AbstractDissecting the genetic basis of seed traits in wheat is impeded by limited genetic polymorphisms and significant variations caused by environmental conditions and seed position in a spikelet. Seed performance is largely determined by endosperm development controlled by spatiotemporal variation in gene activities, which is greatly affected by chromatin status.

摘要有限的遗传多态性和由环境条件和小穗种子位置引起的显着变异阻碍了对小麦种子性状遗传基础的剖析。。

Here, we map genome-wide dynamic distributions of H3K27me3, H3K4me3 and H3K9ac modifications and profile gene transcription across wheat endosperm development. The combinatorial effects of active and repressive marks ensure spatiotemporal dynamic gene expression, especially for starch biosynthesis. By scanning the transcription factor binding motifs in the ATAC-seq peaks, hub regulators are identified from the regulatory network.

在这里，我们绘制了H3K27me3，H3K4me3和H3K9ac修饰的全基因组动态分布图，并在小麦胚乳发育过程中分析了基因转录。活性和抑制性标记的组合效应确保了时空动态基因表达，特别是淀粉生物合成。通过扫描ATAC-seq峰中的转录因子结合基序，可以从调控网络中识别中枢调节因子。

In addition, we observe significant correlations between sequence polymorphisms of hub regulators and variations in seed traits in a germplasm population. Thus, the analysis of genomic regulatory activities together with genetic variation provides a robust approach to dissect seed traits in bread wheat..

此外，我们观察到中枢调节因子的序列多态性与种质群体中种子性状变异之间存在显着相关性。因此，对基因组调控活性和遗传变异的分析为剖析面包小麦的种子性状提供了一种强有力的方法。。

IntroductionHexaploid wheat (Triticum aestivum L., AABBDD) is a world-wide staple food crop. Seed traits greatly determine the yield and processing quality of wheat. However, performance of seed in wheat is largely affected by environmental conditions like temperature, which changes grain filling rate1.

引言六倍体小麦（Triticum aestivum L.，AABBDD）是世界范围内的主要粮食作物。种子性状在很大程度上决定了小麦的产量和加工品质。然而，小麦种子的表现在很大程度上受温度等环境条件的影响，这会改变籽粒灌浆速率1。

Even within one spike, different position of spikelet and flowers in a spikelet which usually contains more than three flowers produces different sizes of seeds2. In addition, the composition of three sub-genomes results in low frequency of recombination and genetic polymorphism in wheat3. The above facts bring difficulties to dissect genetic basis of seed traits in wheat.Performance of seed depends on the development of endosperm4.

即使在一个穗内，通常含有三朵花以上的小穗中小穗和花的不同位置也会产生不同大小的种子2。此外，三个亚基因组的组成导致小麦3的重组频率和遗传多态性较低。上述事实给剖析小麦种子性状的遗传基础带来了困难。种子的表现取决于胚乳的发育4。

The development of endosperm involves several important events. 0–4 day-post-anthesis (DPA) is defined as endosperm coenocytes, which undergoes rapid proliferation of nuclei without cytokinesis5. Subsequently, cellularization of the coenocyte (5–7 DPA) starts and all free nuclei are surrounded by newly formed cell wall.

胚乳的发育涉及几个重要事件。花后0-4天（DPA）被定义为胚乳腔细胞，其经历细胞核的快速增殖而没有胞质分裂5。随后，腔细胞（5-7 DPA）开始细胞化，所有游离核都被新形成的细胞壁包围。

Repeated rounds of mitosis produce cells that eventually occupy the central vacuole completely6,7. From 7 DPA on, the endosperm begins to differentiate into specialized cell types, such as aleurone, starchy endosperm and so on. This period lasts for one week (7–14 DPA) and it is featured by the initiation of starch and protein accumulation.

反复的有丝分裂产生最终完全占据中央液泡的细胞6,7。从7 DPA开始，胚乳开始分化为特殊的细胞类型，如糊粉，淀粉胚乳等。这一时期持续一周（7-14 DPA），其特征是淀粉和蛋白质积累的开始。

Afterwards, endosperm enters effective filling period, accompanied by grain maturity and drying8.The synthesis and accumulation of starch and seed storage protein (SSP) have been extensively studied in rice and maize9,10, while the knowledge in wheat is relatively limited. In addition to the transcriptomic analysis during development and maturation of wheat endosperm8,11,12, only a few gene.

