title: Regenerant Arabidopsis lineages display a distinct genome-wide spectrum of mutations conferring variant phenotypes.
abstract: Multicellular organisms can be regenerated from totipotent differentiated somatic cell or nuclear founders [1-3]. Organisms regenerated from clonally related isogenic founders might a priori have been expected to be phenotypically invariant. However, clonal regenerant animals display variant phenotypes caused by defective epigenetic reprogramming of gene expression [2], and clonal regenerant plants exhibit poorly understood heritable phenotypic ("somaclonal") variation [4-7]. Here we show that somaclonal variation in regenerant Arabidopsis lineages is associated with genome-wide elevation in DNA sequence mutation rate. We also show that regenerant mutations comprise a distinctive molecular spectrum of base substitutions, insertions, and deletions that probably results from decreased DNA repair fidelity. Finally, we show that while regenerant base substitutions are a likely major genetic cause of the somaclonal variation of regenerant Arabidopsis lineages, transposon movement is unlikely to contribute substantially to that variation. We conclude that the phenotypic variation of regenerant plants, unlike that of regenerant animals, is substantially due to DNA sequence mutation.
authors.affiliation: Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
authors.forename: Caifu
authors.initials: C
authors.lastname: Jiang
authors.forename: Aziz
authors.initials: A
authors.lastname: Mithani
authors.forename: Xiangchao
authors.initials: X
authors.lastname: Gan
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Belfield
authors.forename: John P
authors.initials: JP
authors.lastname: Klingler
authors.forename: Jian-Kang
authors.initials: JK
authors.lastname: Zhu
authors.forename: Jiannis
authors.initials: J
authors.lastname: Ragoussis
authors.forename: Richard
authors.initials: R
authors.lastname: Mott
authors.forename: Nicholas P
authors.initials: NP
authors.lastname: Harberd
mesh_terms: D017360:Arabidopsis / Q000033:anatomy & histology / Q000235:genetics*; D001483:Base Sequence; D004252:DNA Mutational Analysis; D004251:DNA Transposable Elements; D018745:Genome, Plant; D008969:Molecular Sequence Data; D009154:Mutation; D059645:Mutation Rate; D010641:Phenotype; D012038:Regeneration / Q000502:physiology*; D016415:Sequence Alignment
chemical_list: D004251:DNA Transposable Elements