Establishment of Saccharum spontaneum L. Core Collections

Qi, Yongwen; Fan, Lina; Luo, Qiong; Wang, Qinnan; Chen, Yongsheng; Huang, Zhidong; Liu, Rui; Liu, Shao-Mou; Deng, Hai-hua; Li, Qiwei

doi:10.3724/sp.j.1006.2013.00649

Cited by 6 publications

(3 citation statements)

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“…The nuclear extraction reagent formulas of various Gramineae plants were used to extract nuclei and build libraries for ATAC-Seq from zoysiagrass (Qi et al ., 2023). The Novoprotein Chromatin Profile Kit for Illumina extracted nuclei and fragment chromatin in zoysiagrass.…”

Section: Methodsmentioning

confidence: 99%

Integration of ATAC-seq and RNA-seq identifies novel candidate genes associated with drought tolerance inZoysia japonicaSteud

Shen,

Qi,

et al. 2023

Preprint

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HighlightIntegration of ATAC-seq and RNA-seq identifies novel candidate genes associated with drought tolerance inZoysia japonicaSteud.The warm-season turfgrass Zoysia japonica is renowned for its drought resistance and serves as an exceptional domestic turfgrass in China. In order to unlock the potential of this native grass, identify drought-resistant genes, enhance the genetic transformation system, and maximize its utilization benefits, we conducted physiological characterization, multi-omics analysis, and RT-qPCR experimental verification in Zoysia japonica. This study suggested that 63 high-confidence genes related to drought stress and 6 motifs regulating drought responses were identified using a combined omics approach and RT-qPCR validation. The study discovered a positive correlation between ATAC-Seq peak intensity and gene expression levels. The expression of high-confidence genes was linked toZoysia japonicaresistance evaluation and phenotypic traits, implying that these genes are involved in responding to external drought stress. This study combined ATAC-seq and RNA-seq technologies for the first time to identify drought-related genes inZoysia japonica, elucidating the grass’s adaptation to environmental stress and the regulatory mechanisms underlying stress responses, and laying the groundwork forZoysia japonicaimprovement and breeding.

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Section: Methodsmentioning

confidence: 99%

Integration of ATAC-seq and RNA-seq identifies novel candidate genes associated with drought tolerance inZoysia japonicaSteud

Shen,

Qi,

et al. 2023

Preprint

View full text Add to dashboard Cite

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“…Micro/nano-scale electromechanical systems (MEMS/NEMS) with micro/nano-scaled channels have gained widespread applications in diverse fields such as physics, chemistry, aerospace, environmental monitoring, biological detection, targeted drug delivery, DNA manipulation, and biomedicine. [1][2][3] The efficient transfer of fluids in microchannels is a prerequisite for the smooth operation of these microfluidic systems. [4] Due to the larger surface-to-volume ratio, micro/nano-scaled channels render the flow of the fluid more susceptible to surface properties such as roughness, hydrophobicity, and surface forces than in macro-scaled channels.…”

Section: Intorductionmentioning

confidence: 99%

Influence of surface roughness on the fluid flow in microchannel

Li,

Zhang,

et al. 2024

J. Phys.: Conf. Ser.

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Surface roughness is a crucial factor of fluid flow in microfluidic channels. Most of the existing studies focus on the effect of regular microstructured surfaces on fluid flow, while researchs about the impact of random rough surfaces on fluid flow remains limited. Therefore, in this study, a random rough surface model and two microstructured surface models were established, and the effects surface roughness on the fluid flow at Wenzel state and Cassie-Baxter state were studied using COMSOL multi-physics simulation software. Our findings reveal that both the flow velocity and the fluid flow rate at the microchannel outlet decreases with the surface roughness increases. Notably, the flow rate and velocity of the fluid flow at Cassie-Baxter state is higher than that of fluid flow at Wenzel state.

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“…The nuclear extraction reagent formulas of various Gramineae plants were used to extract nuclei and build libraries for ATAC-seq from zoysiagrass [50]. The Novoprotein Chromatin Pro le Kit for Illumina extracted nuclei and fragment chromatin in zoysiagrass.…”

Section: Rna Extraction and Atac Libraries Preparationmentioning

confidence: 99%

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

Shen,

Li,

et al. 2024

Preprint

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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.

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Establishment of Saccharum spontaneum L. Core Collections

Cited by 6 publications

References 0 publications

Integration of ATAC-seq and RNA-seq identifies novel candidate genes associated with drought tolerance inZoysia japonicaSteud

Integration of ATAC-seq and RNA-seq identifies novel candidate genes associated with drought tolerance inZoysia japonicaSteud

Influence of surface roughness on the fluid flow in microchannel

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

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