,*西南大学水稻研究所/西南大学农业科学研究院, 重庆 400715Identification of rice chromosome segment substitution Line Z747 with increased grain number and QTL mapping for related traits
WANG Da-Chuan, WANG Hui, MA Fu-Ying, DU Jie, ZHANG Jia-Yu, XU Guang-Yi, HE Guang-Hua, LI Yun-Feng, LING Ying-Hua, ZHAO Fang-Ming,*Rice Research Institute, Southwest University/Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China通讯作者:
收稿日期:2019-04-15接受日期:2019-08-9网络出版日期:2019-09-11
| 基金资助: |
Received:2019-04-15Accepted:2019-08-9Online:2019-09-11
| Fund supported: |
作者简介 About authors
E-mail:wangdachuan6@163.com。
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王大川, 汪会, 马福盈, 杜婕, 张佳宇, 徐光益, 何光华, 李云峰, 凌英华, 赵芳明. 增加穗粒数的水稻染色体代换系Z747鉴定及相关性状QTL定位[J]. 作物学报, 2020, 46(1): 140-146. doi:10.3724/SP.J.1006.2020.92022
WANG Da-Chuan, WANG Hui, MA Fu-Ying, DU Jie, ZHANG Jia-Yu, XU Guang-Yi, HE Guang-Hua, LI Yun-Feng, LING Ying-Hua, ZHAO Fang-Ming.
水稻是世界上最重要的粮食作物之一[1], 提高水稻产量以保障世界粮食安全刻不容缓。水稻产量主要由穗数、粒数、粒重和结实率构成。每穗粒数由穗长、一次枝梗和二次枝梗数决定[2], 所以增加每穗粒数是提高水稻产量的途径之一。然而粒数属于数量性状, 由多基因控制。水稻染色体片段代换系可将多位点控制的复杂性状分解, 使QTL定位更加准确, 尤其定位出的QTL可直接应用于育种实践, 因而是理想的遗传材料。到目前为止, 已经克隆了许多与水稻粒数相关的基因。其中一些涉及细胞分裂素、生长素和茉莉酸等激素信号途径。如Gn1a (Grain number 1a) [3]表达量降低引起花序分生组织中细胞分裂素的积累, 从而增加水稻粒数。GNP1 (Grain Number per Panicle 1) [4]通过增加水稻穗分生组织中的细胞分裂素活性, 提高籽粒数目和产量。An-1 (Awn-1)[5]基因表达上调会引起一个重要的细胞分裂素调控基因LOG的表达下调, 使分生组织的活性降低, 减少每穗粒数。OsGRF6[6]能与OsTAWAWA1及OsMADS34启动子结合, 正调控生长素的生物合成和信号转导, 促进花序发育, 增加穗粒数。PAY1 (Plant Architecture and Yield 1)[7]通过影响生长素极性运输和改变内源吲哚-3-乙酸的分布改善水稻株型, 进而增加水稻穗粒数。NOG1 (NUMBER OF GRAINS 1) [8]启动子区域12 bp的插入使其表达增强, 降低植物体内脂肪酸和茉莉酸水平, 增加水稻穗粒数。也有一些基因通过其他途径调控水稻粒数发育。如GSN1 (Grain Size and Number1) [9]编码双特异性磷酸酶使OsMPK6去磷酸化, GSN1-MAPK模块通过整合细胞定域分化和增殖来协调籽粒数和大小之间的平衡关系。Ghd7 (Grain number, plant height, and heading data7)[10]基因编码CCT结构域蛋白家族成员, 其表达和功能受光周期调控, 在长日照条件下, 该基因的表达增强使稻穗变大和粒数增多。OsCOL13[11]是一个转录因子, 其表达受节律钟的调控和光的诱导, 引起一次枝梗数、二次枝梗数和每穗粒数增加。此外, 还有一些未被克隆的粒数相关QTL, 如qGN4-1[12]、qSSP7[13]、SPP1[14]等。近年来, 还相继发现多花小穗基因fon4[15]和LF1[16], 使得水稻具有形成多花小穗的潜力, 为水稻粒数的增加提供了一条新的可能途径。然而, 目前克隆的基因仍不能完全解释水稻粒数发育的分子机制, 因此有必要鉴定更多粒数相关基因。本研究鉴定了一个以日本晴为受体亲本、西恢18为供体亲本的增加穗粒数的水稻染色体片段代换系Z747, 本文将全面分析该代换系,并进行水稻粒数等重要农艺性状的QTL定位, 为发现增加每穗粒数的QTL奠定基础。
1 材料与方法
1.1 试验材料
增加穗粒数的水稻染色体片段代换系Z747是以日本晴为受体亲本、西恢18为供体亲本, 经过多代回交和自交并结合全基因组SSR分子标记辅助选择选育而成, 西恢18是西南大学选育的优良恢复系。QTL定位材料为日本晴和Z747杂交构建的次级F2群体。1.2 试验方法
1.2.1 材料种植 2017年在西南大学水稻基地, 以日本晴与Z747杂交, 收取杂交种并于同年在海南基地种植F1, 收取F2种子。2018年3月8日, 在西南大学水稻基地育苗, 4月15日, 以株、行距分别为16.67 cm和26.67 cm移栽日本晴和Z747各30株以及280个F2单株于同一试验田, 按常规模式进行田间管理。1.2.2 Z747代换系培育与代换片段的鉴定 首先使用均匀分布于水稻全基因组的429个SSR标记, 进行日本晴和西恢18的多态性分析, 选出263个多态性标记[17], 然后用这些多态性标记从BC2F1代进行分子标记辅助选择(molecular marker assisted selection, MAS), 从中选出20个单株种成株系自交, 每个株系每代取10株继续进行分子标记辅助选择, 在BC2F4选择了一个较理想的单株与日本晴回交, 再自交, 同样从每代每个株系取10株进行分子标记辅助选择, 直至F6代选育成15代换片段的优良多粒染色体片段代换系Z747。鉴定染色体代换片段参照崔国庆等[18]描述的方法, 参照Paterson等[19]的方法计算代换片段长度。
1.2.3 表型分析和农艺性状调查 成熟后, 平地面收取日本晴和Z747各10株以及280株F2群体。考察株高、有效穗数、穗长、一次枝梗数、二次枝梗数、粒长、粒宽、每穗实粒数、每穗总粒数、千粒重和单株产量共11个性状。参照崔国庆等[18]描述的方法测定穗长、一次枝梗数、二次枝梗数、每穗实粒数和每穗总粒数的整株平均值。结实率以每穗实粒数占每穗总粒数的百分比表示。谷粒长宽比以粒长与粒宽的比值计算。最后, 使用Microsoft Excel 2010统计10株日本晴和Z747及F2群体各参数如最小值、最大值、平均值、标准差、偏度、峰度, 并进行t测验。
1.3 QTL定位
用CTAB法提取亲本和280个F2单株的DNA, 参照崔国庆等[18]描述的方法进行PCR扩增和非变性聚丙烯酰胺凝胶电泳。将日本晴带型、Z747带型、双亲带型、缺失带型分别用“-1”、“1”、“0”和“.”来表示基因型赋予值。结合280个F2单株对应的表型值, 在SAS统计软件上, 使用加州大学河滨分校徐世忠教授编写的HPMIXED程序的限制性最大似然(REML)法[20]进行QTL定位, 以P < 0.01为阈值决定QTL是否存在。2 结果与分析
2.1 Z747的代换片段鉴定
用Z747代换片段上的所有多态性SSR标记及代换片段外的24个SSR标记对10株Z747进行进一步代换片段鉴定和遗传背景纯度检测发现10个Z747单株的代换片段一致, 且没有检出除代换片段外的西恢18其他残留片段, 说明Z747基因型已经稳定。Z747共含有来自西恢18的15个染色体代换片段, 分布于水稻1号、2号、3号、5号、6号、9号、11号和12号染色体上。其中1号、2号、3号、6号、9号、11号和12号染色体上均含有2个代换片段, 第5染色体上有1个代换片段。代换区间见图1。总代换片段长度为67.42 Mb, 最长代换片段长度为8.33 Mb, 最短代换片段长度为0.75 Mb, 平均代换片段长度为4.49 Mb。图1
新窗口打开|下载原图ZIP|生成PPT图1Z747的代换片段及携带的QTL
每条染色体左侧为物理距离(Mb)、定位的QTL; 右侧为标记名称、代换区间(框内标记)和代换长度(黑箭头指向)。PH: 株高; PL: 穗长; NPB: 一次枝梗数; NSB: 二次枝梗数; GPP: 每穗实粒数; SPP: 每穗总粒数; SSR: 结实率; GL: 粒长; GW: 粒宽; RLW: 谷粒长宽比; GWT: 千粒重。部分有上标[20]~[30]的QTL表示可能与已克隆的基因等位。[20]: OsRLCK102; [21]: HTD2; [22]: pbr2; [23]: JMJ703; [24]: ND1; [25]: DFO1; [26]: OsMCA1; [27]: OsFRDL1; [28]: PTB1; [29]: DCM1; [30]: OsVPE3。
Fig. 1Substitution segments and detected QTL of Z747
Physical distances (Mb) and mapped QTL are marked at the left of each chromosome; Markers, substitution interval squared by frame, and substitution length (black arrow direction) are displayed at the right of each chromosome. PH: plant height; PL: panicle length; NPB: number of primary branches; NSB: number of secondary branches; GPP: grain number per panicle; SPP: spikelet number per panicle; SSR: seed setting rate; GL: grain length; GW: grain width; RLW: rate of length to width; GWT: 1000-grains weight. Partial QTL noted superscript [20]-[30] indicate that these QTLs are possible alleles with the cloned genes. [20]: OsRLCK102; [21]: HTD2; [22]: pbr2; [23]: JMJ703; [24]: ND1; [25]: DFO1; [26]: OsMCA1, [27]: OsFRDL1; [28]: PTB1; [29]: DCM1; [30]: OsVPE3.
