Utilisation of transposons to alter genomic and epigenomic diversity in crop plants

Abstract

Plant genetic improvement relies on the presence of a wide range of genetic variation in both form and function to deliver phenotypes of importance to agriculture and horticulture. Often, however, this pool of important allelic variation is constrained either through previous breeding efforts or a lack of suitable populations from which to draw allelic diversity to generate new phenotypes for key agronomic and quality traits. With the democratisation of sequencing technologies and the concomitant drop in sequencing costs an ever growing range of plant genomes are being sequenced uncovering the underlying drivers of genetic variation. Among the many forms of genome variation contributing to phenotype, it is becoming clear that transposons are a key driver of genetic and phenotypic diversity in crop systems. Aside from obvious roles in loss-offunction mutation through insertion, transposons have also been shown to be potent manipulators of gene regulatory networks via genetic and epigenetic pathways. Our work has focused on understanding the roles of transposons in 2 crop plants, grapevine (Vitis Vinifera), and Hops (Humulus lupulus) as well as Pilosella (Mendel’s Hawkweed) and the native Australian tobacco, Nicotiana benthamiana. We have recently shown transposons are the causative agent for parthenogenesis in Piosella. In addition we have proven it is possible to elevate and capture new transposable element activity in crop plants and are currently evaluating the impact of this activity in genetic, epigenetic and phenotypic contexts. We present a case for the importance of transposons in providing new and novel sources of (epi)genetic variation, which in combination with high throughput sequencing allows both the identification of novel insertions and their exploitation of insertions impacting phenotype, to drive genetic gain in a wide range of plant species.