Super hybrid rice varieties with ideal plant architecture (IPA) have been critical in enhancing food security worldwide. However, the molecular mechanisms underlying their improved yield remain unclear. Here, we report the identification of a QTL, qWS8/ipa1-2D, in the super rice Yongyou12 (YY12) and related varieties. In-depth genetic molecular characterization of qWS8/ipa1-2D reveals that this newly identified QTL results from three distal naturally occurring tandem repeats upstream of IPA1, a key gene/locus previously shown to shape rice ideal plant architecture and greatly enhance grain yield. The qWS8/ipa1-2D locus is associated with reduced DNA methylation and a more open chromatin state at the IPA1 promoter, thus alleviating the epigenetic repression of IPA1 mediated by nearby heterochromatin. Our findings reveal that IPA traits can be fine-tuned by manipulating IPA1 expression and that an optimal IPA1 expression/dose may lead to an ideal yield, demonstrating a practical approach to efficiently design elite super rice varieties.

中文翻译：

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天然串联排列减轻了IPA1的表观遗传抑制，并导致了高产水稻。

具有理想植物结构（IPA）的超级杂交水稻品种对于增强全球粮食安全至关重要。然而，提高产量的分子机制尚不清楚。在这里，我们报告了超级稻永优12（YY12）及其相关品种中的QTL鉴定，即qWS8 / ipa1-2D。对qWS8 / ipa1-2D的深入遗传分子表征显示，该新鉴定的QTL来自IPA1上游的三个远端自然发生的串联重复序列，而IPA1的关键基因/基因座先前显示出可塑造水稻理想的植物结构并大大提高谷物产量。qWS8 / ipa1-2D基因座与IPA1启动子处的DNA甲基化降低和染色质更开放状态相关，从而减轻了附近异染色质介导的IPA1的表观遗传抑制。