欢迎访问作物学报，今天是
作物学报

作物学报 ›› 2023, Vol. 49 ›› Issue (9): 2398-2411.doi: 10.3724/SP.J.1006.2023.22059

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

低温胁迫下组蛋白H3K18cr在水稻全基因组上的动态变化特征解析

刘凯1(), 陈积金1, 刘帅2, 陈旭1, 赵新茹2, 孙尚2, 薛超2, 龚志云1,2,*()   

  1. 1江苏省作物基因组学和分子育种重点实验室 / 植物功能基因组学教育部重点实验室 / 江苏省作物遗传生理重点实验室 / 扬州大学农学院, 江苏扬州 225009
    2江苏省粮食作物现代产业技术协同创新中心 / 扬州大学, 江苏扬州 225009
  • 收稿日期:2022-10-07 接受日期:2023-02-10 出版日期:2023-09-12 网络出版日期:2023-02-27
  • 通讯作者: *龚志云, E-mail: zygong@yzu.edu.cn
  • 作者简介:刘凯, E-mail: lkss1730@foxmail.com
  • 基金资助:
    国家自然科学基金项目(31871232)

Dynamic change profile of histone H3K18cr on rice whole genome under cold stress

LIU Kai1(), CHEN Ji-Jin1, LIU Shuai2, CHEN Xu1, ZHAO Xin-Ru2, SUN Shang2, XUE Chao2, GONG Zhi-Yun1,2,*()   

  1. 1Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, Jiangsu, China
    2Jiangsu Co-innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, Jiangsu, China
  • Received:2022-10-07 Accepted:2023-02-10 Published:2023-09-12 Published online:2023-02-27
  • Supported by:
    National Natural Science Foundation of China(31871232)

RichHTML

18

PDF

173

摘要：

组蛋白修饰在水稻响应非生物胁迫的过程中发挥着重要作用。巴豆酰化是一种新型的组蛋白修饰方式, 其在水稻受到低温逆境时如何变化目前很少有见报道。本研究对正常生长和低温处理的水稻日品种本晴幼苗进行RNA-seq和ChIP-seq高通量测序, 然后联合分析组蛋白H3赖氨酸18特异位点上巴豆酰化修饰(H3K18cr)在低温胁迫下对基因表达的调控特征。研究表明, 在基因组中H3K18cr主要富集在第1外显子和基因间区, 且与基因表达和基因长度呈现正相关。低温胁迫下, H3K18cr在水稻基因组上的分布区域没有变化, 但是蛋白免疫印记和ChIP-seq结果均表明整体修饰水平下降; 差异修饰分析发现低温胁迫后有899个和409个基因分别表现出修饰显著增加和减少。通过与RNA-seq关联分析显示共有199个基因H3K18cr修饰水平增高且表达水平上调, GO富集分析发现这些基因主要参与转录活性的调控等过程。进一步验证表明组蛋白H3K18cr通过调控OsDREB1A、OsEATB、OsAP2-39、OsNAC9等转录因子的表达来参与水稻低温胁迫的响应过程。相关研究结果为解析组蛋白巴豆酰化调控植物响应低温胁迫的表观遗传机制提供理论基础。

关键词: 水稻, 低温胁迫, H3K18cr, 基因表达

Abstract:

Histone modifications play an important role in response to abiotic stresses in rice. Crotonylation is a novel histone modification, and the changes of crotonylation in rice subjected to low temperature stress are rarely reported. In this study, RNA-seq and ChIP-seq were performed on normal-grown and cold-treated rice seedlings of rice variety ‘Nipponbare’, followed by combined analysis of the regulatory characteristics of the crotonylation modification at the histone H3 lysine 18-specific site (H3K18cr) on gene expression under cold stress. The results showed that H3K18cr was mainly enriched in the first exon and intergenic region and had positive correlation with gene expression and gene length. The global distribution of H3K18cr in rice genome did not change under cold stress, but WB and ChIP-seq results indicated that the overall modification level decreased. The differential modification analysis revealed that there were significant increase and decrease of 899 genes and 409 genes in the modification after cold stress, respectively. Association analysis with RNA-seq showed that a total of 199 genes had increased levels of H3K18cr modification and up-regulated expression levels. GO enrichment revealed that these genes were mainly involved in the processes such as the regulation of transcriptional activity. Further analysis indicated that histone H3K18cr was involved in the response process of cold stress by regulating the expression of transcription factors such as OsDREB1A, OsEATB, OsAP2-39, and OsNAC9 in rice. The results provide a theoretical basis for further understanding the epigenetic mechanisms of histone crotonylation in response to cold stress in plants.

