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.

Complete mitochondrial genome and draft chloroplastic genome of Haslea ostrearia (Simonsen 1974).

The first completed, circular mitochondrial genome and the first draft, linear chloroplastic genome of the blue diatom Haslea ostrearia (Simonsen 1974, Naviculaceae, Bacillariophyceae) were assembled from Illumina and PacBio sequencing. The mitochondrial genome was composed of 38,696 bases and contained 64 genes, including 31 protein-coding genes (CDS), 2 ribosomal RNA (rRNA) genes and 23 transfer RNA (tRNA) genes. For the chloroplast, the genome was composed of 130,200 bases with 169 genes (131 CDS, 6 rRNA genes, 31 tRNA genes, and 1 transfer messenger RNA gene). Phylogenetic trees, using the maximum-likehood method and partial genes currently available for Haslea ostrearia and other diatom species, suggested the proximity of all the Haslea ostrearia strains/isolates and the possibility of using these genomes as future references.

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.

Genomic introgressions from African rice (Oryza glaberrima) in Asian rice (O. sativa) lead to the identification of key QTLs for panicle architecture.

BACKGROUND: Developing high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativa L.) and the African rice (O. glaberrima Steud.). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, with O. sativa displaying a highly branched panicle, which in turn produces a larger number of grains than that of O. glaberrima. The gene regulatory network that governs intra- and interspecific panicle diversity is still under-studied. RESULTS: To identify genetic factors linked to panicle architecture diversity in the two species, we used a set of 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC3DH) and carrying genomic segments from O. glaberrima cv. MG12 in the genetic background of O. sativa Tropical Japonica cv. Caiapó. Phenotypic data were collected for rachis and primary branch length, primary, secondary and tertiary branch number and spikelet number. A total of 15 QTLs were localized on chromosomes 1, 2, 3, 7, 11 and 12, QTLs associated with enhanced secondary and tertiary branch numbers were detected in two CSSLs. Furthermore, BC4F3:5 lines carrying different combinations of substituted segments were produced to decipher the effects of the identified QTL regions on variations in panicle architecture. A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand how O. glaberrima introgression events may lead to alterations in panicle traits. CONCLUSION: Our analysis led to the detection of genomic variations between O. sativa cv. Caiapó and O. glaberrima cv. MG12 in regions associated with enhanced panicle traits in specific CSSLs. These regions contain a number of key genes that regulate panicle development in O. sativa and their interspecific genomic variations may explain the phenotypic effects observed.

Chlorophyll fluorescence-based high-throughput phenotyping facilitates the genetic dissection of photosynthetic heat tolerance in African (Oryza glaberrima) and Asian (Oryza sativa) rice.

Rising temperatures and extreme heat events threaten rice production. Half of the global population relies on rice for basic nutrition, and therefore developing heat-tolerant rice is essential. During vegetative development, reduced photosynthetic rates can limit growth and the capacity to store soluble carbohydrates. The photosystem II (PSII) complex is a particularly heat-labile component of photosynthesis. We have developed a high-throughput chlorophyll fluorescence-based screen for photosynthetic heat tolerance capable of screening hundreds of plants daily. Through measuring the response of maximum PSII efficiency to increasing temperature, this platform generates data for modelling the PSII-temperature relationship in large populations in a small amount of time. Coefficients from these models (photosynthetic heat tolerance traits) demonstrated high heritabilities across African (Oryza glaberrima) and Asian (Oryza sativa, Bengal Assam Aus Panel) rice diversity sets, highlighting valuable genetic variation accessible for breeding. Genome-wide association studies were performed across both species for these traits, representing the first documented attempt to characterize the genetic basis of photosynthetic heat tolerance in any species to date. A total of 133 candidate genes were highlighted. These were significantly enriched with genes whose predicted roles suggested influence on PSII activity and the response to stress. We discuss the most promising candidates for improving photosynthetic heat tolerance in rice.

TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.

Transposable Element MOnitoring with LOng-reads (TrEMOLO) is a new software that combines assembly- and mapping-based approaches to robustly detect genetic elements called transposable elements (TEs). Using high- or low-quality genome assemblies, TrEMOLO can detect most TE insertions and deletions and estimate their allele frequency in populations. Benchmarking with simulated data revealed that TrEMOLO outperforms other state-of-the-art computational tools. TE detection and frequency estimation by TrEMOLO were validated using simulated and experimental datasets. Therefore, TrEMOLO is a comprehensive and suitable tool to accurately study TE dynamics. TrEMOLO is available under GNU GPL3.0 at https://github.com/DrosophilaGenomeEvolution/TrEMOLO .

Rapid evolution of an RNA virus to escape recognition by a rice nucleotide-binding and leucine-rich repeat domain immune receptor.

