Crop genetic improvement requires balancing complex tradeoffs caused by gene pleiotropy and linkage drags, as exemplified by IPA1 (Ideal Plant Architecture 1), a typical pleiotropic gene in rice that increases grains per panicle but reduces tillers. In this study, we identified a 54-base pair cis-regulatory region in IPA1 via a tiling-deletion-based CRISPR–Cas9 screen that, when deleted, resolves the tradeoff between grains per panicle and tiller number, leading to substantially enhanced grain yield per plant. Mechanistic studies revealed that the deleted fragment is a target site for the transcription factor An-1 to repress IPA1 expression in panicles and roots. Targeting gene regulatory regions should help dissect tradeoff effects and provide a rich source of targets for breeding complementary beneficial traits.
作物遺傳改良需要平衡由基因多效性和連鎖阻力引起的復(fù)雜權(quán)衡，如理想株型基因IPA1，這是水稻中典型的多效基因，可以增加每穗粒數(shù)，但減少分蘗。在本研究中，我們將IPA1基因的表達(dá)調(diào)控區(qū)像“瓦片”一樣，分成很多段，對(duì)其用CRISPR/Cas9技術(shù)分別刪除，從中發(fā)掘出了一個(gè)可以同時(shí)提高分蘗數(shù)和穗粒數(shù)的編輯材料IPA1-Pro10及其對(duì)應(yīng)的54bp關(guān)鍵順式作用元件。IPA1-Pro10具有穗重和穗數(shù)同時(shí)增加、株高變高、莖稈和根系粗壯的表型。經(jīng)田間小區(qū)測(cè)產(chǎn)鑒定，IPA1-Pro10與對(duì)照品種中花11相比能夠增產(chǎn)15.9%，大大提高了水稻產(chǎn)量。當(dāng)該54bp區(qū)域被刪除時(shí)，可以解決每穗粒數(shù)和分蘗數(shù)之間的權(quán)衡，從而顯著提高單株籽粒產(chǎn)量。機(jī)理研究表明，發(fā)現(xiàn)馴化關(guān)鍵轉(zhuǎn)錄因子An-1能通過(guò)結(jié)合54bp關(guān)鍵順式作用元件中的一個(gè)GCGCGTGT基序特異調(diào)控IPA1在幼穗的表達(dá)水平，進(jìn)而特異調(diào)控穗部表型。以基因調(diào)控區(qū)域?yàn)榘悬c(diǎn)可以幫助分析權(quán)衡效應(yīng)，為培育互補(bǔ)優(yōu)勢(shì)性狀提供豐富的靶點(diǎn)來(lái)源。