2.2 Z747的农艺性状分析
2018年在重庆, 代换系Z747的生育期为86 d, 比受体日本晴的生育期(95 d)早9 d。与日本晴相比, Z747的每穗总粒数、穗长、一次枝梗数和二次枝梗数显著增加(图2和表1), 分别增加了56.3%、18.3%、64.9%和183.2%, 说明Z747每穗总粒数的增加主要由穗长、一次枝梗和二次枝梗数的共同增加所致, 尤其是二次枝梗数增加了将近2倍。此外, Z747的粒长也增加10.6%, 差异极显著; 粒宽显著变窄、结实率显著降低, 分别减少了5.0%和11.0%, 但其结实率仍达81.0%。Z747的株高、有效穗数、每穗实粒数、千粒重和单株产量与日本晴无显著差异(表1)。图2
新窗口打开|下载原图ZIP|生成PPT图2日本晴和Z747的表型
Fig. 2Phenotype of Nipponbare and Z747
Table 1
表1
表1日本晴和Z747及F2群体各性状统计参数
Table 1
| 性状 Trait | 平均值±标准差(亲本) Mean±SD (parents) | F2群体 F2 population | |||||
|---|---|---|---|---|---|---|---|
| 日本晴 Nipponbare | Z747 | 平均值±标准差 Mean±SD | 范围 Range | 偏度 Skewness | 峰度 Kurtosis | ||
| 株高 Plant height (cm) | 88.1±3.4 | 91.8±6.9 | 91.9±8.2 | 68.0-130.8 | 0.39 | 0.31 | |
| 穗长Panicle length (cm) | 19.7±1.2 | 23.3±1.3** | 19.3±1.6 | 14.8-27.3 | -0.18 | 0.57 | |
| 有效穗数Panicle number | 19.3±5.1 | 15.5±6.4 | 15.6±5.5 | 3.0-36.0 | 0.40 | -0.03 | |
| 一次枝梗数Number of primary branch | 7.4±0.5 | 12.2±1.3** | 8.5±1.1 | 6.9-13.4 | -0.15 | 0.27 | |
| 二次枝梗数Number of secondary branch | 14.3±1.7 | 40.5±1.2** | 15.1±4.3 | 7.4-45.6 | 0.03 | 0.71 | |
| 每穗总粒数Spikelet number per panicle | 110.7±16.4 | 173.0±49.6** | 94.3±19.9 | 21.9-221.7 | -0.19 | 0.39 | |
| 每穗实粒数Grain number per panicle | 101.4±16.5 | 139.8±41.2 | 79.4±15.6 | 10.1-142.5 | -0.23 | 0.65 | |
| 结实率Seed setting rate (%) | 91.0±2.0 | 81.0±0.7** | 85.1±12.9 | 10.9-96.3 | -2.17 | 10.44 | |
| 粒长Grain length (mm) | 7.17±0.24 | 7.93±0.04** | 7.45±0.47 | 6.61-10.05 | 0.36 | 1.81 | |
| 粒宽Grain width (mm) | 3.40±0.08 | 3.23±0.05* | 3.34±0.13 | 2.38-3.52 | -0.38 | 0.26 | |
| 千粒重1000-grain weight (g) | 24.6±1.6 | 25.5±0.7 | 25.5±1.8 | 21.0-32.3 | 0.28 | 1.27 | |
| 单株产量Yield per plant (g) | 38.6±9.8 | 40.9±5.3 | 31.7±12.4 | 2.4-72.5 | 0.45 | 0.20 | |
新窗口打开|下载CSV
2.3 Z747代换片段携带的粒数等重要农艺性状QTL定位
Z747携带46个水稻重要农艺性状QTL, 分布于其12个代换片段上, 贡献率在1.19%~63.73%之间。包括5个株高QTL、2个穗长QTL、4个一次枝梗数QTL、6个二次枝梗数QTL、3个每穗总粒数的QTL、4个每穗实粒数QTL、9个结实率QTL、3个粒长QTL、2个粒宽QTL、6个谷粒长宽比QTL、2个千粒重QTL。其中有13个是贡献率大于10%的主效QTL, 包括株高qPH-3-3和qPH5、总粒数qSPP9、实粒数qGPP-9-1、二次枝梗数qNSB-9-1、结实率qSSR1、qSSR5和qSSR-9-1、粒长qGL3、谷粒长宽比qRLW-3-2、qRLW5和qRLW6及千粒重qGWT3 (表2和图1)。Table 2
表2
表2Z747携带的水稻重要农艺性状QTL
Table 2
| 性状 Trait | QTL | 染色体 Chr. | 连锁标记 Linked marker | 加性效应 Additive effect | 贡献率 Var. (%) | P值 P-value | 可能的等位基因 Possible alleles |
|---|---|---|---|---|---|---|---|
| 株高 | qPH-3-1 | 3 | RM5474 | -7.79 | 9.45 | 0.0004 | OsRLCK102[20] |
| Plant height | qPH-3-2 | 3 | RM3417 | 5.74 | 5.15 | 0.0003 | HTD2 [21] |
| qPH-3-3 | 3 | RM6266 | 5.03 | 10.30 | <0.0001 | — | |
| qPH5 | 5 | RM5874 | 13.67 | 27.54 | 0.0003 | — | |
| qPH11 | 11 | RM7120 | 5.31 | 4.39 | 0.0090 | — | |
| 穗长 | qPL3 | 3 | RM6266 | 0.51 | 2.70 | 0.0020 | — |
| Panicle length | qPL11 | 11 | RM7120 | 1.28 | 6.61 | 0.0012 | — |
| 一次枝梗数 | qNPB2 | 2 | RM1385 | 0.59 | 6.07 | 0.0002 | Pbr2[22] |
| Number of primary branch | qNPB3 | 3 | RM3766 | 0.83 | 7.45 | 0.0012 | — |
| qNPB9 | 9 | RM24537 | 1.79 | 9.96 | <0.0001 | — | |
| qNPB12 | 12 | RM247 | -1.07 | 8.14 | 0.0049 | — | |
| 二次枝梗数 | qNSB2 | 2 | RM6378 | 2.33 | 1.65 | 0.0004 | — |
| Number of secondary branch | qNSB3 | 3 | RM3766 | 3.86 | 7.83 | 0.0005 | — |
| qNSB5 | 5 | RM18067 | 3.59 | 5.92 | 0.0036 | JMJ703[23] | |
| qNSB6 | 6 | RM494 | -2.46 | 7.10 | 0.0004 | — | |
| qNSB-9-1 | 9 | RM7048 | -7.39 | 20.71 | 0.0007 | — | |
| qNSB-9-2 | 9 | RM24537 | 6.29 | 6.05 | 0.0001 | — | |
| 实粒数 | qGPP2 | 2 | RM1385 | 8.89 | 4.53 | 0.0014 | — |
| Grain number per panicle | qGPP-9-1 | 9 | RM7048 | -28.08 | 19.83 | 0.0008 | — |
| qGPP-9-2 | 9 | RM24537 | 18.49 | 3.66 | 0.0038 | — | |
| qGPP12 | 12 | RM3331 | -18.64 | 8.21 | <0.0001 | ND1[24] | |
| 总粒数 | qSPP3 | 3 | RM3766 | 20.73 | 9.66 | 0.0002 | — |
| Spikelet number per panicle | qSPP5 | 5 | RM18067 | 20.07 | 7.90 | 0.0015 | — |
| qSPP9 | 9 | RM7048 | -29.51 | 14.15 | 0.0044 | — | |
| 结实率 | qSSR1 | 1 | RM259 | -24.38 | 11.97 | 0.0001 | DFO1[25] |
| Seed setting rate | qSSR2 | 2 | RM1385 | 4.65 | 1.19 | 0.0069 | — |