Viral diseases are a major limitation for crop production, and their control is crucial for sustainable food supply. We investigated by a combination of functional genetics and experimental evolution the resistance of rice to the rice yellow mottle virus (RYMV), which is among the most devastating rice pathogens in Africa, and the mechanisms underlying the extremely fast adaptation of the virus to its host. We found that the RYMV3 gene that protects rice against the virus codes for a nucleotide-binding and leucine-rich repeat domain immune receptor (NLRs) from the Mla-like clade of NLRs. RYMV3 detects the virus by forming a recognition complex with the viral coat protein (CP). The virus escapes efficiently from detection by mutations in its CP, some of which interfere with the formation of the recognition complex. This study establishes that NLRs also confer in monocotyledonous plants immunity to viruses, and reveals an unexpected functional diversity for NLRs of the Mla clade that were previously only known as fungal disease resistance proteins. In addition, it provides precise insight into the mechanisms by which viruses adapt to plant immunity and gives important knowledge for the development of sustainable resistance against viral diseases of cereals.

On the importance of metadata when sharing and opening data.

While data sharing increases, most open data are difficult to re-use or to identify due to the lack of related metada. In this editorial, I discussed about the importance of those metadata in the context of genomic, and why they are mandatory to ensure the success of data sharing.

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.

Ten simple rules for switching from face-to-face to remote conference: An opportunity to estimate the reduction in GHG emissions.

In 2020, the world faced the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic that drastically altered people's lives. Since then, many countries have been forced to suspend public gatherings, leading to many conference cancellations, postponements, or reorganizations. Switching from a face-to-face to a remote conference became inevitable and the ultimate solution to sustain scientific exchanges at the national and the international levels. The same year, as a committee, we were in charge of organizing the major French annual conference that covers all computational biology areas: The "Journées Ouvertes en Biologie, Informatique et Mathématiques" (JOBIM). Despite the health crisis, we succeeded in changing the conference format from face to face to remote in a very short amount of time. Here, we propose 10 simple rules based on this experience to modify a conference format in an optimized and cost-effective way. In addition to the suggested rules, we decided to emphasize an unexpected benefit of this situation: a significant reduction in greenhouse gas (GHG) emissions related to travel for scientific conference attendance. We believe that even once the SARS-CoV-2 crisis is over, we collectively will have an opportunity to think about the way we approach such scientific events over the longer term.

Panache: a web browser-based viewer for linearized pangenomes.

MOTIVATION: Pangenomics evolved since its first applications on bacteria, extending from the study of genes for a given population to the study of all of its sequences available. While multiple methods are being developed to construct pangenomes in eukaryotic species there is still a gap for efficient and user-friendly visualization tools. Emerging graph representations come with their own challenges, and linearity remains a suitable option for user-friendliness. RESULTS: We introduce Panache, a tool for the visualization and exploration of linear representations of gene-based and sequence-based pangenomes. It uses a layout similar to genome browsers to display presence absence variations and additional tracks along a linear axis with a pangenomics perspective. AVAILABILITY AND IMPLEMENTATION: Panache is available at github.com/SouthGreenPlatform/panache under the MIT License.

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.

Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima.

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 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. 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.

A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore.

Transposable elements (TEs) are the main components of genomes. However, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies. Here, we describe an efficient pipeline to accurately recover TE insertion (TEI) sites and sequences from long reads obtained by Oxford Nanopore Technology (ONT) sequencing. With this pipeline, we could precisely describe the landscapes of the most recent TEIs in wild-type strains of Drosophila melanogaster and Drosophila simulans. Their comparison suggests that this subset of TE sequences is more similar than previously thought in these two species. The chromosome assemblies obtained using this pipeline also allowed recovering piRNA cluster sequences, which was impossible using short-read sequencing. Finally, we used our pipeline to analyze ONT sequencing data from a D. melanogaster unstable line in which LTR transposition was derepressed for 73 successive generations. We could rely on single reads to identify new insertions with intact target site duplications. Moreover, the detailed analysis of TEIs in the wild-type strains and the unstable line did not support the trap model claiming that piRNA clusters are hotspots of TE insertions.

MooSciTIC: Training of trainers in West African research and higher education.

The MooSciTIC project is a capacity-building initiative targeting West African research scientists and higher education teachers. The project aimed to improve the self-reliance of researchers and upgrade research practices by providing on-site summer schools on trans-disciplinary topics such as scientific writing, communication, and integrity. Here, we explain how this program was designed and implemented and share the positive responses from our trainees, hoping to inspire similar initiatives.

Long-fragment targeted capture for long-read sequencing of plastomes.

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.

The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes.

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.

Evolutionary forces affecting synonymous variations in plant genomes.

Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic dataset based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that at synonymous positions, base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.