Philippe Cubry

Institut de Recherche pour le Développement

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Yves Vigouroux

Université de Montpellier

Olivier François

AZ Groeninge

Marie Couderc

Institut de Recherche pour le Développement

Anne‐Céline Thuillet

Institut de Recherche pour le Développement

François Sabot

Institut de Recherche pour le Développement

Cédric Mariac

Université de Montpellier

Ndjido Ardo Kane

Institut Sénégalais de Recherches Agricoles

Thierry Leroy

Centre de Coopération Internationale en Recherche Agronomique pour le Développement

Alain Ghesquière

Diversité, adaptation et développement des plantes

Christine Tranchant‐Dubreuil

Institut de Recherche pour le Développement

Cooperative Institutions

Centre de Coopération Internationale en Recherche Agronomique pour le Développement

136

Université de Montpellier

133

Agropolis International

116

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

101

Institut de Recherche pour le Développement

100

Institut Agro Montpellier

Diversité, adaptation et développement des plantes

Genetic Improvement and Adaptation of Mediterranean and Tropical Plants

Centre National de la Recherche Scientifique

International Crops Research Institute for the Semi-Arid Tropics

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Genomic evidence of genuine wild versus admixed olive populations evolving in the same natural environments in western Mediterranean Basin

PLoS ONE (2024)

Lison Zunino Philippe Cubry Gautier Sarah Pierre Mournet Ahmed El Bakkali

Crop-to-wild gene flow is a mechanism process widely documented, both in plants and animals. This can have positive or negative impacts on the evolution of admixed populations in natural environments, yet the phenomenon is still misunderstood in long-lived woody species, contrary to short-lived crops. Wild olive Olea europaea L. occurs in the same eco-geographical range as domesticated olive, i.e. the Mediterranean Basin (MB). Moreover, it is an allogamous and anemophilous species whose seeds are disseminated by birds, i.e. factors that drive gene flow between crops and their wild relatives. Here we investigated the genetic structure of western MB wild olive populations in natural environments assuming a homogenous gene pool with limited impact of cultivated alleles, as previously suggested. We used a target sequencing method based on annotated genes from the Farga reference genome to analyze 27 western MB olive tree populations sampled in natural environments in France, Spain and Morocco. We also target sequenced cultivated olive tree accessions from the Worldwide Olive Germplasm Bank of Marrakech and Porquerolles and from an eastern MB wild olive tree population. We combined PCA, sNMF, pairwise F ST and TreeMix and clearly identified genuine wild olive trees throughout their natural distribution range along a north-south gradient including, for the first time, in southern France. However, contrary to our assumption, we highlighted more admixed than genuine wild olive trees. Our results raise questions regarding the admixed population evolution pattern in this environment, which might be facilitated by crop-to-wild gene flow.

Mediterranean Basin

Olive trees

Germ plasm

Olea

Gene pool

10.1371/journal.pone.0295043

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Yam genomics supports West Africa as a major cradle of crop domestication

Zenodo (CERN European Organization for Nuclear Research) (2019)

Nora Scarcelli Philippe Cubry Roland Akakpo Anne‐Céline Thuillet Jude Obidiegwu

167 yam samples were fully resequenced (WGS, Illumina HiSeq) and mapped (BWA) to the Dioscorea rotundata genome (BDMI01000001.1 to BDMI01000021.1). Calling_ALL_Rotundata_Allc05.vcf.gz is the result of the SNP calling (GATK). See associated publication for details;

10.5281/zenodo.2540773

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Impact of past climatic and recent anthropogenic factors on wild yam genetic diversity

Molecular Ecology (2011)

Hâna Chaïr Pierre‐Olivier Duroy Philippe Cubry Brice Sinsin J. L. Pham

Forests of the Dahomey Gap are considered as refugia for many species. They play a crucial role in providing ecosystem services in an area devoid of forests. However, the impact of the way they are managed on the biodiversity they host has barely been investigated. Wild yams existing in these forests play a crucial role in maintaining the genetic diversity of cultivated yams. Indeed, studies of farmer practices have shown that, by way of ennoblement, wild yams collected and selected in the forests and old fallow areas are integrated into the cultivated pool. However, the genetic structure of wild yams is poorly understood. Using nine microsatellite loci, we investigated the population genetics of Dioscorea praehensilis in five forests in Benin, involving different management strategies and bioclimatic areas. Populations of D. praehensilis were strongly differentiated, consistent with an ancient separation of the forests. While the D. praehensilis population in a holly forest was undergoing mutation and drift equilibrium, the population collected from the most conserved forest was in a bottleneck. Moreover, in two forests with different management strategies, accessions from other forests were found, resulting from the displacement of yams following farmer migrations. No isolation by distance was detected, but a differentiation was found between populations of the Sudano-Guinean climate and the Guineo-Congolian climate. Our findings suggest differentiation due to forest isolations under past climatic conditions and more recent tuber flow through anthropogenic impacts.

