Developmental and environmental variation in genomes

Abstract

The genetic make-up of an organism, established at fertilization, is not conventionally expected to change during development unless mutation occurs. However, there is actually evidence that considerable variation can arise. Some of these changes may occur in response to the environment. This article reviews such variations in genome size or DNA content (excluding ploidy-level changes). The variation can be generated by processes, including high-frequency chromosomal recombination, transposition, cis-element-enhanced gene amplification and repetitive-sequence-based changes in nuclear DNA content. Environmentally induced and developmentally regulated genomic variation (ED-genomic variation or ED-genetic variation) can be found in both coding and non-coding sequences, and is often non-Mendelian in its inheritance pattern. Changes can depend on development (for example, propagation method, seed/fruit position on plants, embryo stage, etc.) and occur in response to the environment (for example, light, temperature, herbicide, salinity, fertilizer, land slope direction, pathogen infection, etc.). Some plants have meiotic (or rejuvenation) corrections, which restore their genome sizes to a certain degree. However, Mendelian inheritance and acquired inheritance of the variants occur, and both inheritance types may be different expressions evolved for the same adaptive responses. With this perspective, the terms 'pure-breeding line' or 'stable cultivar' may only be appropriate for a given mode of reproduction or propagation, and for a given environment. ED-genomic variation appears to be an essential component of differentiation, development and adaptation. Consequently, modern molecular biology tools, such as microarray hybridization and new sequencing technology, should be directed towards a more comprehensive evaluation of ED-genomic variation.