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Summary: Understanding the molecular regulation of plant cold response is the basis for cold resistance germplasm improvement. Here, we revealed that the apple histone deacetylase MdHDA6 can perform histone deacetylation on cold‐negative regulator genes and repress their expression, leading to the positive regulation of cold tolerance in apples. Moreover, MdHDA6 directly interacts with the transcription factor MdTCP15. Phenotypic analysis of MdTCP15 transgenic apple lines and wild types reveals that MdTCP15 negatively regulates cold tolerance in apples. Furthermore, we found that MdHDA6 can facilitate histone deacetylation of MdTCP15 and repress the expression of MdTCP15, which positively contributes to cold tolerance in apples. Additionally, the transcription factor MdTCP15 can directly bind to the promoter of the cold‐negative regulator gene MdABI1 and activate its expression, and it can also directly bind to the promoter of the cold‐positive regulator gene MdCOR47 and repress its expression. However, the co‐expression of MdHDA6 and MdTCP15 can inhibit MdTCP15‐induced activation of MdABI1 and repression of MdCOR47, suggesting that MdHDA6 suppresses the transcriptional regulation of MdTCP15 on its downstream genes. Our results demonstrate that histone deacetylase MdHDA6 plays an antagonistic role in the regulation of MdTCP15‐induced transcriptional activation or repression to positively regulate cold tolerance in apples, revealing a new regulatory mechanism of plant cold response. [ABSTRACT FROM AUTHOR]

Drought resistance in plants is influenced by multiple signaling pathways that involve various transcription factors, many target genes, and multiple types of epigenetic modifications. Studies on epigenetic modifications of drought focus on DNA methylation and histone modifications, with fewer on chromatin remodeling. Changes in chromatin accessibility can play an important role in abiotic stress in plants by affecting RNA polymerase binding and various regulatory factors. However, the changes in chromatin accessibility during drought in apples are not well understood. In this study, the landscape of chromatin accessibility associated with the gene expression of apple (GL3) under drought conditions was analyzed by Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) and RNA-seq. Differential analysis between drought treatment and control identified 23,466 peaks of upregulated chromatin accessibility and 2447 peaks of downregulated accessibility. The drought-induced chromatin accessibility changed genes were mainly enriched in metabolism, stimulus, and binding pathways. By combining results from differential analysis of RNA-seq and ATAC-seq, we identified 240 genes with higher chromatin accessibility and increased gene expression under drought conditions that may play important functions in the drought response process. Among them, a total of nine transcription factor genes were identified, including ATHB7, HAT5, and WRKY26. These transcription factor genes are differentially expressed with different chromatin accessibility motif binding loci that may participate in apple response to drought by regulating downstream genes. Our study provides a reference for chromatin accessibility under drought stress in apples and the results will facilitate subsequent studies on chromatin remodelers and transcription factors. [ABSTRACT FROM AUTHOR]

• Herein, we identify lncRNAs involved in four stages from early to fully-ripening stage of apple (Malus domestica) fruit. • 12,570 differentially expressed mRNAs and 3571 differentially expressed lncRNAs were identified. • The targeted relationship of lncRNA-mRNA was analyzed by using co-location, co-expression, and cluster networks. • Three lncRNAs (TCONS_00131720, TCONS_00025525, TCONS_00032426) were identified to target the mRNAs of IAA32, SAUR36, and PA2 which were involved in apple fruit development process. • The related lncRNAs (TCONS_00060619, TCONS_00178112, TCONS_00065854) were analyzed by combining with miRNAs data and GAMYB-miR159a regulation was identified which might related to apple coloring. Long noncoding RNAs (lncRNAs) have been reported to play a regulatory role during fresh fruit ripening. However, the functions of lncRNAs during apple fruit ripening have received relatively little attention. Here, we performed strand-specific RNA-seq and lncRNA identification at four developmental stages of 'Pinova' apple (Malus domestica) fruits. A total of 12,570 differentially expressed mRNAs and 3571 differentially expressed lncRNAs were identified among the four fruit developmental stages. Co-localization and co-expression principles were used to explore lncRNA–mRNA target relationships. Interestingly, most lncRNA targeted mRNAs appeared to participate in various fruit ripening pathways involving the cell wall, photosystems, biosynthesis and metabolic processes. To further explore the potential correlations between lncRNAs and mRNAs, a group of 8239 mRNAs and 3566 lncRNAs were used for cluster and co-expression network analysis, and 15 clusters were obtained. Four different clusters were selected for functional analysis and the construction of co-expression networks. mRNAs differentially expressed in the early ripening stages were mainly involved with photosynthesis, whereas those differentially expressed at later stages were associated with metabolic pathways, consistent with the dynamic accumulation of metabolites in ripening fruits. Based on these analyses, we identified a series of genes that play vital roles in fruit ripening and are regulated by lncRNAs; these included IAA32, SAUR36 , and PA2. qRT-PCR analysis also validated these regulatory relationships. Previous studies have shown that lncRNAs can repress miRNA–mRNA targeting by acting as endogenous target mimics (eTMs). We therefore investigated the involvement of lncRNAs in miRNA targeting of mRNA, and eTMs of lncRNAs involved in the targeting of GAMYB (transcriptional factor in anthocyanin synthesis) by miR159 were identified. These results provide insight for future studies of lncRNA regulation during apple fruit ripening. [ABSTRACT FROM AUTHOR]

GABA (γ-aminobutyric acid) plays a multifaceted role in plant growth, fruit quality, and tolerance to abiotic stresses. However, its physiological roles and mechanisms in the fruit quality and response to long-term drought stress in apple remain unelucidated. To investigate the effect of GABA on apple fruit quality and drought tolerance, we sprayed exogenous GABA on apple cultivar "Cripps Pink" and irrigated rootstock M.9-T337 with GABA, respectively. Results showed that exogenous GABA could effectively improve the fruit quality of "Cripps Pink", including increased sugar-to-acid ratio, flesh firmness, pericarp malleability, and GABA content, as well as reduced fruit acidity. In addition, pretreatment of M.9-T337 plants with GABA improved their tolerance to both long- and short-term drought stress. Specifically, 1 mM exogenous GABA increased the net photosynthetic rate, relative leaf water content, root-to-shoot ratio, and water use efficiency under long-term drought stress, and delayed the increased of the relative electrolyte leakage under short-term drought stress. RNA-seq analysis identified 1271 differentially expressed genes (DEGs) between nontreated and GABA-pretreated plants under short-term drought stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these DEGs revealed that GABA may enhance plant drought resistance by upregulating the expression of genes related to "Biosynthesis of secondary metabolites", "MAPK signaling pathway", "Glutathione metabolism", and "Carbon fixation in photosynthetic organisms". In conclusion, these results revealed that exogenous GABA can improve fruit quality and enhance drought tolerance in apple. [ABSTRACT FROM AUTHOR]