Salt stress affects rice seed germination and seedling formation, seriously restricting rice production. Screening salt-tolerant rice varieties and analyzing the genetic mechanisms underlying salt tolerance are therefore very important to ensure rice production. In this study, 313 Oryza sativa ssp. japonica germplasm were used to conduct a genome-wide association study (GWAS) using 1% NaCl as a salt stress treatment during germination stage. The germination potential (GP) on different days and the germination index (GI) under salt stress were used as salt tolerance indicators. The results of population structure analysis showed that the 313 germplasm studied could be divided into two subpopulations, consistent with the geographical origins of the materials. There were 52 loci significantly related to salt tolerance during germination, and the phenotypic contribution rate of 29 loci was > 10%. A region on chromosome 11 (17049672–17249672 bp) was repeatedly located, and the candidate gene LOC_Os11g29490, which encodes a plasma membrane ATPase, was identified in this locus. Further haplotype analysis showed the GP of germplasm with different haplotypes at that locus significantly differed under salt stress (p < 0.05), and germplasm carrying Hap2 displayed strong salt tolerance during the germination stage. Two other promising candidate genes for salt tolerance were identified: LOC_Os01g27170 (OsHAK3), which encodes a potassium transporter, and LOC_Os10g42550 (OsITPK5), which encodes an inositol 1, 3, 4-trisphosphate 5/6-kinase. The results of this study provide a theoretical basis for salt-tolerant gene cloning and molecular design breeding in rice.

Rice adaptation to low temperatures involves changes in their genetic and physiological architecture, caused by complex and variable transcriptional regulatory networks to regulate between growth and stress resistance. Overwintering rice survives cold winter and germinates the following spring. The perennial and cold‐tolerant properties present great potential regarding rice breeding and food security. In this study, the cold‐tolerant overwintering cultivar rice, “glutinous rice 89‐1” (Gr 89‐1), and an indica cultivar rice, “R07,” were placed at 4°C at the tillering stage and sampled at 0, 12, 24, and 96 h, and recovery 7 days. Physiological indicators of each sample were measured, and transcriptome analysis was performed. The results revealed that the overwintering cultivar rice Gr 89‐1 exhibited a pattern of physiological parameters consistent with the cold‐tolerant phenotype, less membrane damage accumulation and water loss with increasing duration of low temperature, and a stable increase in peroxidase activities, catalase activities, and soluble sugar content. Transcriptome analysis of two cultivars at 0, 12, and 24 h under 4°C revealed different gene expression patterns to low temperatures. Compared with R07, gene ontology terms of nuclear lumen, endomembrane system, organelle membrane, and envelope were enriched in Gr 89‐1, suggesting an alteration of membrane composition during cold acclimation. Specific upregulated transcription factors and cold‐tolerance regulators indicated a coordinated response between signal transduction, energy regulation, cell cycle, and circadian rhythm, which might help maintain cell homeostasis and improve Gr 89‐1 survival under cold stress. Two candidate genes OsETR3 and NAC78 were screened out, they significantly upregulated at 12 and 24 h of cold treatment in Gr 89‐1 and were higher than R07, and they were involved in cell wall remodeling and endoplasmic reticulum homeostasis under stress, respectively, which may relate to the cold‐tolerant trait of Gr 89‐1.