A curated list of genes that affect the plant ionome

Abstract

Understanding the mechanisms underlying plants' adaptation to their environment will require knowledge of the genes and alleles underlying elemental composition. Modern genetics is capable of quickly, and cheaply indicating which regions of DNA are associated with particular phenotypes in question, but most genes remain poorly annotated, hindering the identification of candidate genes. To help identify candidate genes underlying elemental accumulations, we have created the known ionome gene (KIG) list: a curated collection of genes experimentally shown to change uptake, accumulation, and distribution of elements. We have also created an automated computational pipeline to generate lists of KIG orthologs in other plant species using the PhytoMine database. The current version of KIG consists of 176 known genes covering 5 species, 23 elements, and their 1588 orthologs in 10 species. Analysis of the known genes demonstrated that most were identified in the model plant Arabidopsis thaliana, and that transporter coding genes and genes altering the accumulation of iron and zinc are overrepresented in the current list.

Keywords: curated; ionomics; mineral nutrition.

FIGURE 1

Number of genes for each species that are primary, inferred from other primary genes in other species, or both

FIGURE 2

Number of primary genes from each species listing each element

FIGURE 3

Number of primary genes each type of tissue contributes to the known ionome gene list. Above ground is a summary of anther, leaf, seed, and shoot, while below ground is a summary of root and nodule

FIGURE 4

Known ionome genes relating to different terms from the GO complete biological process dataset. Ontology groups of GO Enrichment Analysis from PANTHER