Coffea stenophylla is a wild coffee species of growing interest in West Africa due to its resilience and potential for crop improvement. Understanding its phenotypic diversity and trait relationships is critical for conservation and breeding programmes. This study assessed phenotypic diversity, generated a representative core collection and determined trait associations in C. stenophylla accessions using agro-morphological markers. A total of 179 accessions were assessed across 21 morphological traits. Principal component analysis (PCA), factor analysis (FA) and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram were used to unravel variability and clustering patterns. Core Hunter 3 software was applied to select the core subsets. Traits that discriminated the most between the genotypes included: leaf length, leaf width, leaf area, circumference, plant height, stem diameter, length of longest primary branch, angle of primary branches, length of primary branch, pair number of plagiotropic branch per plant, number of orthotropic shoot internode, number of internodes on longest primary branch, internode length of plagiotropic branch and internode length of orthotropic stem. FA had seven factors, which explained 63.35% of the total genetic variation in the dependence structure. A putative core set of 18 accessions was identified. The contributions by the communalities were fairly high, with nine traits exhibiting higher communality over the specificity (12 traits). Factor 5 had the highest negative associations (15 traits); whereas factor 6 had the least (9 traits). This study revealed wide genetic diversity in coffee genotypes grown in Sierra Leone, which could be used to breed high yielding genotypes and other desired traits such as resistance to local pests and diseases.
Cassava (Manihot esculenta Crantz) underpins food security for millions of people across sub-Saharan Africa (SSA). The local landraces maintained by smallholder farmers constitute a vital reservoir of agrobiodiversity, underpinning the identification of varieties tolerant to pests and diseases, and providing raw material for crop improvement. In the Democratic Republic of Congo (DRC), this diversity remains poorly characterised across the southwestern provinces, where cassava mosaic disease and the recurrent use of infected farmer-saved cuttings erode the genetic base. Filling this gap is essential for targeted conservation and CMD-tolerance pre-breeding. The objective of this study was to evaluate the morpho-agronomic diversity and Cassava Mosaic Disease (CMD) severity of local cultivars in southwestern Democratic Republic of Congo to establish a baseline for germplasm management and identify the status of varietal disease severity for breeding. A total of 374 cultivars inventoried across 226 farms were assessed using tree standardised qualitative descriptors (leaf colour at apex, petiole colour, vein colour) and two quantitative variables (cassava age, CMD severity). Multivariate analyses revealed a robust nine-cluster structure independently validated by an alternative classification (both at 97.3%). Leaf pigmentation, petiole colour and CMD severity drove the first five dimensions (46.8% of variance). Cluster 1 (n = 27; mean CMD = 1.52), Cluster 4 (n = 32; mean = 1.78), and Cluster 9 (n = 34; mean = 1.56) showed consistently low severity and represented priority candidates for CMD-tolerance pre-breeding. This study delivers the first comprehensive baseline of local cassava diversity in southwestern DRC. The low-CMD clusters identified provide actionable leads for tolerance-based breeding and underscore the importance of integrating in situ agrobiodiversity into formal conservation programmes to strengthen CMD resistance.
Cassava mosaic disease (CMD) is a major constraint on cassava production in sub-Saharan Africa (SSA). However, the genetic diversity and evolutionary dynamics of the B-DNA components of associated begomoviruses remain poorly documented, particularly in West Africa and especially in Côte d’Ivoire. The objective of this study was to characterise the molecular diversity and evolution of DNA-B components of begomoviruses associated with DCM in Côte d’Ivoire. A total of 844 cassava leaf samples analysed by PCR, revealed infection by at least one begomovirus in 509 samples (60.3%). Mixed ACMV+EACMCMV infections were predominant (34.0%), followed by single infections with ACMV (16.0%) and EACMCMV (10.3%). Genetic diversity was highly variable in ACMV. Neutrality statistics (Tajima’s D and Fu &Li’s D) indicated more active evolutionary dynamics in ACMV, in contrast with EACMCMV, which exhibited a more conserved genetic structure. Phylogenetic analyses showed a close relationship between Ivorian isolates and those from West Africa, suggesting regional circulation of viral populations. These results highlight the differentiated evolution of DNA-B components of ACMV and EACMCMV in Côte d’Ivoire; and underscore the importance of ongoing molecular surveillance to anticipate the emergence of viral variants and improve sustainable management strategies for CMD.
