BackgroundAccurate identification of crop cultivars is crucial in assessing the impact of crop improvement research outputs. Two commonly used identification approaches, elicitation of variety names from farmer interviews and morphological plant descriptors, have inherent uncertainty levels. Genotyping-by-sequencing (GBS) was used in a case study as an alternative method to track released varieties in farmers’ fields, using cassava, a clonally propagated root crop widely grown in the tropics, and often disseminated through extension services and informal seed systems. A total of 917 accessions collected from 495 farming households across Ghana were genotyped at 56,489 SNP loci along with a “reference library” of 64 accessions of released varieties and popular landraces.ResultsAccurate cultivar identification and ancestry estimation was accomplished through two complementary clustering methods: (i) distance-based hierarchical clustering; and (ii) model-based maximum likelihood admixture analysis. Subsequently, 30 % of the identified accessions from farmers’ fields were matched to specific released varieties represented in the reference library. ADMIXTURE analysis revealed that the optimum number of major varieties was 11 and matched the hierarchical clustering results. The majority of the accessions (69 %) belonged purely to one of the 11 groups, while the remaining accessions showed two or more ancestries. Further analysis using subsets of SNP markers reproduced results obtained from the full-set of markers, suggesting that GBS can be done at higher DNA multiplexing, thereby reducing the costs of variety fingerprinting. A large proportion of discrepancy between genetically unique cultivars as identified by markers and variety names as elicited from farmers were observed. Clustering results from ADMIXTURE analysis was validated using the assumption-free Discriminant Analysis of Principal Components (DAPC) method.ConclusionWe show that genome-wide SNP markers from increasingly affordable GBS methods coupled with complementary cluster analysis is a powerful tool for fine-scale population structure analysis and variety identification. Moreover, the ancestry estimation provides a framework for quantifying the contribution of exotic germplasm or older improved varieties to the genetic background of contemporary improved cultivars.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0273-1) contains supplementary material, which is available to authorized users.

Twenty cassava genotypes were arranged in a randomised complete block design with three replications and assessed for growth and yield stability using the additive main effect and multiplicative interaction (AMMI) analysis. Highly significant (P<0.001) effects of genotype, environment, and genotype ⁎ environment interaction were observed for all traits studied. The AMMI analysis of variance indicated that genotype accounted for 51% of the total sum of squares for height at first branching followed by environment (33%) and interaction (15%). For fresh root yield, environment effects accounted for 37% of the total sum of squares, whilst genotype and interaction accounted for 32% and 29%, respectively. Genotypic variances for harvest index (HI), plant height, storage root yield, and dry matter content contributed a greater proportion of the phenotypic variance indicating stronger genetic control. This suggests better chance of progress in the genetic improvement of these traits. Genotype MM96/1751 combined high yield with stability according to the yield stability index ranking across environments. On the other hand genotypes UCC 2001/449 and 96/1708 though high yielding were unstable according to AMMI stability value scores. However they can be tested further in more environments to ascertain their specific adaptability for release to farmers for cultivation to boost cassava production and ensure food security.

Sweetpotato is used in various food preparations in place of rice, cassava, yam and plantain in Ghana. In spite of this it does not have the same importance in Ghanaian diet as other root and tuber crops. Consumer taste, preference and acceptance are critical in determining the suitability of sweetpotato cultivars to any locality. A study was carried out in some selected communities of Ghana where sweetpotato is popular which span all five ecozones of Ghana in February, 2012. The main objective was to investigate why sweetpotato has low utilization compared with other root and tuber crops and to increase its utilization through breeding. The study employed Focus Group Discussion (FGD) followed by administration of Semi-structured Questionnaire (SSQ). Data collected were analysed using Genstat and Statistical Package for Social Sciences. Seventy-nine people consisting of 63% males and 37% females, and 178 people consisting of 52% female and 48% males were involved in the FGD and SSQ, respectively. Majority (94%) of farmers' ranked sweetpotato from 1 to 5 among 24 cultivated crops. Only about 28% of consumers ate sweetpotato at least six days per week. The survey revealed that consumers in Ghana desired non-sweet, high dry matter sweetpotato cultivars. Therefore, there is need for Research and Development to adjust sweetpotato breeding objectives and selection procedures to develop high dry matter non-sweet sweetpotato varieties in Ghana.

A participatory breeding programme involving farmers in two Ghanaian communities and scientists from CRI (Ghana) and NRI (UK) to develop superior cassava cultivars is described. Initial situation analyses of the communities indicated that cassava is increasing in importance both as a food and a cash crop. Most farmers utilised landraces of cassava; modern varieties were scarcely mentioned. Seeds of 16 half-sib families obtained from a crossing block in Nigeria at the International Institute of Tropical Agriculture were planted in a field in each community. During seedling and subsequent clonal generations, accessions selected either by farmers or scientists were retained to the next generation. This selection process has identified 29 superior accessions from amongst 1350 original seedlings. Farmers were relatively consistent in their selection from year to year and their selections corresponded with their stated criteria. Official variety release requires additional multilocational and inspection trials and postharvest assays but otherwise seems harmonious with a participatory breeding approach; our early involvement of farmers may facilitate early release, an important factor in cost-effectiveness. A stakeholder workshop confirmed the need for improved markets for cassava; surveys of current and potential markets have led to field trials with cassava processors. Adoption of a participatory approach, with farmers and scientists taking on new roles and decentralisation of activities, implies a concomitant transfer of influence and resources.

Lack of differentiation in Africa is most likely due to postintroduction hybridization between bitter and sweet manioc. Inconsistent transfer from South America to Africa of ethnobotanical knowledge surrounding use-category management may contribute to increased hybridization in Africa. Investigating this issue requires more data on the variation in cyanogenesis in roots within and among manioc populations and how manioc diversity is managed on the farm.