之后，胚乳进入有效灌浆期，伴随着籽粒成熟和干燥8。水稻和玉米中淀粉和种子贮藏蛋白（SSP）的合成和积累已被广泛研究9,10，而小麦的知识相对有限。除了小麦胚乳发育和成熟过程中的转录组学分析8,11,12外，只有少数基因。

Data availability

数据可用性

The sequencing data generated in this study have been deposited in the Genome Sequence Archive at the Beijing Institute of Genomics (BIG) Data Center, Chinese Academy of Sciences, under accession code CRA009416. The processed ChIP-seq data are available in the Open Archive for Miscellaneous Data (OMIX) under accession code OMIX002851.

。处理后的ChIP-seq数据可在Open Archive for Miscellaneous data（OMIX）中获得，登录号为OMIX002851。

The public DAP-seq data were downloaded from the Gene Expression Omnibus database under the accession code GSE192815 and GSE188699. Source data are provided with this paper..

公共DAP-seq数据是从Gene Expression Omnibus数据库下载的，登录号为GSE192815和GSE188699。本文提供了源数据。。

Code availability

代码可用性

The scripts and codes for this study can be found at GitHub repository [https://github.com/hcph/wheat-endosperm-development]77.

这项研究的脚本和代码可以在GitHub存储库中找到[https://github.com/hcph/wheat-endosperm-development]77页。

ReferencesAkter, N. & Rafiqul Islam, M. Heat stress effects and management in wheat. Agron. Sustain. Dev. 37, 37 (2017).

参考文献Sakter，N。＆Rafiqul Islam，M。小麦的热应激效应和管理。阿格伦。维持。德文37，37（2017）。

Google Scholar

谷歌学者

Boz, H., Gerçekaslan, K. E., Karaoğlu, M. M. & Kotancilar, H. G. Differences in some physical and chemical properties of wheat grains from different parts within the spike. Turkish J. Agric. Forestry 36, 309–316 (2012).CAS

Boz，H.，Gerçekaslan，K.E.，Karaoğlu，M.M。和Kotancilar，H.G。穗内不同部位小麦籽粒某些物理和化学性质的差异。土耳其J.Agric。。中科院

Google Scholar

谷歌学者

Gardiner, L. J. et al. Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency. Genome Biol. 20, 69 (2019).PubMed

Gardiner，L.J.等人对六倍体面包小麦重组景观的分析揭示了控制重组和基因转化频率的基因。基因组生物学。20,69（2019）。PubMed出版社

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Evers, T. & Millar, S. Cereal grain structure and development: Some implications for quality. J. Cereal Sci. 36, 261–284 (2002).

Evers，T。＆Millar，S。谷物谷物结构和发育：对质量的一些影响。J、 谷物科学。36261-284（2002）。

Google Scholar

谷歌学者

Gao, X., Francis, D., Ormrod, J. C. & Bennett, M. D. Changes in cell number and cell division activity during endosperm development in allohexaploid wheat, Triticum aestivum L. J. Exp. Bot. 43, 1603–1609 (1992).

Gao，X.，Francis，D.，Ormrod，J.C.＆Bennett，M.D.异六倍体小麦胚乳发育过程中细胞数量和细胞分裂活性的变化，Triticum aestivum L.J.Exp.Bot.431603-1609（1992）。

Google Scholar

谷歌学者

Leroux, B. M. et al. Maize early endosperm growth and development: from fertilization through cell type differentiation. Am. J. Bot. 101, 1259–1274 (2014).PubMed

Leroux，B.M.等。玉米早期胚乳生长发育：从受精到细胞类型分化。《美国法学杂志》第1011259-1274页（2014年）。PubMed出版社

Google Scholar

谷歌学者

Olsen, O. A. ENDOSPERM DEVELOPMENT: Cellularization and cell fate specification. Annu Rev. Plant Physiol. Plant Mol. Biol. 52, 233–267 (2001).CAS

Olsen，O.A。胚乳发育：细胞化和细胞命运规范。Annu Rev.植物生理学。植物分子生物学。52233-267（2001）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Shewry, P. R. et al. An integrated study of grain development of wheat (cv. Hereward). J. Cereal Sci. 56, 21–30 (2012).ADS

Shewry，P.R.等人，《小麦籽粒发育的综合研究》（cv。Hereward）。J、 谷物科学。56,21-30（2012）。广告

Google Scholar

谷歌学者

Huang, L., Tan, H., Zhang, C., Li, Q. & Liu, Q. Starch biosynthesis in cereal endosperms: An updated review over the last decade. Plant Commun. 2, 100237 (2021).CAS

