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

TL;DR

This study provides a complete genome of a key hybrid rice line and identifies genes linked to lodging resistance, helping improve rice breeding for food security.

Contribution

The first telomere-to-telomere genome assembly of a two-line sterile rice line, revealing lodging resistance genes and strain-specific genetic advantages.

Findings

The 1892S rice line's genome includes 12 complete chromosomes and 40,560 protein-coding genes.

Lodging resistance genes like SD1, Sdt97, and OsTB1 have unique alleles in 1892S.

Pan-genome analysis identified 2347 strain-specific genes in 1892S.

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.

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