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.

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.

The diversity of cassava was studied in 10 communities spanning a range of socio-economic circumstances and located in the four main agro-ecological zones in Ghana. On average, each farmer grew about two cultivars, mostly landraces, both for home consumption and sale of the storage roots. In total, 35 differently-named landraces were mentioned, 26 in only single communities. Most communities had grown cassava for >100 years and seem to have acquired an additional landrace about every decade. Landraces were also abandoned. The attributes mentioned of newly-acquired landraces were generally the reverse of landraces abandoned and most were related to the storage roots. All the current landraces in all the communities seem to have been obtained from other communities. None of the almost 300 interviewed farmers understood the role of pollination in setting seed and providing variation amongst seedlings, none purposely planted seeds and most farmers ignored or weeded out cassava seedlings. However, some did use planting material (stem cuttings) from self-sown seedlings, often when planting material from their crops was scarce, and some purposely grew cuttings from a few such seedlings, apparently as experiments. That many seedlings were both reported and seen in newly-planted crops suggests that some may be accidentally used as planting material, especially those seedlings that are perceptually indistinct from the planted crop, resulting in polyclonal landraces.

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.

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Background: Early bulking in cassava (Manihot esculenta Crantz) is a very important trait in semi-arid ecologies of the tropics. Farmers tend to select early-maturing cassava varieties to escape terminal drought and destruction by domestic animals during the dry season. However, early harvesting is associated with yield penalty due to unavailability of high-yielding early-maturing cassava varieties. In order to develop early-bulking cassava varieties for the savanna ecologies, this study was carried out to assess genetic variation in the pattern of storage root bulking and as well as traits associated with early storage root bulking under moisture stress and well-watered conditions. Methods:Twenty cassava genotypes were arranged in a randomised complete block design with three replications under irrigation and no irrigation. The genotypes were sequentially harvested at 6, 8, 10 and 12 months after planting to study their pattern of dry matter accumulation. Irrigation water was supplied using a drip irrigation system with a discharge capacity of 1.6 l/h.Results: Analysis of variance indicated significant effect of genotype, harvesting time and irrigation on most of the yield traits studied. The interaction between genotype and irrigation effect was significant for all traits except mean storage root weight, storage root girth, storage root length and storage root dry matter content. Apart from storage root girth and storage root dry matter content, genotype × harvesting time interaction was not significant. Pearson correlation analysis of root yield at different times showed significant positive correlation between early storage root yield and final root yield indicating the possibility of selecting early-bulking genotypes with high yield potential. Conclusion:The study indicated that dry matter is partitioned more for root elongation than expansion in root girth under moisture stress conditions compared with irrigation, resulting in high storage root length: girth ratio. This ratio can be used to study the pattern of photosynthates accumulation in cassava roots under stress conditions. The study helped to provide improved understanding of the genetic basis and the mechanism of storage root bulking in cassava under moisture stress conditions, which can be exploited to develop high-yielding cassava varieties for droughtprone areas to ensure food security.