Yves Vigouroux

• Institute of Research for Development

Pearl millet (Pennisetum glaucum) thrives in arid and nutrient-poor environments, establishing its role as a crucial cereal crop for food security in sub-Saharan Africa. Despite its remarkable adaptability, its yields remain below genetic potential, primarily due to limited water and nutrient availability. In this study, we conducted ionomic profil...

Transpiration efficiency (TE), the biomass produced per unit of water transpired, is a key trait for crop performance under limited water. As water becomes scarce, increasing TE would contribute to increase crop drought tolerance. This study is a first step to explore pearl millet genotypic variability for TE on a large and representative diversity...

Transpiration efficiency (TE), the biomass produced per unit of water transpired, is a key trait for crop performance under limited water. As water becomes scarce, increasing TE would contribute to increase crop drought tolerance. This study is a first step to explore pearl millet genotypic variability for TE on a large and representative diversity...

Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet’s early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Saheli...

Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet’s early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Saheli...

Societal Impact Statement Fonio ( Digitaria exilis —Kippist—Stapf) is a neglected cereal crop that plays a crucial role in the food and nutritional security of sub‐Saharan populations. Currently threatened with extinction in many countries, fonio, like other minor species, could help give insights into the history of African agriculture and provide...

The use of neglected and underutilized species (NUS) in agrosystems is a potential solution to the challenges arising from global change. These species could contribute to the equitable diversification of agricultural systems. Providing knowledge on their genetic diversity and fostering access to data and results is essential for the development of...

Effective approaches to study inversions taking advantage of high throughput sequencing have recently emerged. This has led to a renewed interest to study the role of inversions in adaptation. We used a population genomic approach to analyze 126 samples of an African cereal pearl millet. We identified 5 large candidate regions displaying a populati...

Genomic offset statistics predict the maladaptation of populations to rapid habitat alteration based on association of genotypes with environmental variation. Despite substantial evidence for empirical validity, genomic offset statistics have well-identified limitations, and lack a theory that would facilitate interpretations of predicted values. H...

Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet’s early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Saheli...

Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet’s early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Saheli...

Si l'agriculture mondiale est aujourd'hui dominée par trois céréales (blé, maïs, riz), plusieurs céréales ont accompagné le développement des premières sociétés agricoles dans les 10 000 dernières années. Dans les zones les plus sèches d'Afrique et d'Asie, ces sociétés agricoles se sont principalement reposées sur les millets, des plantes qui s'avè...

Speciation, Darwin's mystery of mysteries, is a continuous process that results in genomic divergence accompanied by the gradual increment of reproductive barriers between lineages. Since the beginning of research on the genetics of speciation, several questions have emerged such as: What are the genetic bases of incompatibilities? How many loci ar...

Humans have had a major influence on the dissemination of crops beyond their native range, thereby offering new hybridization opportunities. Characterizing admixed genomes with mosaic origins generates valuable insight into the adaptive history of crops and the impact on current varietial diversity. We applied the ELAI tool-an efficient local ances...

Pearl millet (Pennisetum glaucum (L.)) R. Br. syn. Cenchrus americanus (L.) Morrone) is an important crop in South Asia and sub-Saharan Africa which contributes to ensuring food security. Its genome has an estimated size of 1.76 Gb and displays a high level of repetitiveness above 80%. A first assembly was previously obtained for the Tift 23D2B1-P1...

We present here FrangiPANe, a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1 306 6...

Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet's early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Saheli...

Pearl millet (Pennisetum glaucum (L.)) R. Br. syn. Cenchrus americanus (L.) Morrone) is an important crop in South Asia and sub-Saharan Africa which contributes to ensure food security. Its genome has an estimated size of 1.76 Gb and displays a high level of repetitiveness above 80%. A first assembly was previously obtained for the Tift 23D2B1-P1-P...

Genomic offset statistics assess the maladaptation of populations to rapid habitat alteration based on association of genotypes with environmental variation. Despite substantial evidence for empirical validity, genomic offset statistics have well-identified limitations, and lack a theory that would facilitate interpretations of predicted values. He...

