劉喜 牟昌鈴 周春雷 程治軍 江玲,* 萬建民,

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水稻粒型基因克隆和調(diào)控機(jī)制研究進(jìn)展

劉喜1牟昌鈴1周春雷1程治軍2江玲1,*萬建民1,2

(1南京農(nóng)業(yè)大學(xué) 作物遺傳與種質(zhì)創(chuàng)新國家重點(diǎn)實(shí)驗(yàn)室, 南京 210095;2中國農(nóng)業(yè)科學(xué)院 作物科學(xué)研究所/農(nóng)作物基因資源與基因改良國家重大科學(xué)工程, 北京 100081;*通訊聯(lián)系人, E-mail: jiangling@njau.edu.cn)

水稻粒型是影響其產(chǎn)量和品質(zhì)的重要性狀，闡明其遺傳調(diào)控機(jī)理，有助于提高水稻單產(chǎn)和改良品質(zhì)。水稻粒型性狀主要包括粒長、粒寬、粒厚、長/寬比，屬于數(shù)量性狀，受胚、胚乳及母體植株等不同遺傳體系的控制。隨著水稻功能基因組學(xué)和重測序技術(shù)的快速發(fā)展，目前已經(jīng)定位超過400個與水稻粒型相關(guān)的數(shù)量性狀位點(diǎn)(QTL)，并已克隆了60個水稻粒型基因，涉及植物激素、泛素-蛋白酶體通路、絲裂原活化蛋白激酶(MAPK)信號通路、G蛋白信號通路及表觀修飾等多個調(diào)控通路。本文對水稻粒型基因克隆及其調(diào)控機(jī)制的研究進(jìn)展進(jìn)行了系統(tǒng)總結(jié)和梳理，并對這些基因在育種上的利用價值進(jìn)行了評價。

水稻；粒型；基因；調(diào)控機(jī)制

矮稈基因及雜種優(yōu)勢的利用實(shí)現(xiàn)了水稻產(chǎn)量的兩次跨越，不過隨著人口的增長，耕地面積的剛性下降，如何保證我國糧食安全仍是當(dāng)前面臨的重要挑戰(zhàn)。水稻粒型不僅是重要產(chǎn)量性狀千粒重的決定因素之一，還影響到稻米的外觀品質(zhì)和商品價值。在中國南方、美國和大多數(shù)亞洲國家，人們更習(xí)慣長或細(xì)長型稻米，而韓國、日本、中國北方和斯里蘭卡則習(xí)慣短圓型稻米[1-3]。此外，粒型也是進(jìn)化中一個易于被選擇的表型，是研究水稻進(jìn)化的一個重要性狀[4]。因此，克隆粒型相關(guān)的基因并深入研究和闡明粒型形成的基因調(diào)控網(wǎng)絡(luò)，可為水稻高產(chǎn)、優(yōu)質(zhì)分子育種提供重要的理論基礎(chǔ)和基因資源。在本文中，筆者對前人的研究結(jié)果進(jìn)行了系統(tǒng)匯總分析，以期為水稻粒型的分子育種提供幫助。

1 水稻粒型性狀的遺傳特點(diǎn)與其關(guān)鍵基因克隆

水稻種子的發(fā)育從雙受精開始，精細(xì)胞和卵細(xì)胞結(jié)合發(fā)育成二倍體的胚，精細(xì)胞和兩個極核結(jié)合發(fā)育成三倍體的胚乳，穎花中的子房壁發(fā)育成果皮，珠被發(fā)育成種皮。胚和胚乳為子代組織，其發(fā)育需要母體組織提供營養(yǎng)。因此，種子的體積受到胚、胚乳及母體植株等不同遺傳體系的控制。

水稻的粒型性狀包括粒長、粒寬、粒厚及長寬比，與粒重呈正相關(guān)[5-6]。其遺傳受多基因控制[5-7]。迄今，檢測到的控制粒型的QTL已超過400個，遍布水稻12條染色體。其中位于第2、第3和第5染色體上的QTL數(shù)較多，分別為58、106和55[7-9]。這3條染色體上克隆出的基因數(shù)也最多，在已克隆出的60個粒型基因中, 位于第2和第3染色體的基因各8個，第5染色體上的基因9個(圖1，表1)。

