important yield losses. For the development of integrated management strategies responding to the farmers’ realities, it is important to document their perceptions, knowledge, and management of rice pests. Surveys involving 418 rice farmers to 21 ethnic groups through 39 villages were performed using rural appraisal tools. RESULTS: Farmers perceived birds, specifically weavers as the most important rice pests. The surveyed farmers also identified the variegated grasshopper, Zonocerus variegatus L. and rice brown leaf spots (Curvularia lunata (Wakker) Boedijn) as the main pests in the northern region, while it is the pink stem borer, Sesamia calamistis Hampson and rice blast (Magnaporthe grisea (Hebert) Barr) in the southern region, and Z. variegatus and rice yellow mottle virus (genus Sobemovirus) in central Benin. The most important rice storage constraint was the rodent attacks and the surveyed farmers proposed thirteen key solutions to minimize constraints related to rice storage. Among various pest control methods recorded, farmers used mainly synthetic chemical pesticides. However, the Beninese National Pesticide Management Committee (CNGP) does not recommend for the rice protection (prohibited pesticides or intended for the protection of other crops) most of pesticides used by farmers. Farming experience, family size, region, and number of observed pests have significantly influenced farmers’ decision to use pesticides. CONCLUSION: The rice pests perceived by farmers as important vary significantly across regions. These results suggest that IPM programs that target rice pests accounting for these regional differences will be more effective. The identified variables that influence the use of pesticides must be taken in account in the development of strategies to encourage farmers to use eco-friendly pest management

On-farm management of rice diversity, varietal preference criteria, and farmers' perceptions of the African (Oryza glaberrima Steud.) versus Asian rice (Oryza sativa L.) in the Republic of Benin (West Africa): implications for breeding and conservation

International audienceRice (Oryza spp.) is an important food and cash crop in the Republic of Benin. However, despite its production increase during the recent years, the yield of cultivated varieties remains low, and the introduction of improved varieties threatens the rice diversity existing in the traditional agriculture. Therefore, documenting the on-farm management of rice diversity, farmers' varietal preferences, and their perceptions of the performance of cultivated varieties and species are important prerequisites for the development of on-site breeding and conservation programs. To fill these gaps in Benin, 418 rice farmers, belonging to 21 ethnic groups, were surveyed in 39 villages using participatory rural appraisal tools. Subject to synonymy, 30 improved varieties and 2 68 local varieties were registered and their folk nomenclature and taxonomy were documented. The north of Benin had the highest diversity of rice with the greatest number of traditional varieties, making this region the best place for an in situ conservation program. The number of rice varieties maintained per village varied from 1 to 15 (six on average). The foursquare analysis revealed that the improved variety IR 841 was by far the most popular variety. Most of NERICA varieties were abandoned in the south, while the north still host a wide range of local varieties. Twenty-one reasons explained varietal abandonment by farmers, varying according to geographic areas and ethnic groups. The seed system was both formal and informal in the study area. The participatory evaluation revealed the necessity to create and introduce tolerant/resistant rice varieties to drought and flooding stresses in Beninese agriculture that meet farmers' preferences. Our results showed that the north Benin would be the most suitable place for in situ conservation of local rice diversity