作物学报 ›› 2024, Vol. 50 ›› Issue (4): 897-813.doi: 10.3724/SP.J.1006.2024.31046
所属专题: 小麦:遗传育种·种质资源·分子遗传学
王添宁1(
), 冯雅岚2, 琚吉浩1, 吴毅1, 张均1, 马超1,*(
)
WANG Tian-Ning1(
), FENG Ya-Lan2, JU Ji-Hao1, WU Yi1, ZHANG Jun1, MA Chao1,*(
)
摘要:
生长调控因子(growth-regulating factor, GRF)在植物的生长发育、逆境响应和激素信号转导中起着重要的调控作用。系统分析小麦及其祖先物种GRF转录因子家族成员在基因组上的分布、结构、进化以及表达特性, 对于深入研究GRF家族的生物学功能和小麦的进化具有重要的意义。本研究利用生物信息学方法, 对乌拉尔图小麦、拟斯卑尔脱山羊草、粗山羊草、栽培二粒小麦和普通小麦5个物种的GRF成员进行全基因组鉴定, 并对其理化性质、系统发育关系、基因结构、启动子顺式作用元件以及表达特性进行了分析。结果表明, 乌拉尔图小麦、拟斯卑尔脱山羊草、粗山羊草、栽培二粒小麦和普通小麦中分别有15、12、19、29和53个GRF成员, 通过种间共线性分析发现, TtGRFs分别有18个和29个成员与TuGRFs和AesGRFs具有共线性, TaGRFs分别有36个和37个成员与TtGRFs和AetGRFs具有共线性。启动子顺式作用元件预测发现GRF基因具有基本的转录元件以及一些与生长发育和逆境响应的结合元件。RT-qPCR分析表明, 多数GRF基因在外源IAA、GA和干旱胁迫条件下呈上调表达趋势, 而在高温胁迫条件下呈下调表达趋势, 表明GRF家族成员在响应激素和逆境胁迫中有重要作用。系统进化分析表明, 小麦与其祖先物种之间的GRF成员存在保守且复杂的进化关系。上述结果为GRF转录因子家族的进化及其功能研究提供了理论基础。
| [1] |
Feng K, Hou X L, Xing G M, Liu J X, Duan A Q, Xu Z S, Li M Y, Zhuang J, Xiong A S. Advances in AP2/ERF super-family transcription factors in plant. Crit Rev Biotechnol, 2020, 40: 750-776.
doi: 10.1080/07388551.2020.1768509 pmid: 32522044 |
| [2] |
Claus S, Michael B. The regulation of transcription factor activity in plants. Trends Plant Sci, 1998, 3: 378-383.
doi: 10.1016/S1360-1385(98)01302-8 |
| [3] |
Karam B S, Rhonda C F, Luis O. Transcription factors in plant defense and stress responses. Curr Opin Plant Biol, 2002, 5: 430-436.
doi: 10.1016/s1369-5266(02)00289-3 pmid: 12183182 |
| [4] |
Du W X, Yang J F, Li Q, Su Q, Yi D X, Pang Y Z. Genome-wide identification and characterization of growth regulatory factor family genes in Medicago. Int J Mol Sci, 2022, 23: 6905.
doi: 10.3390/ijms23136905 |
| [5] |
Wang F D, Qiu N W, Ding Q, Li J J, Zhang Y H, Li H Y, Gao J W. Genome-wide identification and analysis of the growth-regulating factor family in Chinese cabbage (Brassica rapa L. ssp. pekinensis). BMC Genom, 2014, 15: 807.
doi: 10.1186/1471-2164-15-807 |
| [6] |
van der Knaap, Kim J H, Kende H. A novel gibberellin-induced gene from rice and its potential regulatory role in stem growth. Plant Physiol, 2000, 122: 695-704.
doi: 10.1104/pp.122.3.695 pmid: 10712532 |
| [7] |
Kim J H, Choi D, Kende H. The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis. Plant J, 2003, 36: 94-104.
doi: 10.1046/j.1365-313X.2003.01862.x |
| [8] |
Zhang D F, Li B, Jia G Q, Zhang T F, Dai J R, Li J S, Wang S C. Isolation and characterization of genes encoding GRF transcription factors and GIF transcriptional coactivators in maize (Zea mays L.). Plant Sci, 2008, 175: 809-817.
doi: 10.1016/j.plantsci.2008.08.002 |
| [9] |
Choi D, Kim J H, Kende H. Whole genome analysis of the OsGRF gene family encoding plant-specific putative transcription activators in rice (Oryza sativa L.). Plant Cell Physiol, 2004, 45: 897-904.
