Plant clones, because they are the product of asexual reproduction, are populations of genetically identical individuals and are important in agriculture, horticulture, and ecology. Although clones can be maintained for hundreds to thousands of years through repeated cycles of vegetative reproduction, degeneration of plant fitness and/or productivity often occurs with increasing age and/or cycles of propagation. While powerful diagnostics allow increasingly accurate identification of the underlying causes for biotic (diseases, pest, etc., and abiotic (nutrient deficiency, inadequate chill, etc.) breakdowns in normal growth and development, genetic/epigenetic failures remain poorly understood, often being generalized as ‘off-types’. A major impediment to the effective deployment of emerging tools for identifying causes of genetic/epigenetic failures is the uncertainty as to where the failure first occurred, which is necessary to identify the most appropriate tissues for testing. Characteristic patterns of clone degeneration can be used to distinguish among different types of failure as well as recommend appropriate methods and tissues for analysis. Clone degeneration from ‘General-aging’ is due to the accumulation of many small-affect deleterious factors making targeted genetic/epigenetic diagnosis difficult though tracking changes in selected methylation profiles could serve as indicators of ‘clone-age’ particularly when ‘slow-to-age’ epicormic meristems are available for reference. ‘Bud-sports’ results from genetic/epigenetic changes in mitotically active cells resulting in distinct sectoral chimeras in subsequent shoot growth and development that can be targeted for molecular and phenotypic analysis. In contrast, ‘epigenetic-imprinting’ seems to be induced at the tissue rather than single cell level making the determination of initial induction time and site difficult to determine. In addition, because most shoot structure in temperate perennials is largely preformed during the previous growing seasons, the time and location between the initial imprinting and its first phenotypic detection can be months to years. Examples, largely from tree crop production, will be presented showing that expression patterns within these major groups can further delineate the specific nature of clone degeneration including the identification of appropriate tissues for testing.
