Ali Raza, Yiran Li, Farkhandah Jan, Cassandria Geraldine Tay Fernandez, Reyazul Rouf Mir, Zhangli Hu, Rajeev K. Varshney
Super-pangenomes expand species-level pan-genomes to genus-wide frameworks, which integrate cultivated and wild genomes to capture hidden diversity. Super-pangenomes reduce reference bias, discover structural variations, rare alleles, and regulatory elements which drive stress adaptation and trait evolution. By leveraging QTL/GWAS and panomics, super-pangenomes fast-track breeding of stress-smart and high-yielding crops. This review highlights advances, challenges, and prospects, which position super-pangenomes as a “surprise package” for sustainable, food-secure agriculture.