Accurate genotype identification is imperative for effective use of Coffea canephora L. germplasm to breed new varieties with tolerance or resistance to biotic and abiotic stresses (including moisture stress and pest and disease stresses such as coffee berry borer and rust) and for high yield and improved cup quality. The present study validated 192 published single nucleotide polymorphism (SNP) markers and selected a panel of 120 loci to examine parentage and labeling errors, genetic diversity, and population structure in 400 C. canephora accessions assembled from different coffee-producing countries and planted in a field gene bank in Ghana. Of the 400 genotypes analyzed, both synonymous (trees with same SNP profiles but different names, 12.8%) and homonymous (trees with same name but different SNP profiles, 5.8%) mislabeling were identified. Parentage analysis showed that 33.3% of the progenies derived from controlled crossing and 0% of the progenies derived from an open pollinated biclonal seed garden had parentage (both parents) corresponding to breeder records. The results suggest mislabeling of the mother trees used in seed gardens and pollen contamination from unwanted paternal parents. After removing the duplicated accessions, Bayesian clustering analysis partitioned the 270 unique genotypes into two main populations. Analysis of molecular variance (AMOVA) showed that the between-population variation accounts for 41% of the total molecular variation and the genetic divergence was highly significant (Fst = 0.256; P < 0.001). Taken together, our results demonstrate the effectiveness of using the selected SNP panel in gene bank management, varietal identification, seed garden management, nursery verification, and coffee bean authentication for C. canephora breeding programs.

With increasing frequency and intensity of dry spells in the cocoa production zones of West Africa, strategies for mitigating impact of water stress on cocoa seedling survival are urgently required. We investigated the effects of applied potassium on biomass accumulation, physiological processes and survival of cocoa varieties subjected to water stress in pot experiments in a gauzehouse facility. Four levels of potassium (0, 1, 2, or 3 g/plant as muriate of potash) were used. Soil water stress reduced plant biomass accumulation (shoot and roots), relative water content (RWC), chlorophyll content and fluorescence. Leaf phenol and proline contents were increased under water stress. Additionally, compared to the well-watered conditions, soils under water stress treatments had higher contents of exchangeable potassium and available phosphorus at the end of the experimental period. Potassium applied under well-watered conditions reduced leaf chlorophyll content and fluorescence and increased leaf electrolyte leakage, but improved the growth and integrity of physiological functions under soil water stress. Potassium addition increased biomass partitioning to roots, improved RWC and leaf membrane stability, and significantly improved cocoa seedling survival under water stress. Under water stress, the variety with the highest seedling mortality accumulated the highest contents of phenol and proline. A significant effect of variety on plant physiological functions was observed. Generally, varieties with PA 7 parentage had higher biomass partitioning to roots and better seedling survival under soil moisture stress. Proportion of biomass partitioned to roots, RWC, chlorophyll fluorescence and leaf electrolyte leakage appear to be the most reliable indicators of cocoa seedling tolerance to drought.