Assembly of a high-quality reference genome and characterization of a chemical-mutagenized library of an elite soybean cultivar Tianlong 1.

Soybean (Glycine max L.) is a globally vital crop for oil production and food security. High-quality genomic resources are instrumental for both functional genomics and breeding. Here, we report a near-complete, high-quality genome assembly of the elite cultivar Tianlong 1 (TL1), featuring fully resolved telomeres and centromeres, as well as a gap-free assembly of 14 of its 20 chromosomes. On the basis of the genome assembly, we generate an ethyl methanesulfonate (EMS)-mutagenized population comprising 2555 M7 plants. Whole-genome resequencing of 288 EMS mutants uncovers 1,163,869 high-confidence single-nucleotide polymorphisms (SNPs) and 542,709 insertions/deletions (InDels), achieving 91.89% coverage of predicted protein-coding genes. Phenotypic screening demonstrates robust genotype-phenotype associations, with two nonsynonymous mutants displaying pronounced defects in seed and leaf development. Collectively, the chromosome-scale TL1 genome assembly and the extensively characterized mutant population establish valuable resources for functional genomics and precision breeding in soybean and related legume species.