Genetic Analysis of Lodging Resistance in 1892S Based on the T2T Genome: Providing a Genetic Approach for the Improvement of Two-Line Hybrid Rice Varieties

Abstract

Successfully breeding high-yield, lodging-resistant hybrid rice varieties is critical for ensuring food security. Two-line hybrid rice system plays an essential role in rice breeding, and 1892S, an important two-line sterile line, has contributed significantly to the development of over 100 hybrid rice varieties with superior agronomic traits, including lodging resistance. Despite its importance, a comprehensive understanding of the genomic basis underlying these traits in 1892S has been lacking due to the limitations of short-read sequencing technologies. To address this gap, we utilized advanced telomere-to-telomere (T2T) genome assembly techniques to generate a high-quality, gap-free genome of 1892S-the final genome comprises 12 complete chromosomes with 40,560 protein-coding genes. Comparative genomic analysis identified multiple known lodging resistance genes, including SD1, Sdt97, SBI, OsFBA2, APO1, and OsTB1, with unique allelic variations that may enhance resistance. The pan-genome analysis identified 2347 strain-specific genes in 1892S, further supporting its unique genetic advantages. This study represents the complete T2T genome assembly of a two-line sterile line and provides novel insights into the genetic foundation of lodging resistance in hybrid rice. This study highlights the genetic potential of 1892S in hybrid rice breeding and provides a model for the genomic analysis of other two-line sterile lines, offering valuable insights for improving in hybrid rice, including traits lodging resistance, yield stability, and adaptability, which are crucial for global food security.

Keywords: comparative genomics; hybrid rice breeding; lodging resistance genes; telomere-to-telomere genome assembly; two-line sterile line (1892S).

Figure 1

Hi-C interaction heatmap of the 1892S genome. Both the X and Y axes represent genomic positions divided into 100 kb bins (N × 100 kb), and each axis follows chromosome order from Chr01 to Chr12. Color gradients indicate the frequency of interaction between genomic regions, with darker colors indicating stronger chromatin contacts. Note: Although chromatin interaction frequencies in this map can reach values as high as 8, most visible intensities fall within the 2–3 range due to figure rendering limits. Strongest interactions are observed along the diagonal (i.e., between adjacent regions on the same chromosome), as expected. The lower interaction intensities in off-diagonal regions indicate minimal inter-chromosomal noise, which in turn reflects the high accuracy and contiguity of the T2T genome assembly.

Figure 2

This figure illustrates an overview of the high-contiguity the genome assembly of the 1892S, in which each of the 12 chromosomes is assembled as a single contig without gaps. Telomeric repeat sequences have been identified at both ends of all chromosomes, and centromeric regions have been predicted based on repeat density and sequence characteristics.

Figure 3

Comprehensive genomic quality assessment of the 1892S genome assembly, including assembly metrics, sequencing depth, and variant distribution profiles. A. Summary of genome assembly statistics, including genome size. B. Distribution of GC content across the genome, indicating regional variation in nucleotide composition. C. Sequencing depth distribution of Illumina short reads mapped to the 1892S genome. D. Sequencing depth distribution of long reads (PacBio HiFi and ultra-ONT) across the genome. E. BUSCO gene completeness assessment: the outer circle shows the distribution of single-copy BUSCOs, while the inner circle represents duplicated BUSCOs, demonstrating gene completeness and copy number consistency. A complete F. SNP density distribution: the outer ring displays homozygous SNP density, and the inner ring shows heterozygous SNP density across the genome. G. InDel density distribution: the outer ring displays homozygous InDel density, and the inner ring shows heterozygous InDel density. These multi-layered metrics collectively support the high quality and accuracy of the 1892S genome assembly.

Figure 4

Functional Annotation of the 1892S Genome Based on Clusters of Orthologous Groups (COG) Classification. The bar chart summarizes the distribution of predicted protein-coding genes in 1892S across standardized COG categories. Each bar represents a functional class, annotated using single-letter COG codes. The COG classification provides insight into the functional composition of the genome and the major biological processes represented.