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.

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.

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.

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