Agro-morphological and structural diversity of rice germplasm revealed by SSR markers in Benin Republic.

BACKGROUND: In developing countries, rice is a staple food and cash crop for the people. In Benin Republic, paddy rice production has increased over time. Accordingly, local varieties were replaced by improved varieties, leading unfortunatley to a loss of the diversity of Beninese rice germplasm. METHODS AND RESULTS: The investigation focused on the structure and genetic diversity of 72 rice accessions collected throughout 22 villages using 13 quantitative traits and 17 SSR markers. The descriptive analysis of the 13 quantitative parameters showed a significant difference among the accessions, with a grouping in three clusters. Group I (16.66% of samples) was composed of accessions with long, wide and thick grains alongside with four controls TOG5681, TOG5307, Azucena and Moroberekan. Group II (7% of samples) contained accessions with late vegetative cycle. Group III contained most of the accessions (76.39% of the samples), including accessions such as the CG14 and Nipponbare control lines, and almost all the improved varieties. The molecular analysis revealed a significant diversity (mean number of alleles: 4.47 with polymorphism information content of 0.633). Population structure based on molecular markers showed three primary populations with a mixture of phenotypic groupings at ΔK, K = 3. CONCLUSION: This study showed that Beninese rice germplasm was divided into two structures: phenotypically similar cultivars but genotypically distinct (homonyms), and phenotypically different cultivars but genotypically similar (synonyms). Some local cultivars such Bagou19, Bagou20 and Koud44 can be used for large scale production due to their agronomics and molecular traits. The molecular structure obtained in this investigation might be used for future conservation and breeding programs.

Impact of Seed Origin and Genetic Drift of Improved Rice Variety IR841 in Benin.

BACKGROUND: Rice production is important for food security in Benin, with a national production largely dominated by the cultivation of the aromatic ecotype IR841, by far the most appreciated by Beninese consumers. However, to maintain agronomical qualities of a given cultivar, the origin and quality of seeds are mandatory and at the heart of the maintenance of yield and of market requests. Following this idea, the objective of the current study was thus to investigate the genetic purity of IR841 varieties collected from rice producers across 22 villages in Benin in relation to their agronomical performances. RESULTS: For this, agromorphological evaluation of 72 accessions based on 13 quantitative descriptors followed by genotyping with the Illumina Infinium rice 7 K SNP array of 9 accessions was carried out in the presence of 2 controls. Agromorphologic as well as genetic and phylogenetic analyses revealed two groups, the first one Okouta97, Koum47, Nana30, Man118, Ang1 and control sample IR841-2) was characterized by seed accessions provided by the formal seed system, while the second (Koum53, Tchaka41 and Koud46) comprising seeds from local markets or from previous harvests and showing a depression in agronomic performances. CONCLUSION: We showed that IR841 seed purity is mandatory for the completion of agronomical performance, and that the farmers' choice of seeds must be guided and informed to ensure sustainability and food security.

Characterization of rice farming systems, production constraints and determinants of adoption of improved varieties by smallholder farmers of the Republic of Benin.

The identification of technological and policy interventions allowing to improve the performance of Beninese rice systems is necessary to reduce the heavy dependence on rice imports. This study characterized the Beninese rice farming systems, identified the production constraints, and determinants of the adoption of improved varieties by farmers. Four hundred eighteen rice farm households were surveyed across 39 villages using participatory research tools and methods. Cluster analysis was used to classify the surveyed farm households and revealed four typologies of rice farming systems differentiated by 8 variables. These are, the intensive rice farming system (cluster 4; 33.7%), semi-intensive rice farming system (cluster 1; 31.8%), integrated rice-livestock farming system (cluster 3; 11.8%), and subsistence rice farming (cluster 2; 22.7%). The integrated rice-livestock farming system was the dominant type practiced in the northern Benin, while, it is the intensive rice farming system in the south. Fifteen production constraints across rice-growing areas were recorded. Our results suggest that to increase adoption of improved rice varieties, agricultural extension services should target landowners' farmers practicing off-season rice production, and having other sources of income. Initiatives to boost rice production in Benin should prioritize the establishment of formal agricultural credit and mechanization option policies.

