A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis    

Abstract

Despite the widespread use of Arabidopsis (Arabidopsis thaliana) as a model plant, a curated dataset of Arabidopsis genes with mutant phenotypes remains to be established. A preliminary list published nine years ago in Plant Physiology is outdated, and genome-wide phenotype information remains difficult to obtain. We describe here a comprehensive dataset of 2,400 genes with a loss-of-function mutant phenotype in Arabidopsis. Phenotype descriptions were gathered primarily from manual curation of the scientific literature. Genes were placed into prioritized groups (essential, morphological, cellular-biochemical, and conditional) based on the documented phenotypes of putative knockout alleles. Phenotype classes (e.g. vegetative, reproductive, and timing, for the morphological group) and subsets (e.g. flowering time, senescence, circadian rhythms, and miscellaneous, for the timing class) were also established. Gene identities were classified as confirmed (through molecular complementation or multiple alleles) or not confirmed. Relationships between mutant phenotype and protein function, genetic redundancy, protein connectivity, and subcellular protein localization were explored. A complementary dataset of 401 genes that exhibit a mutant phenotype only when disrupted in combination with a putative paralog was also compiled. The importance of these genes in confirming functional redundancy and enhancing the value of single gene datasets is discussed. With further input and curation from the Arabidopsis community, these datasets should help to address a variety of important biological questions, provide a foundation for exploring the relationship between genotype and phenotype in angiosperms, enhance the utility of Arabidopsis as a reference plant, and facilitate comparative studies with model genetic organisms.

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology

“…For users who do not know which gene (or genes) they want to look at, the "Expression Angler" button opens a tool that helps identify genes based on a user-defined expression pattern (Austin et al, 2016), and the "Mutant Phenotype Selector" button opens a tool that helps identify genes based on Lloyd and Meinke's mutant phenotype classification system (Lloyd and Meinke, 2012 Icons appear gray when a module is unavailable, turn black once the data have loaded, and are highlighted green when the module is active (i.e., has been selected for viewing by the user).…”

Repression of Essential Chloroplast Genes Reveals New Signaling Pathways and Regulatory Feedback Loops inChlamydomonas

“…In this case, plastid growth and division are maintained in the absence of plastid protein synthesis. Moreover, many mutations that disrupt the splicing of chloroplast tRNAs or ribosomal protein mRNAs in maize lead to a complete loss of plastid ribosomes without affecting embryo development (Bryant et al, 2011;Lloyd and Meinke, 2012). Many additional albino mutants of maize and rice (Oryza sativa) lack plastid ribosomes, although the underlying mechanisms are not yet clear.…”

“…This is in contrast with the situations in tobacco in which transplastomic plants with a homoplasmic disruption of the rpoB gene are still viable (Allison et al, 1996) and in barley (Hordeum vulgare) mutants in which plastid translation is fully deficient (Hess et al, 1994a). Similarly, in maize (Zea mays) or rapeseed (Brassica napus), embryo development is not arrested in the absence of chloroplast translation (Bryant et al, 2011;Lloyd and Meinke, 2012), whereas loss of plastid translation results in embryo lethality in Arabidopsis thaliana (Lloyd and Meinke, 2012). We show that, similar to the case of land plants, abrogation of either chloroplast protein synthesis or transcription in C. reinhardtii activates plastid-to-nucleus signaling pathways, causing the induction of several nuclear-encoded stress-responsive plastid proteins prior to cell death.…”

Tissue-Specific Profiling Reveals Transcriptome Alterations inArabidopsisMutants Lacking Morphological Phenotypes

“…Because redundancy is assessed by comparing differences in single and multiple mutants, conclusions regarding genetic redundancy are necessarily dependent on the nature of the phenotypic analysis performed (Pickett and Meeks-Wagner, 1995;Pérez-Pérez et al, 2009;Lloyd and Meinke, 2012).…”

“…However, this approach relies on the availability of mutants that exhibit observable differences in phenotype. Unfortunately, the majority of single-gene mutants lack detectable alterations, due to genetic redundancy, other compensatory mechanisms, or difficulties in phenotypic assessment, which limits the usefulness of a genetic approach for defining gene function (Pickett and Meeks-Wagner, 1995;Bouché and Bouchez, 2001;Hanada et al, 2009a;Pérez-Pérez et al, 2009;Lloyd and Meinke, 2012).…”