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.

转座因子（TEs）构成了植物基因组中最丰富的部分，可以在植物进化过程中显着塑造宿主基因组。它们在农作物驯化中也起着重要作用。然而，尚不清楚在作物驯化期间是否也选择了TEs。在这里，我们确定了一个活跃的长末端重复（LTR）逆转录转座子，HUO，作为水稻驯化和育种过程中潜在的选择目标。HUO是低拷贝数的LTR反转录转座子，在自然生长条件下具有活性，并通过雄配子发生传播，优先插入能够转录的基因组区域。O在所有野生稻品种和大约一半的考古稻谷粒（1200-7000年前）和地方品种中都存在这种稻草，但几乎所有现代品种中都没有这种稻草，这表明稻米在驯化和育种过程中已逐渐消失。进一步的分析表明，HUO通过RNA定向的DNA甲基化途径受到严格的基因沉默。我们的结果还表明，多个HUO拷贝可能会通过改变全基因组DNA甲基化和小的RNA生物发生以及改变全局基因表达来触发基因组不稳定，从而导致抗病性和产量下降，这与水稻育种过程中的消除相吻合。总之，我们的研究表明，对活性逆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。