Mapped deletions in a publicly available Fast Neutron mutant collection for gene identification in pea

Abstract Background Fast Neutron induced mutants in the background of Pisum sativum (pea) JI2822 have been described in several studies. Here, we sought to organise this collection of mutagenized lineages to make them accessible, to investigate the type and frequency of mutations and to investigate their utility for systematic screening for mutants. Results We investigated the use of Axiom markers to detect deletion mutations by screening for null alleles, and compared this method to low coverage sequencing, where variation in read mapping depth was used to detect deletions. These mutation screens identified many large deletions, but duplications were also found. The deletion mutations were not necessarily single contiguous spans. Some involved one or more nearby locations, implying that Fast Neutron induced mutations can be complex. We identified PsMYB32 as the Fuscopurpureus (Cr) gene and we propose candidate genes for other mutations affecting floral architecture and wax deposition. The identification of PsMYB32 as Cr suggested PsMYB37 as a candidate for the Roseus (Ce) gene and the evidence for this is discussed. Conclusions Our analysis of 210 M2 derived families by the skim-sequencing method identified deletions that cover a little over 15% of the pea genome. This suggests that the population of approximately 5,000 families should contain deletions covering a substantial fraction of the pea genome. We detected hemizygous deletions, so mutants severely compromised in fertility or viability may be accessible for study in this population. The public availability of this resource should facilitate further gene identification in pea; this study provides the background data to support further characterisation of these lines by sequencing.