# Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane

## TL;DR

Researchers developed a new method using qPCR and transposable elements to study sugarcane genetics and evolution.

## Contribution

A novel genotyping method using transposable elements was developed for sugarcane and related species.

## Key findings

- The qPCR-RBIP method can be used as part of a genotyping system for sugarcane.
- Three transposable elements were found only in one lineage of modern sugarcane cultivars.
- The transposable elements support the current understanding of sugarcane evolution.

## Abstract

qPCR-RBIP was used to examine the dosage of particular markers and evolutionary history in Saccharum and the related genera, Erianthus and Miscanthus. It also differentiated between S. spontaneum and S. officinarum.

Sugarcane is the main source of the world’s sugar and is becoming increasingly important as a source of biofuel. The highly polyploid and heterozygous nature of the sugarcane genome has meant that characterization of the genome has lagged behind that of other important crops. Here we developed a method using a combination of quantitative PCR with a transposable marker system to score the relative number of alleles with a transposable element (TE) present at a particular locus. We screened two genera closely related to Saccharum (Miscanthus and Erianthus), wild Saccharum, traditional cultivars, and 127 modern cultivars from Brazilian and Australian breeding programmes. We showed how this method could be used in various ways. First, we showed that the method could be extended to be used as part of a genotyping system. Secondly, the history of insertion and timing of the three TEs examined supports our current understanding of the evolution of the Saccharum complex. Thirdly, all three TEs were found in only one of the two main lineages leading to the modern sugarcane cultivars and are therefore the first TEs identified that could potentially be used as markers for Saccharum spontaneum.