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Comprehensive Dataset of Genes with Loss-of-function Mutant Phenotypes in Arabidopsis Thaliana

Lloyd, John Paul
Mutant phenotypes of Arabidopsis thaliana have proven to be a powerful tool in the study of plant biology. However, genome-wide information on these mutant phenotypes and the altered genes that give rise to them remains difficult to obtain. This thesis describes the construction of a comprehensive, gene-based dataset of mutant phenotype information in Arabidopsis. The SeedGenes database of embryo-defective genes (www.seedgenes.org) and a preliminary phenotype dataset from a Plant Physiology paper published by the Meinke laboratory nine years ago established a foundation for this project. Additional genes and associated phenotypes were identified through manual literature curation focused on PubMed literature searches and a list of candidate phenotype genes provided by TAIR (www.arabidopsis.org). The final phenotype dataset contains information on 2,400 genes with a documented loss-of-function phenotype in Arabidopsis. A complementary dataset of phenotypes resulting from the disruption of more than one genetically redundant gene was also constructed. This multiple mutant dataset contains phenotype data for an additional 400 genes. The 2,800 total genes identified here represent over 10% of the Arabidopsis genome. Information from this dataset assisted in evaluating Arabidopsis genes with gametophyte phenotypes and helped to address the curious survival of mutant gametophytes lacking basic cellular functions. The complete dataset was used to explore the relationship between mutant phenotype and protein function, subcellular localization, protein connectivity, and genetic redundancy. The degree of similarity in protein sequences and expression levels of fully- and partially-redundant genes was analyzed and the similarity in phenotypes of putative orthologs in rice, maize, and tomato was investigated. The thesis concludes with a discussion of Arabidopsis genes that display no apparent loss-of-function phenotype. Much of the work described here is available through several recent publications (Bryant et al., 2011; Muralla et al., 2011; Lloyd and Meinke, 2012).