Major domestication-related phenotypes in indica rice are due to loss of miRNA-mediated laccase silencing

First author: Chenna Swetha; Affiliations: National Centre for Biological Sciences (印度国家生物科学中心): Bangalore, India

Corresponding author: Padubidri V. Shivaprasad

Domestication of rice included conversion of perennial wild species with few seeds to short plants that produced abundant seeds. Most domestication-associated changes were due to variations in transcription factors and other key genes such as enzymes. Here, we show that multiple yield-related traits associated with indica rice domestication are linked to micro (mi) RNA mediated regulation. Analysis of small (s) RNA datasets from cultivated indica rice lines, a few landraces and two wild relatives of rice revealed the presence of abundant 22-nucleotide (nt) reads in wild relatives that mapped to miR397 precursors. miR397 expressed at very high levels in wild relatives and at negligible (微不足道的) levels in high-yielding cultivated lines. In its genera-specific form of 22-nt, miR397 targeted mRNAs coding for laccases (漆酶) to decay and induce robust secondary cascade silencing in wild species that required RNA-dependent RNA polymerase 6. In wild species of rice, reduced expression of laccases resulted in low lignification. As expected, over-expression of miR397 induced de-domestication phenotypes. Interestingly, nearly 26 unknown QTLs previously implicated for rice yield overlapped with laccases and miR397 genes. These results suggest the involvement of miRNAs in rice domestication-associated phenotypes.

水稻的驯化包括由产种少的多年生物种向丰产且生命周期短的植物转变。大多数驯化相关的改变均是由于转录因子和一些关键酶的基因上的变异所导致的。本文的研究显示籼稻的驯化过程中多个与产量相关的性状与miRNA介导的调控相关。对栽培籼稻、一些地方品种以及野生水稻的小RNA数据集的分析显示在野生水稻种存在22核苷酸reads的富集，这些reads能够很好的比对到miR397的前体上去。该种属特异性的22核酸miR397靶向野生水稻中漆酶的mRNA编码区以延缓及诱导次级级联沉默，这个过程需要RNA依赖性RNA聚合酶6。在野生水稻中，减少漆酶的表达会降低木质化水平。同时，过表达miR397能够诱导去驯化表型。有趣的是，作者发现之前报道的26个与水稻产量相关的未知QTL与漆酶和miR397在基因组上的位置存在重叠。本文的研究揭示了miRNA在水稻驯化相关表型的演化过程中发挥作用。

doi: https://doi.org/10.1105/tpc.18.00472

Journal: Plant Cell

First Published: 19 October, 2018

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