Natural variation in CYCLIC NUCLEOTIDE-GATED ION CHANNEL 4 reveals a novel role of calcium signaling in vegetative phase change in Arabidopsis.

The timing of vegetative phase change (VPC) in plants is regulated by a temporal decline in the expression of miR156. Both exogenous cues and endogenous factors, such as temperature, light, sugar, nutrients, and epigenetic regulators, have been shown to affect VPC by altering miR156 expression. However, the genetic basis of natural variation in VPC remains largely unexplored. Here, we conducted a genome-wide association study on the variation of the timing of VPC in Arabidopsis. We identified CYCLIC NUCLEOTIDE-GATED ION CHANNEL 4 (CNGC4) as a significant locus associated with the diversity of VPC. Mutations in CNGC4 delayed VPC, accompanied by an increased expression level of miR156 and a corresponding decrease in SQUAMOSA PROMOTER BINDING-LIKE (SPL) gene expression. Furthermore, mutations in CNGC2 and CATION EXCHANGER 1/3 (CAX1/3) also led to a delay in VPC. Polymorphisms in the CNGC4 promoter contribute to the natural variation in CNGC4 expression and the diversity of VPC. Specifically, the early CNGC4 variant promotes VPC and enhances plant adaptation to local environments. In summary, our findings offer genetic insights into the natural variation in VPC in Arabidopsis, and reveal a previously unidentified role of calcium signaling in the regulation of VPC.

Genome-wide association study identifies a novel BMI1A QTL allele that confers FLC expression diversity in Arabidopsis thaliana.

Identification and understanding of the genetic basis of natural variations in plants are essential for comprehending their phenotypic adaptation. Here, we report a genome-wide association study (GWAS) of FLOWERING LOCUS C (FLC) expression in 727 Arabidopsis accessions. We identified B LYMPHOMA MOLONEY MURINE LEUKEMIA VIRUS INSERTION REGION 1 HOMOLOG 1A (BMI1A) as a causal gene for one of the FLC expression quantitative trait loci (QTLs). Loss of function in BMI1A increases FLC expression and delays flowering time at 16 °C significantly compared with the wild type (Col-0). BMI1A activity is required for histone H3 lysine 27 trimethylation (H3K27me3) accumulation at the FLC, MADS AFFECTING FLOWERING 4 (MAF4), and MAF5 loci at low ambient temperature. We further uncovered two BMI1A haplotypes associated with the natural variation in FLC expression and flowering time at 16 °C, and demonstrated that polymorphisms in the BMI1A promoter region are the main contributor. Different BMI1A haplotypes are strongly associated with geographical distribution, and the low ambient temperature-sensitive BMI1A variants are associated with a lower mean temperature of the driest quarter of their collection sites compared with the temperature-non-responsive variants, indicating that the natural variations in BMI1A have adaptive functions in FLC expression and flowering time regulation. Therefore, our results provide new insights into the natural variations in FLC expression and flowering time diversity in plants.

Transcriptomic Responses to Chilling Reveal Potential Chilling Tolerance Mechanisms in Cucumber.

Chilling is a devastating stress that has led to a crisis of production for cucumber (Cucumis sativus L.). To determine the molecular mechanisms underlying chilling responses in cucumber, we investigated physiological changes and transcriptomic responses to chilling stress in the chilling-tolerant inbred line CC and chilling-susceptible inbred line R1461. Physiological analysis showed that CC had a higher survival rate, lower H2O2 accumulation, and ion leakage than R1461 after chilling treatment. RNA-seq analysis identified 938 differentially expressed genes (DEGs) in response to chilling and revealed that chilling stress regulated the transcript levels of genes related to hormones, including auxin, salicylic acid (SA), jasmonic acid (JA), and ethylene. RT-qPCR and pharmacological analysis suggested that cucumber chilling tolerance was associated with variation in the gene expression involved in ethylene biosynthesis and signaling. Exogenously applying 1-aminocyclopropane-1-carboxylic acid (ACC), the precursor of ethylene, improved the chilling tolerance of cucumber, while the exogenous application of the ethylene inhibitor AgNO3 impaired the chilling tolerance of cucumber. After ACC treatment, the difference in chilling tolerance between CC and R1461 disappeared, suggesting that the different chilling tolerance level between CC and R1461 is dependent on the ethylene biosynthesis and signaling pathway. In addition, a comparison of cucumber lines with different chilling tolerances revealed that chilling tolerance is highly associated with the up-regulation of C-repeat binding factor (CBF) genes, while natural variation in the promoter of CsCBF1 is associated with chilling response. This study thus provides information on transcriptomic responses in different varieties of chilling-tolerant cucumber and reveals potential chilling tolerance mechanisms that could be used to improve chilling tolerance in cucumber.