Key words: rice, cold stress, H3K18cr, gene expression

表1

本研究所用引物"

引物名称
Primer name		 引物序列
Primer sequence (5'-3')		 引物名称
Primer name		 引物序列
Primer sequence (5'-3')
OsDREB1A-F GACGTCCTGAGTGACATGG OsTPS1-F CATCGTGTCAGAGTTTGTCG
OsDREB1A-R CTAGTAGCTCCAGAGTGGGA OsTPS1-R TCACGTACCTGTAGTGCTTC
OsDREB1B-F GTCCACACTTTTCAGTGCGAG OsLEA5-F CTCACCTACACCCTCAAGTG
OsDREB1B-R AATCTCGCACTGAAAAGTGTGG OsLEA5-R CGAGATGAGGAAGTCGTAGG
OsMYBS3-F CAAGAACCAGAGACCCAAGT OsV5A-F CTTCTGCTGAGAATGGACCT
OsMYBS3-R AAGCTGGAACAATCACTGGA OsV5A-R GAGGGTGGGATGATGAATGT
OsMADS57-F GTTCCAGCACTCCATACAGC ONAC095-F CAGGAGGAGAGGTGGAGG
OsMADS57-R GGCAGATGAAGTCCCAGTTCT ONAC095-R GGGGATGATGTCGAACTTGA

图1

水稻品种日本晴幼苗在低温胁迫下H3K18cr的变化情况 A: 生长2周的水稻幼苗在正常和低温(4℃)处理10 h后的表型; B: 蛋白免疫分析H3K18cr在正常和低温胁迫下的变化情况, 使用ImageJ软件计算灰度值; C: 正常和低温胁迫下H3K18cr peaks的全基因组分布; D: 正常和低温胁迫下H3K18cr在不同类型基因上的分布模式分析, X轴表示不同长度基因转化为百分比的标准化, 包括基因的上下游1 kb区域。Y轴表示H3K18cr的归一化读数。"

表2

ChIP-seq数据统计"

样品名
Sample name		 重复数
Replicate		 总序列数
Total clean reads		 比对序列数
Total aligned reads		 唯一比对序列数
Total unique reads		 Peak数
Total peaks		 共有Peak数
Common peaks		 相关性
Correlation coefficient
H3K18cr-CK 1 45,952,156 45,268,705 (98.51%) 30,248,490 (65.83%) 25,218 20,077 0.92
H3K18cr-CK 2 48,099,538 47,360,155 (98.46%) 32,023,294 (66.58%) 29,127
H3K18cr-Cold 1 47,721,602 46,868,242 (98.21%) 30,382,217 (63.67%) 23,544 17,944 0.92
H3K18cr-Cold 2 48,128,162 47,304,118 (98.29%) 30,250,892 (62.85%) 29,632

图2

低温胁迫下H3K18cr响应基因分析 A: 正常和低温胁迫下被H3K18cr标记基因的数目。红线表示正常生长幼苗, 蓝线表示低温处理10 h的幼苗; B: 正常和低温胁迫下H3K18cr差异修饰基因的数目; C: 低温胁迫下H3K18cr修饰增加基因的GO富集分析。散点图表示对相似GO terms矩阵进行多维缩放得出的二维空间中的聚类图, 气泡颜色和大小使用log10(FDR)表示, X轴和Y轴无实际意义; D: 低温胁迫下H3K18cr修饰降低基因的GO富集分析。Y轴表示富集的GO terms, X轴用-log10(FDR)表示, 图中数字表示富集在该GO terms中的基因数; E: 低温胁迫下H3K18cr修饰增加基因的KEGG富集通路分析。"

表3

RNA-seq数据统计"

样品名
Sample		 重复数
Replicate		 总序列数
Total reads		 比对序列数
Aligned reads		 表达基因数
FPKM>0		 相关性
Correlation coefficient
正常温度Control 1 51,702,548 49,740,100 (92.62%) 26,992 0.94
正常温度Control 2 54,410,846 50,622,035 (93.04%) 24,422
低温Cold 1 61,244,656 52,044,285 (84.98%) 25,474 0.95
低温Cold 2 72,466,862 67,205,195 (92.74%) 27,191

图3

低温胁迫下基因表达情况分析 A: 先前报道的非生物胁迫相关基因的RT-qPCR。红色表示上调基因, 蓝色表示下调基因; B: 正常和低温胁迫下H3K18cr修饰与基因表达的关系; C: 正常和低温胁迫下差异基因的表达情况; D: 表达上调基因的GO和KEGG富集分析; E: 表达下基因的GO和KEGG富集分析。"

图4

低温胁迫下H3K18cr与基因表达关系分析 A: 低温处理后ChIP-seq差异修饰基因和RNA-seq差异表达基因的韦恩图; B: 199个修饰增加且表达上调基因修饰富集热图; C: 199个修饰增加且表达上调基因表达水平的盒形图; D: 199个修饰增加且表达上调基因的GO富集分析。散点图表示对相似GO terms矩阵进行多维缩放得出的二维空间中的聚类图, 气泡颜色和大小使用log10(FDR)表示, X轴和Y轴无实际意义; E: 199个修饰增加且表达上调基因的KEGG富集分析。"

图5

低温胁迫下H3K18cr相关的转录因子分析 A: 199个H3K18cr修饰增加且表达上调基因与水稻中所有转录因子的韦恩图; B: IGV软件显示低温下ERF家族中基因与H3K18cr相关; C: IGV软件显示低温下NAC家族中基因与H3K18cr相关; D: IGV软件显示低温下GRAS家族中基因与H3K18cr相关; E: IGV软件显示低温下DBB家族中基因与H3K18cr相关。"

表4

转录因子功能信息统计"