| qSSR-3-1 | 3 | RM5474 | 18.66 | 9.82 | <0.0001 | OsMCA1[26] | |
| qSSR-3-2 | 3 | RM3766 | -10.38 | 3.58 | 0.0014 | OsFRDL1[27] | |
| qSSR5 | 5 | RM5874 | 42.72 | 46.67 | <0.0001 | PTB1[28] | |
| qSSR6 | 6 | RM5371 | -17.59 | 6.48 | 0.0013 | DCM1[29] | |
| qSSR-9-1 | 9 | RM7048 | -20.74 | 10.33 | 0.0004 | — | |
| qSSR-9-2 | 9 | RM24537 | 23.28 | 5.24 | <0.0001 | — | |
| qSSR12 | 12 | RM3331 | -14.58 | 4.80 | <0.0001 | — | |
| 粒长 | qGL3 | 3 | RM6266 | 0.40 | 63.73 | <0.0001 | — |
| Grain length | qGL5 | 5 | RM18067 | 0.24 | 9.29 | 0.0007 | — |
| qGL12 | 12 | RM3331 | 0.16 | 3.21 | 0.0047 | — | |
| 粒宽 | qGW2 | 2 | RM1385 | -0.07 | 5.59 | 0.0080 | OsVPE3[30] |
| Grain width | qGW5 | 5 | RM18148 | -0.08 | 6.05 | 0.0029 | — |
| 长宽比 | qRLW2 | 2 | RM1385 | 0.08 | 5.35 | 0.0004 | — |
| Rate of length to width | qRLW-3-1 | 3 | RM3766 | 0.10 | 5.42 | 0.0047 | — |
| qRLW-3-2 | 3 | RM6266 | 0.13 | 19.74 | <0.0001 | — | |
| qRLW5 | 5 | RM18148 | 0.13 | 10.17 | 0.0002 | — | |
| qRLW6 | 6 | RM494 | -0.09 | 10.31 | <0.0001 | — | |
| qRLW12 | 12 | RM3331 | 0.15 | 7.70 | <0.0001 | — | |
| 千粒重 | qGWT2 | 2 | RM1385 | -0.80 | 4.01 | 0.0048 | OsVPE3[30] |
| 1000-kernel weight | qGWT3 | 3 | RM6266 | 1.82 | 28.67 | <0.0001 | — |
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3个每穗总粒数QTL (qSPP3、qSPP5、qSPP9)的贡献率分别为9.66%、7.90%和14.15%, 暗示Z747的每穗总粒数由1个减少总粒数的主效QTL和2个增加总粒数的微效QTL共同控制。4个实粒数QTL (qGPP2、qGPP-9-1、qGPP-9-2、qGPP12)的贡献率分别为4.53%、19.83%、3.66%和8.21%。表明Z747的每穗实粒数由1个减少实粒数的主效QTL和3个微效QTL (2个增加和1个减少粒数)共同控制(表2和图1)。
共有30个具有增加对应性状效应值的QTL。有12个QTL如qPH-3-1、qPH-3-2、qGWT2等可能与已克隆基因如OsRLCK102、HTD2、OsVPE3等[20,21,22,23,24,25,26,27,28,29,30]等位(表2和图1)。
3 讨论
水稻染色体片段代换系, 与受体亲本相比, 仅存在少量代换片段的差异, 因而可消除遗传背景的干扰, 使QTL定位更加准确, 尤其是定位结果可直接应用于育种实践, 在水稻功能基因组学研究中有越来越广泛的应用[31]。利用染色体片段代换系, 可挖掘出更多的有利变异基因, 为水稻分子聚合育种提供丰富的基因资源[32]。本研究鉴定出一个以日本晴为受体亲本, 西恢18为供体亲本的15代换片段的增加每穗粒数的水稻染色体片段代换系Z747。Z747含有多个育种有利性状, 不仅穗粒数多, 而且粒也重。其粒数的增加主要是由于穗长、一次枝梗数和二次枝梗数共同增加所致。因而Z747的鉴定对日本晴系列的分子设计育种有重要应用价值。鉴于Z747还存在15个来自西恢18的染色体代换片段, 我们利用以受体日本晴与Z747杂交所产生的次级F2群体进行了水稻粒数等12个重要农艺性状的QTL定位。结果鉴定出46个QTL, 分布于Z747的12个代换片段上。与前人报道的基因相比较, 我们检出的qNPB2与一次枝梗数QTL-pbr2[22]可能是同一QTL。二次枝梗数qNSB5与编码H3K4特异性去甲基酶的JMJ703[23]可能等位。每穗实粒数qGPP12与编码纤维素合酶的ND1(OsCD1)[24]可能等位。结实率QTL-qSSR1、qSSR-3-1、qSSR-3-2、qSSR5和qSSR6分别与编码类EMF1蛋白的DFO1(CCP1)[25]、编码质膜蛋白的OsMCA1(PAP)[26]、编码柠檬酸盐转运蛋白的OsFRDL1[27]、编码RING类E3泛素连接酶的PTB1[28]和编码锌指蛋白的DCM1[29]是等位基因。株高qPH-3-1及qPH-3-2分别与BR信号的OsRLCK102[20]和编码α/β折叠水解酶超家族蛋白的HTD2[21]可能等位。千粒重qGWT2和粒宽qGW2, 连锁于同一标记, 可能是一因多效QTL, 与参与细胞程序化死亡的OsVPE3[30]可能等位。
此外, 一些已克隆的基因虽然在我们所定位的7个QTL的代换片段上, 但连锁标记的物理距离与基因相距较远, 二者可能并不等位。如粒数qSPP3与PLS2[33] 、每穗总粒数qSPP5与QTL-snp5.1[34]、株高qPH5与OsSIZ1[35] 、粒宽qGW5及谷粒长宽比qRLW5与编码钙调素结合蛋白的GW5[36]、每穗实粒数qGPP-9-2和直立密穗基因DEP1[37]、粒长qGL3与编码蛋白磷酸酶的粒长基因qGL3.1[38]。此外, 我们还鉴定出了qSPP9、qNSB2、qGL12、qPL3等27个未被报道的QTL。通过这些QTL的比较, 对于可能是与已克隆基因等位的12个QTL, 我们需进一步对日本晴和Z747进行测序和功能互补验证, 便于进一步培育其单片段代换系。鉴于上述基因多数是利用突变体鉴定出来的, 含有多个育种不利性状, 不利于直接利用, 而这些基因的等位代换系则含有多个育种有利性状, 因而可直接应用于分子设计育种。对于尚未报道的QTL, 尤其具有主效效应者, 可进一步精细定位和克隆, 为解析这些重要农艺性状形成的分子机制奠定基础。
参考文献 原文顺序
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被引期刊影响因子
DOI:10.1007/s12892-012-0093-zURL [本文引用: 1]
[本文引用: 1]
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DOI:10.1126/science.1113373URLPMID:15976269 [本文引用: 1]
Most agriculturally important traits are regulated by genes known as quantitative trait loci (QTLs) derived from natural allelic variations. We here show that a QTL that increases grain productivity in rice, Gn1a, is a gene for cytokinin oxidase/dehydrogenase (OsCKX2), an enzyme that degrades the phytohormone cytokinin. Reduced expression of OsCKX2 causes cytokinin accumulation in inflorescence meristems and increases the number of reproductive organs, resulting in enhanced grain yield. QTL pyramiding to combine loci for grain number and plant height in the same genetic background generated lines exhibiting both beneficial traits. These results provide a strategy for tailormade crop improvement.
