Biology subjects

Verleysen, L.

Publications and source records attributed to Verleysen, L..

4 recordsLinked to original sources

bioRxiv2023

Cultivated Robusta coffee meets wild Coffea canephora: Evidence of cultivated-wild hybridisation in the Democratic Republic of the Congo

Background and aimsPlant breeders are increasingly turning to crop wild relatives (CWRs) to ensure global food security amidst a rapidly changing environment. However, CWR populations are confronted with various human-induced threats, including hybridisation with their nearby cultivated crops, posing a significant threat to the wild gene pool. Here, we focussed on Robusta coffee in the Yangambi region in the DR Congo, where cultivated Robusta coffee coexists with its wild relative (Coffea canephora), creating ample opportunity for genetic exchange. We examined the geographical distribution of cultivated Robusta coffee plants and the incidence of hybridisation between cultivated and wild individuals within the rainforest. MethodsWe used Genotyping-by-Sequencing data from 471 C. canephora individuals across various locations, including natural rainforests, home gardens, and the INERA Coffee Collection, a Robusta coffee field genebank. Our analyses involved establishing robust diagnostic fingerprints that differentiate cultivated from wild coffee, identifying cultivated-wild hybrids and mapping their geographical position. Key resultsWe identified cultivated genotypes and cultivated-wild hybrids in zones with clear anthropogenic activity, and where Robusta coffee cultivated in the home gardens may serve as a source for crop-to-wild gene flow. We found relatively few hybrids and backcrosses in the rainforests, which is so far likely not sufficient for the stable incorporation of alleles from the cultivated gene pool into the CWR gene pool. ConclusionsThe cultivation of Robusta coffee in close proximity to its wild gene pool has led to cultivated genotypes and cultivated-wild hybrids appearing within the natural habitats of C. canephora. Yet, given the high overlap between the cultivated and wild gene pool, together with the relatively low frequency of hybridisation, our results indicate that the overall impact in terms of risk of introgression remains limited so far. Nevertheless, it is important to continue monitoring crop-to-wild gene flow to safeguard the wild gene pool of C. canephora.

ecology↗

bioRxiv2023

Characterization of the genetic composition and establishment of a core collection for the INERA Robusta coffee (Coffea canephora) field genebank from the Democratic Republic of the Congo

Cultivation of Robusta coffee is likely to gain importance because of its high disease resistance and climate envelope, but substantial effort must be made to improve its cupping quality and other agronomic traits. Robusta coffee genetic resources conserved in field genebanks can play an important role in this context, but many of them are limited and poorly characterized. In this study, we aimed to characterize the genetic composition of the historically important but until recently neglected INERA Coffee Collection in Yangambi (Democratic Republic of the Congo) and to propose a Robusta core collection. We combined genome-wide GBS marker sets with a novel versatile multiplex amplicon sequencing (HiPlex) screening assay, for the genetic screening of the INERA Coffee Collection and created tools for future genetic screening. A set of 730 coffee shrubs in the collection were genotyped at 86 HiPlex loci and 263 unique genetic fingerprints were identified. Representative fingerprints were compared to Lula cultivars, Luki cultivars, Congolese subgroup A, and wild genotypes growing in the rainforest of the Yangambi region. The majority of the unique genetic fingerprints were identified as Lula cultivars but also four Congolese subgroup A and nine wild genotypes were found in the collection. Twenty-five percent of the unique genetic fingerprints had a hybrid identity which could result from seed-based propagation of the collection or natural cross-pollination. Moreover, eight unique genetic fingerprints were frequently identified as a parent and these may correspond to the ancient selected mother plants, or direct descendants thereof, of which seed material was widely distributed from 1930 to 1960 for the creation of coffee plantations. Finally, to delineate core collections we tested the maximization strategy and genetic distance method for the INERA Coffee Collection, and proposed i) a core collection conserving the loci diversity of the collection, i.e. 100 accessions and ii) a core collection holding the highest genetic distances between the accessions, i.e. 10 accessions. Our study provides a method for the genetic characterization of Robusta coffee collections in general and contributes to the revaluation and exploitation of the Robusta coffee genetic resources in the Democratic Republic of the Congo in particular.

plant biology↗

bioRxiv2022

Genetic diversity and structure in wild Robusta coffee (Coffea canephora A. Froehner) populations in Yangambi (DR Congo) and their relation with forest disturbance

Degradation and regeneration of tropical forests can strongly affect gene flow in understorey species, resulting in genetic erosion and changes in genetic structure. Yet, these processes remain poorly studied in tropical Africa. Coffea canephora is an economically important species, found in the understorey of tropical rainforests of Central and West Africa, and the genetic diversity harboured in its wild populations is vital for sustainable coffee production worldwide. Here, we aimed to quantify genetic diversity, genetic structure, and pedigree relations in wild C. canephora populations, and we investigated associations between these descriptors and forest disturbance and regeneration. Therefore, we sampled 256 C. canephora individuals within 24 plots across three forest categories in Yangambi (DR Congo), and used genotyping-by-sequencing to identify 18 894 SNPs. Overall, we found high genetic diversity, and no evidence of genetic erosion in C. canephora in disturbed old-growth forest, as compared to undisturbed old-growth forest. Additionally, an overall heterozygosity excess was found in all populations, which was expected for a self-incompatible species. Genetic structure was mainly a result of isolation-by-distance, reflecting geographical location, with low to moderate relatedness at finer scales. Populations in regrowth forest had lower allelic richness than populations in old-growth forest and were characterised by a lower inter-individual relatedness and a lack of isolation-by-distance, suggesting that they originated from different neighbouring populations and were subject to founder effects. Wild Robusta coffee populations in the study area still harbour high levels of genetic diversity, yet careful monitoring of their response to ongoing forest degradation remains required.

ecology↗

bioRxiv2021

Effects of forest disturbance and regeneration on tree species composition and traits in DR Congo

Despite their key role in biodiversity conservation, forests of the Congo Basin are increasingly threatened by human activities. Whereas deforestation is very conspicuous, it remains challenging to monitor the impact of forest degradation under a more or less intact canopy. Likewise, the outcomes of forest regeneration following agricultural abandonment remain poorly studied in the Congo Basin. Here, we surveyed 125 vegetation quadrats across 25 forest inventory plots in the Yangambi region, and based on historical land-use maps. We aimed to assess both the impact of anthropogenic disturbance and forest recovery on tree species diversity, tree functional traits, community composition, canopy cover, and forest structure, as compared to undisturbed old-growth forest. We found that undisturbed old-growth forest harboured more tree individuals, particularly individuals with a smaller diameter, as well as species with a higher wood density when compared to both disturbed old-growth and regrowth forest. Moreover, species diversity was highest in disturbed old-growth forest. Tree species composition was significantly different between undisturbed old-growth forest and the other two forest categories. Our findings indicate that anthropogenic disturbance results in a degraded forest structure and may reduce the forests ability to store carbon. Whereas species diversity recovered 60 years after agricultural abandonment, species composition remained different from undisturbed old-growth forest. Our study illustrates the need for more extensive vegetation surveys in the Congo Basin in order to quantify the effects of human disturbance under a closed canopy.

ecology↗