2 水稻粒型基因調(diào)控機(jī)制

粒型的形成涉及復(fù)雜的遺傳調(diào)控網(wǎng)絡(luò)，自細(xì)胞增殖或伸長開始，直至完成籽粒的灌漿過程為止[8-9]。對已克隆的控制粒型的60個基因進(jìn)行總結(jié)分析，發(fā)現(xiàn)這些基因主要涉及包括植物激素、泛素-蛋白酶體通路、MAPK信號、表觀修飾、G-蛋白信號等分子路徑(圖2)。涉及MAPK信號、G蛋白信號和泛素-蛋白酶體通路的基因是通過控制細(xì)胞增殖，進(jìn)而影響水稻粒型，而植物激素、表觀修飾等通路同時影響細(xì)胞增殖和擴(kuò)張，最終控制粒型。越來越多的研究表明不同粒型調(diào)控路徑之間存在互作調(diào)控關(guān)系[9]。例如，G蛋白α亞基，其突變體對BR不敏感，表明參與G蛋白信號與BR信號轉(zhuǎn)導(dǎo)途徑共同調(diào)控水稻粒型[60-63]。受甲基化調(diào)控的，其突變體表現(xiàn)BR相關(guān)突變體的表型，表明表觀修飾與BR途徑存在聯(lián)系[16]。

2.1 植物激素

2.1.1 油菜素內(nèi)酯(BR)

油菜素內(nèi)酯(BR)是調(diào)控植物生長發(fā)育的重要激素[97]。已報道一些BR合成和信號基因的突變會影響水稻籽粒體積，如、、、、等(表1)。這些基因突變使籽粒變短、植株矮化、葉傾角變小。其中，和編碼細(xì)胞色素P450加氧酶，正向調(diào)節(jié)細(xì)胞伸長，參與油菜素內(nèi)酯的合成[10-11,47-48]。編碼與擬南芥同源的BR信號激酶，包含一個激酶結(jié)構(gòu)域和一個C端的TPR結(jié)構(gòu)域，是BR信號的正向調(diào)控因子，是磷酸化底物，此外，的TPR結(jié)構(gòu)域與其激酶結(jié)構(gòu)域互作，阻止與()互作[50]。Feng等[81]克隆了控制粒型的基因它編碼一個類BAHD?；D(zhuǎn)移酶，抑制細(xì)胞伸長，參與介導(dǎo)油菜素內(nèi)酯穩(wěn)態(tài)的調(diào)控，其突變引起籽粒變長、葉傾角變大。Jiang等[46]克隆了一個控制器官體積的基因，它編碼一個與有33%同源性的LRR激酶結(jié)構(gòu)域蛋白，該基因突變，導(dǎo)致細(xì)胞分裂速度下降，細(xì)胞數(shù)目減少，器官變小，突變體內(nèi)源BR的含量降低，根、胚芽鞘組織伸長對BR的響應(yīng)增強(qiáng)。Hu等[26]克隆了一個水稻粒長基因，編碼生長調(diào)節(jié)因子，促進(jìn)細(xì)胞分裂和擴(kuò)張，從而調(diào)節(jié)粒長和粒寬。Che等[27-28]研究發(fā)現(xiàn)/與BR信號轉(zhuǎn)導(dǎo)通路的負(fù)調(diào)控因子直接互作，其轉(zhuǎn)錄激活活性受抑制，其表達(dá)受調(diào)節(jié)。

圖1 已克隆的控制水稻粒型的基因在12條染色體上的分布

Fig. 1. Distribution of cloned genes for grain shape on the 12 chromosomes in rice.

表1已克隆的控制水稻粒型的基因

Table 1. Cloned genes for grain shape in rice.

水稻粒型是由5個主要的信號途徑調(diào)控，包括激素、泛素-蛋白酶體通路、MAPK信號、表觀修飾與G蛋白信號轉(zhuǎn)導(dǎo)。這些調(diào)控因子通過影響細(xì)胞增殖和擴(kuò)張來控制粒型。

Fig. 2. Major pathways of rice grain shape regulation.