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DOI:10.1371/journal.pgen.1006386URLPMID:27764111 [本文引用: 1]
Cytokinins and gibberellins (GAs) play antagonistic roles in regulating reproductive meristem activity. Cytokinins have positive effects on meristem activity and maintenance. During inflorescence meristem development, cytokinin biosynthesis is activated via a KNOX-mediated pathway. Increased cytokinin activity leads to higher grain number, whereas GAs negatively affect meristem activity. The GA biosynthesis genes GA20oxs are negatively regulated by KNOX proteins. KNOX proteins function as modulators, balancing cytokinin and GA activity in the meristem. However, little is known about the crosstalk among cytokinin and GA regulators together with KNOX proteins and how KNOX-mediated dynamic balancing of hormonal activity functions. Through map-based cloning of QTLs, we cloned a GA biosynthesis gene, Grain Number per Panicle1 (GNP1), which encodes rice GA20ox1. The grain number and yield of NIL-GNP1TQ were significantly higher than those of isogenic control (Lemont). Sequence variations in its promoter region increased the levels of GNP1 transcripts, which were enriched in the apical regions of inflorescence meristems in NIL-GNP1TQ. We propose that cytokinin activity increased due to a KNOX-mediated transcriptional feedback loop resulting from the higher GNP1 transcript levels, in turn leading to increased expression of the GA catabolism genes GA2oxs and reduced GA1 and GA3 accumulation. This rebalancing process increased cytokinin activity, thereby increasing grain number and grain yield in rice. These findings uncover important, novel roles of GAs in rice florescence meristem development and provide new insights into the crosstalk between cytokinin and GA underlying development process.
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DOI:10.1105/tpc.113.113589URL [本文引用: 1]
Long awns are important for seed dispersal in wild rice (Oryza rufipogon), but are absent in cultivated rice (Oryza sativa). The genetic mechanism involved in loss-of-awn in cultivated rice remains unknown. We report here the molecular cloning of a major quantitative trait locus, An-1, which regulates long awn formation in O. rufipogon. An-1 encodes a basic helix-loophelix protein, which regulates cell division. The nearly-isogenic line (NIL-An-1) carrying a wild allele An-1 in the genetic background of the awnless indica Guangluai4 produces long awns and longer grains, but significantly fewer grains per panicle compared with Guangluai4. Transgenic studies confirmed that An-1 positively regulates awn elongation, but negatively regulates grain number per panicle. Genetic variations in the An-1 locus were found to be associated with awn loss in cultivated rice. Population genetic analysis of wild and cultivated rice showed a significant reduction in nucleotide diversity of the An-1 locus in rice cultivars, suggesting that the An-1 locus was a major target for artificial selection. Thus, we propose that awn loss was favored and strongly selected by humans, as genetic variations at the An-1 locus that cause awn loss would increase grain numbers and subsequently improve grain yield in cultivated rice.
DOI:10.1038/nplants.2015.196URLPMID:27250748 [本文引用: 1]
Strategies to increase rice productivity to meet the global demand have been the main concern of breeders around the world. Although a growing number of functional genes related to crop yield have been characterized, our understanding of its associated regulatory pathways is limited. Using rice as a model, we find that blocking miR396 greatly increases grain yield by modulating development of auxiliary branches and spikelets through direct induction of the growth regulating factor 6 (OsGRF6) gene. The upregulation of OsGRF6 results in the coordinated activation of several immediate downstream biological clades, including auxin (IAA) biosynthesis, auxin response factors, and branch and spikelet development-related transcription factors. This study describes a conserved microRNA (miRNA)-dependent regulatory module that integrates inflorescence development, auxin biosynthesis and signalling pathways, and could potentially be used in engineering high-yield crop plants.
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DOI:10.1111/tpj.12905URLPMID:26095647 [本文引用: 1]
Plant architecture, a complex of the important agronomic traits that determine grain yield, is a primary target of artificial selection of rice domestication and improvement. Some important genes affecting plant architecture and grain yield have been isolated and characterized in recent decades; however, their underlying mechanism remains to be elucidated. Here, we report genetic identification and functional analysis of the PLANT ARCHITECTURE AND YIELD 1 (PAY1) gene in rice, which affects plant architecture and grain yield in rice. Transgenic plants over-expressing PAY1 had twice the number of grains per panicle and consequently produced nearly 38% more grain yield per plant than control plants. Mechanistically, PAY1 could improve plant architecture via affecting polar auxin transport activity and altering endogenous indole-3-acetic acid distribution. Furthermore, introgression of PAY1 into elite rice cultivars, using marker-assisted background selection, dramatically increased grain yield compared with the recipient parents. Overall, these results demonstrated that PAY1 could be a new beneficial genetic resource for shaping ideal plant architecture and breeding high-yielding rice varieties.
DOI:10.1038/s41467-017-01501-8URLPMID:29133783 [本文引用: 1]
During rice domestication and improvement, increasing grain yield to meet human needs was the primary objective. Rice grain yield is a quantitative trait determined by multiple genes, but the molecular basis for increased grain yield is still unclear. Here, we show that NUMBER OF GRAINS 1 (NOG1), which encodes an enoyl-CoA hydratase/isomerase, increases the grain yield of rice by enhancing grain number per panicle without a negative effect on the number of panicles per plant or grain weight. NOG1 can significantly increase the grain yield of commercial high-yield varieties: introduction of NOG1 increases the grain yield by 25.8% in the NOG1-deficient rice cultivar Zhonghua 17, and overexpression of NOG1 can further increase the grain yield by 19.5% in the NOG1-containing variety Teqing. Interestingly, NOG1 plays a prominent role in increasing grain number, but does not change heading date or seed-setting rate. Our findings suggest that NOG1 could be used to increase rice production.
