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Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa
Plant Biotechnology Journal ( IF 13.8 ) Pub Date : 2022-03-12 , DOI: 10.1111/pbi.13807
Xu Cai 1 , Runmao Lin 1 , Jianli Liang 1 , Graham J King 2 , Jian Wu 1 , Xiaowu Wang 1
Affiliation  

Transposable element (TE) is prevalent in plant genomes. However, studies on their impact on phenotypic evolution in crop plants are relatively rare, because systematically identifying TE insertions within a species has been a challenge. Here, we present a novel approach for uncovering TE insertion polymorphisms (TIPs) using pan-genome analysis combined with population-scale resequencing, and we adopt this pipeline to retrieve TIPs in a Brassica rapa germplasm collection. We found that 23% of genes within the reference Chiifu-401-42 genome harbored TIPs. TIPs tended to have large transcriptional effects, including modifying gene expression levels and altering gene structure by introducing new introns. Among 524 diverse accessions, TIPs broadly influenced genes related to traits and acted a crucial role in the domestication of B. rapa morphotypes. As examples, four specific TIP-containing genes were found to be candidates that potentially involved in various climatic conditions, promoting the formation of diverse vegetable crops in B. rapa. Our work reveals the hitherto hidden TIPs implicated in agronomic traits and highlights their widespread utility in studies of crop domestication.

中文翻译:

转座因子插入:芸苔驯化表型变异的隐藏主要来源

转座因子 (TE) 在植物基因组中普遍存在。然而,关于它们对作物表型进化影响的研究相对较少,因为系统地识别物种内的 TE 插入一直是一个挑战。在这里,我们提出了一种使用泛基因组分析结合种群规模重测序来揭示 TE 插入多态性 (TIP) 的新方法,并且我们采用该管道来检索芸苔中的 TIP种质采集。我们发现参考 Chiifu-401-42 基因组中 23% 的基因含有 TIP。TIP 往往具有很大的转录效应,包括通过引入新的内含子来改变基因表达水平和改变基因结构。在 524 个不同的种质中,TIP 广泛影响与性状相关的基因,并在B. rapa形态型的驯化中发挥关键作用。例如,发现四种特定的含有 TIP 的基因可能参与各种气候条件,从而促进B. rapa中多种蔬菜作物的形成。我们的工作揭示了迄今为止隐藏的与农艺性状有关的 TIP,并强调了它们在作物驯化研究中的广泛用途。
更新日期:2022-03-12
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