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.

Drought stress caused a significant threat to apple growth and production. Although there is an increasing studies concerning the molecular mechanism in apple response to drought, most of these studies focus on the leaves. However, the roots is the first organism to sense the drought signal and play important role in drought response. The molecular mechanisms underlying the apple roots in response to drought needs to be further explored. In this study, we conducted a comparative transcriptomic analysis of roots from drought-resistant (Malus prunifolia) and drought-susceptible (Malus hupehensis) apple genotypes under different soil water contents with 60% (control), 30% (mild drought), 10% (moderate drought), and 5% (severe drought). The further Mapman pathways analysis showed that Malus prunifolia exhibited more rapid activation of abscisic acid (ABA) biosynthesis (NCED, PYL) and signaling pathway, as well as the induction of transcription factors (NAC, WRKY, MYB) compare to Malus prunifolia under mild and moderate drought treatments. This might be one of the reasons why Malus prunifolia exhibits greater drought resistance. Furthermore, weighted gene co-expression network analysis (WGCNA) was adopted for the identification of core drought-responsive genes. Notably, three hub genes, ubiquitin-conjugating enzyme 32 (UBC32), basic leucine-zipper 4 (bZIP4), and highly ABA-induced PP2C gene 2 (HAI2), were selected from the different modules, suggesting their vital roles in drought response. Taken together, our results gain insights into the global expression alterations in drought-resistance and susceptible germplasms under different drought conditions and identify some key genes involved in drought response, which is helpful for drought-resistant apple breeding in future.

Apples (Malus × domestica Borkh.) can be categorized into early-, medium-, and late-ripening cultivars based on the length of the fruit developmental phases. The lengthening of the apple ripening period has a direct impact on its economic worth and market competitiveness, although the underlying mechanism is mostly unclear. In the current study, the development and maturation of the early-ripening ‘Geneva Early’ (GE) and late-ripening ‘Hanfu’ (HF) cultivars of apple fruit were studied using transcriptomics to detect and identify the changes of differential genes. Results showed that the two varieties had different ripening periods, but in both, the development process of fruit ripening required cell division, cell expansion, starch accumulation, and secondary metabolite accumulation. In the early stages of fruit development (G1 to G2), the GE’s fruit size was larger than HF’s, and the GO analysis revealed an enrichment in genes involved in the metabolism of fatty acids and carbon molecules. In G2 phase, the GE involved numerous regulatory factors of hormonal pathways, while in HF this phase was mainly enriched in the metabolism of sugars and carbohydrates. The results indicated that during GE development, the relevant genes regulating fruit development were expressed earlier than HF, which made fruit development enter the next development phase earlier, thereby shortening the fruit development phase. These findings contributed to an improved understanding of the molecular basis of apple ripening and provide a reliable reference for apple breeding using genomics.