The FAO recently estimated that demand for food will increase by 70% by 2050. The challenge will not only be on increasing the food supply but also on improving its nutritional value under an accelerating rate of environmental and social changes. One solution would be the wider use of underutilized crops to diversify alimentation and develop sustai...

Seed and pollen dispersal contribute to gene flow and shape the genetic patterns of plants over fine spatial scales. We inferred fine‐scale spatial genetic structure (FSGS) and estimated realized dispersal distances in Phytelephas aequatorialis , a Neotropical dioecious large‐seeded palm. We aimed to explore how seed and pollen dispersal shape this...

Pearl millet is among the top three-cereal production in one of the most climate vulnerable regions, sub-Saharan Africa. Its Sahelian origin makes it adapted to grow in poor sandy soils under low soil water regimes. Pearl millet is thus considered today as one of the most interesting crops to face the global warming. Flowering time, a trait highly...

We present here FrangiPANe, a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5,290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1,306,...

Background Bulk segregant analysis (BSA) combined with next generation sequencing is a powerful tool to identify quantitative trait loci (QTL). The impact of the size of the study population and the percentage of extreme genotypes analysed have already been assessed. But a good comparison of statistical approaches designed to identify QTL regions u...

The rhizosheath, the layer of soil that adheres strongly to roots, influences water and nutrients acquisition. Pearl millet is a cereal crop that plays a major role for food security in arid regions of sub-Saharan Africa and India. We previously showed that root-adhering soil mass is a heritable trait in pearl millet and that it correlates with cha...

The assessment of population vulnerability under climate change is crucial for planning conservation as well as for ensuring food security. Coffea canephora is, in its native habitat, an understorey tree that is mainly distributed in the lowland rainforests of tropical Africa. Also known as Robusta, its commercial value constitutes a significant re...

Understanding vulnerabilities of plant populations to climate change could help preserve their biodiversity and reveal new elite parents for future breeding programs. To this end, landscape genomics is a useful approach for assessing putative adaptations to future climatic conditions, especially in long‐lived species such as trees. We conducted a p...

We assessed and optimized a capture protocol in 20 different species from 6 different plant genus using kits from 20,000 to 200,000 baits targeting from 300 to 32,000 genes. We evaluated both the effectiveness of the capture protocol and the fold enrichment in targeted sequences. We proposed a protocol with multiplexing up to 96 samples in a single...

Fungal communities associated with roots play a key role in nutrient uptake and in mitigating the abiotic and biotic stress of their host. In this study, we characterized the roots mycobiome of wild and cultivated pearl millet [ Pennisetum glaucum (L.) R. Br., synonym: Cenchrus americanus (L.) Morrone] in three agro-ecological areas of Senegal foll...

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources ¹ . So far, few chickpea ( Cicer arietinum ) germplasm accessions have been characterized at the genome sequence level ² . Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessio...

The rhizosheath, the layer of soil that adheres strongly to roots, influences water and nutrients acquisition. Pearl millet is a cereal crop that plays a major role for food security in arid regions of sub Saharan Africa and India. We previously showed that root-adhering soil mass is a heritable trait in pearl millet and that it correlates with cha...

De plus en plus de voix appellent à résoudre simultanément la crise du climat et celle de la biodiversité. Cela est justifié par de nombreux arguments. Ainsi, les mêmes mécanismes liés à la surexploitation des ressources et des écosystèmes par les sociétés humaines conduisent conjointement à ces deux crises. On peut donc probablement résoudre les d...

The Amazon basin holds the world’s largest freshwater fish diversity. Information on the intensity and timing of reproductive ecology of Amazonian fish are scant. We use a metabarcoding method by capture using a single probe to quantify species‐level ichthyoplankton dynamics. We sampled monthly for two years the Marañón and the Ucayali rivers in Pe...

The Amazon basin holds the world’s largest freshwater fish diversity. Information on the intensity and timing of reproductive ecology of Amazonian fish are scant. We use a metabarcoding method by capture using a single probe to quantify species‐level ichthyoplankton dynamics. We sampled monthly for two years the Marañón and the Ucayali rivers in Pe...