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DOI:10.1105/tpc.17.00959URLPMID:29588389 [本文引用: 1]
Grain number and size are interactive agronomic traits that determine grain yield. However, the molecular mechanisms responsible for coordinating the trade-off between these traits remain elusive. Here, we characterized the rice (Oryza sativa) grain size and number1 (gsn1) mutant, which has larger grains but sparser panicles than the wild type due to disordered localized cell differentiation and proliferation. GSN1 encodes the mitogen-activated protein kinase phosphatase OsMKP1, a dual-specificity phosphatase of unknown function. Reduced expression of GSN1 resulted in larger and fewer grains, whereas increased expression resulted in more grains but reduced grain size. GSN1 directly interacts with and inactivates the mitogen-activated protein kinase OsMPK6 via dephosphorylation. Consistent with this finding, the suppression of mitogen-activated protein kinase genes OsMPK6, OsMKK4, and OsMKKK10 separately resulted in denser panicles and smaller grains, which rescued the mutant gsn1 phenotypes. Therefore, OsMKKK10-OsMKK4-OsMPK6 participates in panicle morphogenesis and acts on a common pathway in rice. We confirmed that GSN1 is a negative regulator of the OsMKKK10-OsMKK4-OsMPK6 cascade that determines panicle architecture. The GSN1-MAPK module coordinates the trade-off between grain number and grain size by integrating localized cell differentiation and proliferation. These findings provide important insights into the developmental plasticity of the panicle and a potential means to improve crop yields.
DOI:10.1038/ng.143URLPMID:18454147 [本文引用: 1]
Yield potential, plant height and heading date are three classes of traits that determine the productivity of many crop plants. Here we show that the quantitative trait locus (QTL) Ghd7, isolated from an elite rice hybrid and encoding a CCT domain protein, has major effects on an array of traits in rice, including number of grains per panicle, plant height and heading date. Enhanced expression of Ghd7 under long-day conditions delays heading and increases plant height and panicle size. Natural mutants with reduced function enable rice to be cultivated in temperate and cooler regions. Thus, Ghd7 has played crucial roles for increasing productivity and adaptability of rice globally.
DOI:10.1007/s11103-016-0506-3URLPMID:27405463 [本文引用: 1]
Flowering time determines the adaptability of crop plants to different local environments, thus being one of the most important agronomic traits targeted in breeding programs. Photoperiod is one of the key factors that control flowering in plant. A number of genes that participate in the photoperiod pathway have been characterized in long-day plants such as Arabidopsis, as well as in short-day plants such as Oryza sativa. Of those, CONSTANS (CO) as a floral integrator promotes flowering in Arabidopsis under long day conditions. In rice, Heading date1 (Hd1), a homologue of CO, functions in an opposite way, which inhibits flowering under long day conditions and induces flowering under short day conditions. Here, we show that another CONSTANS-like (COL) gene, OsCOL13, negatively regulates flowering in rice under both long and short day conditions. Overexpression of OsCOL13 delays flowering regardless of day length. We also demonstrated that OsCOL13 has a constitutive and rhythmic expression pattern, and that OsCOL13 is localized to the nucleus. OsCOL13 displays transcriptional activation activity in the yeast assays and likely forms homodimers in vivo. OsCOL13 suppresses the florigen genes Hd3a and RFT1 by repressing Ehd1, but has no relationship with other known Ehd1 regulators as determined by using mutants or near isogenic lines. In addition, the transcriptional level of OsCOL13 significantly decreased in the osphyb mutant, but remained unchanged in the osphya and osphyc mutants. Thus, we conclude that OsCOL13 functions as a negative regulator downstream of OsphyB and upstream of Ehd1 in the photoperiodic flowering in rice.
DOI:10.1007/s10142-010-0167-2URLPMID:20376514 [本文引用: 1]
Large number of well-filled grains per panicle is an important yield component trait in rice. A combination of QTL mapping and transcriptome profiling was used to identify candidate genes for grain number. A framework linkage map was constructed using 166 SSR markers evenly distributed over the 12 rice chromosomes. QTL mapping using 3 years phenotyping data on a set of recombinant inbred lines derived from a cross between Pusa 1266 (high grain number) and Pusa Basmati 1 (low grain number) identified one consistent QTL qGN4-1 on the long arm of chromosome 4 with major effect on grain number. This QTL was co-localized with major QTLs for primary and secondary branches per panicle, and number of panicles per plant. The QTL interval was narrowed down to 11.1 cM (0.78 Mbp) by targeted enrichment of the region with six additional markers. Microarray transcriptome profiling revealed eight genes in the qGN4-1 region differentially expressed between the two parents during early panicle development. Synteny of this QTL and potential candidates was examined in wheat, barley, maize, sorghum, and Brachypodium to further validate the association.
DOI:10.1007/s00122-008-0711-9URL [本文引用: 1]
In our previous studies, one putative QTL affecting number of spikelets per panicle (SPP) was identified in the pericentromeric region of rice chromosome 7 using a recombinant inbred population. In order to define the QTL (qSPP7), RI50, a recombinant inbred line with 70% of genetic background same as the female parent of Zhenshan 97, was selected to produce near-isogenic lines for the target region in the present study. In a BC2F2 population consisting of 190 plants, the frequency distribution of SPP was shown to be discontinuous and followed the expected Mendelian ratios (1:2:1 by progeny test) for single locus segregation. qSPP7 was mapped to a 0.4cM region between SSR marker RM3859 and RFLP marker C39 based on tests of the BC2F2 population and its progeny. Its additive and dominant effects on SPP were 51.1 and 24.9 spikelets, respectively. Of great interest, the QTL region also had effects on grain yield per plant (YD), 1,000 grain weight (GW), tillers per plant (TPP) and seed setting ratio (SR). Significant correlations were observed between SPP and YD (r=0.66) and between SPP and SR (r=−0.29) in the progeny test. 1082 extremely small panicle plants of a BC3F2 population containing 8,400 individuals were further used to fine map the QTL. It turns out that qSPP7 co-segregated with two markers, RM5436 and RM5499 spanning a physical distance of 912.4kb. Overall results suggested that recombination suppression occurred in the region and positional cloning strategy is infeasible for qSPP7 isolation. The higher grain yield of Minghui 63 homozygote as compared to the heterozygote suggested that Minghui 63 homozygote at qSPP7 in hybrid rice could further improve its yield.
DOI:10.1007/s00122-009-0999-0URL [本文引用: 1]
Near isogenic lines (NILs) can be used to efficiently handle a target quantitative trait locus (QTL) by blocking genetic background noise. One QTL, SPP1, which controls the number of spikelets per panicle (SPP), was located on chromosome 1, near Gn1a, a cloned gene for rice production in a recombinant inbred line population. NILs of the SPP1 regions were quickly obtained by self-crossing recombinant inbred line 30 which is heterozygous around SPP1. Using a random NIL-F2 population of 210 individuals, we mapped SPP1 to a 2.2-cM interval between RM1195 and RM490, which explained 51.1% of SPP variation. The difference in SPP between the two homozygotes was 44. F2-1456, one NIL-F2 plant, was heterozygous in the SPP1 region but was fixed in the region of Gn1a gene. This plant F3 family showed a very wide variation in SPP, which suggested that it was SPP1 but Gn1a affected the variation of SPP in this population. In a word, SPP1 is a novel gene distinct from Gn1a. Four newly developed InDel markers were used for high-resolution mapping of SPP1 with a large NIL-F2 population. Finally, it was narrowed down to a bacterial artificial chromosome clone spanning 107kb; 17 open reading frames have been identified in the region. Of them, LOC_Os01g12160, which encodes an IAA synthetase, is the most interesting candidate gene.