2.1.2 生長素(IAA)和細(xì)胞分裂素(CK)

是一個生長素響應(yīng)基因，是生長素響應(yīng)和轉(zhuǎn)運(yùn)的正調(diào)控因子，促進(jìn)穎殼細(xì)胞伸長與擴(kuò)張，調(diào)控植物的器官體積[30]?？刂扑玖Ｖ丶肮酀{速率的主效QTL，編碼IAA-葡萄糖水解酶，能水解IAA-葡萄糖成游離的IAA和葡萄糖，在胚乳發(fā)育過程中調(diào)控生長素平衡[64]。編碼一個生長素響應(yīng)因子，負(fù)向調(diào)節(jié)細(xì)胞伸長，受生長素和BR誘導(dǎo)，與編碼油菜素內(nèi)酯受體基因的啟動子結(jié)合，直接影響的表達(dá)，過表達(dá)導(dǎo)致轉(zhuǎn)基因植株小粒、矮稈、窄葉和葉傾角增大[69]。

調(diào)控水稻粒長、穗粒數(shù)和芒長的基因，編碼一個表皮模式因子類蛋白EPFL1，通過激活和的表達(dá)降低植株內(nèi)源細(xì)胞分裂素的含量, 從而調(diào)控粒長、穗粒數(shù)和芒發(fā)育[86]。

2.2 泛素-蛋白酶體

泛素-蛋白酶體途徑(ubiquitin-26S proteasome pathway)主要由泛素活化酶(ubiquitin-activating enzyme, E1)、泛素結(jié)合酶(ubiquitin-conjugating enzyme, E2)、泛素蛋白連接酶(ubiquitin protein ligase, E3)和26S蛋白酶體組成。泛素化過程先是E1激活泛素分子，并把激活的泛素連接到E2上，此過程需要ATP提供能量，E3識別靶蛋白，促進(jìn)E2將泛素轉(zhuǎn)移到靶蛋白上，泛素化水平達(dá)到一定程度，靶蛋白就被運(yùn)輸?shù)?6S蛋白酶體進(jìn)行降解[98]?？刂扑玖挼幕?，編碼一個環(huán)型的E3泛素連接酶，與擬南芥和小麥同源[23-25]。將其底物錨定到蛋白酶體進(jìn)行降解，從而負(fù)調(diào)節(jié)細(xì)胞分裂。該基因突變使得本應(yīng)降解的底物不能被特異識別降解，從而激活穎花外殼細(xì)胞的分裂，進(jìn)而增加穎花外殼的寬度，另外灌漿速率也得到了提高，胚乳也隨之增大，最終使粒寬、粒重以及產(chǎn)量都得到提高[23]?？赡芡ㄟ^參與泛素蛋白酶體途徑來調(diào)控粒型[52-53]，但最新的結(jié)果表明，該基因是通過影響B(tài)R信號途徑基因的磷酸化來實(shí)現(xiàn)對粒型的調(diào)控(劉家范等，未發(fā)表資料)。編碼一個有功能的U-box E3泛素連接酶，且與存在遺傳互作，上位于[45]。促進(jìn)細(xì)胞分裂，突變體對BR不敏感，表現(xiàn)為粒變短、第2節(jié)間變短、葉片直立，這說明水稻存在-介導(dǎo)的BR信號途徑[45]。調(diào)控水稻抽穗期和粒重的基因(), 編碼一個含有泛素相關(guān)結(jié)構(gòu)域的蛋白，正向調(diào)控細(xì)胞增殖，與泛素通路上各組分的基因存在共表達(dá)，說明其可能通過泛素途徑調(diào)控水稻抽穗期和粒重[70]。

