Although many horticulturists and botanists are familiar with the economic aspects of somatic mutation, the role somatic mutation plays as a mechanism for evolutionary change is unknown. The modular and layered nature of plant tissues provides the basis for mutations to occur and be perpetuated through cell division and differentiation, potentially creating mosaics of genetic variability (within plant genetic variability). Genetically altered tissues can be perpetuated sexually through gametes or asexually through the production of tubers, bulbs, runners, rhizomes, and seeds, leading to the divergence of parental and somatically altered offspring.

In spite of wide acknowledgment that somatic mutation can occur, it is unknown how much variation can be generated and perpetuated within an individual plant. To address this issue we propose conducting a genome-wide scan of genetic (gene level) variation within different plant parts of the same individual (roots, stems, leaves) using the model plant system black cottonwood, Populus trichocarpa, and Illumina sequencing (resequencing), specifically addressing how common mutations are at the level of the gene within an individual.

Ultimately, the results of this study will take an initial step toward resolving a long-standing debate over the importance of somatic mutations in nature and their evolutionary importance, including ways in which plants may be able to evolutionarily cope with changing environmental conditions and whether within plant genetic variation can prevent pests and pathogens from breaking the defenses of their host plants. One graduate and one undergraduate student will gain training in genomics and bioinformatics.

Project Report

Fundamentally we think of individual organisms as genetically uniform at the gene level with an occasional mutation arising that can be recombined into the next generation through sexual recombination. If the mutation is beneficial it will gradually predominate within the population through recombination and natural selection. Thus, populations evolve, not individuals. Plants unlike most animals are unusual in that there is no sequestering of the germ line from somatic cells, i.e., a mutation in a somatic cell can be easily incorporated into the germ line and perpetuated. Even if a somatic mutation is not incorporated into a cell line that differentiates as gametes, it can still be perpetuated through asexual means of reproduction via cloning by root runners, stolons, rhizomes, branch layering, etc. Because no genetic recombination is involved in asexual reproduction the genetic composition of the parent plant tissues is maintained and somatic mutations in all plant derivatives (e.g., roots, stems, inflorescences) can become independent of the parent plant and the individual can evolve. Thus, it has been argued that somatic mutations may be an important source of heritable variation in plants through naturally occurring mechanisms of sexual and asexual reproduction. The somatic mutation hypothesis proposes that individual plants accumulate spontaneous mutations and ultimately develop as genetic mosaics. Somatic mutations would be particularly favored in long-lived, clonally propagating plants such as trees and could be of evolutionary importance by providing a way in which plants could keep up with, or out-run, their pests and pathogens in a coevolutionary arms race or serve in fine-tuning an individual to changing environmental conditions. Over the past thirty-two years this idea has been bantered about with no clear resolution as to its ecological or evolutionary importance because it is not known how much variation can be generated and perpetuated within an individual plant at the level of the gene. Here we assessed the magnitude of within plant genetic variation in the model system black cottonwood and the prospects for evolutionary change in their clonally derived offspring as measured by gene level changes in amino acids. Tissue samples from eleven individual trees and their clonally derived offspring were collected from Washington State near Mount Rainier. Five tissues per individual tree, three from the parental tree (floral or leaf buds from the top of the tree, stem tissue from the middle of the tree and root material between the parent and offspring and two tissues from their clonally derived offspring (stem tissue from the middle of the tree and floral or leaf bud tissue from the top of the tree), were sequenced. High levels of unique amino acid change were observed among tissues within all individual trees (on the average 4,840 unique amino acid changes per tissue. Clonally derived offspring also acquired a unique suite of amino acid changes through time, differentiating them from their parents (over 8,000 unique amino acid changes based on two tissues within the offspring). In addition, overrepresentation of amino acid change in genes involved in reproductive cellular processes in floral buds supports the notion that within plant genetic variation can be perpetuated through sexual reproduction. Thus, an individual can evolve as delineated by the gene level changes shown here - changes observed within the parent or offspring and from parent to clonally derived offspring. It will now be necessary to initiate the task of tying within-plant genetic variation to the adaptive significance of such variation. It has been argued that somatic mutations could be of evolutionary importance by providing a way in which long-lived plants could keep up with, or potentially out-run, their rapidly evolving pests and pathogens in a coevolutionary arms race. Our results are consistent with such a notion in that there is an overrepresentation of amino acid change in genes involved in plant defense to pathogen attack including the R genes. In addition, once genetic differences exist there is the potential for natural selection to modify gene frequencies within an individual through the process of differential growth. We show that there is differential spread of a subset of approximately 1,500-1,600 mutations across two to three tissues within an individual tree; whether these results reflect selective spread remains to be determined. We also illustrate that half of the genetic diversity within the tree population is generated within the individual plant via somatic mutation. This result potentially has important implications for conservation biology in that it is unlikely that such plants will suffer the effects of inbreeding, typical of small populations, given the high levels of somatic mutation generated. In addition, results may address the observation that asexual populations can often be as genetically diverse as sexual ones. Such variation could also have unexpected consequences for ecological, evolutionary, and plant molecular genetic studies that assume the maintenance of genetically identical clonally-derived lineages.

National Science Foundation (NSF)
Division of Environmental Biology (DEB)
Standard Grant (Standard)
Application #
Program Officer
George Gilchrist
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Illinois Urbana-Champaign
United States
Zip Code