National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
Mol Plant. 2019 Oct 7;12(10):1395-1407. doi: 10.1016/j.molp.2019.06.004. Epub 2019 Jun 20.
Transposable elements (TEs) constitute the most abundant portions of plant genomes and can dramatically shape host genomes during plant evolution. They also play important roles in crop domestication. However, whether TEs themselves are also selected during crop domestication has remained unknown. Here, we identify an active long terminal repeat (LTR) retrotransposon, HUO, as a potential target of selection during rice domestication and breeding. HUO is a low-copy-number LTR retrotransposon, and is active under natural growth conditions and transmitted through male gametogenesis, preferentially inserting into genomic regions capable of transcription. HUO exists in all wild rice accessions and about half of the archaeological rice grains (1200-7000 years ago) and landraces surveyed, but is absent in almost all modern varieties, indicating its gradual elimination during rice domestication and breeding. Further analyses showed that HUO is subjected to strict gene silencing through the RNA-directed DNA methylation pathway. Our results also suggest that multiple HUO copies may trigger genomic instability through altering genome-wide DNA methylation and small RNA biogenesis and changing global gene expression, resulting in decreased disease resistance and yield, coinciding with its elimination during rice breeding. Together, our study suggests that negative selection of an active retrotransposon might be important for genome stability during crop domestication and breeding.
转座元件 (TEs) 构成了植物基因组中最丰富的部分，在植物进化过程中可以显著塑造宿主基因组。它们在作物驯化中也起着重要作用。然而，TEs 本身是否也在作物驯化过程中受到选择，仍然未知。在这里，我们鉴定出一个活跃的长末端重复 (LTR) 反转录转座子 HUO，作为水稻驯化和育种过程中潜在的选择靶标。HUO 是一个低拷贝数的 LTR 反转录转座子，在自然生长条件下活跃，并通过雄性配子发生传递，优先插入能够转录的基因组区域。HUO 存在于所有野生稻品种和大约一半的考古稻粒（1200-7000 年前）和调查的地方品种中，但几乎不存在于所有现代品种中，表明它在水稻驯化和育种过程中逐渐被淘汰。进一步的分析表明，HUO 通过 RNA 指导的 DNA 甲基化途径受到严格的基因沉默。我们的研究结果还表明，多个 HUO 拷贝可能通过改变全基因组 DNA 甲基化和小 RNA 生物发生以及改变全局基因表达来引发基因组不稳定，导致抗病性和产量下降，这与它在水稻育种过程中的消除相一致。总之，我们的研究表明，活跃反转录转座子的负选择可能对作物驯化和育种过程中的基因组稳定性很重要。