Huang，L.，Tan，H.，Zhang，C.，Li，Q。＆Liu，Q。谷物胚乳中的淀粉生物合成：过去十年的最新综述。植物群落。210027（2021）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Dai, D., Ma, Z. & Song, R. Maize endosperm development. J. Integr. Plant Biol. 63, 613–627 (2021).CAS

Dai，D.，Ma，Z。＆Song，R。玉米胚乳发育。J、 整数。植物生物学。63613-627（2021）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Pfeifer, M. et al. Genome interplay in the grain transcriptome of hexaploid bread wheat. Science 345, 1250091 (2014).PubMed

Pfeifer，M.等人。六倍体面包小麦籽粒转录组中的基因组相互作用。科学3451250091（2014）。PubMed出版社

Google Scholar

谷歌学者

Guan, J. et al. Transcriptome analysis of developing wheat grains at rapid expanding phase reveals dynamic gene expression patterns. Biology-Basel. 11, 281 (2022).Song, Y. et al. TubZIP28, a novel bZIP family transcription factor from Triticum urartu, and TabZIP28, its homologue from Triticum aestivum, enhance starch synthesis in wheat.

。巴塞尔生物学。11281（2022）。Song，Y.等人，TubZIP28是一种来自小麦urartu的新型bZIP家族转录因子，而TabZIP28是来自普通小麦的同源物，可增强小麦的淀粉合成。

N. Phytol. 226, 1384–1398 (2020).CAS .

N、 植物醇。2261384-1398（2020）。CAS。

Google Scholar

谷歌学者

Liu, G. et al. Virus-induced gene silencing identifies an important role of the TaRSR1 transcription factor in starch synthesis in bread wheat. Int. J. Mol. Sci. 17, 1557 (2016).Guo, D. et al. Over-expressing TaSPA-B reduces prolamin and starch accumulation in wheat (Triticum aestivum L.) grains.

Liu，G。等人。病毒诱导的基因沉默确定了TaRSR1转录因子在面包小麦淀粉合成中的重要作用。Int.J.Mol.Sci。171557（2016）。郭，D。等人。过表达TaSPA-B可减少小麦（Triticum aestivum L.）籽粒中的醇溶蛋白和淀粉积累。

Int. J. Mol. Sci. 21, 3257 (2020).Liu, Y. et al. The NAC transcription factor NAC019-A1 is a negative regulator of starch synthesis in wheat developing endosperm. J. Exp. Bot. 71, 5794–5807 (2020).CAS .

Int.J.Mol.Sci。213257（2020）。。J、 实验Bot 715794–5807（2020）。CAS。

PubMed

PubMed

Google Scholar

谷歌学者

Gao, Y. et al. The endosperm-specific transcription factor TaNAC019 regulates glutenin and starch accumulation and its elite allele improves wheat grain quality. Plant Cell 33, 603–622 (2021).PubMed

胚乳特异性转录因子TaNAC019调节谷蛋白和淀粉的积累，其精英等位基因改善小麦籽粒品质。植物细胞33603-622（2021）。PubMed出版社

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Berger, S. L. The complex language of chromatin regulation during transcription. Nature 447, 407–412 (2007).ADS

Berger，S.L。转录过程中染色质调控的复杂语言。《自然》447407–412（2007）。广告

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Lauberth, S. M. et al. H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation. Cell 152, 1021–1036 (2013).CAS

。细胞1521021-1036（2013）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Kratz, A. et al. Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. Bmc Genomics 11, 257 (2010).PubMed

Kratz，A。等人。核心启动子结构和基因组背景反映了组蛋白3赖氨酸9乙酰化模式。Bmc基因组学11257（2010）。PubMed出版社

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039–1043 (2002).ADS

Cao，R。等人。组蛋白H3赖氨酸27甲基化在Polycomb组沉默中的作用。科学2981039-1043（2002）。广告

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Oka, R. et al. Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biol. 18, 137 (2017).PubMed

Oka，R.等人。使用玉米中的DNA和染色质特征对转录增强子候选物进行全基因组定位。基因组生物学。18137（2017）。PubMed出版社

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Du, Z. et al. Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica. Mol. Plant. 6, 1463–1472 (2013).CAS

Du，Z.等人。组蛋白修饰的全基因组分析：水稻中的H3K4me2，H3K4me3，H3K9ac和H3K27ac。摩尔植物。61463-1472（2013）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Huang, Y. et al. Wide Grain 7 increases grain width by enhancing H3K4me3 enrichment in the OsMADS1 promoter in rice (Oryza sativa L.). Plant J. 102, 517–528 (2020).CAS

