Uncovering the historic genetic diversity of Ugandan Robusta coffee germplasm: a foundation for core collection design

Abstract

Background Uganda is a primary centre of diversity for Coffea canephora (Robusta coffee), a crop that underpins both the national coffee sector and global breeding programs. The National Coffee Research Institute (NaCORI) of Uganda conserves more than 2058 accessions that were collected from different agroecological zones of the country. However, their genetic diversity has been only partly characterized, limiting their effective use in conservation and breeding. Results A total of 909 C. canephora accessions from the NaCORI collection was genotyped, using 236 KASPar SNP markers. To investigate genetic structure and diversity we combined multivariate analyses, genetic diversity and differentiation metrics as well as hierarchical clustering. Genetic clusters were then spatially mapped according to the agroecological regions of origin across Uganda. Using reference genotypes from known wild Ugandan forests and major African genetic groups we observed that accessions from NaCORI were majorly related to the genetic group O from Uganda (and to a lesser extent Congolese group E). Despite the low differentiation among regional subpopulations of origin, reflecting gene flow driven by historical dissemination and admixture within the collection, the cultivated accessions were separated into six distinct clusters using Ward’s hierarchical method. From these genetic clusters, two core collections were designed using Core Hunter 3. The first comprised 109 accessions with high allelic coverage (CV = 0.981), while the second comprised 328 accessions that, in addition to allelic coverage, optimized the representation of both geographical origin and genetic clusters. These corresponded to 13% and 42% of the entire studied collection, respectively. The core collection of 328 accessions was defined as the GWAS population for downstream association studies. Including representative wild Ugandan accessions in the analyses reveals that some forests may harbour unique diversity absent from the cultivated germplasm. Conclusion Characterizing this diversity and designing representative core and GWAS collections are essential to optimize resource management and enable the targeted development of climate-resilient cultivars. The multi-regional origin of our core collections revealed the influence of ecological and socio-cultural factors on germplasm diversity. Our results also suggest that including wild accessions from Ugandan forests could greatly enhance the cultivated genetic pool.