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DOI:10.1111/pbi.13083URLPMID:30677211 [本文引用: 1]
DOI:10.1073/pnas.1700504114URLPMID:28847935 [本文引用: 1]
The spikelet is a unique inflorescence structure in grass. The molecular mechanisms behind the development and evolution of the spikelet are far from clear. In this study, a dominant rice mutant, lateral florets 1 (lf1), was characterized. In the lf1 spikelet, lateral floral meristems were promoted unexpectedly and could generally blossom into relatively normal florets. LF1 encoded a class III homeodomain-leucine zipper (HD-ZIP III) protein, and the site of mutation in lf1 was located in a putative miRNA165/166 target sequence. Ectopic expression of both LF1 and the meristem maintenance gene OSH1 was detected in the axil of the sterile lemma primordia of the lf1 spikelet. Furthermore, the promoter of OSH1 could be bound directly by LF1 protein. Collectively, these results indicate that the mutation of LF1 induces ectopic expression of OSH1, which results in the initiation of lateral meristems to generate lateral florets in the axil of the sterile lemma. This study thus offers strong evidence in support of the "three-florets spikelet" hypothesis in rice.
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[本文引用: 3]
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URLPMID:1673106 [本文引用: 1]
As part of ongoing studies regarding the genetic basis of quantitative variation in phenotype, we have determined the chromosomal locations of quantitative trait loci (QTLs) affecting fruit size, soluble solids concentration, and pH, in a cross between the domestic tomato (Lycopersicon esculentum Mill.) and a closely-related wild species, L. cheesmanii. Using a RFLP map of the tomato genome, we compared the inheritance patterns of polymorphisms in 350 F2 individuals with phenotypes scored in three different ways: (1) from the F2 progeny themselves, grown near Davis, California; (2) from F3 families obtained by selfing each F2 individual, grown near Gilroy, California (F3-CA); and (3) from equivalent F3 families grown near Rehovot, Israel (F3-IS). Maximum likelihood methods were used to estimate the approximate chromosomal locations, phenotypic effects (both additive effects and dominance deviations), and gene action of QTLs underlying phenotypic variation in each of these three environments. A total of 29 putative QTLs were detected in the three environments. These QTLs were distributed over 11 of the 12 chromosomes, accounted for 4.7-42.0% of the phenotypic variance in a trait, and showed different types of gene action. Among these 29 QTLs, 4 were detected in all three environments, 10 in two environments, and 15 in only a single environment. The two California environments were most similar, sharing 11/25 (44%) QTLs, while the Israel environment was quite different, sharing 7/20 (35%) and 5/26 (19%) QTLs with the respective California environments. One major goal of QTL mapping is to predict, with maximum accuracy, which individuals will produce progeny showing particular phenotypes. Traditionally, the phenotype of an individual alone has been used to predict the phenotype of its progeny. Our results suggested that, for a trait with low heritability (soluble solids), the phenotype of F3 progeny could be predicted more accurately from the genotype of the F2 parent at QTLs than from the phenotype of the F2 individual. For a trait with intermediate heritability (fruit pH), QTL genotype and observed phenotype were about equally effective at predicting progeny phenotype. For a trait with high heritability (mass per fruit), knowing the QTL genotype of an individual added little if any predictive value, to simply knowing the phenotype. The QTLs mapped in the L. esculentum X L. cheesmanii F2 appear to be at similar locations to many of those mapped in a previous cross with a different wild tomato (L. chmielewskii).(ABSTRACT TRUNCATED AT 400 WORDS)
DOI:10.1111/tpj.14093URLPMID:30222251 [本文引用: 4]
Plants have evolved many receptor-like cytoplasmic kinases (RLCKs) to modulate their growth, development, and innate immunity. Broad-Spectrum Resistance 1 (BSR1) encodes a rice RLCK, whose overexpression confers resistance to multiple diseases, including fungal rice blast and bacterial leaf blight. However, the mechanisms underlying resistance remain largely unknown. In the present study, we report that BSR1 is a functional protein kinase that autophosphorylates and transphosphorylates an artificial substrate in?vitro. Although BSR1 is classified as a serine/threonine kinase, it was shown to autophosphorylate on tyrosine as well as on serine/threonine residues when expressed in bacteria, demonstrating that it is a dual-specificity kinase. Protein kinase activity was found to be indispensable for resistance to rice blast and leaf blight in BSR1-overexpressing plants. Importantly, tyrosine phosphorylation of BSR1 was critical for proper localization of BSR1 in rice cells and played a crucial role in BSR1-mediated resistance to multiple diseases, as evidenced by compromised disease resistance in transgenic plants overexpressing a mutant BSR1 in which Tyr-63 was substituted with Ala. Overall, our data indicate that BSR1 is a non-receptor dual-specificity kinase and that both tyrosine and serine/threonine kinase activities are critical for the normal functioning of BSR1 in the resistance to multiple pathogens. Our results support the notion that tyrosine phosphorylation plays a major regulatory role in the transduction of defense signals from cell-surface receptor complexes to downstream signaling components in plants.
DOI:10.1007/s00425-009-0975-6URL [本文引用: 3]
Tiller number is highly regulated by controlling the formation of tiller bud and its subsequent outgrowth in response to endogenous and environmental signals. Here, we identified a rice mutant htd2 from one of the 15,000 transgenic rice lines, which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not affect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud. To isolate the htd2 gene, a map-based cloning strategy was employed and 17 new insertions-deletions (InDels) markers were developed. A high-resolution physical map of the chromosomal region around the htd2 gene was made using the F2 and F3 population. Finally, the gene was mapped in 12.8kb region between marker HT41 and marker HT52 within the BAC clone OSJNBa0009J13. Cloning and sequencing of the target region from the mutant showed that the T-DNA insertion caused a 463bp deletion between the promoter and first exon of an esterase/lipase/thioesterase family gene in the 12.8kb region. Furthermore, transgenic rice with reduced expression level of the gene exhibited an enhanced tillering and dwarf phenotype. Accordingly, the esterase/lipase/thioesterase family gene (TIGR locus Os03g10620) was identified as the HTD2 gene. HTD2 transcripts were expressed mainly in leaf. Loss of function of HTD2 resulted in a significantly increased expression of HTD1, D10 and D3, which were involved in the strigolactone biosynthetic pathway. The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway.
DOI:10.1111/j.1469-8137.2005.01647.xURLPMID:16539615 [本文引用: 3]
With a small and sequenced genome, rice provides an excellent system for studying the genetics of cereal domestication. We conducted a quantitative trait locus (QTL) analysis of key domestication traits using an F2 population derived from a cross between the cultivated rice, Oryza sativa, and the annual wild species, O. nivara. We found that the QTL of large phenotypic effects were targeted by domestication selection for effective harvest and planting, including a reduction in seed shattering and seed dormancy and the synchronization of seed maturation. Selection for higher yield was probably responsible for the fixation of mutations at a cluster of QTL on chromosome 7 and a few other chromosomal locations that could have substantially improved plant architecture and panicle structure, resulting in fewer erect tillers and longer and more highly branched panicles in cultivated rice. In comparison with the wild perennial species, O. rufipogon, rice domestication from O. nivara would have involved QTL with a greater degree of chromosomal co-localization and required little genetic change associated with life history or mating system transitions. The genetic analyses of domestication traits with both wild relatives will open opportunities for the improvement of rice cultivars utilizing natural germplasm.
DOI:10.1073/pnas.1217020110URLPMID:23319643 [本文引用: 3]
Transposable elements (TEs) are ubiquitously present in plant genomes and often account for significant fractions of the nuclear DNA. For example, roughly 40% of the rice genome consists of TEs, many of which are retrotransposons, including 14% LTR- and ～1% non-LTR retrotransposons. Despite their wide distribution and abundance, very few TEs have been found to be transpositional, indicating that TE activities may be tightly controlled by the host genome to minimize the potentially mutagenic effects associated with active transposition. Consistent with this notion, a growing body of evidence suggests that epigenetic silencing pathways such as DNA methylation, RNA interference, and H3K9me2 function collectively to repress TE activity at the transcriptional and posttranscriptional levels. It is not yet clear, however, whether the removal of histone modifications associated with active transcription is also involved in TE silencing. Here, we show that the rice protein JMJ703 is an active H3K4-specific demethylase required for TEs silencing. Impaired JMJ703 activity led to elevated levels of H3K4me3, the misregulation of numerous endogenous genes, and the transpositional reactivation of two families of non-LTR retrotransposons. Interestingly, loss of JMJ703 did not affect TEs (such as Tos17) previously found to be silenced by other epigenetic pathways. These results indicate that the removal of active histone modifications is involved in TE silencing and that different subsets of TEs may be regulated by distinct epigenetic pathways.
