Critical insights in cassava functional genomics: from haplotypes to genome editing

Cassava (Manihot esculenta Crantz) sustains food security and a rapidly expanding starch economy, yet genetic gain remains constrained by clonal propagation, high heterozygosity, genetic load, long breeding cycles, genotype-by-environment effects, and persistent threats from cassava mosaic disease, cassava brown streak disease, and post-harvest physiological deterioration. Recent long-read, haplotype-resolved assemblies have reframed cassava genomics by resolving the two chromosome copies within elite clones, revealing structural variants, copy-number and presence/absence variation, and allele-specific regulatory differences that are poorly captured by collapsed references. We review how phased assemblies, pangenomes, haplotype maps, and graph-based imputation can shift cassava improvement from proxy single nucleotide polymorphism markers toward causal haplotypes and structural alleles. We discuss how allele-specific expression, transposable-element-associated variation, and methylation divergence connect genome structure to tissue-specific trait biology. Finally, we outline a deployment-oriented framework in which haplotype-informed breeding and allele-specific genome editing provide complementary routes for improving cassava, with parental selection, marker design, quality control, and editing decisions guided by the correct allele and structural context in elite varieties.