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

Abstract

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.

Arabidopsis REI-LIKE proteins activate ribosome biogenesis during cold acclimation

“…9 ). The slight accumulation of abundant RPL3A, an essential gene for Arabidopsis (Meinke, 2019), appears to compensate reduction of RPL3B in our study. In addition, RPL3B decrease in the absence of REIL proteins has a transcriptional component, as the reduction of RPL3B transcript is one of the rare observations of otherwise absent associations between transcriptome and proteome changes of non-translating fractions ( Supplemental Figure S9 ).…”

Epigenetics Regulates Reproductive Development in Plants

“…Seed development is controlled by programmed gene expression. To date, many genes have been identified and characterized as being important for seed development [156]. The research in the last decade has shown epigenetics is important for seed development, but it remains largely unclear how different epigenetic mechanisms interact to regulate seed development.…”

The Flavoproteome of the Model Plant Arabidopsis thaliana

“…Recently, an updated list of 510 EMBRYO-DEFECTIVE (EMB) genes was presented [41], which contains several flavoenzyme-encoding genes. We detected six flavoenzyme-encoding genes (AT1G24340, AT1G48850, AT1G49880, AT3G02280, AT3G54660, AT5G14760), which are assigned to be essential for embryo development [42][43][44][45][46].…”

“…AT1G24340 is predicted to encode a FAD-dependent flavoenzyme (see the third evidence code). Considering that the list of EMB genes is not complete (as 750-1000 EMB genes are estimated in Arabidopsis [41]), it is assumed that more flavoenzymes are essential for embryo development. In continuation, a list of embryo-lethal double mutants (embryo lethality only in combination of two mutated genes) was published.…”