DOI:10.1111/j.1467-7652.2010.00570.xURL [本文引用: 3]
P>The cell wall plays important roles in plant architecture and morphogenesis. The cellulose synthase-like super-families were reported to contain glycosyltransferases motif and are required for the biosynthesis of cell wall polysaccharides. Here, we describe a curled leaf and dwarf mutant, cd1, in rice, which exhibits multiple phenotypic traits such as the reduction of plant height and leaf width, curled leaf morphology and a decrease in the number of grains and in the panicle length. Map-based cloning indicates that a member of the cellulose synthase-like D (CSLD) group is a candidate for OsCD1. RNAi transgenic plants with the candidate CSLD gene display a similar phenotype to the cd1 mutant, suggesting that OsCD1 is a member of the CSLD sub-family. Furthermore, sequence analysis indicates that OsCD1 contains the common D,D,D,QXXRW motif, which is a feature of the cellulose synthase-like super-family. Analysis of OsCD1 promoter with GUS fusion expression shows that OsCD1 exhibits higher expression in young meristem tissues such as fresh roots, young panicle and stem apical meristem. Cell wall composition analysis reveals that cellulose content and the level of xylose are significantly reduced in mature culm owing to loss of OsCD1 function. Take together, the work presented here is useful for expanding the understanding of cell wall biosynthesis.
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DOI:10.1111/tpj.12784URLPMID:25647350 [本文引用: 3]
Floral organ specification is controlled by various MADS-box genes in both dicots and monocots, whose expression is often subjected to both genetic and epigenetic regulation in Arabidopsis thaliana. However, little information is known about the role of epigenetic modification of MADS-box genes during rice flower development. Here, we report the characterization of a rice gene, curved chimeric palea 1 (CCP1) that functions in palea development. Mutation in CCP1 resulted in abnormal palea with ectopic stigmatic tissues and other pleiotropic phenotypes. We found that OsMADS58, a C-class gene responsible for carpel morphogenesis, was ectopically expressed in the ccp1 palea, indicating that the ccp1 palea was misspecified and partially acquired carpel-like identity. Constitutive expression of OsMADS58 in the wild-type rice plants caused morphological abnormality of palea similar to that of ccp1, whereas OsMADS58 knockdown by RNAi in ccp1 could rescue the abnormal phenotype of mutant palea, suggesting that the repression of OsMADS58 expression by CCP1 is critical for palea development. Map-based cloning revealed that CCP1 encodes a putative plant-specific emBRYONIC flower1 (EMF1)-like protein. Chromatin immunoprecipitation assay showed that the level of the H3K27me3 at the OsMADS58 locus was greatly reduced in ccp1 compared with that in the wild-type. Taken together, our results show that CCP1 plays an important role in palea development through maintaining H3K27me3-mediated epigenetic silence of the carpel identity-specifying gene OsMADS58, shedding light on the epigenetic mechanism in floral organ development.
DOI:10.1007/s11103-014-0257-yURLPMID:25307286 [本文引用: 3]
Plant architecture directly affects biomass in higher plants, especially grain yields in agricultural crops. In this study, we characterized a recessive mutant, plant architecture determinant (pad), derived from the Oryza sativa ssp. indica cultivar MH86. The mutant exhibited severe dwarf phenotypes, including shorter and stunted leaves, fewer secondary branches during both the vegetative and reproductive growth stages. Cytological studies revealed that pad mutant growth defects are primarily due to the inhibition of cell expansion. The PAD gene was isolated using a map-based cloning strategy. It encodes a plasma membrane protein OsMCA1 and a SNP responsible for a single amino acid change was found in the mutant. PAD was universally expressed in rice tissues from the vegetative to reproductive growth stages, especially in seedlings, nodes and rachillae. Quantitative real-time PCR analysis revealed that the most of the genes responding to gibberellin (GA) metabolism were up-regulated in pad mutant internodes. The endogenous GA content measurement revealed that the levels of GA1 were significantly decreased in the third internode of pad mutants. Moreover, a GA response assay suggested that OsMCA1/PAD might be involved in the regulation of GA metabolism and signal transduction. Our results revealed the pad is a loss-of-function mutant of the OsMCA1/PAD, leading to upregulation of genes related to GA deactivation, which decreased bioactive GA levels.
DOI:10.1093/jxb/erw314URLPMID:27555544 [本文引用: 3]
Iron (Fe) is essential for plant growth and development, but the molecular mechanisms underlying its distribution to different organs are poorly understood. We found that OsFRDL1 (FERRIC REDUCTASE DEFECTIVE LIKE 1), a plasma membrane-localized transporter for citrate, was highly expressed in the upper nodes of rice at the reproductive growth stage. OsFRDL1 was expressed in most cells of enlarged vascular bundles, diffuse vascular bundles, and the interjacent parenchyma cell bridges of uppermost node I, as well as vascular tissues of the leaf blade, leaf sheath, peduncle, rachis, husk, and stamen. Knockout of OsFRDL1 decreased pollen viability and grain fertility when grown in a paddy field. Iron was deposited in the parenchyma cell bridges, a few of the cell layers of the parenchyma tissues outside of the bundle sheath of enlarged vascular bundles in node I in both the wild-type rice and osfrdl1 mutant, but the mutant accumulated more Fe than the wild-type rice in this area. A stem-fed experiment with stable isotope 57Fe showed that the distribution of Fe in the anther and panicle decreased in the knockout line, but that in the flag leaf it increased compared with the wild-type rice. Taken together, our results show that OsFRDL1 expressed in the upper nodes is required for the distribution of Fe in the panicles through solubilizing Fe deposited in the apoplastic part of nodes in rice.
DOI:10.1038/ncomms3793URLPMID:24240868 [本文引用: 3]
Grain number, panicle seed setting rate, panicle number and grain weight are the most important components of rice grain yield. To date, several genes related to grain weight, grain number and panicle number have been described in rice. However, no genes regulating the panicle seed setting rate have been functionally characterized. Here we show that the domestication-related POLLEN TUBE BLOCKED 1 (PTB1), a RING-type E3 ubiquitin ligase, positively regulates the rice panicle seed setting rate by promoting pollen tube growth. The natural variation in expression of PTB1 which is affected by the promoter haplotype and the environmental temperature, correlates with the rice panicle seed setting rate. Our results support the hypothesis that PTB1 is an important maternal sporophytic factor of pollen tube growth and a key modulator of the rice panicle seed setting rate. This finding has implications for the improvement of rice yield.
DOI:10.1371/journal.pgen.1007769URLPMID:30419020 [本文引用: 3]
Meiotic cytokinesis influences the fertility and ploidy of gametes. However, limited information is available on the genetic control of meiotic cytokinesis in plants. Here, we identified a rice mutant with low male fertility, defective callose in meiosis 1 (dcm1). The pollen grains of dcm1 are proved to be defective in exine formation. Meiotic cytokinesis is disrupted in dcm1, resulting in disordered spindle orientation during meiosis II and formation of pollen grains with varied size and DNA content. We demonstrated that meiotic cytokinesis defect in dcm1 is caused by prematurely dissolution of callosic plates. Furthermore, peripheral callose surrounding the dcm1 pollen mother cells (PMCs) also disappeared untimely around pachytene. The DCM1 protein contains five tandem CCCH motifs and interacts with nuclear poly (A) binding proteins (PABNs) in nuclear speckles. The expression profiles of genes related to callose synthesis and degradation are significantly modified in dcm1. Together, we propose that DCM1 plays an essential role in male meiotic cytokinesis by preserving callose from prematurely dissolution in rice.
