Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security

Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.

Automated summary

Underutilized crops have valuable traits and are important for addressing climate change and increasing global population. Going beyond reference genomes is crucial to identify specific genes and adaptive alleles. Population genomic and pangenomic approaches have identified stress- and disease-tolerant alleles in staple crops, but this research is limited for underutilized crops. Genomic advances have benefited previously underutilized crops, and breeding targets in these crops often align with those in staple crops. Cross-crop population-level resequencing can help understand the genetic basis of adaptive traits in underutilized crops. This level of investment is important for fully understanding the value of these crops before they are lost.