doi: 10.1093/pcp/pch098 |
| [10] |
Huang W D, He Y Q, Yang L, Lu C, Zhu Y X, Sun C, Ma D F, Yin J L. Genome-wide analysis of growth-regulating factors (GRFs) in Triticum aestivum. PeerJ, 2021, 9: e10701.
doi: 10.7717/peerj.10701 |
| [11] |
Yi W, Luan A P, Liu C Y, Wu J, Zhang W, Zhong Z Q, Wang Z P, Yang M Z, Chen C J, He Y H. Genome-wide identification, phylogeny, and expression analysis of GRF transcription factors in pineapple (Ananas comosus). Front Plant Sci, 2023, 14: 1159223.
doi: 10.3389/fpls.2023.1159223 |
| [12] |
Zan T, Zhang L, Xie T T, Li L Q. Genome-Wide identification and analysis of the growth-regulating factor (GRF) gene family and GRF-Interacting factor family in Triticum aestivum L. Biochem Genet, 2020, 58: 1-20.
doi: 10.1007/s10528-019-09927-z |
| [13] |
Kim J H, Kende H. A transcriptional coactivator, AtGIF1, is involved in regulating leaf growth and morphology in Arabidopsis. Proc Natl Acad Sci USA, 2004, 101: 13374-13379.
doi: 10.1073/pnas.0405450101 |
| [14] |
Kim J H. Biological roles and an evolutionary sketch of the GRF-GIF transcriptional complex in plants. BMB Rep, 2019, 52: 227-238.
pmid: 30885290 |
| [15] |
Liang G, He H, Li Y, Wang F, Yu D Q. Molecular mechanism of microRNA396 mediating pistil development in Arabidopsis. Plant Physiol, 2014, 164: 249-258.
doi: 10.1104/pp.113.225144 pmid: 24285851 |
| [16] |
Liu X, Guo L X, Jin L F, Liu Y Z, Liu T, Fan Y H, Peng S A. Identification and transcript profiles of citrus growth-regulating factor genes involved in the regulation of leaf and fruit development. Mol Biol Rep, 2016, 43: 1059-1067.
doi: 10.1007/s11033-016-4048-1 pmid: 27491940 |
| [17] |
Kuijt S J H, Greco R, Agalou A, Shao J, Hoen C C J, Overnäs E, Osnato M, Curiale S, Meynard D, van Gulik R, de Faria M S, Atallah M, de Kam R J, Lamers G E M, Guiderdoni E, Rossini L, Meijer A H, Ouwerkerk P B F. Interaction between the growth-regulating factor and knotted1-like homeobox families of transcription factors. Plant Physiol, 2014, 164: 1952-1966.
doi: 10.1104/pp.113.222836 pmid: 24532604 |
| [18] |
Li S C, Gao F Y, Xie K L, Zeng X H, Cao Y, Zeng J, He Z S, Ren Y, Li W B, Deng Q M, Wang S Q, Zheng A P, Zhu J, Liu H N, Wang L X, Li P. The OsmiR396c-OsGRF4-OsGIF1 regulatory module determines grain size and yield in rice. Plant Biotechnol J, 2016, 14: 2134-2146.
doi: 10.1111/pbi.12569 pmid: 27107174 |
| [19] |
Wang P, Xiao Y, Yan M, Yan Y, Lei X J, Di P, Wang Y P. Whole- genome identification and expression profiling of growth- regulating factor (GRF) and GRF-interacting factor (GIF) gene families in Panax ginseng. BMC Genom, 2023, 24: 334.
doi: 10.1186/s12864-023-09435-w |
| [20] |
Zhang S W, Li G G, Wang Y D, Anwar A, He B, Zhang J W, Chen C M, Hao Y W, Chen R Y, Song S W. Genome-wide identification of BcGRF genes in flowering Chinese cabbage and preliminary functional analysis of BcGRF8 in nitrogen metabolism. Front Plant Sci, 2023, 14: 1144748.
doi: 10.3389/fpls.2023.1144748 |
| [21] |
Yarra R, Krysan P J. GRF-GIF duo and GRF-GIF-BBM: novel transformation methodologies for enhancing regeneration efficiency of genome-edited recalcitrant crops. Planta, 2023, 257: 60.
