Simple sequence repeats and their expansions: role in plant development, environmental response and adaptation

Repetitive DNA is a feature of all organisms, ranging from archaea and plants to humans. DNA repeats can be seen both in coding and in noncoding regions of the genome. Due to the recurring nature of the sequences, simple DNA repeats tend to be more prone to errors during replication and repair, resulting in variability in their unit length. This feature of simple sequence repeats led to their use as molecular markers for mapping traits in diverse organisms. Advances in genomics, and the ever-reducing costs of genome sequencing have empowered us to assess the functional impacts of DNA repeats. The variability in repeat lengths can cause phenotypic differences depending on where they are present in the genome. Variability in the repeat length in coding regions of genes results in poly amino acid stretches that appear to interfere with protein function, including the perturbation of protein-protein interactions with diverse phenotypic impacts. These are often common allelic variations that can significantly impact evolutionary dynamics. In extreme situations, repeats can undergo massive expansions and appear as outliers. Repeat expansions underlie several genetic defects in plants to diseases in humans. This review systematically analyses tandem DNA repeats in plants, their role in development and environmental response and adaptation in plants. We identify and synthesise emerging themes, differentiate repeat length variability and repeat expansions, and argue that many repeat-associated phenotypes in plants are yet to be discovered. We emphasise the underexplored nature and immense potential of this area of research, particularly in plants, and suggest ways in which this can be achieved and how it might contribute to evolution and agricultural productivity.