TF 家族
TF family		 基因 ID
Gene ID		 基因名字
Gene name		 功能
Function		 参考文献References
Dof LOC_Os01g15900 RDD1; OsDof-2 产量相关 Yield-related [45]
LOC_Os10g26620 OsDof-26; OsDof27 非生物逆境抗性 Abiotic stress tolerance [46]
ERF LOC_Os09g35030 OsDREB1A 非生物逆境抗性 Abiotic stress tolerance [28]
LOC_Os09g28440 OsEATB 株高发育; 非生物逆境抗性
Plant growth; Abiotic stress tolerance		 [37-38]
LOC_Os04g52090 OsAP2-39 非生物逆境抗性 Abiotic stress tolerance [39]
ARF LOC_Os04g36054 OsARF9 — —
NAC LOC_Os03g60080 SNAC1; OsNAC9 非生物逆境抗性 Abiotic stress tolerance [41]
LOC_Os07g12340 OsNAC3 非生物逆境抗性 Abiotic stress tolerance [40]
CO-like LOC_Os09g06464 OsCO3 调控光周期 Regulate photoperiodic [47]
LOC_Os02g39710 OsCOL4 调控抽穗期 Regulate heading date [48]
HD-ZIP LOC_Os04g45810 Oshox22 非生物逆境抗性 Abiotic stress tolerance [49]
bZIP LOC_Os02g16680 RITA-1; OsbZIP20 非生物逆境抗性; 重金属胁迫
Abiotic stress tolerance; High metal stress		 [50-51]
HSF LOC_Os02g13800 OsHsfC2a 非生物逆境抗性 Abiotic stress tolerance [52]
DBB LOC_Os02g39360 OsBBX4; OsBBX25 非生物逆境抗性 Abiotic stress tolerance [44]
LOC_Os09g35880 OsBBX29 非生物逆境抗性 Abiotic stress tolerance [43]
LOC_Os04g41560 OsBBX11 非生物逆境抗性 Abiotic stress tolerance [43]
bHLH LOC_Os01g50940 OsMYL1 调控JA信号 Regulate JA signal [53]
LOC_Os04g41229 OsbHLH111 调控糖信号 Regulate sugar signal [54]
LOC_Os09g29930 OsbHLH032 调控BR信号 Regulate BR signal [55]
GRAS LOC_Os02g44360 SCL6-IIb; OsHAM1 非生物逆境抗性 Abiotic stress tolerance [42]
LOC_Os02g45760 OsGRAS-10 — —
LOC_Os01g62460 OsGRAS-2 — —
MYB_related LOC_Os04g49450 OsMYBR1 非生物逆境抗性 Abiotic stress tolerance [56]
LOC_Os02g46030 OsMYB1R 非生物逆境抗性 Abiotic stress tolerance [57]
LOC_Os02g45670 — — —
LOC_Os01g41900 OsDLN13 — —
[1] Zhou Y, Simpson S, Holloway A F, Charlesworth J, van der Mei I, Taylor B V. The potential role of epigenetic modifications in the heritability of multiple sclerosis. Mult Scler, 2014, 20: 135-140.
doi: 10.1177/1352458514520911
[2] Peach S E, Rudomin E L, Udeshi N D, Carr S A, Jaffe J D. Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules. Mol Cell Proteomics, 2012, 11: 128-137.
doi: 10.1074/mcp.M111.015941 pmid: 22442256
[3] Kouzarides T. Chromatin modifications and their function. Cell, 2007, 128: 693-705.
doi: 10.1016/j.cell.2007.02.005 pmid: 17320507
[4] 薛超. 水稻盐胁迫下组蛋白乙酰化修饰特征及HATs相关基因的功能研究. 扬州大学博士学位论文, 江苏扬州, 2018.
Xue C. Characteristic Analysis of Histone Acetylation Dynamics under Salt Stress and Functional Analysis of HATs in Rice. PhD Dissertation of Yangzhou University, Yangzhou, Jiangsu, China, 2018. (in Chinese with English abstract)
[5] Bao X C, Wang Y, Li X, Li X M, Liu Z, Yang T P, Wong C F, Zhang J W, Hao Q, Li X D. Identification of ‘erasers’ for lysine crotonylated histone marks using a chemical proteomics approach. eLife, 2014, 3: e02999.
doi: 10.7554/eLife.02999
[6] Tan M J, Luo H, Lee S, Jin F L, Yang J S, Montellier E, Buchou T, Cheng Z Y, Rousseaux S, Rajagopal N, Lu Z K, Ye Z, Zhu Q, Wysocka J, Ye Y, Khochbin S, Ren B, Zhao Y M. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell, 2011, 146: 1015-1027.
[7] Sabari B R, Tang Z Y, Huang H, Yong-Gonzalez V, Molina H, Kong H E, Dai L Z, Shimada M, Cross J R, Zhao Y M, Roeder R G, Allis C D. Intracellular crotonyl-CoA stimulates transcription through p300-catalyzed histone crotonylation. Mol Cell, 2015, 58: 203-215.
doi: 10.1016/j.molcel.2015.02.029 pmid: 25818647
[8] Sun H J, Liu X W, Li F F, Li W, Zhang J, Xiao Z X, Shen L L, Li Y, Wang F L, Yang J G. First comprehensive proteome analysis of lysine crotonylation in seedling leaves of Nicotiana tabacum. Sci Rep, 2017, 7: 3013.
doi: 10.1038/s41598-017-03369-6
[9] Liu K D, Yuan C C, Li H L, Chen K Y, Lu L S, Shen C J, Zheng X L. A qualitative proteome-wide lysine crotonylation profiling of papaya (Carica papaya L.). Sci Rep, 2018, 8: 8230.
