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

Abstract

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.

Keywords: crop improvement; food security; genomics; pangenome; population genomics; reference genome; underutilized crops.

Fig. 1

Schematic diagram highlighting the main sequencing and breeding approaches discussed in this article. First (left), by comparing the reference genomes of underutilized crops and staple/main crops, genome variants responsible for superior agronomic traits (such as specific resistance and nutrient quality or quantity) of underutilized crops could be explored. In addition (right), the combination of genome resequencing and phenotyping through genome‐wide association study could help to identify candidate genes responsible for agronomic traits of underutilized crops. Through genetic transformation or genome editing, the function of these candidate genes could be verified. Finally, by associating genomic data to phenotypic information of different accessions, germplasm resources can be effectively screened and bred by means of molecular marker‐assisted breeding and crossing, to improve the resistance and nutritional value of underutilized crops in addition to staple crops.

Fig. 2

Schematic diagram highlighting common breeding targets for any crop, and whether the genetic basis has been investigated in underutilized crops (UCs) and/or staple crops. ANF, antinutrient factor.