doi: 10.1007/s00425-023-04096-1 pmid: 36801980 |
| [22] |
Liu Y T, Guo P, Wang J, Xu Z Y. Growth-regulating factors: conserved and divergent roles in plant growth and development and potential value for crop improvement. Plant J, 2022, 113: 1122-1145.
doi: 10.1111/tpj.v113.6 |
| [23] |
Daniela L, Javier F P. MicroRNA miR396, GRF transcription factors and GIF co-regulators: a conserved plant growth regulatory module with potential for breeding and biotechnology. Curr Opin Plant Biol, 2020, 53: 31-42.
doi: S1369-5266(19)30077-9 pmid: 31726426 |
| [24] |
Montenegro J D, Golicz A A, Bayer P E, Hurgobin B, Lee H, Chan C K, Visendi P, Lai K, Doležel J, Batley J, Edwards D. The pangenome of hexaploid bread wheat. Plant J, 2017, 90: 1007-1013.
doi: 10.1111/tpj.2017.90.issue-5 |
| [25] |
Etienne P, Pierre S, Jérôme S, Cyrille S, Frédéric C, Philippe L, Abraham K, Monika M, Shahryar K, Wolfgang S, Evans L, Daryl S, Andrzej K, Michael A, Sonia V, Hélène B, Kellye E, Rudi A, Jan S, Hana S, Jaroslav D, Michel B, Catherine F. A physical map of the 1-Gigabase bread wheat chromosome 3B. Science, 2008, 322: 101-104.
doi: 10.1126/science.1161847 pmid: 18832645 |
| [26] |
Zhang M, Qiu X B. Genetic basis of genome size variation of wheat. Funct Integr Genomic, 2023, 23: 285-285.
doi: 10.1007/s10142-023-01194-x pmid: 37648783 |
| [27] |
El B M, Murat F, Veyssiere M, Molinier M, Flores R, Burlot L, Alaux M, Quesneville H, Pont C, Salse J. Reconciling the evolutionary origin of bread wheat (Triticum aestivum). New Phytol, 2017, 213: 1477-1486.
doi: 10.1111/nph.14113 pmid: 27551821 |
| [28] | 魏益民. 中国小麦的起源、传播及进化. 麦类作物学报, 2021, 41: 305-309. |
| Wei Y M. Origin, spread and evolution of wheat in China. J Triticeae Crops, 2021, 41: 305-309. (in Chinese with English abstract) | |
| [29] |
Chen F, Yang Y Z, Luo X F, Zhou W G, Dai Y J, Zheng C, Liu W G, Yang W Y, Shu K. Genome-wide identification of GRF transcription factors in soybean and expression analysis of GmGRF family under shade stress. BMC Plant Biol, 2019, 19: 1-13.
doi: 10.1186/s12870-018-1600-2 |
| [30] |
Chen H L, Ge W N. Identification, molecular characteristics, and evolution of GRF gene family in foxtail millet (Setaria italica L.). Front Genet, 2022, 12: 727674.
doi: 10.3389/fgene.2021.727674 |
| [31] |
Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol, 2021, 38: 3022-3027.
doi: 10.1093/molbev/msab120 pmid: 33892491 |
| [32] |
Chen C J, Chen H, Zhang Y, Thomas H R, Margaret H F, He Y H, Xia R. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant, 2020, 13: 1194-1202.
doi: S1674-2052(20)30187-8 pmid: 32585190 |
| [33] |
Li C, Li Q G, Dunwell J M, Zhang Y M. Divergent evolutionary pattern of starch biosynthetic pathway genes in grasses and dicots. Mol Biol Evol, 2012, 29: 3227-3236.
pmid: 22586327 |
| [34] | Timothy L B, Charles E. Fitting a Mixture Model by Expectation Maximization to Discover Motifs in Biopolymers. Menlo Park, California: AAAI Press, 1994. pp 28-36. |
| [35] |
Wang Y P, Tang H B, Debarry J D, Tan X, Li J P, Wang X Y, Lee T H, Jin H Z, Marler B, Guo H, Kissinger J C, Paterson A H. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res, 2012, 40: e49.
doi: 10.1093/nar/gkr1293 |
| [36] |
Khadiza K, Arif H K R, Park J, Ujjal K N, Chang K K, Ki-Byung L, Ill S N, Mi-Young C, Hikmet B. Molecular characterization and expression profiling of tomato GRF transcription factor family genes in response to abiotic stresses and phytohormones. Int J Mol Sci, 2017, 18: 1056.
