Liu Zhen, Zhao Han, Yan Yan, Wei Ming-Xiao, Zheng Yun-Chao, Yue Er-Kui, Alam Mohammad Shah, Smartt Kwesi Odel, Duan Ming-Hua, Xu Jian-Hong
Hainan Institute, Zhejiang University, Sanya, China.
Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China.
Front Plant Sci. 2021 Sep 28;12:745526. doi: 10.3389/fpls.2021.745526. eCollection 2021.
Active transposable elements (TEs) have drawn more attention as they continue to create new insertions and contribute to genetic diversity of the genome. However, only a few have been discovered in rice up to now, and their activities are mostly induced by artificial treatments (e.g., tissue culture, hybridization etc.) rather than under normal growth conditions. To systematically survey the current activity of TEs in natural rice accessions and identify rice accessions carrying highly active TEs, the transposon insertion polymorphisms (TIPs) profile was used to identify singleton insertions, which were unique to a single accession and represented the new insertion of TEs in the genome. As a result, 10,924 high-confidence singletons from 251 TE families were obtained, covering all investigated TE types. The number of singletons varied substantially among different superfamilies/families, perhaps reflecting distinct current activity. Particularly, eight TE families maintained potentially higher activity in 3,000 natural rice accessions. Sixty percent of rice accessions were detected to contain singletons, indicating the extensive activity of TEs in natural rice accessions. Thirty-five TE families exhibited potentially high activity in at least one rice accession, and the majority of them showed variable activity among different rice groups/subgroups. These naturally active TEs would be ideal candidates for elucidating the molecular mechanisms underlying the transposition and activation of TEs, as well as investigating the interactions between TEs and the host genome.
活跃的转座元件（TEs）由于持续产生新的插入并促进基因组的遗传多样性而受到更多关注。然而，截至目前在水稻中仅发现了少数转座元件，并且它们的活性大多是由人工处理（如组织培养、杂交等）诱导的，而非在正常生长条件下。为了系统地调查天然水稻种质中转座元件的当前活性，并鉴定携带高活性转座元件的水稻种质，利用转座子插入多态性（TIPs）图谱来识别单拷贝插入，这些单拷贝插入是单个种质所特有的，代表了转座元件在基因组中的新插入。结果，从251个转座元件家族中获得了10924个高可信度的单拷贝插入，涵盖了所有研究的转座元件类型。不同超家族/家族中的单拷贝插入数量差异很大，这可能反映了当前不同的活性。特别地，8个转座元件家族在3000份天然水稻种质中保持着潜在的较高活性。检测到60%的水稻种质含有单拷贝插入，这表明转座元件在天然水稻种质中具有广泛的活性。35个转座元件家族在至少一份水稻种质中表现出潜在的高活性，并且它们中的大多数在不同的水稻组/亚组中表现出可变的活性。这些天然活跃的转座元件将是阐明转座元件转座和激活的分子机制以及研究转座元件与宿主基因组之间相互作用的理想候选对象。
