The role of pan-genomics in understanding genetic diversity and structural variations for developing climate-resilient crops

Abstract

Exploring and utilization of genetic variation within the gene pool of modern crop species is a critical step in maintaining and improving crop productivity. Genetic variation, ranging from SNP’s (single nucleotide polymorphisms) to large structural variations, can result in variation in the gene content between individuals of the same species. The pan-genome concept was proposed to better capture this variation, as a single reference genome is inadequate to capture the complete genetic diversity of a species. By combining genomic data from multiple accessions, the pan-genome allows for the detection of structural variants, including copy number variations (CNV), presence/absence variation (PAV), inversions and translocations. Advances in sequencing technologies have enabled the assembly of high-quality genome sequences at a low cost, making it possible to construct genus-level pan-genomes across all species. The analysis provides a platform to evaluate the genetic diversity of a species via investigation of its entire genome repertoire and can also be applied to breeding climate resilience into existing crops or to re-domesticate crops, combining environmental adaptation traits with crop productivity. It has been constructed for major crops like rice, maize, Brassica and soybean, this has led to the discovery of valuable genes linked to disease resistance and yield components. High-quality pan-genomes coupled with phenotypic data can identify variant alleles and CRISPR-Cas9 target sites, enhancing editing efficiency. Using a pan-genome graph as a reference aid in comparative analyses for developing climate-resilient, high-performance crops. With diverse species pan-genomes available, we can understand species and higher taxa at the genomic level, offering insights into plant evolution and domestication.