Huang，Y。等人。宽粒7通过增强水稻（Oryza sativa L.）中OsMADS1启动子中H3K4me3的富集来增加粒宽。工厂J.102517–528（2020）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Nallamilli, B. R. et al. Polycomb group gene OsFIE2 regulates rice (Oryza sativa) seed development and grain filling via a mechanism distinct from Arabidopsis. Plos Genet 9, e1003322 (2013).CAS

Nallamilli，B.R。等人，Polycomb组基因OsFIE2通过不同于拟南芥的机制调节水稻（Oryza sativa）种子发育和籽粒灌浆。Plos Genet 9，e1003322（2013）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Liu, X. et al. SDG711 is involved in rice seed development through regulation of starch metabolism gene expression in coordination with other histone modifications. Rice 14, 25 (2021).CAS

Liu，X。等人。SDG711通过与其他组蛋白修饰协同调节淀粉代谢基因表达，参与水稻种子发育。赖斯14，25（2021）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Kim, E. D. et al. Spatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development. Sci. Rep. 7, 3838 (2017).ADS

Kim，E.D.等人。玉米胚乳发育过程中编码和长非编码转录本的时空分析。科学。代表73838（2017）。广告

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Tian, Q. et al. Riboflavin integrates cellular energetics and cell cycle to regulate maize seed development. Plant Biotechnol. J. 20, 1487–1501 (2022).CAS

Tian，Q。等人。核黄素整合细胞能量学和细胞周期来调节玉米种子发育。植物生物技术。J、 201487-1501（2022）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Weinhofer, I., Hehenberger, E., Roszak, P., Hennig, L. & Kohler, C. H3K27me3 profiling of the endosperm implies exclusion of polycomb group protein targeting by DNA methylation. PLoS Genet. 6, e1001152 (2010).Dong, X. et al. Dynamic and antagonistic allele-Specific epigenetic modifications controlling the expression of imprinted genes in maize endosperm.

Weinhofer，I.，Hehenberger，E.，Roszak，P.，Hennig，L。＆Kohler，C。胚乳的H3K27me3分析意味着排除了通过DNA甲基化靶向的多梳组蛋白。PLoS Genet。6，e1001152（2010）。Dong，X。等人。控制玉米胚乳印迹基因表达的动态和拮抗等位基因特异性表观遗传修饰。

Mol. Plant. 10, 442–455 (2017).CAS .

摩尔植物。。CAS。

PubMed

PubMed

Google Scholar

谷歌学者

Makarevitch, I. et al. Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27. Plant Cell 25, 780–793 (2013).CAS

Makarevitch，I。等人。H3K27三甲基化标记的玉米兼性异染色质的基因组分布。植物细胞25780-793（2013）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Zhao, L. et al. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biol. 24, 7 (2023).Gillies, S. A., Futardo, A. & Henry, R. J. Gene expression in the developing aleurone and starchy endosperm of wheat. Plant Biotechnol. J. 10, 668’679 (2012).Barthole, G.

赵，L。等。六倍体小麦胚胎发生过程中的动态染色质调控程序。基因组生物学。24，7（2023）。Gillies，S.A.，Futardo，A。＆Henry，R.J。小麦糊粉和淀粉胚乳发育中的基因表达。植物生物技术。J、 10668'679（2012）。Barthole，G。

et al. MYB118 represses endosperm maturation in seeds of Arabidopsis. Plant Cell 26, 3519–3537 (2014).CAS .

MYB118抑制拟南芥种子中胚乳的成熟。植物细胞263519-3537（2014）。CAS。

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Liu, H. et al. Pleiotropic ZmICE1 is an important transcriptional regulator of maize endosperm starch biosynthesis. Front. Plant Sci. 13, 895763 (2022).PubMed

Liu，H。等人。多效性ZmICE1是玉米胚乳淀粉生物合成的重要转录调节因子。正面。植物科学。13895763（2022）。PubMed出版社

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Chen, Z. et al. Expression of AtAAP gene family and endosperm-specific expression of AtAAP1 gene promotes amino acid absorption in Arabidopsis thaliana and maize. Agronomy 11, 1668 (2021).

