TY - JOUR
T1 - A curated list of genes that affect the plant ionome
AU - Whitt, Lauren
AU - Ricachenevsky, Felipe Klein
AU - Ziegler, Greg Ziegler
AU - Clemens, Stephan
AU - Walker, Elsbeth
AU - Maathuis, Frans J.M.
AU - Kear, Philip
AU - Baxter, Ivan
N1 - Publisher Copyright:
© 2020 The Authors. Plant Direct published by American Society of Plant Biologists, Society for Experimental Biology and John Wiley & Sons Ltd.
PY - 2020/10/1
Y1 - 2020/10/1
N2 - 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.
AB - 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.
KW - curated
KW - ionomics
KW - mineral nutrition
UR - http://www.scopus.com/inward/record.url?scp=85094667432&partnerID=8YFLogxK
U2 - 10.1002/pld3.272
DO - 10.1002/pld3.272
M3 - Article
AN - SCOPUS:85094667432
SN - 2475-4455
VL - 4
JO - Plant Direct
JF - Plant Direct
IS - 10
M1 - e00272
ER -