The shea tree is a well-known carbon sink in Africa that requires a sustainable conservation of its gene pool. However, the genetic structure of its population is not well studied, especially in Côte d’Ivoire. In this study, 333 superior shea tree genotypes conserved in situ in Côte d’Ivoire were collected and genotyped with the aim of investigating its genetic diversity and population structure to facilitate suitable conservation and support future breeding efforts to adapt to climate change effects. A total of 7,559 filtered high-quality single nucleotide polymorphisms (SNPs) were identified using the genotyping by sequencing technology. The gene diversity (HE) ranged between 0.1 to 0.5 with an average of 0.26, while the polymorphism information content (PIC) value ranged between 0.1 to 0.5 with an average of 0.24, indicating a moderate genetic diversity among the studied genotypes. The population structure model classified the 333 genotypes into three genetic groups (GP1, GP2, and GP3). GP1 contained shea trees that mainly originated from the Poro, Tchologo, and Hambol districts, while GP2 and GP3 contained shea trees collected from the Bagoué district. Analysis of molecular variance (AMOVA) identified 55% variance within populations and 45% variance within individuals, indicating a very low genetic differentiation (or very high gene exchange) between these three groups (FST = 0.004, gene flow Nm = 59.02). Morphologically, GP1 displayed spreading tree growth habit, oval nut shape, higher mean nut weight (10.62 g), wide leaf (limb width = 4.63 cm), and small trunk size (trunk circumference = 133.4 cm). Meanwhile, GP2 and GP3 showed similar morphological characteristics: erect and spreading tree growth habit, ovoid nut shape, lower mean nut weight (GP2: 8.89 g; GP3: 8.36 g), thin leaf (limb width = 4.45 cm), and large trunk size ( GP2: 160.5 cm, GP3: 149.1 cm). A core set of 100 superior shea trees, representing 30% of the original population size and including individuals from all four study districts, was proposed using the “maximum length sub-tree function” in DARwin v. 6.0.21. These findings provide new knowledge of the genetic diversity and population structure of Ivorian shea tree genetic resources for the design of effective collection and conservation strategies for the efficient use of inbreeding.

Caractères morphologiques et durabilité des arbres plus de karité (Vitellaria paradoxa C.F.Gaertn.) en Côte d’Ivoire Description du sujet. Le karité (Vitellaria paradoxa C.F.Gaertn.) est une plante essentielle des savanes naturelles/semi-naturelles et des systèmes agroforestiers d'Afrique, contribuant aux revenus des ménages ruraux et représentant une importante culture de rente pour l'exportation. Il est donc important d'améliorer nos connaissances sur la viabilité et la diversité génétique des génotypes des « Arbres Plus de Karité » (APK : arbres à karité dont la supériorité génétique n'a pas encore été prouvée par un test de descendance approprié) afin de conserver la diversité génétique et d’améliorer le potentiel de production de cette espèce. Objectifs. Nous avons caractérisé la diversité de la collection in situ de APK en Côte d'Ivoire et évalué sa durabilité à long terme. Méthode. Douze traits morphologiques qualitatifs ont été étudiés sur 220 APK échantillonnés au hasard parmi 405 APK également sélectionnés aléatoirement dans les collections in situ des districts de la Bagoué et du Tchologo dans le nord de la Côte d'Ivoire, afin d'évaluer la durabilité de la conservation in situ. Résultats. La plupart des traits morphologiques qualitatifs étaient très diversifiés d'après l'indice de diversité de Shannon (varie de 0,55 à 0,98) avec des différences significatives entre les districts. La classification ascendante hiérarchique a permis de classer les spécimens APK en trois groupes. Il est important de noter que nous avons confirmé que la collecte in situ n'était pas une option réalisable pour la conservation à long terme de cette espèce car elle est menacée par un taux de mortalité élevé (8,15 % après trois ans) et des niveaux élevés d'infestation par les Loranthaceae (83,68 %). Conclusions. Ainsi, nous recommandons l'établissement d'une collection ex situ d'arbres à karité, gérée par une organisation de recherche, afin de sauvegarder la durabilité et la préservation de cet important patrimoine génétique. Pour maximiser la diversité génétique de la future collection ex situ recommandée, nous suggérons d'établir une collection noyau basée sur la diversité moléculaire caractérisée par des marqueurs moléculaires, tels que le polymorphisme d’un seul nucléotide (SNP). Description of the subject. Shea tree (Vitellaria paradoxa C.F.Gaertn.) is an essential component of natural/semi-natural savannas and agroforestry systems of Africa. It contributes to local household incomes and represents an important cash crop for export. It is important to improve our knowledge about the viability and genetic diversity of “plus shea tree” (PST: shea trees whose genetic superiority has not yet been proven by an appropriate progeny test) genotypes to conserve the genetic diversity of the species and the potential for producing improved species. Objectives. We characterized the diversity of an in situ PST collection in Côte d’Ivoire and evaluated its long-term sustainability. Method. Twelve qualitative morphological traits were studied on 220 PSTs randomly sampled among 405 PSTs also randomly selected from in situ collections in the Bagoué and Tchologo districts of northern Côte d’Ivoire to assess in situ conservation sustainability. Results. Most qualitative morphological traits were highly diverse based on the Shannon diversity index (0.55-0.98 range) with significant differences between districts. Hierarchical ascending classification gathered the PSTs into three groups. The lack of sustainability of the in situ collection for long-term conservation of the species was confirmed because it is endangered by a high mortality rate (8.15% after three years) and high levels of infestation by Loranthaceae (83.68%). Conclusions. We recommend the establishment of an ex situ collection of shea trees managed by a research organization to preserve this important genetic heritage. To maximize the genetic diversity of the future ex situ collection, we suggest establishing a core collection based on molecular diversity characterized from molecular markers, such as single nucleotide polymorphism (SNP).