2.3 MAPK信號

絲裂原活化蛋白激酶(MAPK)是一系列細(xì)胞內(nèi)級聯(lián)反應(yīng)的成分，能響應(yīng)多種胞外刺激，MAPK信號轉(zhuǎn)導(dǎo)以三級激酶級聯(lián)的方式進(jìn)行，首先MAPKKK(MAP kinase kinase kinase)受有絲分裂原刺激磷酸化而激活，在此基礎(chǔ)上MAPKKK進(jìn)而磷酸化激活MAPKK(MAP kinase kinase)，最后由MAPKK 磷酸化MAPK，使其活化進(jìn)而轉(zhuǎn)入核內(nèi)，從而參與細(xì)胞生長、發(fā)育、分裂和分化等多種發(fā)育過程，生物體內(nèi)重要的信號轉(zhuǎn)導(dǎo)途徑之一[99]。()編碼一個水稻絲裂原活化蛋白激酶激酶，促進(jìn)細(xì)胞細(xì)胞分裂，該基因突變導(dǎo)致籽粒變小，株高變矮，穗形直立、密穗[19]。()編碼一個與擬南芥同源的絲裂原活化蛋白激酶()，具有磷酸化活性，該基因突變導(dǎo)致籽粒變小、千粒重降低，植株矮化，節(jié)間縮短，葉片直立。與互作，可能位于下游[71]。BR信號途徑與MAPK信號途徑在功能上存在交叉(Crosstalk)，如突變體對BR敏感性降低，且其內(nèi)源BR水平降低，可能也參與影響B(tài)R穩(wěn)態(tài)以及信號途徑，在種子生長發(fā)育中可能作為MAPK通路和BR信號間的連接因子[71]。在擬南芥中BR信號負(fù)調(diào)控因子磷酸化，進(jìn)而抑制其下游MAPK活性[100]。水稻的同源基因是否能磷酸化, 進(jìn)而抑制活性，這需要進(jìn)一步研究。

2.4 表觀修飾

在單子葉植物如水稻胚乳是發(fā)生基因組印跡的主要部位?；蚪M印跡通過抑制靶基因的表達(dá)調(diào)控胚乳發(fā)育，從而控制種子體積[101-102]。甲基化在調(diào)控表達(dá)中發(fā)揮重要作用，研究發(fā)現(xiàn)水稻半顯性突變體植株中表現(xiàn)出葉傾角增大和籽粒變小，是由于基因()啟動子區(qū)域低甲基化[16]。編碼一個H3K36甲基轉(zhuǎn)移酶，其表達(dá)下調(diào)導(dǎo)致多種缺陷，包括植株矮化、節(jié)間縮短、葉片直立和種子變小。轉(zhuǎn)錄組分析發(fā)現(xiàn)，功能喪失，導(dǎo)致包括、和等參與油菜素內(nèi)酯合成及信號通路的相關(guān)基因表達(dá)下調(diào)[17-18]。編碼一個新型的類GNAT蛋白，促進(jìn)細(xì)胞分裂，調(diào)控粒長。具有組蛋白乙酰轉(zhuǎn)移酶活性()，提高該基因表達(dá)會導(dǎo)致轉(zhuǎn)基因植株中組蛋白H4的乙?；教岣撸黾臃N子穎殼細(xì)胞數(shù)目并加速籽粒灌漿，從而增加粒重和產(chǎn)量[65]。

2.5 G-蛋白信號

植物中G蛋白以異源三聚體的形式存在，在多個信號通路中起重要調(diào)控作用[104]。在擬南芥中，Gα()和Gβ()影響葉片和花的發(fā)育，而Gγ()影響種子和器官發(fā)育，功能缺失突變體產(chǎn)生小粒[105-106]。水稻G蛋白α亞基功能缺失突變體表現(xiàn)矮稈小粒表型，對BR的敏感性降低，表明介導(dǎo)的異源三聚體G蛋白與BR信號轉(zhuǎn)導(dǎo)途徑共同調(diào)控水稻粒型[60-63]。G蛋白β亞基()表達(dá)量的降低也會導(dǎo)致水稻出現(xiàn)籽粒變小的表型[32-33]。但G蛋白γ亞基()功能的缺失卻促進(jìn)細(xì)胞伸長，進(jìn)而產(chǎn)生長粒[34-38]，說明水稻中G蛋白γ亞基和α亞基、β亞基的功能是不同的。同時，G蛋白γ亞基對粒型調(diào)控作用在水稻與擬南芥中是相反的，說明水稻與擬南芥中G蛋白γ亞基可能具有不同的作用因子。

