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.

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.

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

The first completed, circular mitochondrial genome and the first draft, linear chloroplastic genome of the blue diatom (Simonsen 1974, ) 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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

De Novo Assemblies of Three Oryza glaberrima Accessions Provide First Insights about Pan-Genome of African Rices.

Oryza glaberrima is one of the two cultivated species of rice, and harbors various interesting agronomic traits, especially in biotic and abiotic resistance, compared with its Asian cousin O. sativa. A previous reference genome was published but newer studies highlighted some missing parts.

Fine mapping of RYMV3: a new resistance gene to Rice yellow mottle virus from Oryza glaberrima.

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.

LTRclassifier: A website for fast structural LTR retrotransposons classification in plants.

Automatic classification of LTR retrotransposons is a big challenge in the area of massive genomics. Many tools were developed to detect them but automatic classification is somehow challenging. Here we propose a simple approach, , based on recognition followed by analyses () to classify plant LTR retrotransposons in their respective superfamily, and () to provide automatically a basic functional annotation of these elements.

A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives.

We produced a unique large data set of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose, we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short-read assemblies using data from two crops for which an annotated reference genome was available, namely grapevine and sorghum.