10.1111/j.1365-294x.2011.05041.x

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Analyse de la diversité et évaluation du déséquilibre de liaison chez quelques populations naturelles et cultivées de caféiers Coffea canephora

Philippe Cubry

Le cafe Robusta, produit par Coffea canephora, represente environ 35% de la production mondiale de cafe. Dans le cadre de recherches visant a l'amelioration de la qualite a la tasse du cafe, la connaissance de la diversite genetique des populations naturelles et cultivees presente un interet important. Dans un premier temps, une etude de diversite a ete realisee a l'aide de 34 marqueurs SSR repartis sur l'ensemble du genome. Cette etude comprend des populations d'individus des grands groupes genetiques prealablement identifies ainsi que des populations sauvages et cultivees d'Afrique de l'Est jamais analysees pour leur diversite. Les resultats obtenus confirment la structuration en groupes decrite precedemment et indiquent l'originalite des populations d'Afrique de dans l'espece Coffea canephora. Ces populations pourraient constituer une variabilite genetique utilisable par les selectionneurs. Une evaluation du desequilibre de liaison pour des marqueurs entre lesquels la distance genetique est connue a ensuite ete menee pour 25 marqueurs microsatellites sur les populations analysees en diversite. Les resultats de cette etude pourront etre utilises pour les programmes d'amelioration des populations en cours et serviront de base a la definition de populations utilisables pour de futures etudes d'association. (Resume d'auteur)

Coffea canephora

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Simulated genetic data in a hierarchical metapopulation structure

Zenodo (CERN European Organization for Nuclear Research) (2021)

Philippe Cubry Sylvie Oddou‐Muratorio Ivan Scotti François Lefèvre

We simulated a hierarchical metapopulation structure with four populations, two environments per population and three patches per environment, in a two-step procedure: an initialization step without selection, with eight combinations of mutation type, selfing rate and QTL number parameters (2 modes each); out of 200,000 simulated generations in each case, we chose one with appropriate characteristics as a starting point for the next step; a selection step with all possible combinations of the following parameters: environmental pattern (4 modes), environmental range (5 modes), selection intensity (4 modes), fecundity (3 modes). This resulted in 240 scenarios for each initialized metapopulation, i.e. 1,920 scenarios in total. Each scenario was replicated 10 times, i.e. 19,200 simulation runs. The archive includes all data needed to reproduce the simulations and analyses, or to re-use the simulated metapopulations for other analyses. It has the following structure (further detailed below): NemoScripts directory contains the Nemo input files used to perform simulations for the initialization step and the selection step; RScripts directory contains the R scripts to read the Nemo output files, compute synthetic variables(*), and produce the figures as they appear in the publication and supplementary material (*: long computations, therefore we also directly provide those synthetic variables in the Data directory); Data directory contains the Nemo output files, the synthetic variables, and other data needed to reproduce the figures; this directory can be used as a working directory for the R scripts (recommended). Running the following command in a terminal tar –xzvf Archive_PC_SOM_IS_FL.tar will create a directory named Archive_PC_SOM_IS_FL, which detailed content is described in the README.pdf file.
Warning: the extracted archive is large (460Go, >40,000 files) and extraction may take some time.

Metapopulation

Genetic data

10.5281/zenodo.5211159

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Additional file 4 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

Figshare (2020)

Philippe Cubry Hélène Pidon Kim Nhung Ta Christine Tranchant‐Dubreuil Anne‐Céline Thuillet

Additional file 4: Table S3. Heritability estimates of the different traits. Heritability was estimated for each phenotypic trait: flowering time, panicule morphology and resistance to RYMV virus. The analysis was done for flowering time (FT), spikelet number (SpN), primary branch number (PBN), secondary branch number (SBN), rachis length (RL), primary branch average length (PBL), secondary branch average length (SBL), primary branch internode average length (PBintL), secondary branch internode average length (SBintL) and RYMV virus content based on the mean of estimation at 17 and 20 days after infection (RYMV). We used a mixed model to estimate the inbred line variance, the bloc, the year and the residual variance. Heritability was calculated as the ratio of the line variance divided by the line variance and the residual variance ( https://plant-breeding-genomics.extension.org/estimating-heritability-and-blups-for-traits-using-tomato-phenotypic-data/ ). (ODS 10 kb)

Oryza

10.6084/m9.figshare.12965418

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Additional file 2 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

Figshare (2020)

Philippe Cubry Hélène Pidon Kim Nhung Ta Christine Tranchant‐Dubreuil Anne‐Céline Thuillet

Additional file 2: Table S2. Statistics of the Shapiro-Wilkinson and Anderson-Darling normality tests, applied to the different non-transformed (a) and transformed variables (b).

Oryza

10.6084/m9.figshare.12965412

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Pearl millet genomic vulnerability to climate change in West Africa highlights the need for regional collaboration

Nature Communications (2020)

Bénédicte Rhoné Dimitri Defrance Cécile Berthouly‐Salazar Cédric Mariac Philippe Cubry

Abstract 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 Africa. We analyze the genomic diversity of 173 landraces collected in West Africa together with an extensive climate dataset composed of metrics of agronomic importance. Mapping the pearl millet genomic vulnerability at the 2050 horizon based on the current genomic-climate relationships, we identify the northern edge of the current areas of cultivation of both early and late flowering varieties as being the most vulnerable to climate change. We predict that the most vulnerable areas will benefit from using landraces that already grow in equivalent climate conditions today. However, such seed-exchange scenarios will require long distance and trans-frontier assisted migrations. Leveraging genetic diversity as a climate mitigation strategy in West Africa will thus require regional collaboration.

Vulnerability

Crop Diversity

10.1038/s41467-020-19066-4

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Consequences of multiple-scale variation in selection on microgeographic adaptation

HAL (Le Centre pour la Communication Scientifique Directe) (2015)

Philippe Cubry Sylvie Muratorio Ivan Scotti François Lefèvre

Variation (astronomy)

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Une histoire de la génomique des riz cultivés

Philippe Cubry Mathias Lorieux François Sabot Alain Ghesquière

Les riz ont été domestiqués indépendamment dans trois continents, Asie, Afrique et Amérique, à partir d’espèces ancestrales différentes. Le séquençage de milliers de génomes a permis de mettre en évidence l’importance de la notion de « pan-génome » et éclaire le déterminisme génétique des transformations des caractères agro-morphologiques et de la qualité des grains consécutifs à la domestication.

10.51926/iste.9167.ch10

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