Integration of ATAC-seq and RNA-seq Reveals the Dynamics of Chromatin Accessibility and Gene Expression in Zoysiagrass Response to Drought

Abstract

Abstract Background Zoysiagrass is renowned for its drought resistance and serves as an exceptional domestic turfgrass in China. However, the changes in chromatin accessibility during drought in zoysiagrass are not well understood. Methods We assessed the drought tolerance of six ecotypes zoysiagrass varieties based on their growth characteristics and physiological traits under drought conditions. Additionally, we utilized an integrated multi-omics strategy, encompassing whole-genome sequencing (WGS), RNA sequencing (RNA-seq), Assay for Transposase Accessible Chromatin using high-throughput sequencing (ATAC-seq), and RT-qPCR verification experiments, to gain a deeper understanding of the chromatin accessibility patterns linked to gene expression in response to drought stress in zoysiagrass. Results The correlation analysis between proline levels and drought tolerance in zoysiagrass revealed that the variety 'X4' exhibited notably high drought resistance compared to the other six zoysiagrass varieties. The KEGG pathway enrichment analysis revealed that zoysiagrass responded to environmental stress by regulating stress response and antioxidant defense pathways. Notably, the expression levels of genes Zja03G031540 and Zja11G000860 were notably increased in the 'X4' zoysiagrass genotype with improved drought tolerance compared to the 'X1' zoysiagrass genotype with reduced drought tolerance. This study suggested that 63 high-confidence genes related to drought stress and 6 motifs regulating drought responses were unearthed. The study discovered a positive correlation between ATAC-seq peak intensity and gene expression levels. The expression of high-confidence genes was linked to zoysiagrass resistance evaluation and phenotypic traits, implying that these genes are involved in responding to external drought stress. Conclusions This study combined ATAC-seq and RNA-seq technologies for the first time to identify drought-related genes expression in zoysiagrass, elucidating the grass adaptation to environmental stress and the regulatory mechanisms underlying stress responses, and laying the groundwork for zoysiagrass improvement and breeding.