Chen，Z。等人。AtAAP基因家族的表达和AtAAP1基因的胚乳特异性表达促进拟南芥和玉米中的氨基酸吸收。农学111668（2021）。

Google Scholar

谷歌学者

Gehring, M., Missirian, V. & Henikoff, S. Genomic analysis of parent-of-origin allelic expression in Arabidopsis thaliana seeds. PLoS One 6, e23687 (2011).ADS

Gehring，M.，Missirian，V。＆Henikoff，S。拟南芥种子中起源亲本等位基因表达的基因组分析。PLoS One 6，e23687（2011）。广告

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Ramirez-Gonzalez, R. H. et al. The transcriptional landscape of polyploid wheat. Science. 361, eaar6089 (2018).Zhao, T., Zhan, Z. & Jiang, D. Histone modifications and their regulatory roles in plant development and environmental memory. J. Genet. Genomics. 46, 467–476 (2019).CAS

Ramirez-Gonzalez，R.H.等人。多倍体小麦的转录景观。科学。361，eaar6089（2018）。Zhao，T.，Zhan，Z。＆Jiang，D。组蛋白修饰及其在植物发育和环境记忆中的调节作用。J、 基因。基因组学。。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Ma, C. et al. iTRAQ-based quantitative proteome and phosphoprotein characterization reveals the central metabolism changes involved in wheat grain development. BMC Genomics 15, 1029 (2014).PubMed

基于iTRAQ的定量蛋白质组和磷蛋白表征揭示了小麦籽粒发育中涉及的中枢代谢变化。BMC Genomics 151029（2014）。PubMed出版社

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Kaufmann, K., Pajoro, A. & Angenent, G. C. Regulation of transcription in plants: mechanisms controlling developmental switches. Nat. Rev. Genet. 11, 830–842 (2010).CAS

Kaufmann，K.，Pajoro，A。＆Angenent，G.C。植物转录调控：控制发育开关的机制。Genet自然Rev。11830-842（2010）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Pei, H. et al. Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat. Sci. China Life Sci. 66, 819–834 (2023).Zhang, Y. et al. Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat. Nat. Commun.

Pei，H。等人。低亲和力SPL结合位点有助于异源六倍体小麦的亚基因组表达差异。科学。中国生命科学。66819-834（2023）。Zhang，Y。等人。转座因子协调普通小麦中的亚基因组会聚和发散转录。国家公社。

13, 6940 (2022).Sun, F. et al. Functional characterization of TaFUSCA3, a B3-Superfamily transcription factor gene in the wheat. Front. Plant Sci. 8, 1133 (2017).PubMed .

136940（2022年）。Sun，F。等人。小麦B3超家族转录因子基因TaFUSCA3的功能表征。正面。植物科学。81133（2017）。PubMed。

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Zhu, J. et al. 5-Azacytidine treatment and TaPBF-D over-expression increases glutenin accumulation within the wheat grain by hypomethylating the Glu-1 promoters. Theor. Appl. Genet. 131, 735–746 (2018).CAS

。理论。应用。。131735-746（2018）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Guo, W. et al. The wheat transcription factor TaGAMyb recruits histone acetyltransferase and activates the expression of a high-molecular-weight glutenin subunit gene. Plant J. 84, 347–359 (2015).CAS

Guo，W。等人。小麦转录因子TaGAMyb募集组蛋白乙酰转移酶并激活高分子量谷蛋白亚基基因的表达。植物J.84347–359（2015）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Yoo, S. D., Cho, Y. H., Tena, G., Xiong, Y. & Sheen, J. Dual control of nuclear EIN3 by bifurcate MAPK cascades in C2H4 signalling. Nature 451, 789–795 (2008).ADS

Yoo，S.D.，Cho，Y.H.，Tena，G.，Xiong，Y。＆Sheen，J。通过C2H4信号传导中的分叉MAPK级联对核EIN3进行双重控制。自然451789-795（2008）。广告

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Pan, Y. et al. An ethylene response factor (ERF5) promoting adaptation to drought and salt tolerance in tomato. Plant Cell Rep. 31, 349–360 (2012).CAS

Pan，Y。等人。一种乙烯反应因子（ERF5），促进番茄对干旱和耐盐性的适应。植物细胞代表31349-360（2012）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Troncoso-Ponce, M. A. et al. Transcriptional activation of two delta-9 Palmitoyl-ACP desaturase genes by MYB115 and MYB118 is critical for biosynthesis of omega-7 monounsaturated fatty acids in the endosperm of Arabidopsis seeds. Plant Cell 28, 2666–2682 (2016).CAS