doi: 10.1038/s41598-018-26676-y
[10] Sun J H, Qiu C, Qian W J, Wang Y, Sun L T, Li Y S, Ding Z T. Ammonium triggered the response mechanism of lysine crotonylome in tea plants. BMC Genomics, 2019, 20: 340.
doi: 10.1186/s12864-019-5716-z pmid: 31060518
[11] Dong Y B, Chen C. Comprehensive profiling of paper mulberry (Broussonetia papyrifera) crotonylome reveals the significance of lysine crotonylation in young leaves. Int J Mol Sci, 2022, 23: 1173.
doi: 10.3390/ijms23031173
[12] Xu M L, Luo J D, Li Y, Shen L L, Zhang X, Yu J, Guo Z Q, Wu J X, Chi Y C, Yang J G. First comprehensive proteomics analysis of lysine crotonylation in leaves of peanut (Arachis hypogaea L.). Proteomics, 2021, 21: e2000156.
[13] Liu S, Xue C, Fang Y, Chen G, Peng X J, Zhou Y, Chen C, Liu G Q, Gu M H, Wang K, Zhang W L, Wu Y F, Gong Z Y. Global involvement of lysine crotonylation in protein modification and transcription regulation in rice. Mol Cell Proteomics, 2018, 17: 1922-1936.
doi: 10.1074/mcp.RA118.000640 pmid: 30021883
[14] Yuan L Y, Liu X C, Luo M, Yang S G, Wu K Q. Involvement of histone modifications in plant abiotic stress responses. J Integr Plant Biol, 2013, 55: 892-901.
doi: 10.1111/jipb.12060
[15] Li H, Yan S H, Zhao L, Tan J J, Zhang Q, Gao F, Wang P, Hou H L, Li L J. Histone acetylation associated up-regulation of the cell wall related genes is involved in salt stress induced maize root swelling. BMC Plant Biol, 2014, 14: 105.
doi: 10.1186/1471-2229-14-105 pmid: 24758373
[16] Kim J M, To T K, Ishida J, Morosawa T, Kawashima M, Matsui A, Toyoda T, Kimura H, Shinozaki K, Seki M. Alterations of lysine modifications on the histone H3 N-tail under drought stress conditions in Arabidopsis thaliana. Plant Cell Physiol, 2008, 49: 1580-1588.
doi: 10.1093/pcp/pcn133
[17] Van D K, Ding Y, Malkaram S, Riethoven J J M, Liu R, Yang J Y, Laczko P, Chen H, Xia Y N, Ladunga I, Avramova Z, Fromm M. Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana. BMC Plant Biol, 2010, 10: 238.
doi: 10.1186/1471-2229-10-238
[18] Vlachonasios K E, Thomashow M F, Triezenberg S J. Disruption mutations of ADA2b and GCN5 transcriptional adaptor genes dramatically affect Arabidopsis growth, development, and gene expression. Plant Cell, 2003, 15: 626-638.
doi: 10.1105/tpc.007922
[19] Kwon C S, Lee D, Choi G, Chung W I. Histone occupancy- dependent and -independent removal of H3K27 trimethylation at cold-responsive genes in Arabidopsis. Plant J, 2009, 60: 112-121.
doi: 10.1111/tpj.2009.60.issue-1
[20] Roy D, Paul A, Roy A, Ghosh R, Ganguly P, Chaudhuri S. Differential acetylation of histone H3 at the regulatory region of OsDREB1b promoter facilitates chromatin remodelling and transcription activation during cold stress. PLoS One, 2014, 9: e100343.
[21] Zheng D Y, Wang L, Chen L F, Pan X C, Lin K D, Fang Y, Wang X E, Zhang W L. Salt-responsive genes are differentially regulated at the chromatin levels between seedlings and roots in rice. Plant Cell Physiol, 2019, 60: 1790-1803.
doi: 10.1093/pcp/pcz095 pmid: 31111914
[22] Lu Y, Xu Q T, Liu Y, Yu Y, Cheng Z Y, Zhao Y, Zhou D X. Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence. Genome Biol, 2018, 19: 144.
doi: 10.1186/s13059-018-1533-y pmid: 30253806
[23] 徐青山, 黄晶, 孙爱军, 洪小智, 朱练峰, 曹小闯, 孔亚丽, 金千瑜, 朱春权, 张均华. 低温影响水稻发育机理及调控途径研究进展. 中国水稻科学, 2022, 36: 118-130.
doi: 10.16819/j.1001-7216.2022.210602
Xu Q S, Huang J, Sun A J, Hong X Z, Zhu L F, Cao X C, Kong Y L, Jin Q Y, Quan C, Zhang J H. Effects of low temperature on the growth and development of rice plants and the advance of regulation pathways: a review. Chin J Rice Sci, 2022, 36: 118-130. (in Chinese with English abstract)
