Jean-Pierre Labouisse

Ce mémoire, rédigé pour l'obtention d'un doctorat en agriculture par validation des acquis de l'expérience, retrace mon parcours professionnel qui s'est entièrement déroulé au sein du CIRAD de 1983 à 2022. Ingénieur agronome de formation, j'ai consacré en grande partie ma carrière à la conservation, à la caractérisation et à l'exploitation de la diversité de trois plantes pérennes tropicales : le caféier (robusta Coffea canephora et arabica C. arabica), le cocotier (Cocos nucifera) et, dans une moindre mesure, l'arbre à pain (Artocarpus altilis). Au-delà de la description phénotypique et génétique, j'ai eu à cœur de comprendre comment la diversité actuelle a pu se constituer sous l'action de facteurs aussi divers que la biologie de l'espèce, l'environnement, l'histoire et l'organisation des sociétés qui cultivent, sélectionnent et diffusent des variétés adaptées à leurs usages et besoins.Après une description chronologique de mon parcours, je détaille mes travaux portant sur :• Le caféier robusta en Afrique de l'Ouest avec i) la mise en place d'un programme de recherche en Guinée comprenant l' établissement de collections, d'essais agronomiques, d'essais comparatifs clonaux et la création d'un laboratoire pour l'expertise commerciale et l'évaluation de la qualité du café ; ii) une étude de la structure et de la répartition géographique de la diversité des C. canephora d'Afrique de l'Ouest en exploitant les ressources biologiques d'herbiers anciens grâce à un génotypage par microsatellites ; iii) l'étude génétique de caféiers C. canephora nouvellement collectés en Guinée.• Le cocotier et l'arbre à pain dans le Pacifique avec i) des travaux d'amélioration génétique du cocotier, menés sur station de recherche dans l'archipel du Vanuatu et qui ont abouti à la sélection d'un Grand local amélioré et d'un hybride tolérant à la maladie virale du dépérissement foliaire du cocotier ; ii) à l'échelle de l'archipel, des enquêtes participatives auprès des populations rurales sur la diversité du cocotier et de l'arbre à pain, qui ont révélé une riche nomenclature et une grande diversité d'usages ; iii) plusieurs projets et expertises menés dans la région Pacifique, sur la création et la production d'hybrides de cocotier, et au sein du réseau international des ressources génétiques du cocotier COGENT.• Diverses opérations de gestion de ressources génétiques avec l'organisation de collectes, la conservation en collections vivantes et la gestion de données pour plusieurs espèces dont le caféier arabica en Éthiopie.Une synthèse générale de mes activités de recherche, une auto-analyse de compétences et mes principales publications complètent ce mémoire.

Aibika [ Abelmoschus manihot (L.) Medik.], also known as island cabbage, is a highly nutritious leafy vegetable crop which is traditionally cultivated in Southwest Pacific countries. The study presents the results of genetic analyses of 227 aibika accessions conserved in the genebanks of three Melanesian countries (New Caledonia, Papua New Guinea, and Vanuatu), and French Polynesia. Genotyping with 21 novel microsatellite markers revealed that 216 accessions had a diploid genome, while eleven exhibited a third allele at one locus or more. Among the diploid accessions, we observed a total of 196 unique multilocus genotypes. Using K-means clustering method, we identified six genetic groups, including one specific to Papua New Guinea. Discriminant analysis of principal components revealed the relations between these groups, the probability of membership, and the level of admixture of the accessions. Genetic analyses by country also shown that Papua New Guinea accessions exhibited the highest genetic diversity, allelic richness, and number of private alleles, which is consistent with the history of the introductions of the crop in the Pacific. The genetic diversity observed is likely the result of a cultivation process combining selection of seedlings issued from natural sexual reproduction and clonal propagation. Morphological analyses of 76 accessions conserved in Vanuatu national ex situ germplasm collection were also conducted using a set of four quantitative and five qualitative morphological descriptors. We further discussed future challenges for the conservation and breeding of this neglected crop that contributes to the diversification and quality of the diets of Pacific Islands communities.

Aibika ( Abelmoschus manihot ) is a tropical leafy vegetable with great potential in the prevention of malnutrition. Its high fibre and micronutrient content makes it a valuable complement to staple foods such as rice and starchy crops consumed in South Asia and the Pacific. The present study is the first to report the development of a set of 21 nuclear single sequence repeat (SSR) markers of A. manihot from genomic sequence data obtained using NGS technology. The DNA library was prepared from a pool of four aibika accessions and sequenced using an Illumina MiSeq system. A total of 1,295,217 pair-end reads were generated. Raw data are available in the European Nucleotide Archive (accession number PRJEB88210; https://www.ebi.ac.uk/ena/browser/view/PRJEB88210 ). The sequences were assembled using the ABySS software. In total 651,320 contigs were generated. Using MISA Perl script and Primer3 software, we identified 8014 SSR motifs, of which 4637 had a suitable primer design. The contigs were blasted with NCBI-BLAST on okra reference genome. After selection based on motif type, repeat length, amplicon size and occurrence blast, we retained 91 candidate SSR loci, which were tested on 23 aibika accessions. Finally, we validated 21 high quality SSR loci by genotyping 45 accessions from three Pacific countries. The number of alleles per locus ranged from 3 to 21 with an average of 7.81 alleles/locus. The 21 selected SSRs were found to be useful in discriminating between accessions and revealing the diversity structure of A. manihot . They will help to optimize genebanks management and breeding programmes, and guide future collection activities.

