Rice is the leading global staple crop. Low temperatures pose negative impacts on rice’s optimal growth and development. Rice cultivars acclimating to low temperatures exhibited improved seedling emergence under direct-seeded sowing conditions, yet little is known about the genes that regulate germination at low temperatures (LTG). In this research investigation, we’ve performed whole genome sequencing for the 273 rice plant materials. Using the best linear unbiased prediction (BLUP) values for each rice material, we identified 7 LTG-related traits and performed the efficient genetic analysis and genome-wide association study (GWAS). As a result of this, 95 quantitative trait loci (QTLs) and 1001 candidate genes associated with LTG in rice were identified. Haplotype analysis and functional annotation of the candidate genes resulted in the identification of three promising candidate genes (LOC_Os08g30520 for regulating LTG4 and LTG5, LOC_Os10g02625 for regulating LTG6, LTg7 and LTG8, and LOC_Os12g31460 for regulating LTG7, LTg8 and LTG9) involving in the regulation of LTG in rice. This research provides a solid foundation for addressing the LTG issue in rice and will be valuable in future direct-seeded rice breeding programs.

Rice is an important grain crop widely cultivated across the world. Its yield and quality have always been the focus of breeders’ attention, significantly impacting world food security. Rice grain shape, primarily characterized by grain length and width, is an important quantitative trait controlled by multiple genes, which not only directly affects rice yield but is also closely related to rice quality. Therefore, mining and utilizing the main QTLs and genes responsible for grain shape regulation is significant for breeding high-yielding rice varieties. In this study, 265 natural population materials were used to characterize the related phenotypes of grain length (GL), grain width (GW), and the grain length-width ratio (GLWR) over 2 years, revealing abundant phenotypic variations. Genome-wide association studies (GWAS) combined with 4,451,085 single-nucleotide polymorphism (SNP) markers distributed on 12 chromosomes, identified 61 significantly related QTLs, 14 of which are similar to previously reported rice grain type-related loci. Among these 61, three GL related QTLs (qGL3.1, qGL3.2 and qGL10.2), 1 GW related QTL (qGW5.1) and 11 GLWR related QTLs (qGLWR2.1, qGLWR2.3, qGLWR3.3, qGLWR3.4, qGLWR3.5, qGLWR4.2, qGLWR5.2, qGLWR5.3, qGLWR6.1, qGLWR9.2 and qGLWR10.2) were detected in two consecutive years. Three candidate genes, LOC_Os03g39710, LOC_Os05g09480, and LOC_Os09g36350, were identified through functional annotation and haplotype analysis of these co-existing QTLs. In brief, we detected 14, 12, and 35 QTLs associated with GL, GW, and GLWR, respectively. We further screened the grain shape-related candidate genes by functional annotation and haplotype analysis of all genes in the QTL regions. This study lays the foundation for further cloning and genetic regulation of rice grain-shape genes, providing innovative insights for rice molecular breeding designs.

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.