Troncoso Ponce，M.A。等人。MYB115和MYB118对两个δ-9棕榈酰ACP去饱和酶基因的转录激活对于拟南芥种子胚乳中ω-7单不饱和脂肪酸的生物合成至关重要。植物细胞282666-2682（2016）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Zhang, Y., Cao, G., Qu, L. J. & Gu, H. Involvement of an R2R3-MYB transcription factor gene AtMYB118 in embryogenesis in Arabidopsis. Plant Cell Rep. 28, 337–346 (2009).CAS

Zhang，Y.，Cao，G.，Qu，L.J。＆Gu，H。R2R3-MYB转录因子基因AtMYB118参与拟南芥的胚胎发生。植物细胞代表28337-346（2009）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Franken, P., Schrell, S., Peterson, P. A., Saedler, H. & Wienand, U. Molecular analysis of protein domain function encoded by the myb-homologous maize genes C1, Zm 1 and Zm 38. Plant J. 6, 21–30 (1994).CAS

Franken，P.，Schrell，S.，Peterson，P.A.，Saedler，H。＆Wienand，U。myb同源玉米基因C1，Zm 1和Zm 38编码的蛋白质结构域功能的分子分析。植物J.6，21-30（1994）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Villagomez-Aranda, A. L. et al. Activating stress memory: eustressors as potential tools for plant breeding. Plant Cell Rep. 41, 1481–1498 (2022).CAS

Villagomez-Aranda，A.L.等人，《激活应激记忆：正应激源作为植物育种的潜在工具》。植物细胞代表411481-1498（2022）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Angel, A., Song, J., Dean, C. & Howard, M. A Polycomb-based switch underlying quantitative epigenetic memory. Nature 476, 105–108 (2011).CAS

Angel，A.，Song，J.，Dean，C。＆Howard，M。基于Polycomb的定量表观遗传记忆开关。自然476105-108（2011）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

He, C., Chen, X., Huang, H. & Xu, L. Reprogramming of H3K27me3 is critical for acquisition of pluripotency from cultured Arabidopsis tissues. Plos Genet 8, e1002911 (2012).CAS

He，C.，Chen，X.，Huang，H。＆Xu，L。H3K27me3的重编程对于从培养的拟南芥组织中获得多能性至关重要。Plos Genet 8，e1002911（2012）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Atlasi, Y. & Stunnenberg, H. G. The interplay of epigenetic marks during stem cell differentiation and development. Nat. Rev. Genet. 18, 643–658 (2017).CAS

Atlasi，Y。＆Stunnenberg，H.G。干细胞分化和发育过程中表观遗传标记的相互作用。Genet自然Rev。18643-658（2017）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Jia, H., Suzuki, M. & McCarty, D. R. Regulation of the seed to seedling developmental phase transition by the LAFL and VAL transcription factor networks. Wiley Interdiscip. Rev. Dev. Biol. 3, 135–145 (2014).CAS

Jia，H.，Suzuki，M。＆McCarty，D.R。通过LAFL和VAL转录因子网络调节种子到幼苗的发育相变。Wiley Interdiscip公司。。3135-145（2014）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Kagaya, Y. et al. LEAFY COTYLEDON1 controls seed storage protein genes through its regulation of FUSCA3 and ABSCISIC ACID INSENSITIVE3. Plant Cell Physiol. 46, 399–406 (2005).CAS

Kagaya，Y。等人。叶子叶1通过调节FUSCA3和脱落酸不敏感来控制种子贮藏蛋白基因3。植物细胞生理学。46399-406（2005）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Ravindran, P., Verma, V., Stamm, P. & Kumar, P. P. A novel RGL2-DOF6 complex contributes to primary seed dormancy in Arabidopsis thaliana by regulating a GATA transcription factor. Mol. Plant. 10, 1307–1320 (2017).CAS

Ravindran，P.，Verma，V.，Stamm，P。＆Kumar，P.P。一种新型RGL2-DOF6复合物通过调节GATA转录因子促进拟南芥的初级种子休眠。摩尔植物。101307-1320（2017）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Zinsmeister, J. et al. The seed-specific heat shock factor A9 regulates the depth of dormancy in Medicago truncatula seeds via ABA signalling. Plant Cell Environ. 43, 2508–2522 (2020).CAS

Zinsmeister，J。等人。种子比热休克因子A9通过ABA信号调节蒺藜苜蓿种子的休眠深度。植物细胞环境。432508-2522（2020）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

van Ginkel, M. & Ogbonnaya, F. Novel genetic diversity from synthetic wheats in breeding cultivars for changing production conditions. Field Crop. Res. 104, 86–94 (2007).