我國進(jìn)入經(jīng)濟(jì)新常態(tài)以來，隨著經(jīng)濟(jì)發(fā)展越來越接近發(fā)達(dá)經(jīng)濟(jì)體，技術(shù)創(chuàng)新和技術(shù)轉(zhuǎn)移與擴(kuò)散在影響產(chǎn)業(yè)升級時的角色逐漸發(fā)生轉(zhuǎn)變。根據(jù)以上研究結(jié)果，本文圍繞著經(jīng)濟(jì)新形勢下我國如何優(yōu)化金融結(jié)構(gòu)以更好地促進(jìn)產(chǎn)業(yè)結(jié)構(gòu)升級這一現(xiàn)實(shí)課題，提出以下幾點(diǎn)建議：

2.6 其他通路

MicroRNA在水稻粒型調(diào)控中起重要作用。過表達(dá)的水稻植株出現(xiàn)小粒的表型，對油菜素內(nèi)酯敏感性降低。研究發(fā)現(xiàn)通過降解靶基因，調(diào)控BR生物合成，最終影響植株葉夾角和種子大小[57]。能夠通過下調(diào)的表達(dá)，促進(jìn)油菜素內(nèi)酯的信號轉(zhuǎn)導(dǎo)，進(jìn)而促進(jìn)幼穗分枝、增加種子體積，提高水稻產(chǎn)量[58]。

和都是非典型的不結(jié)合DNA的堿性螺旋-環(huán)-螺旋蛋白, 都是水稻籽粒長度的正向調(diào)節(jié)子。通過與拮抗因子形成異源二聚體抑制的功能，從而正向調(diào)節(jié)水稻粒長[29,31]。編碼包含SBP結(jié)構(gòu)域的轉(zhuǎn)錄因子，該基因的高表達(dá)促進(jìn)細(xì)胞分裂和籽粒灌漿，增加水稻粒寬及產(chǎn)量[83]。編碼植物特有的轉(zhuǎn)錄因子，其高表達(dá)促進(jìn)細(xì)胞伸長，進(jìn)而產(chǎn)生大粒。5′-UTR的一個串聯(lián)重復(fù)序列通過影響轉(zhuǎn)錄和翻譯從而改變其表達(dá)，正向調(diào)控水稻穎殼的細(xì)胞體積，進(jìn)而增加粒長和產(chǎn)量[75]。此外，可以結(jié)合和的啟動子，調(diào)控其表達(dá)，但具體的遺傳互作關(guān)系仍然未知。

Kitagawa等[59]克隆了一個粒型基因，它編碼一個由819個氨基酸組成的kinesin-13家族成員蛋白，與擬南芥高度同源，該基因突變導(dǎo)致細(xì)胞長度變小，從而使突變體表現(xiàn)出籽粒圓而小，株高降低。Li等[87]發(fā)現(xiàn)編碼一種具有轉(zhuǎn)錄調(diào)控活性的類驅(qū)動蛋白，通過調(diào)控水稻中GA的合成來調(diào)節(jié)細(xì)胞伸長, 矮稈突變體表現(xiàn)出短小的根、莖、穗和種子。這些結(jié)果說明驅(qū)動蛋白在水稻粒型調(diào)控中也起到重要作用。

3 粒型基因間互作及其在水稻高產(chǎn)優(yōu)質(zhì)育種中的應(yīng)用

粒型性狀是由多基因控制的數(shù)量性狀，不同粒型基因之間存在著不同程度的互作。編碼一個含有泛素相關(guān)結(jié)構(gòu)域蛋白，作為一個重要的上游調(diào)控蛋白促進(jìn)抽穗和粒重相關(guān)基因的表達(dá)。在突變體中，、和等基因的表達(dá)降低，其中基因的表達(dá)量降低最為明顯[70]。Gao等[107]研究發(fā)現(xiàn)和在水稻粒長調(diào)控上具有累加效應(yīng)。和對的表達(dá)為正調(diào)控，同時，又能夠抑制的轉(zhuǎn)錄，從而降低其表達(dá)水平?？梢匝谏w對粒長的影響，而又可以掩蓋對粒寬的影響[38]。

