Suitability of two distinct approaches for the high-throughput study of the post-embryonic effects of embryo-lethal mutations in Arabidopsis

Muñoz-Nortes, Tamara; Candela, Héctor; Micol, José Luis

doi:10.1038/s41598-017-17218-z

Cited by 3 publications

(2 citation statements)

References 23 publications

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“…One important outcome of this approach was the identification of the leafy cotyledon phenotype in Arabidopsis . Mosaic analysis using marked genetic sectors has also been explored, although not fully utilized (Latvala-Kilby & Kilby, 2006;Muñoz-Nortes et al, 2017). One of the most intriguing examples of post-embryonic development involves a mutant defective in a cell wall glycoprotein (EXTENSIN3) in which 'self-rescue' generates viable homozygotes (phenotypic revertants) that activate alternative gene expression programs (Saha et al, 2013).…”

Section: Reviewmentioning

confidence: 99%

Genome‐wide identification of EMBRYO‐DEFECTIVE (EMB) genes required for growth and development in Arabidopsis

Meinke

2019

New Phytologist

140

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Summary With the emergence of high‐throughput methods in plant biology, the importance of long‐term projects characterized by incremental advances involving multiple laboratories can sometimes be overlooked. Here, I highlight my 40‐year effort to isolate and characterize the most common class of mutants encountered in Arabidopsis (Arabidopsis thaliana): those defective in embryo development. I present an updated dataset of 510 EMBRYO‐DEFECTIVE (EMB) genes identified throughout the Arabidopsis community; include important details on 2200 emb mutants and 241 pigment‐defective embryo (pde) mutants analyzed in my laboratory; provide curated datasets with key features and publication links for each EMB gene identified; revisit past estimates of 500–1000 total EMB genes in Arabidopsis; document 83 double mutant combinations reported to disrupt embryo development; emphasize the importance of following established nomenclature guidelines and acknowledging allele history in research publications; and consider how best to extend community‐based curation and screening efforts to approach saturation for this diverse class of mutants in the future. Continued advances in identifying EMB genes and characterizing their loss‐of‐function mutant alleles are needed to understand genotype‐to‐phenotype relationships in Arabidopsis on a broad scale, and to document the contributions of large numbers of essential genes to plant growth and development.

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Section: Reviewmentioning

confidence: 99%

Genome‐wide identification of EMBRYO‐DEFECTIVE (EMB) genes required for growth and development in Arabidopsis

Meinke

2019

New Phytologist

140

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“…Other methods include the conditional knockout of genes in specific cell types or tissues using a CRE recombinase (Sieburth et al, 1998). These approaches, however, can be cumbersome and difficult to scale (Muñoz-Nortes et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

CRISPR-TSKO: A Technique for Efficient Mutagenesis in Specific Cell Types, Tissues, or Organs in Arabidopsis

et al. 2019

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Detailed functional analyses of many fundamentally important plant genes via conventional loss-of-function approaches are impeded by the severe pleiotropic phenotypes resulting from these losses. In particular, mutations in genes that are required for basic cellular functions and/or reproduction often interfere with the generation of homozygous mutant plants, precluding further functional studies. To overcome this limitation, we devised a clustered regularly interspaced short palindromic repeats (CRISPR)-based tissue-specific knockout system, CRISPR-TSKO, enabling the generation of somatic mutations in particular plant cell types, tissues, and organs. In Arabidopsis (Arabidopsis thaliana), CRISPR-TSKO mutations in essential genes caused well-defined, localized phenotypes in the root cap, stomatal lineage, or entire lateral roots. The modular cloning system developed in this study allows for the efficient selection, identification, and functional analysis of mutant lines directly in the first transgenic generation. The efficacy of CRISPR-TSKO opens avenues for discovering and analyzing gene functions in the spatial and temporal contexts of plant life while avoiding the pleiotropic effects of systemwide losses of gene function.

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Taking the Wheel – de novo DNA Methylation as a Driving Force of Plant Embryonic Development

et al. 2021

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During plant embryogenesis, regardless of whether it begins with a fertilized egg cell (zygotic embryogenesis) or an induced somatic cell (somatic embryogenesis), significant epigenetic reprogramming occurs with the purpose of parental or vegetative transcript silencing and establishment of a next-generation epigenetic patterning. To ensure genome stability of a developing embryo, large-scale transposon silencing occurs by an RNA-directed DNA methylation (RdDM) pathway, which introduces methylation patterns de novo and as such potentially serves as a global mechanism of transcription control during developmental transitions. RdDM is controlled by a two-armed mechanism based around the activity of two RNA polymerases. While PolIV produces siRNAs accompanied by protein complexes comprising the methylation machinery, PolV produces lncRNA which guides the methylation machinery toward specific genomic locations. Recently, RdDM has been proposed as a dominant methylation mechanism during gamete formation and early embryo development in Arabidopsis thaliana, overshadowing all other methylation mechanisms. Here, we bring an overview of current knowledge about different roles of DNA methylation with emphasis on RdDM during plant zygotic and somatic embryogenesis. Based on published chromatin immunoprecipitation data on PolV binding sites within the A. thaliana genome, we uncover groups of auxin metabolism, reproductive development and embryogenesis-related genes, and discuss possible roles of RdDM at the onset of early embryonic development via targeted methylation at sites involved in different embryogenesis-related developmental mechanisms.

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Suitability of two distinct approaches for the high-throughput study of the post-embryonic effects of embryo-lethal mutations in Arabidopsis

Cited by 3 publications

References 23 publications

Genome‐wide identification of EMBRYO‐DEFECTIVE (EMB) genes required for growth and development in Arabidopsis

Genome‐wide identification of EMBRYO‐DEFECTIVE (EMB) genes required for growth and development in Arabidopsis

CRISPR-TSKO: A Technique for Efficient Mutagenesis in Specific Cell Types, Tissues, or Organs in Arabidopsis

Taking the Wheel – de novo DNA Methylation as a Driving Force of Plant Embryonic Development

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