doi: 10.16819/j.1001-7216.2022.210602
[24] Hu Y F, Zhu N, Wang X M, Yi Q P, Zhu D Y, Lai Y, Zhao Y. Analysis of rice Snf2 family proteins and their potential roles in epigenetic regulation. Plant Physiol Biochem, 2013, 70: 33-42.
doi: 10.1016/j.plaphy.2013.05.001
[25] Sharma R, Singh R K M, Malik G, Deveshwar P, Tyagi A K, Kapoor S, Kapoor M. Rice cytosine DNA methyltransferases: gene expression profiling during reproductive development and abiotic stress. FEBS J, 2009, 276: 6301-6311.
doi: 10.1111/j.1742-4658.2009.07338.x pmid: 19788421
[26] Xue C, Liu S, Chen C, Zhu J, Yang X B, Zhou Y, Guo R, Liu X Y, Gong Z Y. Global proteome analysis links lysine acetylation to diverse functions in Oryza sativa. Proteomics, 2018, 18: 1700036.
doi: 10.1002/pmic.v18.1
[27] Nagaki K, Talbert P B, Zhong C X, Dawe R K, Henikoff S, Jiang J M. Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics, 2003, 163: 1221-1225.
doi: 10.1093/genetics/163.3.1221
[28] Ito Y, Katsura K, Maruyama K, Taji T, Kobayashi M, Seki M, Shinozaki K, Yamaguchi-Shinozaki K. Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant Cell Physiol, 2006, 47: 141-153.
doi: 10.1093/pcp/pci230 pmid: 16284406
[29] Mao D H, Chen C Y. Colinearity and similar expression pattern of rice DREB1s reveal their functional conservation in the cold-responsive pathway. PLoS One, 2012, 7: e47275.
doi: 10.1371/journal.pone.0047275
[30] Huang L, Hong Y B, Zhang H J, Li D Y, Song F M. Rice NAC transcription factor ONAC095 plays opposite roles in drought and cold stress tolerance. BMC Plant Biol, 2016, 16: 203.
doi: 10.1186/s12870-016-0897-y pmid: 27646344
[31] Liu H J, Li Q Z, Yang F, Zhu F Y, Sun Y, Tao Y Z, Lo C. Differential regulation of protochlorophyllide oxidoreductase abundances by VIRESCENT 5A (OsV5A) and VIRESCENT 5B (OsV5B) in rice seedlings. Plant Cell Physiol, 2016, 57: 2392-2402.
pmid: 27565208
[32] He S, Tan L L, Hu Z L, Chen G P, Wang G X, Hu T Z. Molecular characterization and functional analysis by heterologous expression in E. coli under diverse abiotic stresses for OsLEA5, the atypical hydrophobic LEA protein from Oryza sativa L. Mol Genet Genomics, 2012, 287: 39-54.
doi: 10.1007/s00438-011-0660-x
[33] Li H W, Zang B S, Deng X W, Wang X P. Overexpression of the trehalose-6-phosphate synthase gene OsTPS1 enhances abiotic stress tolerance in rice. Planta, 2011, 234: 1007-1018.
doi: 10.1007/s00425-011-1458-0
[34] Yu C Y, Su S, Xu Y C, Zhao Y Q, Yan A, Huang L L, Ali I, Gan Y B. The effects of fluctuations in the nutrient supply on the expression of five members of the AGL17 clade of MADS-Box genes in rice. PLoS One, 2014, 9: e105597.
doi: 10.1371/journal.pone.0105597
[35] Su C F, Wang Y C, Hsieh T H, Lu C A, Tseng T H, Yu S M. A novel MYBS3-dependent pathway confers cold tolerance in rice. Plant Physiol, 2010, 153: 145-158.
doi: 10.1104/pp.110.153015
[36] Jin J P, Tian F, Yang D C, Meng Y Q, Kong L, Luo J C, Gao G. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res, 2017, 45: D1040-D1045.
doi: 10.1093/nar/gkw982
[37] Tripathi A K, Pareek A, Sopory S K, Singla-Pareek S L. Narrowing down the targets for yield improvement in rice under normal and abiotic stress conditions via expression profiling of yield- related genes. Rice, 2012, 5: 37.
doi: 10.1186/1939-8433-5-37 pmid: 24280046
[38] Qi W W, Sun F, Wang Q J, Chen M L, Huang Y Q, Feng Y Q, Luo X J, Yang J S. Rice ethylene-response AP2/ERF factor OsEATB restricts internode elongation by down-regulating a gibberellin biosynthetic gene. Plant Physiol, 2011, 157: 216-228.
doi: 10.1104/pp.111.179945