Trees are a traditional component of urban spaces where they provide ecosystem services critical to urban wellbeing. In the Tropics, urban trees' seed origins have rarely been characterized. Yet, understanding the social dynamics linked to tree planting is critical given their influence on the distribution of associated genetic diversity. This stud...

Trees are a traditional component of urban spaces where they provide ecosystem services critical to urban wellbeing. In the Tropics, urban trees’ seed origins have rarely been characterized. Yet, understanding the social dynamics linked to tree planting is critical given their influence on the distribution of associated genetic diversity. This stud...

Trees are a traditional component of urban spaces where they provide ecosystem services critical to urban wellbeing. In the Tropics, urban trees’ seed origins have rarely been characterized. Yet, understanding the social dynamics linked to tree planting is critical given their influence on the distribution of associated genetic diversity. This stud...

Background Pearl millet, a nutritious food for around 100 million people in Africa and India, displays extensive genetic diversity and a high degree of admixture with wild relatives. Two major morphotypes can be distinguished in Senegal: early-flowering Souna and late-flowering Sanio. Phenotypic variabilities related to flowering time play an impor...

Climate change is already affecting agro-ecosystems and threatening food security by reducing crop productivity and increasing harvest uncertainty. Mobilizing crop diversity could be an efficient way to mitigate its impact. We test this hypothesis in pearl millet, a nutritious staple cereal cultivated in arid and low-fertility soils in sub-Saharan...

Pearl millet is a key cereal for food security in arid and semi-arid regions but its yield is increasingly threatened by water stress. Physiological mechanisms relating to conservation of soil water or increased water use efficiency can alleviate that stress. Aquaporins (AQP) are water channels that mediate root water transport, thereby influencing...

Significance The emergence of noxious weeds poses a serious threat to agricultural production. Understanding their origin and evolution is therefore of major importance. Here we analyzed the intriguing case of teosinte, a wild relative of maize originating from Mexico that recently emerged as an invasive weed in maize fields in Europe. Patterns of...

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...

Cultivated diversity is considered an insurance against major climatic variability. However, since the 1980s, several studies have shown that climate variability and agricultural changes may already have locally eroded crop genetic diversity. We studied pearl millet diversity in Senegal through a comparison of pearl millet landraces collected 40 ye...

Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio i...

Pearl millet is a key cereal for food security in arid and semi-arid regions but its yield is increasingly threatened by water stress. Physiological mechanisms consisting in saving water or increasing water use efficiency can alleviate that stress. Aquaporins (AQP) are water channels contributing to plant hydraulic balance that are supposedly invol...

Background Pearl millet, a dietary food for around 100 million people in Africa and in India, has a large diversity due to an extensive genetic diversity combined with a high degree of admixture with wild relatives. In Senegal, two major morphotypes are distinguished: early-flowering and late-flowering millets. The phenotypic variabilities accordin...

Background: Pearl millet, a dietary food for around 100 million people in Africa and in India, has a large diversity due to an extensive genetic diversity combined with a high degree of admixture with wild relatives. In Senegal, two major morphotypes are distinguished: early-flowering and late-flowering millets. The phenotypic variabilities accordi...

Background: Pearl millet, a nutritious food for around 100 million people in Africa and India, displays extensive genetic diversity and a high degree of admixture with wild relatives. Two major morphotypes can be distinguished in Senegal: early-flowering Souna and late-flowering Sanio. Phenotypic variabilities related to flowering time play an impo...

Background: Pearl millet, a nutritious food for around 100 million people in Africa and India, displays extensive genetic diversity and a high degree of admixture with wild relatives. Two major morphotypes can be distinguished in Senegal: early-flowering Souna and late-flowering Sanio. Phenotypic variabilities related to flowering time play an impo...

Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet ( Digitaria exilis ) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we established high-quality genomic resources to facilitate fon...

A detailed understanding of the origins of domesticated species is important for many disciplines. Recent advances in this field have been made with the use of genome-wide polymorphisms and improved statistical methods. In this chapter, we review the most important developments of coalescent models for the inference of demographic history from geno...

