Table 2 Short- vs long-term benefits of super-pangenomes for fast-forward breeding
From: From the genome to super-pangenome: a new paradigm for accelerated crop improvement
Benefits | Key impacts and description |
|---|---|
Short-term | |
Comprehensive variant discovery | Reduces reference bias and discovers rare alleles and SVs missed by SNP-only approaches; improves trait resolution for stress, yield, and quality |
Improved marker-trait associations | Improves QTL/GWAS accuracy and guides more effective marker-assisted selection |
Bridging wild and elite genomes | Aids the introgression of lost diversity from CWRs and landraces without restarting domestication |
Better decision support in pre-breeding | Guides the selection of introgression lines and breeding parents, uniquely for traits regulated by SVs |
Long-term | |
Haplotype-assisted genomic prediction | Improves prediction accuracy for complex traits by integrating SVs and haplotype blocks into GS models |
Pan-genome-driven genome editing | Delivers a broad catalogue of functional targets for gene editing, including TEs, CREs, CNSs, and motifs |
Guiding improvement in underutilized crops | Discovers novel traits and domestication avenues in orphan crops and increases improvement efforts across germplasm pools |
Systems-level future crop design | Combines pan-genomics, multi-omics, and AI to enable de novo design of crop genotypes based on trait architecture rather than phenotype alone |
