Chromosome-level genome assembly of soybean cultivar Qinong 5 (QN5) reveals the genetic basis of disease resistance and breeding potential

Soybean ( Glycine max (L.) Merr.) is a globally important oil and protein crop. A high-quality reference genome of elite cultivars is essential for molecular breeding. Here, we report a chromosome-level genome assembly of the disease-resistant, high-oil soybean cultivar Qinong 5 (QN5) from Northeast China, generated using PacBio HiFi and Hi-C technologies. The assembled genome was 1,091.67 Mb in size with a scaffold N50 of 51.76 Mb. Repetitive sequences accounted for 53.38% of the genome, with long terminal repeat (LTR) retrotransposons being the dominant class. We predicted 55,336 protein-coding genes, 97.70% of which were functionally annotated. We predicted 186 Nucleotide-binding domain and Leucine-rich Repeat-type disease (NLR) resistance genes, mainly TNL and CNL types, which were significantly enriched in the plant-pathogen interaction pathway, suggesting their potential association with soybean cyst nematode resistance. Comparative genomics revealed 6,212 structural variations (SVs), including 434 QN5-specific SVs. QN5 harbored abundant favorable alleles for disease resistance, quality, and yield. Pedigree resequencing and identity-by-descent (IBD) analysis showed that 46.80-77.72% of the progeny genome was inherited from QN5, with 1,631 conserved IBD segments covering 7,637 genes. This high-quality QN5 genome enriches soybean genomic resources, reveals its genetic basis as an elite founder parent, and supports molecular breeding for disease resistance, high oil content, and high yield.