DOI:10.1186/s12284-016-0138-xURLPMID:27900724 [本文引用: 4]
Vacuolar processing enzymes (VPEs) are cysteine proteinases that act as crucial mediators of programmed cell death (PCD) in plants. In rice, however, the role of VPEs in abiotic stress-induced PCD remains largely unknown. In this study, we generated OsVPE3 overexpression and suppression transgenic lines to elucidate the function of this gene in rice.
DOI:10.1556/0806.44.2016.022URL [本文引用: 1]
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DOI:10.3389/fpls.2018.00560URLPMID:29755498 [本文引用: 1]
Premature leaf senescence (PLS), which has a significant impact on yield, is caused by various underlying mechanisms. Glycosyltransferases, which function in glycosyl transfer from activated nucleotides to aglycones, are involved in diverse biological processes, but their roles in rice leaf senescence remain elusive. Here, we isolated and characterized a leaf senescence-related gene from the Premature Leaf Senescent mutant (pls2). The mutant phenotype began with leaf yellowing at tillering and resulted in PLS during the reproductive stage. Leaf senescence was associated with an increase in hydrogen peroxide (H2O2) content accompanied with pronounced decreases in net photosynthetic rate, stomatal conductance, and transpiration rate. Map-based cloning revealed that a mutation in LOC_Os03g15840 (PLS2), a putative glycosyltransferase- encoding gene, was responsible for the defective phenotype. PLS2 expression was detected in all tissues surveyed, but predominantly in leaf mesophyll cells. Subcellular localization of the PLS2 was in the endoplasmic reticulum. The pls2 mutant accumulated higher levels of sucrose together with decreased expression of sucrose metabolizing genes compared with wild type. These data suggested that the PLS2 allele is essential for normal leaf senescence and its mutation resulted in PLS.
DOI:10.1186/1471-2156-6-1URL [本文引用: 1]
Background
The human Prader-Willi syndrome (PWS) domain and its mouse orthologue include a cluster of paternally expressed genes which imprinted expression is co-ordinately regulated by an imprinting center (IC) closely associated to the Snurf-Snrpn gene. Besides their co-regulated imprinted expression, two observations suggest that the spatio-temporal expression of these genes could also be co-regulated. First, the PWS genes have all been reported to be expressed in the mouse nervous system. Second, Snurf-Snrpn and its associated IC are the most ancient elements of the domain which later acquired additional functional genes by retrotransposition. Although located at least 1.5 megabases from the IC, these retroposons acquired the same imprinted regulation as Snurf-Snrpn. In this study, we ask whether the IC, in addition to its function in imprinting, could also be involved in the spatio-temporal regulation of genes in the PWS domain.DOI:10.1111/j.1469-8137.2010.03538.xURLPMID:21083564 [本文引用: 1]
? Sumoylation, a post-translational modification, has important functions in both animals and plants. However, the biological function of the SUMO E3 ligase, SIZ1, in rice (Oryza sativa) is still under investigation. ? In this study, we employed two different genetic approaches, the use of siz1 T-DNA mutant and SIZ1-RNAi transgenic plants, to characterize the function of rice SIZ1. ? Genetic results revealed the co-segregation of single T-DNA insertional recessive mutation with the observed phenotypes in siz1. In addition to showing reduced plant height, tiller number and seed set percentage, both the siz1 mutant and SIZ1-RNAi transgenic plants showed obvious defects in anther dehiscence, but not pollen viability. The anther indehiscence in siz1 was probably a result of defects in endothecium development before anthesis. Interestingly, rice orthologs of AtIRX and ZmMADS2, which are essential for endothecium development during anther dehiscence, were significantly down-regulated in siz1. Compared with the wild-type, the sumoylation profile of high-molecular-weight proteins in mature spikelets was reduced significantly in siz1 and the SIZ1-RNAi line with notably reduced SIZ1 expression. The nuclear localization signal located in the SIZ1 C-terminus was sufficient for its nuclear targeting in bombarded onion epidermis. ? The results suggest the functional role of SIZ1, a SUMO E3 ligase, in regulating rice anther dehiscence.
DOI:10.1038/nplants.2017.43URLPMID:28394310 [本文引用: 1]
Grain size is a major determinant of grain yield in cereal crops. qSW5/GW5, which exerts the greatest effect on rice grain width and weight, was fine-mapped to a 2,263-bp/21-kb genomic region containing a 1,212-bp deletion, respectively. Here, we show that a gene encoding a calmodulin binding protein, located ～5?kb downstream of the 1,212-bp deletion, corresponds to qSW5/GW5. GW5 is expressed in various rice organs, with highest expression level detected in young panicles. We provide evidence that the 1,212-bp deletion affects grain width most likely through influencing the expression levels of GW5. GW5 protein is localized to the plasma membrane and can physically interact with and repress the kinase activity of rice GSK2 (glycogen synthase kinase 2), a homologue of Arabidopsis BIN2 (BRASSINOSTEROID INSENSITIVE2) kinase, resulting in accumulation of unphosphorylated OsBZR1 (Oryza sativa BRASSINAZOLE RESISTANT1) and DLT (DWARF AND LOW-TILLERING) proteins in the nucleus to mediate brassinosteroid (BR)-responsive gene expression and growth responses (including grain width and weight). Our results suggest that GW5 is a novel positive regulator of BR signalling and a viable target for genetic manipulation to improve grain yield in rice and perhaps in other cereal crops as well.
DOI:10.1038/ng.352URLPMID:19305410 [本文引用: 1]
Grain yield is controlled by quantitative trait loci (QTLs) derived from natural variations in many crop plants. Here we report the molecular characterization of a major rice grain yield QTL that acts through the determination of panicle architecture. The dominant allele at the DEP1 locus is a gain-of-function mutation causing truncation of a phosphatidylethanolamine-binding protein-like domain protein. The effect of this allele is to enhance meristematic activity, resulting in a reduced length of the inflorescence internode, an increased number of grains per panicle and a consequent increase in grain yield. This allele is common to many Chinese high-yielding rice varieties and likely represents a relatively recent introduction into the cultivated rice gene pool. We also show that a functionally equivalent allele is present in the temperate cereals and seems to have arisen before the divergence of the wheat and barley lineages.
DOI:10.1038/cr.2012.151URL [本文引用: 1]
Increased crop yields are required to support rapid population growth worldwide. Grain weight is a key component of rice yield, but the underlying molecular mechanisms that control it remain elusive. Here, we report the cloning and characterization of a new quantitative trait locus (QTL) for the control of rice grain length, weight and yield. This locus, GL3.1, encodes a protein phosphatase kelch (PPKL) family - Ser/Thr phosphatase. GL3.1 is a member of the large grain WY3 variety, which is associated with weaker dephosphorylation activity than the small grain FAZ1 variety. GL3.1-WY3 influences protein phosphorylation in the spikelet to accelerate cell division, thereby resulting in longer grains and higher yields. Further studies have shown that GL3.1 directly dephosphorylates its substrate, Cyclin-T1; 3, which has only been rarely studied in plants. The downregulation of Cyclin-T1; 3 in rice resulted in a shorter grain, which indicates a novel function for Cyclin-T in cell cycle regulation. Our findings suggest a new mechanism for the regulation of grain size and yield that is driven through a novel phosphatase-mediated process that affects the phosphorylation of Cyclin-T1; 3 during cell cycle progression, and thus provide new insight into the mechanisms underlying crop seed development. We bred a new variety containing the natural GL3.1 allele that demonstrated increased grain yield, which indicates that GL3.1 is a powerful tool for breeding high-yield crops.
