Genotyping-by-sequencing (GBS) technology has made dense genotyping cost-effective for many species. However, the high levels of missing data can result in a large loss of information. The popularity of GBS makes the development of efficient imputation approaches a priority. Here we consider imputation under the further difficulty caused by multi-parental experimental crosses. We present an approach to imputing founder genotypes which allows recovery of a large proportion of markers. Once these have been imputed, we compare three approaches to imputing progeny genotypes and apply our strategy to an eight-parent rice population to demonstrate the potential gain from imputation.