近日，中國農(nóng)業(yè)科學(xué)院深圳農(nóng)業(yè)基因組研究所（嶺南現(xiàn)代農(nóng)業(yè)科學(xué)與技術(shù)廣東省實(shí)驗(yàn)室深圳分中心）聯(lián)合崖州灣國家實(shí)驗(yàn)室,、沈陽農(nóng)業(yè)大學(xué)等單位在《國家科學(xué)評(píng)論（National Science Review）（IF=20.6）上在線發(fā)表了題為“A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice”的研究論文,。研究基于全球野生稻和栽培稻核心種質(zhì)資源,，構(gòu)建了群體水平,、最全面和高精度的水稻泛轉(zhuǎn)座子變異圖譜,，全面評(píng)估了轉(zhuǎn)座子對(duì)水稻馴化和育種改良中的重要作用,，挖掘到多個(gè)與重要農(nóng)藝性狀相關(guān)的優(yōu)異自然變異位點(diǎn),，豐富了水稻育種的可用變異庫，對(duì)水稻全基因組設(shè)計(jì)育種及遺傳育種改良提供了重要資源,。

1950年Barbara Mclintock首次在玉米中發(fā)現(xiàn)轉(zhuǎn)座子（Transposable element,，轉(zhuǎn)座子），并由此獲得諾貝爾獎(jiǎng)（Mclintock,，Cold Spring Harbor Symposia on Quantitative Biology,，1951）。長期以來,，轉(zhuǎn)座子本身被認(rèn)為是垃圾DNA,，但現(xiàn)在它們被認(rèn)為是一類DNA中不同尋常的高度重復(fù)片段，不僅在生物體內(nèi)甚至生物體之間具有驚人的移動(dòng)能力,，也能影響基因,、創(chuàng)造新性狀、增加不同個(gè)體的獨(dú)特性,，更會(huì)在壓力條件下被激活,，并幫助生物體適應(yīng)復(fù)雜多變的自然環(huán)境。大量文獻(xiàn)表明,，基因組結(jié)構(gòu)變異在調(diào)控水稻農(nóng)藝性狀具有重要作用,，而水稻基因組中的結(jié)構(gòu)變異大多源自于轉(zhuǎn)座子。轉(zhuǎn)座子主要包含non-LTR（Long terminal Repeat, SINE和LINE）型逆轉(zhuǎn)座子,、LTR型逆轉(zhuǎn)座子（Copia,、Gypsy等）、TIR（terminal Inverted Repeat）型DNA轉(zhuǎn)座子（Stowaway MITE,、Tourist MITE,、DTC、DTA,、DTT,、DTM、DTH等）和Helitron型DNA轉(zhuǎn)座子（Wicker et al., Nature Reviews Genetics, 2007）,。高度重復(fù)的轉(zhuǎn)座子序列為其本身的充分注釋和精確鑒定帶來了挑戰(zhàn),，極大地阻礙了轉(zhuǎn)座子變異對(duì)作物馴化和農(nóng)藝性狀的深度系統(tǒng)解析,。得益于測序技術(shù)的進(jìn)步，有機(jī)會(huì)從群體的層面上全面地研究轉(zhuǎn)座子的分布特征,，并揭示轉(zhuǎn)座子在水稻馴化和育種中的作用,。

為了獲得高質(zhì)量的泛轉(zhuǎn)座子變異圖譜，本研究利用247份全球水稻核心種質(zhì)資源高質(zhì)量基因組,，構(gòu)建了大規(guī)模群體的亞洲稻泛轉(zhuǎn)座子變異圖譜（圖1）,，包含169,798個(gè)（647.9 Mb）衍生的轉(zhuǎn)座子變異，其中占比最多的是Gypsy,、Helitron和Copia家族,，也是迄今為止質(zhì)量最高的水稻群體水平泛轉(zhuǎn)座子變異圖譜,。

圖1. 泛轉(zhuǎn)座子變異圖譜構(gòu)建

利用該泛轉(zhuǎn)座子變異圖譜,，研究人員比較了普通野生稻與秈稻、普通野生稻與粳稻,、秈稻和粳稻之間的轉(zhuǎn)座子變異,，發(fā)現(xiàn)轉(zhuǎn)座子變異顯著富集在馴化和分化的選擇性區(qū)域內(nèi)，表明轉(zhuǎn)座子參與了水稻馴化和分化,。進(jìn)一步分析,，發(fā)現(xiàn)在水稻馴化分化過程中，不同的轉(zhuǎn)座子家族富集也具有特異性,，例如幾乎所有的LTR,、MITE和Helitron都顯著富集在馴化和分化過程中，而SINE和LINE家族僅顯著富集在從普通野生稻到粳稻的馴化過程中（圖2）,。同時(shí),，研究人員也鑒定到參與水稻馴化和分化過程的轉(zhuǎn)座子變異分別有3,935和2,108個(gè)，并受到這些轉(zhuǎn)座子變異影響的候選基因分別有2,992和1,750個(gè)（圖2）,，包括重要抽穗基因RFT1等,、分蘗基因RFL、D10等,、以及粒型基因GW2,、DAO、LG1等,。例如一個(gè)Tourist MITE插入到耐冷基因LIP19的啟動(dòng)子區(qū),，顯著影響了該基因的表達(dá)水平，功能分析和單倍型分析表明,，該Tourist MITE通過影響LIP19的表達(dá)量而調(diào)控水稻的耐冷表型,。

