Multi-Knock—a multi-targeted genome-scale CRISPR toolbox to overcome functional redundancy in plants

Abstract

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Root Walker: an automated pipeline for large scale quantification of early root growth responses at high spatial and temporal resolution

“…The scale of root growth measurements enables genetic screens such as GWAS and subsequent candidate gene identification and validation. Since treatments with chemicals, nutrients, small bioactive molecules, and plant hormones will be easy using this platform, this opens up opportunities to bring about new biological insight using large-scale genetic approaches on fast root growth responses by utilizing natural variation or other collections suitable for genetic discovery (Hauser et al ., 2013; Coego et al ., 2014; 1001 Genomes Consortium, 2016; Hu et al ., 2023). We note that we were able to conduct this experiment in less than 2 weeks with a single person, while in our hands efforts studies that involve the treatment of GWAS accession panels with a single person usually take significantly more time (more than one or two months due to growing plants; re-opening/treating/resealing and scanning plates).…”

Tackling redundancy: genetic mechanisms underlying paralog compensation in plants

“…This strategy must start with the identification of redundancy and compensation patterns. Genome editing technologies now allow for the implementation of multiplex loss-offunction studies (Ewen-Campen et al, 2017;Hu et al, 2023), which can then inform us about the redundant relationships among paralogs. A genome-wide application of this approach has recently been demonstrated in Arabidopsis thaliana (Hu et al, 2023).…”

“…Genome editing technologies now allow for the implementation of multiplex loss-offunction studies (Ewen-Campen et al, 2017;Hu et al, 2023), which can then inform us about the redundant relationships among paralogs. A genome-wide application of this approach has recently been demonstrated in Arabidopsis thaliana (Hu et al, 2023). However, its implementation in other plant species must first address the challenges associated with large-scale transformation efforts but could become a new frontier in plant functional studies.…”

Establishment of a high‐efficiency transformation and genome editing method for an essential vegetable and medicine Solanum nigrum

“…There are three developed targeted genome editing tools: the zinc finger nucleases (Lloyd et al, 2005), transcription activator-like effector endonucleases (Bogdanove & Voytas, 2011;Cermak et al, 2011), and the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein (Cas) system (Doudna & Emmanuelle, 2014;Li et al, 2013). The RNAguided CRISPR-Cas9 system is a simple and extremely efficient tool for generating heritable genome editing modifications in many plant species (Chen et al, 2019;Dahan-Meir et al, 2018;Hu et al, 2023;Shimatani et al, 2017;Svitashev et al, 2015). The CRISPR-Cas9 system is typically conducted through delivering reagents, such as Cas9 and single-guide RNAs, using conventional gene delivery systems, including particle bombardment, electroporation, and Agrobacteriummediated delivery (Altpeter et al, 2016;Char et al, 2017;Rodrigues et al, 2021;Sardesai & Subramanyam, 2018).…”