Sorghum T2T pangenome highlights comprehensive genomic variation

Three newly assembled telomere-to-telomere (T2T) genomes representing wild, landrace, and transformable germplasm were integrated with seven publicly available T2T genomes to construct a graph-based pangenome. Comparative analyses revealed extensive centromere divergence, including distinct CEN137 monomer and CEN274 dimer organization, and showed that conserved noncoding sequences (CNSs) are more abundant around core genes than dispensable genes. Although TE composition was highly conserved across genomes, individual transposable element (TE) families exhibited substantial copy number variation. TE-based Genome-wide association study (GWAS) identified a Long Terminal Repeat (LTR)/Gypsy insertion upstream of Tx430Chr5G00146410 associated with increased gene expression and grain yield per plant. Heterologous overexpression of Tx430Chr5G00146410 in Setaria viridis further supported its role in regulating yield-related traits.