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

BACKGROUND: 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, 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 rodent attacks and the surveyed farmers proposed 13 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 most of pesticides used by farmers for rice protection (prohibited pesticides or intended for the protection of other crops). 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 integrated pest management programmes which 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 which will encourage farmers to use ecofriendly pest management.

Genetic divergence in northern Benin sorghum (Sorghum bicolor L. Moench) landraces as revealed by agromorphological traits and selection of candidate genotypes.

Sorghum [Sorghum bicolor (L.) Moench] is an important staple food crop in northern Benin. In order to assess its diversity in Benin, 142 accessions of landraces collected from Northern Benin were grown in Central Benin and characterised using 10 qualitative and 14 quantitative agromorphological traits. High variability among both qualitative and quantitative traits was observed. Grain yield (0.72-10.57 tons/ha), panicle weight (15-215.95 g), days to 50% flowering (57-200 days), and plant height (153.27-636.5 cm) were among traits that exhibited broader variability. Correlations between quantitative traits were determined. Grain yield for instance exhibited highly positive association with panicle weight (r = 0.901, P = 0.000) and 100 seed weight (r = 0.247, P = 0.000). UPGMA cluster analysis classified the 142 accessions into 89 morphotypes. Based on multivariate analysis, twenty promising sorghum genotypes were selected. Among them, AT41, AT14, and AT29 showed early maturity (57 to 66 days to 50% flowering), high grain yields (4.85 to 7.85 tons/ha), and shorter plant height (153.27 to 180.37 cm). The results obtained will help enhancing sorghum production and diversity and developing new varieties that will be better adapted to the current soil and climate conditions in Benin.

Large-scale pattern of genetic differentiation within African rainforest trees: insights on the roles of ecological gradients and past climate changes on the evolution of Erythrophleum spp (Fabaceae).

BACKGROUND: The evolutionary events that have shaped biodiversity patterns in the African rainforests are still poorly documented. Past forest fragmentation and ecological gradients have been advocated as important drivers of genetic differentiation but their respective roles remain unclear. Using nuclear microsatellites (nSSRs) and chloroplast non-coding sequences (pDNA), we characterised the spatial genetic structure of Erythrophleum (Fabaceae) forest trees in West and Central Africa (Guinea Region, GR). This widespread genus displays a wide ecological amplitude and taxonomists recognize two forest tree species, E. ivorense and E. suaveolens, which are difficult to distinguish in the field and often confused. RESULTS: Bayesian-clustering applied on nSSRs of a blind sample of 648 specimens identified three major gene pools showing no or very limited introgression. They present parapatric distributions correlated to rainfall gradients and forest types. One gene pool is restricted to coastal evergreen forests and corresponds to E. ivorense; a second one is found in gallery forests from the dry forest zone of West Africa and North-West Cameroon and corresponds to West-African E. suaveolens; the third gene pool occurs in semi-evergreen forests and corresponds to Central African E. suaveolens. These gene pools have mostly unique pDNA haplotypes but they do not form reciprocally monophyletic clades. Nevertheless, pDNA molecular dating indicates that the divergence between E. ivorense and Central African E. suaveolens predates the Pleistocene. Further Bayesian-clustering applied within each major gene pool identified diffuse genetic discontinuities (minor gene pools displaying substantial introgression) at a latitude between 0 and 2°N in Central Africa for both species, and at a longitude between 5° and 8°E for E. ivorense. Moreover, we detected evidence of past population declines which are consistent with historical habitat fragmentation induced by Pleistocene climate changes. CONCLUSIONS: Overall, deep genetic differentiation (major gene pools) follows ecological gradients that may be at the origin of speciation, while diffuse differentiation (minor gene pools) are tentatively interpreted as the signature of past forest fragmentation induced by past climate changes.

Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2012 - 30 September 2012.

This article documents the addition of 83 microsatellite marker loci and 96 pairs of single-nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Bembidion lampros, Inimicus japonicus, Lymnaea stagnalis, Panopea abbreviata, Pentadesma butyracea, Sycoscapter hirticola and Thanatephorus cucumeris (anamorph: Rhizoctonia solani). These loci were cross-tested on the following species: Pentadesma grandifolia and Pentadesma reyndersii. This article also documents the addition of 96 sequencing primer pairs and 88 allele-specific primers or probes for Plutella xylostella.