圖2. 轉(zhuǎn)座子變異在水稻馴化和分化中的重要作用

另外，基于該泛轉(zhuǎn)座子變異圖譜,，研究人員發(fā)現(xiàn)轉(zhuǎn)座子與鄰近的SNPs/InDels存在完全連鎖的比例較低,，揭示轉(zhuǎn)座子變異可以作為補(bǔ)充提升挖掘基因的潛力,。結(jié)合全基因組關(guān)聯(lián)分析和群體表達(dá)數(shù)量性狀位點(diǎn)（expression quantitative trait loci，eQTL）分析,，研究人員鑒定到多個(gè)與水稻農(nóng)藝性狀顯著相關(guān)的轉(zhuǎn)座子變異新位點(diǎn),，而這些新位點(diǎn)無法利用SNP數(shù)據(jù)鑒定，例如Gypsy插入顯著影響耐冷下水稻的結(jié)實(shí)率（圖3）,。同時(shí),，研究人員利用SNP和轉(zhuǎn)座子的cis-eQTL分析鑒定到轉(zhuǎn)座子變異調(diào)控的基因3,868個(gè)，其中轉(zhuǎn)座子比起SNP標(biāo)記特有調(diào)控的基因1,246個(gè)（圖3）,，例如發(fā)現(xiàn)一個(gè)PILE TIR插入基因OsRbohB的啟動(dòng)子區(qū),，顯著影響了該基因的表達(dá)水平，進(jìn)一步顯著影響了水稻的千粒重,，這些結(jié)果得到了實(shí)驗(yàn)的驗(yàn)證,。這些新的轉(zhuǎn)座子變異位點(diǎn)有助于挖掘更多與重要農(nóng)藝性狀相關(guān)的優(yōu)異基因，為水稻基因組輔助育種提供了新靶點(diǎn),。

圖3. 轉(zhuǎn)座子變異影響水稻基因表達(dá)和農(nóng)藝性狀

中國農(nóng)業(yè)科學(xué)院深圳農(nóng)業(yè)基因組研究所商連光研究員,、崖州灣國家實(shí)驗(yàn)室錢前院士和基因組所周永鋒研究員為論文的共同通訊作者?；蚪M所在讀博士生李笑霞,、在讀博士生戴小凡、副研究員賀慧英,、在讀博士生呂陽和在讀碩士生楊龍波為論文共同第一作者,。該研究得到國家自然科學(xué)基金基礎(chǔ)科學(xué)中心、廣東省自然科學(xué)基金杰出青年基金,、中國農(nóng)業(yè)科學(xué)院科技創(chuàng)新工程科學(xué)中心和中國農(nóng)科院青年創(chuàng)新專項(xiàng)資金資助,。該工作得到了基因組所、中國水稻所和崖州灣科技城超級(jí)計(jì)算平臺(tái)的支持,。

原文鏈接：https://academic.oup.com/nsr/advance-article/doi/10.1093/nsr/nwae188/7687832

商連光團(tuán)隊(duì)長期從事利用全世界野生稻和栽培稻種質(zhì)資源進(jìn)行優(yōu)異自然變異挖掘與利用和種質(zhì)創(chuàng)新工作,。團(tuán)隊(duì)前期為了更好地挖掘和利用水稻種質(zhì)資源中對(duì)育種有價(jià)值的優(yōu)異自然變異，完成了水稻日本晴完整參考基因組的組裝和高質(zhì)量注釋來提高對(duì)水稻自然變異的檢測準(zhǔn)確度（Shang et al., Molecular Plant, 2023）,；基于全世界核心種質(zhì)群體捕獲稻屬的豐富遺傳多樣性的自然變異資源,，進(jìn)而構(gòu)建了水稻圖形超級(jí)泛基因組和高精度的結(jié)構(gòu)變異圖譜，大大提高了產(chǎn)量和耐鹽等性狀優(yōu)異等位基因挖掘的速度（Shang et al., Cell Research, 2022,；Lin et al., Journal of Integrative Plant Biology, 2023）,，挖掘到的耐鹽關(guān)鍵等位基因STG5（Wei et al., National Science Review，2024）具有重要育種價(jià)值,，將該基因優(yōu)異單倍型導(dǎo)入到主栽品種中可以大大提高鹽堿地耐鹽性,，利用結(jié)構(gòu)變異和鹽脅迫下的表達(dá)譜成功挖掘到OsMADS56基因上1Kb的結(jié)構(gòu)變異影響耐鹽性狀（Cui et al., New Phytologist, 2024）；基于水稻圖形超級(jí)泛基因組做參考解析了萬份規(guī)模的水稻群體變異組,，揭示了稀有自然變異在育種中的重要性(Wang et al., Nucleic Acids Research, 2023),；同時(shí)破譯了水稻基因組中最為復(fù)雜的著絲粒區(qū)域變異圖譜,，挖掘到復(fù)雜結(jié)構(gòu)變異控制水稻農(nóng)藝性狀的關(guān)鍵基因OsMAB（Lv et al., Journal of Integrative Plant Biology, 2024），揭示了倒位結(jié)構(gòu)變異（He et al., Science Bulletin,，2023）對(duì)水稻重要性狀的作用,。綜上，團(tuán)隊(duì)構(gòu)建全世界水稻核心種質(zhì)圖形超級(jí)泛基因組和高質(zhì)量結(jié)構(gòu)變異圖譜,，系統(tǒng)地解析大片段插入和缺失,、轉(zhuǎn)座子、倒位,、著絲粒,、稀有變異等變異對(duì)水稻農(nóng)藝性狀和耐鹽等性狀的調(diào)控分子機(jī)制，并成功用于水稻的種質(zhì)創(chuàng)新和育種,。

商連光課題組簡介: https://agis.caas.cn/kydw/kydwyjzx/zwjyzyjzx/94d48f75df6943cb9ecc5d97ffa79f7c.htm

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