[39] Wan L Y, Zhang J F, Zhang H W, Zhang Z J, Quan R D, Zhou S R, Huang R F. Transcriptional activation of OsDERF1 in OsERF3 and OsAP2-39 negatively modulates ethylene synthesis and drought tolerance in rice. PLoS One, 2011, 6: e25216.
doi: 10.1371/journal.pone.0025216
[40] Zhang X, Long Y, Chen X X, Zhang B L, Xin Y F, Li L Y, Cao S L, Liu F H, Wang Z G, Huang H, Zhou D G, Xia J X. A NAC transcription factor OsNAC3 positively regulates ABA response and salt tolerance in rice. BMC Plant Biol, 2021, 21: 546.
doi: 10.1186/s12870-021-03333-7 pmid: 34800972
[41] Redillas M C F R, Jeong J S, Kim Y S, Jung H, Bang S W, Choi Y D, Ha S H, Reuzeau C, Kim J K. The overexpression of OsNAC9 alters the root architecture of rice plants enhancing drought resistance and grain yield under field conditions. Plant Biotechnol J, 2012, 10: 792-805.
doi: 10.1111/j.1467-7652.2012.00697.x pmid: 22551450
[42] Um T, Choi J, Park T, Chung P J, Jung S E, Shim J S, Kim Y S, Choi I Y, Park S C, Oh S J, Seo J S, Kim J K. Rice microRNA171f/SCL6 module enhances drought tolerance by regulation of flavonoid biosynthesis genes. Plant Direct, 2022, 6: e374.
[43] 刘兰兰. 水稻OsBBX基因响应热胁迫的初步研究. 湖南农业大学硕士学位论文, 湖南长沙, 2015.
Liu L L. Preliminary Study on OsBBX Genes under Heat Stress in Rice. MS Thesis of Hunan Agricultural University, Changsha, Hunan, China, 2015. (in Chinese with English abstract)
[44] 刘焱, 邢立静, 李俊华, 戴绍军. 水稻含有B-box锌指结构域的OsBBX25蛋白参与植物对非生物胁迫的响应. 植物学报, 2012, 47: 366-378.
doi: 10.3724/SP.J.1259.2012.00366
Liu Y, Xing L J, Li J H, Dai S J. Rice B-box zinc finger protein OsBBX25 is involved in the abiotic response. Chin Bull Bot, 2012, 47: 366-378. (in Chinese with English abstract)
[45] Iwamoto M, Higo K, Takano M. Circadian clock- and phytochrome-regulated Dof-like gene, Rdd1, is associated with grain size in rice. Plant Cell Environ, 2009, 32: 592-603.
doi: 10.1111/pce.2009.32.issue-5
[46] Gandass N, Kajal, Salvi P. Intrinsically disordered protein, DNA binding with one finger transcription factor (OsDOF27) implicates thermotolerance in yeast and rice. Front Plant Sci, 2022, 13: 956299.
doi: 10.3389/fpls.2022.956299
[47] Kim S K, Yun C H, Lee J H, Jang Y H, Park H Y, Kim J K. OsCO3, a CONSTANS-LIKE gene, controls flowering by negatively regulating the expression of FT-like genes under SD conditions in rice. Planta, 2008, 228: 355-365.
doi: 10.1007/s00425-008-0742-0
[48] Lee Y S, Jeong D H, Lee D Y, Yi J, Ryu C H, Kim S L, Jeong H J, Choi S C, Jin P, Yang J, Cho L H, Choi H, An G. OsCOL4 is a constitutive flowering repressor upstream of Ehd1 and downstream of OsphyB. Plant J, 2010, 63: 18-30.
[49] Zhang S X, Haider I, Kohlen W, Jiang L, Bouwmeester H, Meijer A H, Schluepmann H, Liu C M, Ouwerkerk P B F. Function of the HD-Zip I gene Oshox22 in ABA-mediated drought and salt tolerances in rice. Plant Mol Biol, 2012, 80: 571-585.
doi: 10.1007/s11103-012-9967-1
[50] Sun L, Di D W, Li G, Kronzucker H J, Wu X, Shi W. Endogenous ABA alleviates rice ammonium toxicity by reducing ROS and free ammonium via regulation of the SAPK9-bZIP20 pathway. J Exp Bot, 2020, 71: 4562-4577.
doi: 10.1093/jxb/eraa076 pmid: 32064504
[51] Wang B X, Xu B, Liu Y, Li J F, Sun Z G, Chi M, Xing Y G, Yang B, Li J, Liu J B, Chen T M, Fang Z W, Lu B G, Xu D Y, Bello B K. A novel mechanisms of the signaling cascade associated with the SAPK10-bZIP20-NHX1 synergistic interaction to enhance tolerance of plant to abiotic stress in rice (Oryza sativa L.). Plant Sci, 2022, 323: 111393.
doi: 10.1016/j.plantsci.2022.111393
[52] Mittal D, Chakrabarti S, Sarkar A, Singh A, Grover A. Heat shock factor gene family in rice: Genomic organization and transcript expression profiling in response to high temperature, low temperature and oxidative stresses. Plant Physiol Biochem, 2009, 47: 785-795.