doi: 10.3390/ijms18051056 |
| [37] |
Noon J B, Hewezi T, Baum T J. Homeostasis in the soybean miRNA396-GRF network is essential for productive soybean cyst nematode infections. J Exp Bot, 2019, 70: 1653-1668.
doi: 10.1093/jxb/erz022 pmid: 30715445 |
| [38] | 张立全, 张浩林, 李丛丛, 姚磊, 魏建华, 张杰伟. 谷子GRF基因家族鉴定与分析. 西南农业学报, 2021, 34: 2340-2347. |
| Zhang L Q, Zhang H L, Li C C, Yao L, Wei J H, Zhang J W. Genome-wide analysis and identification of GRF gene family in foxtail millet (Setaria italica). Southwest China J Agric Sci, 2021, 34: 2340-2347. (in Chinese with English abstract) | |
| [39] |
时丕彪, 何冰, 费月跃, 王军, 王伟义, 魏福友, 吕远大, 顾闽峰. 藜麦GRF转录因子家族的鉴定及表达分析. 作物学报, 2019, 45: 1841-1850.
doi: 10.3724/SP.J.1006.2019.94049 |
| Shi P B, He B, Fei Y Y, Wang J, Wang W Y, Wei F Y, Lyu Y D, Gu M F. Identification and expression analysis of GRF transcription factor family of Chenopodium quinoa. Acta Agron Sin, 2019, 45: 1841-1850. (in Chinese with English abstract) | |
| [40] |
马超, 宋鹏, 尚申申, 杨夏夏, 杨金华, 韩群威, 李记民, 冯雅岚. 二穗短柄草GRFs基因家族的鉴定及表达模式分析. 核农学报, 2020, 34: 1152-1162.
doi: 10.11869/j.issn.100-8551.2020.06.1152 |
| Ma C, Song P, Shang S S, Yang X X, Yang J H, Han Q W, Li J M, Feng Y L. Whole genome identification and analysis of GRFs gene family in Brachypodium distachyon. Acta Agric Nucl Sci, 2020, 34: 1152-1162. (in Chinese with English abstract) | |
| [41] |
Jiao Y N, Wickett N J, Ayyampalayam S, Chanderbali A S, Landherr L, Ralph P E, Tomsho L P, Hu Y, Liang H Y, Soltis P S, Soltis D E, Clifton S W, Schlarbaum S E, Schuster S C, Ma H, Leebens-Mack J, de Pamphilis C W. Ancestral polyploidy in seed plants and angiosperms. Nature, 2011, 473: 97-100.
doi: 10.1038/nature09916 |
| [42] |
赵旭博, 李爱丽, 毛龙. 植物多倍化过程中小分子RNA调控基因表达机制研究进展. 作物学报, 2013, 39: 1331-1338.
doi: 10.3724/SP.J.1006.2013.01331 |
|
Zhao X B, Li A L, Mao L. Progress on gene regulatory mechanisms by small RNAs during plant poly-ploidization. Acta Agron Sin, 2013, 39: 1331-1338. (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2013.01331 |
|
| [43] |
Panchy N, Lehti-Shiu M, Shiu S H. Evolution of gene duplication in plants. Plant Physiol, 2016, 171: 2294-2316.
doi: 10.1104/pp.16.00523 pmid: 27288366 |
| [44] |
Kong F L, Wang J, Cheng L, Liu S Y, Wu J, Peng Z, Lu G. Genome-wide analysis of the mitogen-activated protein kinase gene family in Solanum lycopersicum. Gene, 2012, 499: 108-120.
doi: 10.1016/j.gene.2012.01.048 |
| [45] |
Tao Y, Wang F T, Jia D M, Li J T, Zhang Y M, Jia C G, Wang D P, Pan H Y. Cloning and functional analysis of the promoter of a stress-inducible gene (ZmRXO1) in maize. Plant Mol Biol Rep, 2015, 33: 200-208.
doi: 10.1007/s11105-014-0741-1 |
| [46] |
Lee S C, Kim S H, Kim S R. Drought inducible OsDhn1 promoter is activated by OsDREB1A and OsDREB1D. J Plant Biol, 2013, 56: 115-121.
doi: 10.1007/s12374-012-0377-3 |
| [47] |
Lee S J, Lee B H, Jung J H, Park S K, Song J T, Kim J H. Growth- regulating factor and GRF-interacting factor specify meristematic cells of gynoecia and anthers. Plant Physiol, 2018, 176: 717-729.
