Retrotranspositional landscape of Asian rice revealed by 3000 genomes

First author: Marie-Christine Carpentier; Affiliations: Université de Perpignan Via Domitia (佩皮尼昂大学): Perpignan Cedex, France

Corresponding author: Olivier Panaud 

The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.

最近3000份水稻遗传资源的公布为从物种水平研究水稻遗传多样性提供了可能。作者基于这些水稻遗传资源研究了水稻基因组的反转录转座子特性。作者开发了一个叫做TRACKPOSON的软件能够从大数据中特异性的检测转座元件插入多态性TIP。作者将该软件应用在32个反转录转座子家族中，成功在3000份水稻资源中鉴定到了超过50,000个TIP。大多数的多态性发现频率较低，说明这些可能是进入到农业时代后在近期形成的。全基因组关联分析显示，相比于转座元件沉默通路上相关遗传因子的改变，这些水稻有活性的反转录转座子更可能是受到外部刺激所诱导的。最终，作者利用TIP数据集进行了水稻驯化起源的追踪研究。本文的研究显示水稻起源于三个不同的驯化事件。

doi: https://doi.org/10.1038/s41467-018-07974-5

Journal: Nature Communications

Published date: 03 January, 2019