Promoter editing for the genetic improvement of crops

L Shi, J Su, MJ Cho, H Song, X Dong… - Journal of …, 2023 - academic.oup.com
Gene expression plays a fundamental role in the regulation of agronomically important traits
in crop plants. The genetic manipulation of plant promoters through genome editing has …

Integrating omics databases for enhanced crop breeding

H Chao, S Zhang, Y Hu, Q Ni, S Xin, L Zhao… - Journal of Integrative …, 2024 - degruyter.com
Crop plant breeding involves selecting and developing new plant varieties with desirable
traits such as increased yield, improved disease resistance, and enhanced nutritional value …

PlantPAN 4.0: Updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters

CN Chow, CW Yang, NY Wu, HT Wang… - Nucleic acids …, 2024 - academic.oup.com
Abstract PlantPAN 4.0 (http://PlantPAN. itps. ncku. edu. tw/) is an integrative resource for
constructing transcriptional regulatory networks for diverse plant species. In this release, the …

Systematic identification of wheat spike developmental regulators by integrated multi-omics, transcriptional network, GWAS, and genetic analyses

X Lin, Y Xu, D Wang, Y Yang, X Zhang, X Bie, L Gui… - Molecular Plant, 2024 - cell.com
The spike architecture of wheat plays a crucial role in determining grain number, making it a
key trait for optimization in wheat breeding programs. In this study, we used a multi-omic …

Capture of regulatory factors via CRISPR–dCas9 for mechanistic analysis of fine-tuned SERRATE expression in Arabidopsis

W Chen, J Wang, Z Wang, T Zhu, Y Zheng, A Hawar… - Nature Plants, 2024 - nature.com
SERRATE (SE) plays an important role in many biological processes and under biotic stress
resistance. However, little about the control of SE has been clarified. Here we present a …

Integration of multi-omics technologies for crop improvement: status and prospects

R Zhang, C Zhang, C Yu, J Dong, J Hu - Frontiers in Bioinformatics, 2022 - frontiersin.org
With the rapid development of next-generation sequencing (NGS), multi-omics techniques
have been emerging as effective approaches for crop improvement. Here, we focus mainly …

scPlant: A versatile framework for single-cell transcriptomic data analysis in plants

S Cao, Z He, R Chen, Y Luo, LY Fu, X Zhou, C He… - Plant …, 2023 - cell.com
Single-cell transcriptomics has been fully embraced in plant biological research and is
revolutionizing our understanding of plant growth, development, and responses to external …

PPGR: a comprehensive perennial plant genomes and regulation database

S Yang, W Zong, L Shi, R Li, Z Ma, S Ma… - Nucleic Acids …, 2024 - academic.oup.com
Perennial woody plants hold vital ecological significance, distinguished by their unique
traits. While significant progress has been made in their genomic and functional studies, a …

Nitrogen sensing and regulatory networks: it's about time and space

CM Shanks, K Rothkegel, MD Brooks, CY Cheng… - The Plant …, 2024 - academic.oup.com
A plant's response to external and internal nitrogen signals/status relies on sensing and
signaling mechanisms that operate across spatial and temporal dimensions. From a …

Genome‐wide enhancer identification by massively parallel reporter assay in Arabidopsis

Y Tan, X Yan, J Sun, J Wan, X Li, Y Huang… - The Plant …, 2023 - Wiley Online Library
Enhancers are critical cis‐regulatory elements controlling gene expression during cell
development and differentiation. However, genome‐wide enhancer characterization has …