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The mining of favorable SNP loci and haplotypes is of great significance for the further cloning and molecular-assisted breeding of alkalinity-tolerance genes in rice. To improve the utilization rate of saline–alkaline lands and the yield of rice, we used the 1,322,884 SNPs obtained from the sequencing 173 of rice accessions in this study. Alkalinity-tolerance-related traits, including the germination energy (GE), germination rate (GR), seedling length (SL), root length (RL), relative alkaline damage rate (RADR) of the GERADR of the GR, RADR of the SL and RADR of the RL, were evaluated in 2019 and 2020 and revealed abundant phenotypes in the studied population. A genome-wide association analysis detected 10 quantitative trait loci (QTLs) related to alkalinity tolerance. In addition, a transcriptome sequencing analysis of the alkalinity-tolerant rice variety 'Yuedao 9' and the alkali-sensitive rice variety 'Tijin' under alkalinity stress and control conditions was performed. Three candidate genes that were predicted to be related to alkalinity tolerance in rice, namely LOC_Os06g06600, LOC_Os011g44680 and LOC_Os011g44600, were screened based on gene annotation, coding sequences and haplotype analysis. The results of this study provide important genetic information for the molecular improvement of rice. [ABSTRACT FROM AUTHOR]

Mining salt tolerance genes is significant for breeding high-quality salt-tolerant rice varieties in order to improve the utilization of saline–alkaline land. In this study, 173 rice accessions were measured for their germination potential (GP), germination rate (GR), seedling length (SL), root length (RL), germination potential relative to salt damage rate (GPR), germination rate relative to salt damage rate (GRR), seedling length relative to salt damage rate (SLR), relative salt damage rate at the germination stage (RSD) and comprehensive relative salt damage rate in the early seedling stage (CRS) under normal and salt stress conditions. Genome-wide association analysis was performed with 1,322,884 high-quality SNPs obtained by resequencing. Eight quantitative trait loci (QTLs) related to salt tolerance traits at the germination stage were detected in 2020 and 2021. They were related to the GPR (qGPR2) and SLR (qSLR9), which were newly discovered in this study. Three genes were predicted as salt tolerance candidate genes: LOC_Os02g40664, LOC_Os02g40810, and LOC_Os09g28310. At present, marker-assisted selection (MAS) and gene-edited breeding are becoming more widespread. Our discovery of candidate genes provides a reference for research in this field. The elite alleles identified in this study may provide a molecular basis for cultivating salt-tolerant rice varieties. [ABSTRACT FROM AUTHOR]

The shape of the rice flag leaf affects rice yield. Therefore, the detection of quantitative trait loci (QTLs) and alleles related to rice flag leaf shape is of great significance for rice yield improvement. Therefore, in 2019 and 2020, we carried out a genome-wide association study of flag leaf length (FLL), flag leaf width (FLW), flag leaf length–width ratio (FLR), and flag leaf area (FLA), considering 1.3 million single-nucleotide polymorphisms (SNPs) in 173 rice accessions, in order to investigate the effects of various genes on flag leaf shape. An abundance of phenotypic variation was found, with respect to the four flag leaf shape parameters of these accessions. We identified one significant SNP position associated with FLL and FLR on chromosome 5 and one significant SNP position associated with FLW on chromosome 2, which were detected in both of the two years of the study period through general linear model (GLM) and mixed linear model (MLM). Furthermore, three candidate genes—LOC_Os02g56760, LOC_Os05g34380, and LOC_Os05g34600—were found to possibly be significantly related to flag leaf shape in rice. Haplotype analysis indicated that LOC_Os05g34380 is highly associated with flag leaf length and flag leaf length–width ratio, LOC_Os05g34600 is highly associated with flag leaf length, and LOC_Os02g56760 is highly associated with flag leaf width. Our results provide important genetic information for the molecular improvement of rice flag leaf shape, laying the foundation for further cloning and molecular-assisted breeding of flag leaf genes. [ABSTRACT FROM AUTHOR]

Maintaining Na+/K+ homeostasis is a critical feature for plant survival under salt stress, which depends on the operation of Na+ and K+ transporters. Although some K+ transporters mediating root K+ uptake have been reported to be essential to the maintenance of Na+/K+ homeostasis, the effect of K+ long‐distance translocation via phloem on plant salt tolerance remains unclear. Here, we provide physiological and genetic evidence of the involvement of phloem‐localized OsAKT2 in rice salt tolerance. OsAKT2 is a K+ channel permeable to K+ but not to Na+. Under salt stress, a T‐DNA knock‐out mutant, osakt2 and two CRISPR lines showed a more sensitive phenotype and higher Na+ accumulation than wild type. They also contained more K+ in shoots but less K+ in roots, showing higher Na+/K+ ratios. Disruption of OsAKT2 decreases K+ concentration in phloem sap and inhibits shoot‐to‐root redistribution of K+. In addition, OsAKT2 also regulates the translocation of K+ and sucrose from old leaves to young leaves, and affects grain shape and yield. These results indicate that OsAKT2‐mediated K+ redistribution from shoots to roots contributes to maintenance of Na+/K+ homeostasis and inhibition of root Na+ uptake, providing novel insights into the roles of K+ transporters in plant salt tolerance. In Oryza sativa, a Shaker K+ channel, OsAKT2 mediates K+ redistribution from shoots to roots, contributing to maintenance of Na+/K+ homeostasis and inhibition of root Na+ uptake under salt stress. [ABSTRACT FROM AUTHOR]

