The role of pangenomics in orphan crop improvement

Abstract

Global food security depends heavily on a few staple crops, while orphan crops, despite being less studied, offer the potential benefits of environmental adaptation and enhanced nutritional traits, especially in a changing climate. Major crops have benefited from genomics-based breeding, initially using single genomes and later pangenomes. Recent advances in DNA sequencing have enabled pangenome construction for several orphan crops, offering a more comprehensive understanding of genetic diversity. Orphan crop research has now entered the pangenomics era and applying these pangenomes with advanced selection methods and genome editing technologies can transform these neglected species into crops of broader agricultural significance.

Fig. 1. Three primary methods for pangenome construction.

a de novo assembly and comparison; (b), reference genome-based iterative assembly; and (c), graph-based pangenome construction.

Fig. 2. Application of pangenomics for the improvement of orphan crops.

Since a pangenome can capture the complete genetic diversity of a species and identify different types of genomic variations, it offers multiple advantages in genomic analyses and molecular breeding. a The pangenome serves as a powerful framework for multi-omics studies, facilitating more comprehensive analyses of differential gene expression, regulatory networks, post-translational modifications and protein interactions through transcriptomic, proteomic, metabolomics and epigenomic approaches. (b) With additional SNPs and SVs markers, a pangenome can provides further insights into population-wide variation and the selection patterns acting on different populations, such as crop wild relatives and domesticated species. c Pangenome-wide association studies utilising PAVs and SVs uncovers missing heritability, efficiently pinpointing functional genes associated with complex traits. d Pangenomes facilitate more efficient and precise genomic selection by enabling accurate haplotype construction and providing an expanded set of SNP and SV markers, thereby enhancing the dissection of complex traits and informing breeding decisions. e Pangenome-wide cross-genus comparison among different species allows the translation of knowledge between major crops and orphan crops. f New genetic variations and genes captured by pangenomes can be used as novel target sites for gene/genome editing, increasing the efficiency of the editing process of targeted trait.