doi: 10.1104/pp.17.00960 |
| [1] | 翟胜男, 曹新有, 李豪圣, 李吉虎, 李法计, 刘金栋, 夏先春, 吕莹莹, 马瑞峰, 王颖, 耿洪伟, 刘建军. 小麦Pod-A1、Pod-D1和Pod-2D位点等位变异对籽粒过氧化物酶活性的遗传效应分析[J]. 作物学报, 2026, 52(6): 1593-1603. |
| [2] | 习千辉, 徐梓瑗, 刘梦梦, 王宏艺, 郎凯琳, 井震海, 陈锋, 赵磊. 小麦籽粒铜含量的全基因组关联分析及候选基因预测[J]. 作物学报, 2026, 52(6): 1604-1617. |
| [3] | 毛嘉琦, 黄朋雨, 赵佳佳, 郑兴卫, 武棒棒, 郝宇琼, 屈非, 刘成, 马朋涛, 郑军. 山西小麦品种白粉病抗性评价及抗病基因分子检测[J]. 作物学报, 2026, 52(6): 1669-1681. |
| [4] | 胡川, 赵凯男, 黄修利, 吴金芝, 任开明, 王贺正, 付国占, 黄明, 李友军. 一次灌溉下耕作方式和氮肥用量对旱地小麦产量和品质的影响[J]. 作物学报, 2026, 52(6): 1830-1846. |
| [5] | 陈雪燕, 何华川, 李政嘉, 董新盼, 李藕琪, 刘小云, 李丹萍, 陈志伟, 刘国霞, 吕胜源, 吴印莹, 赵振东, 曹新有, 万何平. 水培盐碱复合胁迫下‘济麦60’苗期根系有机酸分泌动态变化及其转录调控机制[J]. 作物学报, 2026, 52(6): 1859-1875. |
| [6] | 高沛阳, 李瑾璇, 董宇奎, 石玉, 张振, 张永丽. 测墒补灌下小麦分蘖发生和成穗对施氮量的响应[J]. 作物学报, 2026, 52(6): 1847-1858. |
| [7] | 胡赵, 钱润, 谢丰璞, 应素平. 水稻SPX基因家族鉴定及响应磷处理的表达分析[J]. 作物学报, 2026, 52(6): 1902-1912. |
| [8] | 张献丰, 郭利建, 李康春, 孔斌雪, 刘玉芳, 车卓, 杨德龙. 小麦ABHD6基因家族鉴定与粒重功能标记开发[J]. 作物学报, 2026, 52(6): 1711-1727. |
| [9] | 王壮壮, 武紫君, 张永新, 张芯源, 袁丽雪, 陈如雪, 刘世举, 段剑钊, 冯伟, 王同朝, 王永华. 豫东南黏壤潮土区水氮优化协同提高冬小麦产量和氮素利用效率[J]. 作物学报, 2026, 52(5): 1501-1521. |
| [10] | 何万龙, 耿洪伟, 张飞飞, 米克热阿依·阿巴白克热, 罗紫洋, 李鹏程, 周钊宇, 程宇坤. 基于深度学习的小麦重要病害图像识别系统的研究[J]. 作物学报, 2026, 52(5): 1401-1417. |
| [11] | 张振, 冯连杰, 石玉, 于振文, 张永丽. 节水补灌下不同穗型小麦产量形成差异研究[J]. 作物学报, 2026, 52(5): 1522-1535. |
| [12] | 侯思宇, 王国璀, 韦金贵, 谢玮欣, 殷文, 樊志龙, 柴强, 胡发龙. 绿肥配施化学氮肥对西北干旱灌区小麦干物质积累及产量形成的影响[J]. 作物学报, 2026, 52(4): 1208-1219. |
| [13] | 尚云秋, 赵竹, 陈欢, 丁永刚, 乔玉强, 李玮, 张向前, 曹承富, 杜世州. 长期定位耕作方式对雨养小麦籽粒灌浆和产量形成的影响[J]. 作物学报, 2026, 52(4): 1236-1250. |
| [14] | 乔宇馨, 李程越, 康晓玉, 张鑫琪, 贾绍辉, 刘倩, 曹亚丽, 史鑫蕊, 郝兴宇, 李萍. 基于APSIM模型的长期免耕秸秆覆盖对旱地小麦增产效应研究[J]. 作物学报, 2026, 52(4): 1181-1192. |
| [15] | 李灿, 张喜伟, 朱博涛, 张沛沛. 小麦GSK激酶TaSK41的功能分析及互作蛋白的筛选[J]. 作物学报, 2026, 52(3): 677-687. |
|
||