Fat content (FC) and fatty acids (FA) are the most important traits in shea tree breeding, controlled by several genes with relatively small effects. Therefore, determining the genes involved in the biosynthesis of such traits is crucial for improving oil quantity and quality and for the domestication process of the species. To identify the quantitative trait nucleotides (QTNs) controlling FC and FA, we conducted a multi-locus genome-wide association study (GWAS) using six multi-locus GWAS methods for FC and FA in 122 superior shea trees (SSTs). SSTs were genotyped using DArTseq, resulting in 7,559 non-redundant single nucleotide polymorphism markers. Fat content varied from 36 to 58% with a mean of 50%. Fatty acid composition was 51.26 ± 4.21, 38.76 ± 4.67, 6.45 ± 0.76 and 3.53 ± 0.52% for oleic, stearic, linoleic and palmitic acids, respectively. A very high negative correlation coefficient (-0.98) was found between stearic and oleic acids. A total of 47 significant QTNs associated with fat-related traits were detected by the GWAS methods. Among these QTNs, 25 were identified as common QTNs based on their detection by multiple GWAS methods. Using the superior allele information of the 4 common QTNs associated with fat content in 17 high-fat and 21 low-fat SSTs, we found a higher percentage of superior alleles in SSTs with high FC (47.1%) than in SSTs with low FC (14.3%). Pathway analysis of the common QTNs identified 24 potential candidate genes likely involved in the biosynthesis of FC and FA composition in shea tree seeds. These findings will contribute to the discovery of the polygenic networks controlling FC in shea tree, improve our understanding of the genetic basis and regulation of FC, and be useful for molecular breeding of high-fat shea tree cultivars.

This study investigated the influence of various fermentation supports on cocoa bean quality, aiming to identify alternatives to banana leaves, which are facing scarcity issues. Supports tested included banana leaves (support used as a reference), palm leaves, cocoa pods, jute bags, polypropylene tarpaulins and polypropylene bags. Key parameters monitored during fermentation included temperature, pH, microbial dynamics and concentrations of reducing sugars and organic acids. The beans underwent physicochemical characterisation and market value evaluation after fermentation and drying. The results revealed that fermentation in cocoa pods and polypropylene bags was suboptimal. Cocoa pods exhibited low fermentation temperatures, delayed microbial activity, high pH and increased mould proliferation, leading to poor marketability with low cut‐test scores. Polypropylene bags retained higher humidity levels, posing a risk for mould contamination, although they showed higher phenolic compound content. By contrast, beans fermented on jute bags, palm leaves and reusable polypropylene tarpaulins displayed fermentation profiles and final product characteristics similar to banana leaves, making them viable alternatives for local producers. Further analysis of the aromatic characteristics of beans fermented on these supports is needed to provide a holistic evaluation. This study offers valuable insights into identifying sustainable alternatives for cocoa fermentation and serves as a reference for resource optimisation in other food production systems.