The impact of transposable elements on the structure, evolution and function of the rice genome

Transposable elements (TEs) are ubiquitous in plants and are the primary genomic component of the majority of taxa. Knowledge of their impact on the structure, function and evolution of plant genomes is therefore a priority in the field of genomics. Rice, as one of the most prevalent crops for food security worldwide, has been subjected to intense research efforts over recent decades. Consequently, a considerable amount of genomic resources has been generated and made freely available to the scientific community. These can be exploited both to improve our understanding of some basic aspects of genome biology of this species and to develop new concepts for crop improvement. In this review, we describe the current knowledge on how TEs have shaped rice chromosomes and propose a new strategy based on a genome-wide association study (GWAS) to address the important question of their functional impact on this crop.