The origin and functionality of long noncoding RNA (lncRNA) remain poorly understood. Here, we show that multiple quantitative trait loci modulating distinct domestication traits in soybeans are pleiotropic effects of a locus composed of two tandem lncRNA genes. These lncRNA genes, each containing two inverted repeats, originating from coding sequences of the MYB genes, function in wild soybeans by generating clusters of small RNA (sRNA) species that inhibit the expression of their MYB gene relatives through post-transcriptional regulation. By contrast, the expression of lncRNA genes in cultivated soybeans is severely repressed, and, consequently, the corresponding MYB genes are highly expressed, shaping multiple distinct domestication traits as well as leafhopper resistance. The inverted repeats were formed before the divergence of the Glycine genus from the Phaseolus–Vigna lineage and exhibit strong structure–function constraints. This study exemplifies a type of target for selection during plant domestication and identifies mechanisms of lncRNA formation and action.

长链非编码 RNA (lncRNA) 的起源和功能仍然知之甚少。在这里，我们表明，调节大豆不同驯化性状的多个数量性状基因座是由两个串联 lncRNA 基因组成的基因座的多效性效应。这些 lncRNA 基因各自包含两个反向重复序列，源自 MYB 基因的编码序列，在野生大豆中通过生成小 RNA (sRNA) 簇发挥作用，这些小 RNA (sRNA) 物种通过转录后调控抑制其 MYB 基因相关基因的表达。相比之下，栽培大豆中lncRNA基因的表达受到严重抑制，因此相应的MYB基因高度表达，形成多种不同的驯化性状以及叶蝉抗性。反向重复序列是在大豆属从菜豆-豇豆谱系分化之前形成的，并且表现出强烈的结构-功能限制。这项研究举例说明了植物驯化过程中选择的一种靶标，并确定了 lncRNA 形成和作用的机制。