Summary: The plant Shaker K+ channel AtAKT2 has been identified as a weakly rectifying channel that can stabilize membrane potentials to promote photoassimilate phloem loading and translocation. Thus, studies on functional characterization and regulatory mechanisms of AtAKT2‐like channels in crops are highly important for improving crop production. Here, we identified the rice OsAKT2 as the ortholog of Arabidopsis AtAKT2, which is primarily expressed in the shoot phloem and localized at the plasma membrane. Using an electrophysiological assay, we found that OsAKT2 operated as a weakly rectifying K+ channel, preventing H+/sucrose‐symport‐induced membrane depolarization. Three critical amino acid residues (K193, N206, and S326) are essential to the phosphorylation‐mediated gating change of OsAKT2, consistent with the roles of the corresponding sites in AtAKT2. Disruption of OsAKT2 results in delayed growth of rice seedlings under short‐day conditions. Interestingly, the lipid second messenger phosphatidic acid (PA) inhibits OsAKT2‐mediated currents (both instantaneous and time‐dependent components). Lipid dot‐blot assay and liposome‐protein binding analysis revealed that PA directly bound with two adjacent arginine residues in the ANK domain of OsAKT2, which is essential to PA‐mediated inhibition of OsAKT2. Electrophysiological and phenotypic analyses also showed the PA‐mediated inhibition of AtAKT2 and the negative correlation between intrinsic PA level and Arabidopsis growth, suggesting that PA may inhibit AKT2 function to affect plant growth and development. Our results functionally characterize the Shaker K+ channel OsAKT2 and reveal a direct link between phospholipid signaling and plant K+ channel modulation. Significance Statement: Phospholipids function as second messengers, modulating some kinds of ion channels in animal cells, but in plants, phospholipid‐mediated modulation of ion channels remains unclear. Herein, we identified OsAKT2 (a Shaker family member in rice) as a weakly rectifying K+ channel and found that phosphatidic acid, a lipid mediator, inhibited OsAKT2 activity by binding with two adjacent arginine residues in the ANK domain, revealing a direct link between phospholipid signaling and plant K+ channel modulation. [ABSTRACT FROM AUTHOR]

Rice leaf angle is an important agronomic trait determining plant architecture and crop yield. Brassinosteroids (BRs) play crucial roles in controlling rice leaf angle, thus an increasing number of researches were focused on the BR signaling pathway in rice. However, the orthologs of some important components in Arabidopsis BR signaling have not yet been characterized in rice. In this study, we identified a rice bHLH transcription factor named OsBIM1, as the closest rice homolog of AtBIM1 (BES1-Interacting MYC-like Protein1). Overexpression of OsBIM1 significantly increases rice leaf angles, whereas the T-DNA knock-out mutant osbim1 and wide type (WT) showed similar leaf inclination. OsBIM1 overexpression enhances the sensitivity and response to BR treatment in rice. Gene expression analysis showed that the overexpression of OsBIM1 significantly increased the transcripts of INCREASED LEAF INCLINATION1 (OsILI1) that functions as a key transcription factor promoting BR signaling and response. Meanwhile, OsBIM1 inhibited the expression of DWARF2 (OsD2 , a key enzyme in BR biosynthesis pathway). OsBIM1 can bind with OsILI1 promoter and enhance OsILI1 expression in response to BR treatment. The promoting effect of OsBIM1 overexpression on leaf angle can still be observed at harvest stage, but overexpression of OsBIM1 resulted in smaller grain size and reduced yield. These results indicate that OsBIM1 functions as a positive regulator in BR signaling, and its overexpression increases rice lamina inclination by promoting BR sensitivity and response. • OsBIM1 , the closest rice homolog of AtBIM1 , positively regulates rice leaf angle. • Overexpression of OsBIM1 enhances the sensitivity and response to BR in rice. • OsBIM1 encodes a nuclear-localized bHLH protein binding with OsILI1 promoter. • OsBIM1 promotes BR signaling by increasing OsILI1 expression. [ABSTRACT FROM AUTHOR]