Tomato (Solanum lycopersicum L.) yield in Ghana remains low ( ~7.5 t ha-1), far below the >40 t ha-1 potential of improved hybrids, due to limited adapted varieties, bacterial wilt, tomato yellow leaf curl virus, and poor shelf life under high ambient temperatures. The objective of this study was to evaluate the combining abilities, heterotic patterns, and gene action governing yield and climate-resilient fruit quality traits in a diverse set of tomato germplasm. Five parental genotypes comprising three lines and two testers were crossed in a 3 × 2 line × tester mating design to develop six F1 hybrids. Parents, hybrids, and the commercial check Shasta were evaluated in a randomised complete block design, with three replications across the major and minor cropping seasons of 2022 at CSIR-Crops Research Institute, Kwadaso, Ghana. Nine traits were measured namely; plant height, fruits per plant, fruit yield, fruit weight, total soluble solids, pericarp thickness, number of locules, number of seeds per fruit, and shelf life. Pooled analysis of variance showed significant differences among lines and testers for most traits; while genotype × environment interactions were non-significant, indicating short-term temporal stability at Kwadaso. General combining ability variance exceeded specific combining ability variance for yield, fruits per plant, fruit weight, and seeds per fruit, with Baker’s predictability ratio >0.8, suggesting predominance of additive gene action. WV009 had significant positive GCA for yield (4.22) and fruits per plant (3.30); while CRI-PHE had positive GCA for fruit weight (9.65**). The hybrid CRI-PHE × WV009 showed significant positive standard heterosis for yield (151.3%) and mid-parent heterosis for fruits per plant (56.5%), but also significant negative better-parent heterosis for shelf life (-44.7%), revealing a yield × shelf-life trade-off. High narrow-sense heritability (83.6%), coupled with high genetic advance as a percentage of mean (71.1%) was observed for yield. Results indicate that pedigree selection and pure-line extraction from segregating F2 populations will be effective for yield improvement in this material. Hybrid CRI-PHE × WV009 is recommended for yield maximisation but requires backcrossing with shelf-life donors before commercial deployment. Traits such as total soluble solids with low genetic advance may need introgression from wild relatives for improvement.
Accurate cultivar identification and genetic characterisation are fundamental for any germplasm conservation, nursery certification, clonal propagation, crop improvement, and intellectual property protection. This study evaluated the genetic integrity and diversity of 270 putative Hass avocado (Persea americana Mill. cv. Hass) accessions maintained in the National Forestry Resources Research Institute (NaFORRI) mother garden in Uganda. Diversity Arrays Technology sequencing (DArTseq) was used to generate genome-wide single nucleotide polymorphism (SNP) and SilicoDArT markers to assess genetic variation and relationships among accessions. Genotyping produced 22,262 SNPs and 21,425 SilicoDArT markers, each derived from 69-bp genomic fragments. Following quality filtering, 3,748 SNPs and 1,398 SilicoDArT markers with high call rates (>95%) and reproducibility (>99%) were retained for analysis. The collection exhibited low levels of observed (Ho = 0.001) and expected (He = 0.002) heterozygosity, indicating a high degree of genomic uniformity consistent with the clonal propagation of Hass avocado. The average polymorphic information content was 0.02 for SNPs and 0.13 for SilicoDArT markers, reflecting differences in marker characteristics. Principal Coordinates Analysis (PCoA) showed that the first principal coordinate explained 60% of the variation in the SNP dataset and 29% in the SilicoDArT dataset, indicating that the SNP markers captured the major axis of genetic variation more effectively than the dominant SilicoDArT axis. Genetic distance and phylogenetic analyses revealed that most accessions clustered closely, supporting the genetic uniformity of the Hass germplasm. Genome-wide SNP similarity analysis indicated that the majority of the 270 Hass avocado accessions shared a high degree of genomic similarity. Forty-five accessions (16.7%) exhibited complete concordance across the evaluated SNP markers relative to the reference SNP profile (GCA_002908915.1), while 116 accessions (43.0%) showed 95–99% SNP similarity. Together, these results indicate that approximately 60% of the sampled germplasm displayed very high genomic similarity. Fifty-one accessions (18.9%) exhibited moderate similarity (85-94%), whereas 58 accessions (21.5%) showed lower similarity (<85%), indicating greater allelic divergence; which, based on mother garden management records, corresponded predominantly to unmanaged rootstock escapes that had developed into mature trees, indicating presence of seedling-derived rootstocks rather than Hass scions. This confirms the presence of non-Hass germplasm rather than genetic variation within the Hass cultivar. These findings demonstrate the value of genome-wide SNP markers for monitoring the genetic integrity of avocado mother gardens, detecting off-type planting material, and strengthening nursery certification, traceability, and clonal quality assurance systems for commercial Hass avocado production in Uganda.
