Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France.
Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90040-060, Brazil.
Nat Commun. 2019 Jan 3;10(1):24. doi: 10.1038/s41467-018-07974-5.
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.
最近发布的 3000 个水稻品种的基因组序列为该作物的物种水平的遗传多样性提供了访问途径。我们利用这一资源来揭示水稻反转录转座子景观的一些特征。我们专门开发了软件 TRACKPOSON，用于从大型数据集检测转座元件插入多态性（TIPs）。我们将该工具应用于 32 个反转座子家族，并在 3000 个水稻基因组中鉴定出超过 50000 个 TIPs。大多数多态性发现的频率非常低，这表明它们可能是最近在农业中发生的。全基因组关联研究表明，这些在水稻中的激活可能是由外部刺激触发的，而不是由参与转座元件沉默途径的遗传因素的改变引起的。最后，TIPs 数据集被用来追踪水稻驯化的起源。我们的结果表明，水稻起源于三次不同的驯化事件。