doi: 10.1016/j.plaphy.2009.05.003
[53] Ogawa S, Miyamoto K, Nemoto K, Sawasaki T, Yamane H, Nojiri H, Okada K. OsMYC2, an essential factor for JA-inductive sakuranetin production in rice, interacts with MYC2-like proteins that enhance its transactivation ability. Sci Rep, 2017, 7: 40175.
doi: 10.1038/srep40175 pmid: 28067270
[54] 李梦琪. 转录因子OsbHLH111抑制水稻幼苗生长机理的初步研究. 河南农业大学硕士学位论文, 河南郑州, 2018.
Li M Q. Preminary Study on the Mechanism for Rice Seedling Growth-inhibition of bHLH111. MS Thesis of Henan Agricultural University, Zhengzhou, Henan, China, 2018. (in Chinese with English abstract)
[55] Tian Q X, Luan J X, Guo C X, Shi X Y, Deng P, Zhou Z Z, Zhang W H, Shen L K. A bHLH protein, OsBIM1, positively regulates rice leaf angle by promoting brassinosteroid signaling. Biochem Biophys Res Commun, 2021, 578: 129-135.
doi: 10.1016/j.bbrc.2021.09.035
[56] Yin X, Cui Y, Wang M, Xia X. Overexpression of a novel MYB-related transcription factor, OsMYBR1, confers improved drought tolerance and decreased ABA sensitivity in rice. Biochem Biophys Res Commun, 2017, 490: 1355-1361.
doi: 10.1016/j.bbrc.2017.07.029
[57] Rongjun C. Isolation of a novel MYB transcription factor OsMyb1R from rice and analysis of the response of this gene to abiotic stresses. Afr J Biotechnol, 2012, 11: 3731-3737.
[58] Jha U C, Bohra A, Jha R, Parida S K. Salinity stress response and ‘omics’ approaches for improving salinity stress tolerance in major grain legumes. Plant Cell Rep, 2019, 38: 255-277.
doi: 10.1007/s00299-019-02374-5
[59] Zeng Z X, Zhang W L, Marand A P, Zhu B, Buell C R, Jiang J M. Cold stress induces enhanced chromatin accessibility and bivalent histone modifications H3K4me3 and H3K27me3 of active genes in potato. Genome Biol, 2019, 20: 123.
doi: 10.1186/s13059-019-1731-2 pmid: 31208436
[60] Sun L, Song G S, Guo W J, Wang W X, Zhao H K, Gao T T, Lyu Q X, Yang X, Xu F, Dong Y S, Pu L. Dynamic changes in genome-wide histone3 lysine27 trimethylation and gene expression of soybean roots in response to salt stress. Front Plant Sci, 2019, 10: 1031.
doi: 10.3389/fpls.2019.01031 pmid: 31552061
[61] Lee H G, Seo P J. MYB96 recruits the HDA15 protein to suppress negative regulators of ABA signaling in Arabidopsis. Nat Commun, 2019, 10: 1713.
doi: 10.1038/s41467-019-09417-1
[62] Ding Y, Avramova Z, Fromm M. The Arabidopsis trithorax-like factor ATX1 functions in dehydration stress responses via ABA-dependent and ABA-independent pathways. Plant J, 2011, 66: 735-744.
doi: 10.1111/j.1365-313X.2011.04534.x
[63] Pien S, Fleury D, Mylne J S, Crevillen P, Inze D, Avramova Z, Dean C, Grossniklaus U. ARABIDOPSIS TRITHORAX1 dynamically regulates FLOWERING LOCUS C activation via histone 3 lysine 4 trimethylation. Plant Cell, 2008, 20: 580-588.
doi: 10.1105/tpc.108.058172
[64] Ullah F, Xu Q, Zhao Y, Zhou D X. Histone deacetylase HDA710 controls salt tolerance by regulating ABA signaling in rice. J Integr Plant Biol, 2021, 63: 451-467.
doi: 10.1111/jipb.13042
[65] Nakashima K, Ito Y, Yamaguchi-Shinozaki K. Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant Physiol, 2009, 149: 88-95.
doi: 10.1104/pp.108.129791 pmid: 19126699
[66] 陈悦, 孙明哲, 贾博为, 冷月, 孙晓丽. 水稻AP2/ERF转录因子参与逆境胁迫应答的分子机制研究进展. 作物学报, 2022, 48: 781-790.
doi: 10.3724/SP.J.1006.2022.12026
Chen Y, Sun M Z, Jia B W, Leng Y, Sun X L. Research progress regarding the function and mechanism of rice AP2/ERF transcription factor in stress response. Acta Agron Sin, 2022, 48: 781-790. (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2022.12026