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...

In plants, local adaptation across species range is frequent. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Genome scans are popular to uncover outlier loci potentially involved in the genetic architecture of local adaptation, however links between outliers and phenot...

Targeted-sequence capture coupled to high-throughput sequencing has become a powerful method for the study of genome-wide sequence variation. Using the available genome of C. canephora (estimated size of 710 Mb/haploid) as a reference, we designed probes for the 323 selected candidate genes (CGs) to capture their homeologs in 293 accessions of C. c...

Testing whether and how natural populations are adapted to their local environment and predicting their responses to future habitat alterations is of key importance in the face of climate change. This is particularly the case for coffee trees for which the pace of climate change could be too fast and drastic for adaptation of populations. Using the...

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 appli...

We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines sampled from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea...

While there has been progress in our understanding of the origin and history of agriculture in sub-Saharan Africa, a unified perspective is still lacking on where and how major crops were domesticated in the region. Here, we investigated the domestication of African yam (Dioscorea rotundata), a key crop in early African agriculture. Using whole-gen...

Experts discuss the challenges faced in agrobiodiversity and conservation, integrating disciplines that range from plant and biological sciences to economics and political science. Wide-ranging environmental phenomena—including climate change, extreme weather events, and soil and water availability—combine with such socioeconomic factors as food po...

Experts discuss the challenges faced in agrobiodiversity and conservation, integrating disciplines that range from plant and biological sciences to economics and political science. Wide-ranging environmental phenomena—including climate change, extreme weather events, and soil and water availability—combine with such socioeconomic factors as food po...

Local adaptation across species range is widespread. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Because elevation gradients display continuous environmental changes at a short geographical scale, they provide an exceptional opportunity to investigate these question...

Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and...

Abstract Objectives: Digitaria exilis Stapf (white fonio) is a staple crop in West Africa, mainly consumed during food shortage and highly associated to cultural events. The aim of this study was to test the transferability of microsatellite loci developed for D. exilis to other species of the genus Digitaria in order to further investigate the di...

Complete plastomes of 14 African yam species were reconstructed from whole genome sequencing. These plastomes sizes varied from 151,908 to 155,155 bp. We predicted 130 genes, including 18 duplicated genes located in the two inverted regions. Phylogenetic analysis obtained using the maximum likelihood procedure revealed that each species was distinc...

Comment, depuis plusieurs décennies, la recherche scientifique contribue-t-elle au développement des pays du Sud ? À travers plus de 100 succès emblématiques de la recherche en partenariat, cet ouvrage nous plonge au coeur des grandes questions de développement : oeuvrer pour des sociétés plus justes, lutter contre les maladies, faire face aux risq...

Agrobiodiversity supports agriculture globally and is used and stewarded worldwide by farming communities that possess traditional knowledge about their crops. This chapter takes an evolutionary ecological perspective on the ecology, use, and conservation of crops and proposes research objectives to advance the study of agrobiodiversity globally. I...

Agrobiodiversity results from the domestication and continued selection of crop and livestock species. Understanding the evolution and population dynamics of agrobiodiversity in terms of its genetic, reproductive, ecological, or anthropogenic dimensions, requires both long-term and contemporary perspectives. Population genetics can supply valuable...

Simposio de Pesquisa dos Cafés do Brasil, Vitória, BRA, 08-/10/2019 - 10/10/2019

Simposio de Pesquisa dos Cafés do Brasil, Vitória, BRA, 08-/10/2019 - 10/10/2019

Third generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities to better study biodiversity, phylogeography and population genetics. We developed a protocol for in-solution enrichment hybridization capture of long DNA fragments applicable to com...

Third generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities to better study biodiversity, phylogeography and population genetics. We developed a protocol for in-solution enrichment hybridization capture of long DNA fragments applicable to com...

Digitaria exilis is an important indigenous cereal in West Africa. The first fonio reference transcriptome was released and became a key tool for developing new molecular markers contributing to a better understanding of its genetic diversity. A total of 126 new putative primer pairs were successfully designed in 37,327 unigenes from the D. exilis...