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Background  Sainfoin ( Onobrychis viciifolia ) is a promising alternative forage plant of good quality, moderate nutrient demand and a high content of polyphenolic compounds. Its poor adoption is caused by the limited availability of well performing varieties. Sainfoin is characterised as tetraploid and mainly outcrossing, but the extent of self-fertilisation and its consequences was not investigated so far. This study aimed at assessing the rate of self-fertilisation in sainfoin under different pollination regimes and at analysing the consequences on plant performance in order to assist future breeding efforts.    Methods  The self-fertilisation rate was assessed in three sainfoin populations with artificially directed pollination (ADP) and in three populations with non-directed pollination (NDP). Dominant SRAP (sequence-related amplified polymorphism) and codominant SSR (simple sequence repeats) markers were used to detect self-fertilisation in sainfoin for the first time based on molecular marker data.    Results  High rates of self-fertilisation of up to 64.8 % were observed for ADP populations in contrast to only up to 3.9 % for NDP populations. Self-fertilisation in ADP populations led to a reduction in plant height, plant vigour and, most severely, for seed yield.    Conclusions  Although sainfoin is predominantly outcrossing, self-fertilisation can occur to a high degree under conditions of limited pollen availability. These results will influence future breeding efforts because precautions have to be taken when crossing breeding material. The resulting inbreeding depression can lead to reduced performance in self-fertilised offspring. Nevertheless the possibility of self-fertilisation also offers new ways for hybrid breeding based on the development of homogenous inbred lines.    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-015-0275-z) contains supplementary material, which is available to authorized users.

Evidence and consequences of self-fertilisation in the predominantly outbreeding forage legume Onobrychis viciifolia