van Ginkel，M。＆Ogbonnaya，F。用于改变生产条件的育种品种中合成小麦的新型遗传多样性。大田作物。第104、86-94号决议（2007年）。

Google Scholar

谷歌学者

Zhai, H. et al. QTL Analysis of spike morphological traits and plant height in winter wheat (Triticum aestivum L.) using a high-density SNP and SSR-based linkage map. Front. Plant Sci. 7, 1617 (2016).PubMed

翟，H。等人。使用基于高密度SNP和SSR的连锁图谱对冬小麦（Triticum aestivum L.）穗形态性状和株高进行QTL分析。正面。植物科学。71617（2016）。PubMed出版社

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Zhao, L. et al. Deciphering the transcriptional regulatory network governing starch and storage protein biosynthesis in wheat for breeding improvement. Adv. Sci. 11, e2401383 (2024).

Zhao，L.等人。破译控制小麦淀粉和贮藏蛋白生物合成的转录调控网络，以进行育种改进。高级科学。11，e2401383（2024）。

Google Scholar

谷歌学者

Zhao, L. et al. Integrative analysis of reference epigenomes in 20 rice varieties. Nat. Commun. 11, 2658 (2020).ADS

赵，L。等。20个水稻品种参考表观基因组的综合分析。国家公社。112658（2020）。广告

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Wang, X., Chen, C., He, C., Chen, D. & Yan, W. Mapping open chromatin by ATAC-seq in bread wheat. Front. Plant Sci. 13, 1074873 (2022).PubMed

。正面。植物科学。131074873（2022）。PubMed出版社

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525–527 (2016).CAS

Bray，N.L.，Pimentel，H.，Melsted，P。＆Pachter，L。接近最佳概率RNA-seq定量。美国国家生物技术公司。34525-527（2016）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Pimentel, H., Bray, N. L., Puente, S., Melsted, P. & Pachter, L. Differential analysis of RNA-seq incorporating quantification uncertainty. Nat. Methods 14, 687–690 (2017).CAS

Pimentel，H.，Bray，N.L.，Puente，S.，Melsted，P。＆Pachter，L。结合定量不确定性的RNA-seq的差异分析。自然方法14687-690（2017）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Ramirez, F., Dundar, F., Diehl, S., Gruning, B. A. & Manke, T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res 42, W187–W191 (2014).CAS

Ramirez，F.，Dundar，F.，Diehl，S.，Grunning，B.A。＆Manke，T。deepTools：探索深度测序数据的灵活平台。核酸Res 42，W187–W191（2014）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).CAS

Quinlan，A.R。＆Hall，I.M。BEDTools：用于比较基因组特征的灵活实用程序套件。生物信息学26841-842（2010）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Hamilton, N. E. & Ferry, M. ggtern: Ternary diagrams using ggplot2. J. Stat. Softw. 87, 1–17 (2018).Bentsen, M. et al. ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation. Nat. Commun. 11, 4267 (2020).ADS

。J、 统计软件。87,1-17（2018）。Bentsen，M。等人。ATAC-seq足迹揭示了合子基因组激活过程中转录因子结合的动力学。国家公社。114267（2020）。广告

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Khan, A. et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 46, D260–D266 (2018).CAS

Khan，A.等人，《JASPAR 2018：转录因子结合谱开放获取数据库及其网络框架的更新》。核酸研究46，D260–D266（2018）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P. L. & Ideker, T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27, 431–432 (2011).CAS

Smoot，M.E.，Ono，K.，Ruscheinski，J.，Wang，P.L。＆Ideker，T。Cytoscape 2.8：数据集成和网络可视化的新功能。生物信息学27431-432（2011）。中科院

PubMed

PubMed

Google Scholar

谷歌学者

Bates, D. et al. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).ADS

Bates，D.等人使用lme4拟合线性混合效应模型。J、 统计软件。67,1-48（2015）。广告

Google Scholar

谷歌学者

Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).CAS

Purcell，S。等人。PLINK：用于全基因组关联和基于人群的连锁分析的工具集。。81559-575（2007）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

He, C. et al. Cereal: a guide RNA design tool integrating regulome and genomic variation for wheat, maize and rice. Plant Biotechnol. J. 19, 2141–2143 (2021).PubMed

He，C.等人，《谷物：整合小麦，玉米和水稻的调节体和基因组变异的指导RNA设计工具》。植物生物技术。J、 192141-2143（2021）。PubMed出版社