粒型基因的克隆不僅有助于揭示水稻粒型性狀形成的遺傳機(jī)制，也為水稻分子標(biāo)記輔助選擇育種提供了理論依據(jù)和技術(shù)基礎(chǔ)。Song等[23]研究發(fā)現(xiàn)攜帶的NIL，比其原始親本豐矮占1號的粒長、粒寬、粒厚及千粒重分別提高了6.6%、26.2%、10.5%、49.8%，單株籽粒產(chǎn)量提高19.7%，且不影響株型、籽粒灌漿以及稻米的外觀、蒸煮和食用品質(zhì)。Hu等[26]以9311和武運(yùn)粳7號為背景，分別構(gòu)建了攜帶寶大粒等位基因的兩套近等基因系(NIL)，發(fā)現(xiàn)在以9311為背景的NIL()中粒長、粒寬和粒厚分別提高21.0%、17.6%、11.1%，千粒重增加40.26%, 最終小區(qū)產(chǎn)量增加14.26%。在以WYG7為背景的NIL()中，粒長、粒寬和粒厚分別提高27.3%、12.0%、3.6%，千粒重增加59.89%，小區(qū)產(chǎn)量增加13.1%，雖然株高和穗長明顯提高，劍葉、倒2葉和倒3葉變長，但分蘗數(shù)、一次枝梗數(shù)和二次枝梗數(shù)、粒寬等均無明顯差異[28]。Zhang等[41]將來自于大粒品種N411隱性基因?qū)氲?311中，發(fā)現(xiàn)NIL-千粒重提高了37.03%，穗長增加11.76%，小區(qū)產(chǎn)量提高16.2%，而穗粒數(shù)、分蘗數(shù)、抽穗期和株高并未受到影響。Song等[65]利用雜交、回交篩選獲得了含有來自秈稻Kasalath的粒型基因的遺傳背景為粳稻日本晴的NIL-，相比日本晴，谷粒產(chǎn)量增加15.8%。Wang等[72]研究發(fā)現(xiàn)，相比日本晴，遺傳背景含的NIL籽粒長寬比增加，淀粉顆粒更大更致密，稻米堊白度和堊白率顯著降低，外觀品質(zhì)改善，但千粒重、單株產(chǎn)量、整精米率、直鏈淀粉含量、膠稠度和蛋白質(zhì)含量不受影響。這說明可以用于改良水稻谷粒外觀品質(zhì)，而不影響其產(chǎn)量和蒸煮食用品質(zhì)。

4 展望

謝辭：感謝農(nóng)業(yè)部長江中下游粳稻生物學(xué)與遺傳育種重點(diǎn)實(shí)驗(yàn)室、江蘇省植物基因工程技術(shù)研究中心、江蘇省現(xiàn)代作物生產(chǎn)中心、長江流域雜交水稻協(xié)同創(chuàng)新中心的支持！

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Research Progress on Cloning and Regulation Mechanism of Rice Grain Shape Genes

LIU Xi1, MOU Changling1, ZHOU Chunlei1, CHENG Zhijun2, JIANG Ling1,*, WAN Jianmin1,2

(1State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China;2National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China;*Corresponding author,E-mail: jiangling@njau.edu.cn)

Grain shape is an important trait that affects the yield and quality of rice, so it is necessary tounderstand the genetic regulation mechanism of grain shape to improve rice yield and quality. Grain shape is characterized by a combination of grain length, grain width, grain thickness, and grain length-to-width ratio,belonging to quantitative traits, which is controlled by different genetic systems, such as embryo, endosperm and maternal plant. With the rapid development of rice functional genomics and re-sequencing technology, more than 400 QTLs related to rice grain shape have been located at present, and at least 60 genes associated with rice grain traits have been identified. Some rice grain shape regulation pathways were identified, including phytohormones, the ubiquitin-proteasome pathway, the mitogen-activated protein kinase (MAPK) signaling pathway, epigenetic modification, the G protein signaling pathways. In this review, we systematically summarize and sort out the research progress of the cloning and functional analysis of rice grain shape genes, and evaluate the utilization value of rice grain shape genes in rice breeding for high yield and good quality.

rice(L.); grain shape; gene;regulation of mechanism

10.16819/j.1001-7216.2018.7016

S511.032; S511.2+2

A

1001-7216(2018)01-0001-11

2017-02-07;

2017-04-20。

國家自然科學(xué)基金重點(diǎn)項(xiàng)目(91535302)。