Genome resources for underutilised legume crops: genome sizes, genome skimming and marker development

Underutilised crops suffer from under-investigation relative to more mainstream crops, but often possess improved stress tolerance and/or nutrition, making them potentially important for breeding programmes in the context of climate change and an expanding human population. Developing basic genome resources for underutilised crops may therefore catalyse analyses to facilitate their use, through improved understanding of population structure, phylogeny, candidate genes, and linkage mapping. We carried out nuclear and plastid genome sequencing and assembly for five underutilised legumes: jack bean, sword bean, Kersting's groundnut, moth bean, and zombi pea. Using only 'off-the-shelf', free-to-use bioinformatic tools, we also developed a simple but effective pipeline to identify thousands of markers, which could be applied in other species. We assembled 53-68% of the genome and 73-95% of the gene space in the five legumes. The assemblies were fragmented but nevertheless useful for identifying between 34,000-60,000 microsatellites. Examination of 32 markers in zombi pea revealed 16 primer pairs which amplified in at least half of the eight accessions tested and were polymorphic. We also present nuclear genome size estimates for 17 legume taxa (12 for the first time), comprising the above five species as well as other domesticated legume species and crop wild relatives. We aim for the newly developed markers and genome size estimates presented here to be useful for the research community by aiding genomic and population genetic studies for these taxa, and to provide information on approaches that can be applied for investigating other important yet underutilised crops.

Automated summary

Underutilised crops have great potential for breeding programmes in the face of climate change and population growth due to their improved stress tolerance and/or nutrition. Therefore, developing genome resources for these crops can enhance their use by providing insights into population structure, phylogeny, candidate genes, and linkage mapping. In this study, we sequenced and assembled the nuclear and plastid genomes of five underutilised legumes and developed a pipeline to identify thousands of markers that can be used in other species. Our findings provide valuable information for genomic and population genetic studies of these crops and offer approaches for investigating other important yet underutilised crops.