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Zhou, Z. et al. Overcoming genotypic dependency and bypassing immature embryos in wheat transformation by using morphogenic regulators. Sci. China Life Sci. 67, 1535–1538 (2024).PubMed

Zhou，Z.等人。通过使用形态发生调节剂克服小麦转化中的基因型依赖性和绕过未成熟胚。科学。中国生命科学。671535-1538（2024）。PubMed出版社

Google Scholar

谷歌学者

He, C. et al. Dynamic atlas of histone modifications and gene regulatory networks in endosperm of bread wheat. Github. https://doi.org/10.5281/zenodo.13767298 (2024).Download referencesAcknowledgementsThis research was supported by the Biological Breeding-National Science and Technology Major Project (2023ZD0406802) to H.L.M and the Science and Technology Major Program of Hubei Province (NO.2022ABA001) to W.H.Y.

He，C.等。面包小麦胚乳组蛋白修饰和基因调控网络的动态图谱。。https://doi.org/10.5281/zenodo.13767298（2024年）。下载参考文献致谢本研究得到了H.L.M.的生物育种国家科技重大项目（2023ZD046802）和W.H.Y.的湖北省科技重大项目（NO.2022ABA001）的支持。

We thank Prof. Dr. Kerstin Kaufmann from Humboldt-Universität zu Berlin for her critical reading and suggestions on the manuscript. We thank the China National GeneBank and the high-performance computing platform at the National Key Laboratory of Crop Genetic Improvement at Huazhong Agricultural University for data storage and server for data processing.Author informationAuthor notesThese authors contributed equally: Chao He, Siteng Bi, Yuqi Li.Authors and AffiliationsNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, ChinaChao He, Siteng Bi, Yuqi Li, Chengxiang Song, Heping Zhang, Xintong Xu, Qiang Li, Sulaiman Saeed, Wei Chen, Chunjie Zhao, Caixia Lan, Handong Su, Hailiang Mao & Wenhao YanAuthorsChao HeView author publicationsYou can also search for this author in.

。我们感谢中国国家基因库和华中农业大学作物遗传改良国家重点实验室的高性能计算平台提供的数据存储和数据处理服务器。作者信息作者注意到这些作者做出了同样的贡献：Chao He，Siteng Bi，Yuqi Li。作者和附属机构华中农业大学湖北洪山实验室作物遗传改良国家重点实验室，武汉，430070，中国Chao He，Siteng Bi，Yuqi Li，宋承祥，张和平，徐心彤，李强，苏莱曼·赛义德，陈伟，赵春杰，蓝彩霞，苏汉东，毛海良和杨文浩作者Chao HeView作者出版物您也可以在中搜索这位作者。

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PubMed Google ScholarContributionsW.H.Y. and H.L.M. conceived and designed the study. Y.Q.L., C.H. and C.X.S. performed the experiment and collect the data with help from H.P.Z., X.T.X., S.S. and C.J.Z., C.H. and S.T.B. performed the data analyses. C.H. and S.T.B. draft the manuscript with input from H.D.S, C.X.L., Q.L.

PubMed谷歌学术贡献软件。H、 Y.和H.L.M.构思并设计了这项研究。Y、 Q.L.，C.H.和C.X.S.进行了实验，并在H.P.Z.，X.T.X.，S.S.和C.J.Z.的帮助下收集了数据，C.H.和S.T.B.进行了数据分析。C、 H.和S.T.B.在H.D.S，C.X.L.，Q.L.的输入下起草了手稿。

and W.C., W.H.Y. finalized the manuscript. All authors reviewed and approved the manuscript.Corresponding authorsCorrespondence to.

和W.C.，W.H.Y.完成了手稿。所有作者都审查并批准了手稿。通讯作者通讯。

Hailiang Mao or Wenhao Yan.Ethics declarations

毛海良或颜文豪。道德宣言

Competing interests

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The authors declare no competing interests.

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Nature Communications thanks Laura-Jayne Gardiner and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. A peer review file is available.

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Reprints and permissionsAbout this articleCite this articleHe, C., Bi, S., Li, Y. et al. Dynamic atlas of histone modifications and gene regulatory networks in endosperm of bread wheat.

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Nat Commun 15, 9572 (2024). https://doi.org/10.1038/s41467-024-53300-7Download citationReceived: 20 January 2023Accepted: 07 October 2024Published: 06 November 2024DOI: https://doi.org/10.1038/s41467-024-53300-7Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard.

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