The Pacific Islands (Melanesia, Micronesia, Polynesia) were the last region in the world to be colonized by modern humans. In their migrations, they dispersed asexually propagated food plants that were first domesticated in Melanesia and exposed them to further selection in diverse insular environments. Later, staple food crops were introduced from South America. In our search for research on genetic resources characterization and breeding conducted between 1950 and 2022, we retrieved 338 references on 13 crop species. All studies were examined, and a review is presented here. Relatively few were on genetic improvement (92 references) compared to those on morphological diversity (246 references). The paradox is that the Pacific is considered a region exposed to the climatic crisis, perhaps more vulnerable than any other region in the world. This paradox is surprising when we consider that most people in the Pacific are growing staple food crops, for household use and/or for local markets, and occasionally for export. In some countries, it involves more than 75% of the population with a considerable contribution to gross domestic product (GDP). Plant breeding has not been considered a priority to mitigate against forthcoming changes in climate, which is likely to be detrimental to crops with a narrow genetic base. We suggest several possible reasons and that conventional plant breeding should be given high priority based on new approaches that include geographical distribution of allelic diversity.

Backgrounds and aims – Previous studies showed that robusta coffee (Coffea canephora Pierre ex A.Froehner), one of the two cultivated coffee species worldwide, can be classified in two genetic groups: the Guinean group originating in Upper Guinea and the Congolese group in Lower Guinea and Congolia. Although C. canephora of the Guinean group is an important resource for genetic improvement of robusta coffee, its germplasm is under-represented in ex situ gene banks and its genetic diversity and population structure have not yet been investigated. Methods – To overcome the limitations of living collections, we explored old herbarium specimens collected in Guinea and Côte d’Ivoire and conserved at the Muséum National d’Histoire Naturelle, Paris. First, we reviewed the history of collection missions in both countries and how the C. canephora herbaria from the Muséum were assembled. Then, using 23 nuclear microsatellite markers, factorial and model-based Bayesian analyses, we investigated the genetic diversity of 126 specimens and 36 controls, analysed their distribution among the Congolese and Guinean groups, and estimated admixture proportions for each individual.Key results – For the first time, we detected population genetic structure within the Guinean group of C. canephora. The Guinean genotypes can be assigned to five sub-groups with distinct geographic distribution, especially in Guinea where two sub-groups (Maclaudii and Gamé) are characterized by a low level of admixture due to geographical isolation.Conclusions – We showed how combining a literature review and genetic data from old herbarium specimens can shed light on previous observations made by botanists and guide further actions to better preserve native coffee plants in forest remnants of West Africa.

Lipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide association study was performed to identify genomic regions associated with lipid, cafestol and kahweol contents and cafestol/kahweol ratio. Using the diploid Coffea canephora genome as a reference, we identified 6,696 SNPs. Population structure analyses suggested the presence of two to three groups (K = 2 and K = 3) corresponding to the east and west sides of the Great Rift Valley and an additional group formed by wild accessions collected in western forests. We identified 5 SNPs associated with lipid content, 4 with cafestol, 3 with kahweol and 9 with cafestol/kahweol ratio. Most of these SNPs are located inside or near candidate genes related to metabolic pathways of these chemical compounds in coffee beans. In addition, three trait-associated SNPs showed evidence of directional selection among cultivated and wild coffee accessions. Our results also confirm a great allelic richness in wild accessions from Ethiopia, especially in accessions originating from forests in the west side of the Great Rift Valley.

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. In protein coding genes, base composition strongly varies within and among plant genomes, especially at positions where changes do not alter the coded protein (synonymous variations). Some species, such as the model plant Arabidopsis thaliana, are relatively GC-poor and homogeneous while others, such as grasses, are highly heterogeneous and GC-rich. The causes of these variations are still debated: are they mainly due to selective or neutral processes? Answering to this question is important to correctly infer whether variations in base composition may have functional roles or not. We extended a population genetics method to jointly estimate the different forces that may affect synonymous variations and applied it to genomic datasets in 11 flowering plant species. We found that GC-biased gene conversion, a neutral process associated with recombination that mimics selection by favouring G and C bases, is a widespread and stronger process than selection and that it could explain the large variation in base composition observed in plant genomes. Our results bear implications for analysing plant genomes and for correctly interpreting what could be functional or not.