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Background: Maize is the most produced crop in Sub-Saharan Africa, but yields are low and climate change is projected to further constrain smallholder production. The current efforts to breed and disseminate new high yielding and climate ready maize varieties are implemented through the formal seed system; the chain of public and private sector activities and institutions that produce and release certified seeds. These efforts are taking place in contexts currently dominated by informal seed systems; local and informal seed management and exchange channels with a long history of adapting crops to local conditions. We here present a case study of the genetic effects of both formal and informal seed management from the semi-arid zone in Tanzania.

Results: Two open pollinated varieties (OPVs), Staha and TMV1, first released by the formal seed system in the 1980s are cultivated on two-thirds of the maize fields among the surveyed households. Farmer-recycling of improved varieties and seed selection are common on-farm seed management practices. Drought tolerance and high yield are the most important characteristics reported as reason for cultivating the current varieties as well as the most important criteria for farmers’ seed selection. Bayesian cluster analysis, PCA and F-ST analyses based on 131 SNPs clearly distinguish between the two OPVs, and despite considerable heterogeneity between and within seed lots, there is insignificant differentiation between breeder’s seeds and commercial seeds in both OPVs. Genetic separation increases as the formal system varieties enter the informal system and both hybridization with unrelated varieties and directional selection probably play a role in the differentiation. Using a Bayesian association approach we identify three loci putatively under selection in the informal seed system.

Conclusions: Our results suggest that the formal seed system in the study area distributes seed lots that are true to type. We suggest that hybridization and directional selection differentiate farmer recycled seed lots from the original varieties and potentially lead to beneficial creolization. Access to drought tolerant OPVs in combination with farmer seed selection is likely to enhance seed system security and farmers’ adaptive capacity in the face of climate change.