Identification of Rice Accessions Having Cold Tolerance at the Seedling Stage and Development of Novel Genotypic Assays for Predicting Cold Tolerance

Integrating molecular markers and phenotypic analysis to assess cold tolerance in rice germplasm

Rice (Oryza sativa L.) is a crucial staple food for most of the world's population. However, it is highly vulnerable to low temperatures, which can induce growth retardation and yield loss. In this study, we aimed to develop SNP- and Indel-based molecular markers for the key cold tolerance-related genes HAN1, COLD11, and COLD1. The HAN1 marker was designed using a KASP assay, which was effective for fluorescence-based detection, whereas COLD11 and COLD1 markers were gel electrophoresis-compatible, enabling easy application without complex equipment. Considering the polygenic nature of cold tolerance, we analyzed combined markers, which exhibited enhanced prediction accuracy compared to single-marker analysis. Based on these markers, we categorized 372 rice cultivars into seven genotypic groups and assessed their genotypic and phenotypic data. The cold-tolerant HAN1 genotype was absent in the Tongil and indica cultivars but conferred the highest cold tolerance to japonica cultivars, highlighting the crucial role of HAN1 in the cold stress response. The COLD1 genotype and GCG repeat number of COLD11 are crucial for cold tolerance. Analysis of a doubled haploid population derived from a cross between the '93-11' and 'Milyang352' confirmed that the number of COLD11's GCG repeats significantly influence cold tolerance, followed by COLD1. Combining multiple cold-resistant alleles improved overall tolerance and post-stress recovery. Identifying additional alleles associated with cold stress resistance could aid in the selection of Tongil cultivars with enhanced cold tolerance. These markers could potentially contribute to breeding programs for the identification and selection of cold-tolerant rice varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01543-7.

Insights on the enhancement of chilling tolerance in Rice through over-expression and knock-out studies of OsRBCS3

Chilling stress is an important environmental factor that affects rice (Oryza sativa L.) growth and yield, and the booting stage is the most sensitive stage of rice to chilling stress. In this study, we focused on OsRBCS3, a rice gene related to chilling tolerance at the booting stage, which encodes the key enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit in photosynthesis. The aim of this study was to elucidate the role and mechanism of OsRBCS3 in rice chilling tolerance at the booting stage. The expression levels of OsRBCS3 under chilling stress were compared in two japonica rice cultivars with different chilling tolerances: Kongyu131 (KY131) and Longjing11 (LJ11). A positive correlation was found between OsRBCS3 expression and chilling tolerance. Over-expression (OE) and knock-out (KO) lines of OsRBCS3 were constructed using over-expression and CRISPR/Cas9 technology, respectively, and their chilling tolerance was evaluated at the seedling and booting stages. The results showed that OE lines exhibited higher chilling tolerance than wild-type (WT) lines at both seedling and booting stages, while KO lines showed lower chilling tolerance than WT lines. Furthermore, the antioxidant enzyme activities, malondialdehyde (MDA) content and Rubisco activity of four rice lines under chilling stress were measured, and it was found that OE lines had stronger antioxidant and photosynthetic capacities, while KO lines had the opposite effects. This study validated that OsRBCS3 plays an important role in rice chilling tolerance at the booting stage, providing new molecular tools and a theoretical basis for rice chilling tolerance breeding.

The Molecular Mechanism of Cold-Stress Tolerance: Cold Responsive Genes and Their Mechanisms in Rice (Oryza sativa L.)

Rice (Oryza sativa L.) production is highly susceptible to temperature fluctuations, which can significantly reduce plant growth and development at different developmental stages, resulting in a dramatic loss of grain yield. Over the past century, substantial efforts have been undertaken to investigate the physiological, biochemical, and molecular mechanisms of cold stress tolerance in rice. This review aims to provide a comprehensive overview of the recent developments and trends in this field. We summarized the previous advancements and methodologies used for identifying cold-responsive genes and the molecular mechanisms of cold tolerance in rice. Integration of new technologies has significantly improved studies in this era, facilitating the identification of essential genes, QTLs, and molecular modules in rice. These findings have accelerated the molecular breeding of cold-resistant rice varieties. In addition, functional genomics, including the investigation of natural variations in alleles and artificially developed mutants, is emerging as an exciting new approach to investigating cold tolerance. Looking ahead, it is imperative for scientists to evaluate the collective impacts of these novel genes to develop rice cultivars resilient to global climate change.