[67] Zheng Y, Ge J, Bao C, Chang W, Liu J, Shao J, Liu X, Su L, Pan L, Zhou D X. Histone deacetylase HDA9 and WRKY53 transcription factor are mutual antagonists in regulation of plant stress response. Mol Plant, 2020, 13: 598-611.
doi: S1674-2052(19)30408-3 pmid: 31891777
[68] Lamke J, Brzezinka K, Altmann S, Baurle I. A hit-and-run heat shock factor governs sustained histone methylation and transcriptional stress memory. EMBO J, 2016, 35: 162-175.
doi: 10.15252/embj.201592593 pmid: 26657708
[69] Mao Y, Pavangadkar K A, Thomashow M F, Triezenberg S J. Physical and functional interactions of Arabidopsis ADA 2 transcriptional coactivator proteins with the acetyltransferase GCN5 and with the cold-induced transcription factor CBF1. Biochim Biophys Acta, 2006, 1759: 69-79.
[70] Zong W, Yang J, Fu J, Xiong L. Synergistic regulation of drought-responsive genes by transcription factor OsbZIP23 and histone modification in rice. J Integr Plant Biol, 2020, 62: 723-729.
doi: 10.1111/jipb.12850
[71] Huang Q X, Liao X Q, Yang X H, Luo Y C, Lin P, Zeng Q H, Bai H R, Jiang B B, Pan Y Z, Zhang F, Zhang L, Jia Y, Liu Q L. Lysine crotonylation of DgTIL1 at K72 modulates cold tolerance by enhancing DgnsLTP stability in chrysanthemum. Plant Biotechnol J, 2021, 19: 1125-1140.
doi: 10.1111/pbi.13533 pmid: 33368971
[1] 徐高峰, 申时才, 张付斗, 杨韶松, 金桂梅, 郑凤萍, 温丽娜, 张云, 吴冉迪. 土壤微生物对长雄野生稻及其化感潜力后代抑草作用的影响[J]. 作物学报, 2023, 49(9): 2562-2571.
[2] 胡艳娟, 薛丹, 耿嫡, 朱末, 王天穹, 王晓雪. 水稻OsCDF1基因突变效应及其基因组变异分析[J]. 作物学报, 2023, 49(9): 2362-2372.
[3] 唐杰, 龙湍, 吴春瑜, 李新鹏, 曾翔, 吴永忠, 黄培劲. 水稻OsGMS2基因的鉴定及其核不育系种子繁殖体系构建[J]. 作物学报, 2023, 49(8): 2025-2038.
[4] 宋兆建, 冯紫旖, 屈天歌, 吕品苍, 杨晓璐, 湛明月, 张献华, 何玉池, 刘育华, 蔡得田. 四倍体水稻回复二倍体品系的籼粳属性鉴定和杂种优势利用初探[J]. 作物学报, 2023, 49(8): 2039-2050.
[5] 韦新宇, 曾跃辉, 杨旺兴, 肖长春, 候新坡, 黄建鸿, 邹文广, 许旭明. 利用CRISPR-Cas9技术编辑Badh2基因创制优质香型籼稻三系不育系[J]. 作物学报, 2023, 49(8): 2144-2159.
[6] 贾璐绮, 孙悠, 田然, 张学菲, 代永东, 崔志波, 李杨羊, 冯新宇, 桑贤春, 王晓雯. 水稻种子快速萌发突变体rgs1的鉴定及调控基因克隆[J]. 作物学报, 2023, 49(8): 2288-2295.
[7] 丁洪艳, 冯晓溪, 汪柏宇, 张积森. 甘蔗割手密种LRRII-RLK基因家族演化和表达分析[J]. 作物学报, 2023, 49(7): 1769-1784.
[8] 项嘉铭, 戴茜, 刘立军. 外源水杨酸提高云麻1号(Cannabis sativa L.)对铜胁迫的耐受性[J]. 作物学报, 2023, 49(7): 1979-1993.
[9] 邓艾兴, 李歌星, 吕玉平, 刘猷红, 孟英, 张俊, 张卫建. 齐穗后遮阴时长对西北稻区粳稻产量和品质的影响[J]. 作物学报, 2023, 49(7): 1930-1941.
[10] 许娜, 徐铨, 徐正进, 陈温福. 水稻株型生理生态与遗传基础研究进展[J]. 作物学报, 2023, 49(7): 1735-1746.
[11] 魏正欣, 刘昌燕, 陈宏伟, 李莉, 孙龙清, 韩雪松, 焦春海, 沙爱华. 基于干旱胁迫转录组信息的蚕豆ASPAT基因家族分析[J]. 作物学报, 2023, 49(7): 1871-1881.
[12] 林孝欣, 黄明江, 韦祎, 朱洪慧, 王子怡, 李忠成, 庄慧, 李彦羲, 李云峰, 陈锐. 水稻籽粒伸长突变体lgdp的鉴定与基因定位[J]. 作物学报, 2023, 49(6): 1699-1707.
[13] 丁杰荣, 马雅美, 潘发枝, 江立群, 黄文洁, 孙炳蕊, 张静, 吕树伟, 毛兴学, 于航, 李晨, 刘清. 泛素受体蛋白OsDSK2b负向调控水稻叶瘟和渗透胁迫抗性[J]. 作物学报, 2023, 49(6): 1466-1479.
[14] 何永明, 张芳. 生长素调控水稻颖花开放的效应研究[J]. 作物学报, 2023, 49(6): 1690-1698.
[15] 陶玥玥, 盛雪雯, 徐坚, 沈园, 王海候, 陆长婴, 沈明星. 长三角水稻-油菜周年两熟温光资源分配与利用特征[J]. 作物学报, 2023, 49(5): 1327-1338.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
[1] 李绍清, 李阳生, 吴福顺, 廖江林, 李达模. 水稻孕穗期在淹涝胁迫下施肥的优化选择及其作用机理[J]. 作物学报, 2002, 28(01): 115 -120 .
[2] 王兰珍;米国华;陈范骏;张福锁. 不同产量结构小麦品种对缺磷反应的分析[J]. 作物学报, 2003, 29(06): 867 -870 .
[3] 王艳;邱立明;谢文娟;黄薇;叶锋;张富春;马纪. 昆虫抗冻蛋白基因转化烟草的抗寒性[J]. 作物学报, 2008, 34(03): 397 -402 .
[4] 郑希;吴建国;楼向阳;徐海明;石春海. 不同环境条件下稻米组氨酸和精氨酸的胚乳和母体植株QTL分析[J]. 作物学报, 2008, 34(03): 369 -375 .
[5] 邢光南, 周斌, 赵团结, 喻德跃, 邢邯, 陈受宜, 盖钧镒. 大豆抗筛豆龟蝽Megacota cribraria (Fabricius)的QTL分析[J]. 作物学报, 2008, 34(03): 361 -368 .
[6] 郑永美;丁艳锋;王强盛;李刚华;王惠芝;王绍华. 起身肥对水稻分蘖和氮素吸收利用的影响[J]. 作物学报, 2008, 34(03): 513 -519 .
[7] 秦恩华;杨兰芳. 烤烟苗期含硒量和根际硒形态的研究[J]. 作物学报, 2008, 34(03): 506 -512 .
[8] 吕丽华;陶洪斌;夏来坤; 张雅杰; 赵明; 赵久然;王璞. 不同种植密度下的夏玉米冠层结构及光合特性[J]. 作物学报, 2008, 34(03): 447 -455 .
[9] 张书标;杨仁崔. e-杂交稻若干生物学特性研究[J]. 作物学报, 2003, 29(06): 919 -924 .
[10] 邵瑞鑫;上官周平. 外源一氧化氮供体SNP对受旱小麦光合色素含量和PS II光能利用能力的影响[J]. 作物学报, 2008, 34(05): 818 -822 .
京ICP备15008789号-2