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 Congo

Abstract

Cultivation of Robusta coffee is likely to gain importance because of its high disease resistance and climate envelope. Robusta coffee genetic resources conserved in field genebanks can play an important role to further improve its cupping quality and other agronomic traits, but such Coffea canephora collections are limited and still poorly characterized. In this study, we characterized the genetic composition of the historically important but until recently neglected INERA Coffee Collection in Yangambi (the Democratic Republic of Congo). We used GBS to discover genome-wide genetic diversity, created and validated a novel multiplex amplicon sequencing (HiPlex) screening assay to genetically screen 730 coffee shrubs of the Yangambi Coffee Collection, grouped clonal material and delineated 263 accessions with unique genetic fingerprints. Comparison to reference material of three genetic origins revealed that the majority of the Yangambi accessions were assigned a ‘Lula’ cultivar origin, four accessions were assigned to Congolese subgroup A and nine accessions were most closely related to local wild accessions. About one-quarter of the accessions was likely derived from hybridization between these groups, which could result from seed-based propagation of the collection, breeding efforts, or natural cross-pollination. Parental analyses discovered eight preferentially used accessions, which may correspond to historically selected founders, or direct descendants thereof, whose seed material was once widely used to establish coffee plantations. Finally, two core collections were proposed using the maximization strategy (CC-I; 100 accessions) and genetic distance method (CC-X; 10 accessions). Our study demonstrates a method for the genetic characterization of Robusta coffee collections in general and contributes to the re-evaluation and exploration of the Robusta coffee genetic resources in the Democratic Republic of the Congo in particular.

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

“…The GBS data of the 83 newly sampled individuals was complemented with GBS data derived from SRA (Bioproject PRJNA901681) of the 249 C. canephora individuals studied by Depecker et al (2023), and the 139 C. canephora individuals studied by Verleysen et al (2023). GBS data of all 471 C. canephora individuals were mapped onto the C. canephora reference genome sequence (Denoeud et al, 2014) with the BWA-mem algorithm in BWA 0.7.17 with default parameters (Li and Durbin, 2009).…”

“…SMAP grm was run with parameters: locus_completeness 0.1, similarity_coefficient Jaccard, distance_method Euclidean, locus_information_content shared, and partial FALSE creating a pairwise Jaccard Inversed Distance (JID) matrix. The procedure of Verleysen et al (2023) was used to calculate the minimal JID as a threshold to identify all pairs of genetically identical individuals (i.e., clones).…”

“…Notably, the cultivated materials present in the INERA Coffee Collection and distributed in the Yangambi area should be considered as one or more heterogeneous "genetic groups", and not as 'pure' cultivars with a narrow genetic base. The INERA Coffee Collection that is used for the breeding and distribution of germplasm for cultivation encompasses genetic material from several different origins, mostly Lula material, Congolese subgroup A, and wild material from local wild populations, as previously described in detail in Verleysen et al (2023). In addition to Verleysen et al (2023), a novel group with unknown origin was found.…”

“…Furthermore, previous studies have shown that the genetic diversity of these wild populations is significantly higher than material that is currently available for cultivation (Krishnan, 2013;Leroy et al, 2014;Vanden Abeele et al, 2021). (Coste 1955;Capot 1962;Vanden Abeele et al, 2021;Verleysen et al, 2023). Verleysen et al (2023) recently catalogued genetic fingerprints of the accessions of the INERA Coffee Collection and showed that most accessions of the germplasm collection were highly similar to "Lula" cultivar -material originating from the INERA Coffee Research Station in Lula in the DR Congo -, whereas some accessions were more similar to the Congolese subgroup A (Dussert et al, 2003) or to local wild genotypes.…”

“…(Coste 1955;Capot 1962;Vanden Abeele et al, 2021;Verleysen et al, 2023). Verleysen et al (2023) recently catalogued genetic fingerprints of the accessions of the INERA Coffee Collection and showed that most accessions of the germplasm collection were highly similar to "Lula" cultivar -material originating from the INERA Coffee Research Station in Lula in the DR Congo -, whereas some accessions were more similar to the Congolese subgroup A (Dussert et al, 2003) or to local wild genotypes. In the local villages, Robusta coffee is predominantly cultivated in home garden systems, which are often located very closely (sometimes < 1 km) to wild C. canephora populations (Vanden Abeele et al, 2021).…”