Onion has previously posed many challenges for genetic analysis due to huge genome size and population heterozygosity. We describe progress in overcoming these challenges through use of next-generation sequencing and doubled haploids in a wide onion cross. The doubled haploid line ‘CUDH2150’ (Cornell University) was inter-crossed with the open-pollinated Indian landrace ‘Nasik Red’ and large F2 families were developed through asexual propagation and mass pollination of the highly vigorous F1 plants. The families exhibit segregation for multiple economic traits including colour, carbohydrate composition, flowering and vigor. Galaxy pipelines were developed to enable large-scale design of PCR-based markers for validation and mapping of polymorphisms identified between transcriptomes of parent lines. A preliminary linkage map of over 700 cM was developed in a subset of one family using these markers and is mostly aligned with the onion physical map. Bin mapping using a subset of these progeny has confirmed ability to place markers within 10 cM bins, enabling increased efficiency in marker assignment and targeted map refinement. Because all findings to date confirm that this population is very well-suited to genomic analysis, we propose to develop a genomic reference sequence of ‘CUDH2150’ and conduct detailed analysis of economic traits in the F2 families by reduced-representation sequencing of progeny pools. Since the parental lines are publically accessible, the development of genome data and tools for these will greatly expand scope for reproducible and collaborative genetic research in onion.