基于WGCNA的稻谷储藏期间差异基因挖掘与品质调控网络构建

doi:10.3864/j.issn.0578-1752.2025.14.013

Abstract

Abstract:

【Background】Rice grain undergoes various physiological and biochemical changes during long-term storage, impacting both stability and quality. Those factors contribute to rice grain quality deterioration during its storage stage, such as lipid oxidation, starch degradation, protein modifications, membrane homeostasis imbalance, and oxidative stress collectively. However, the molecular mechanisms underlying these changes remain elusive.【Objective】This study aimed to analyze differentially expressed genes (DEGs) in stored rice grian, construct a co-expression network, identify core genes using WGCNA and explore regulatory mechanisms associated with rice storage stability. 【Method】Transcriptomic analysis was conducted on Japonica rice (Nanjing 46) grain stored for different durations (0, 3, 6, 9 and 12 months) to obtain gene expression profiles. WGCNA was employed to identify highly variable genes during storage, construct a weighted gene co-expression network, and identify storage-time-specific modules. Core genes screening was based on network connectivity, followed by functional enrichment analysis and physiological and biochemical assays to explore their potential roles in storage quality regulation.【Result】A total of 9 050 DEGs were identified, with 8 654 showing variations across storage stages, and 396 were expressed consistently across all time points. WGCNA identified 17 gene co-expression modules, of which four showed strong associations with storage duration. Connectivity analysis further highlighted key genes with regulatory potential：OsOLE4 and OsCDAP3, involved in lipid metabolism; OsLEA32, OsAGP24 and OsRHD3 associated with maintaining cellular stability; OsERF064 linked to the ethylene signaling pathway and OsEMF2a, an epigenetic regulator. Additionally, five candidate genes lacking functional annotation were identified for further study.【Conclusion】This study systematically analyzed the molecular regulatory network of rice grain storage using transcriptomics and WGCNA, revealing that rice grain adapts to storage environments through multi-level gene regulatory mechanisms. Core genes within specific modules played pivotal roles in antioxidant activity, nutrient metabolism, membrane stability, and cellular function maintenance. These findings provided a biological basis for delaying rice quality deterioration and offered potential genetic resources for improving rice grain storage stability.

Key words: rice grain (Oryza sativa), quality preservation, transcriptome sequencing, Weighted Gene Co-Expression Network Analysis (WGCNA), core genes

DONG Xue, CHEN MengQiu, SHAO Jin, WU XueYou, TANG PeiAn. Construction of a Differential Gene Expression and Quality Regulation Network in Stored Rice Grain Using WGCNA[J].Scientia Agricultura Sinica, 2025, 58(14): 2885-2903.

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Figures/Tables 14

Table 1

Fig. 1

Fig. 2

Fig. 3

Table 2

Fig. 4

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Table 3

GO functional enrichment of the specific module"

模块 Module		基因数目 Gene number	GO编号 GO ID	类型 Term type	描述 Description	富集因子 Rich factor	P校正值 P-adjust
Brown		5	GO: 0008494	MF	翻译激活剂活性Translation activator activity	0.556	1.10E-04
		5	GO: 0097177	MF	线粒体核糖体结合Mitochondrial ribosome binding	0.417	5.59E-04
		5	GO: 0062125	BP	线粒体基因表达调控 Tegulation of mitochondrial gene expression	0.556	7.26E-04
		5	GO: 0070131	BP	线粒体翻译的正向调控 Positive regulation of mitochondrial translation	0.556	7.26E-04
		5	GO: 0070129	BP	线粒体翻译的调控Tegulation of mitochondrial translation	0.556	7.26E-04
		16	GO:0031974	CC	膜腔Membrane-enclosed lumen	0.083	2.98E-03
Blue		39	GO: 0045735	MF	营养库活动Nutrient reservoir activity	0.351	7.52E-28
		21	GO: 0033095	CC	糊粉粒Aleurone grain	0.600	1.09E-20
		14	GO: 0019865	MF	免疫球蛋白结合Immunoglobulin binding	0.483	1.88E-11
		14	GO: 0019863	MF	IgE 结合IgE binding	0.483	1.88E-11
		29	GO: 0005773	CC	液胞Vacuole	0.092	2.84E-05
		30	GO: 0044042	BP	葡聚糖代谢过程Glucan metabolic process	0.091	6.51E-05
Black		3	GO: 0004865	MF	蛋白丝氨酸/苏氨酸磷酸酶抑制剂活性 Protein serine/threonine phosphatase inhibitor activity	1.000	2.66E-04
		12	GO: 0006869	BP	脂质运输Lipid transport	0.067	1.23E-03
		8	GO: 0009873	BP	乙烯激活信号通路Ethylene-activated signaling pathway	0.094	3.57E-03
		7	GO: 0043621	MF	蛋白质自我结合Protein self-association	0.096	3.79E-03
		4	GO: 0012511	CC	单层环绕脂质贮存体 Monolayer-surrounded lipid storage body	0.400	4.16E-03
		4	GO: 0019915	BP	脂质储存Lipid storage	0.286	6.00E-03
Turquoise		1281	GO: 0005515	MF	蛋白结合Protein binding	0.239	3.23E-53
		841	GO: 0090304	BP	核酸代谢过程Nucleic acid metabolic process	0.260	1.12E-46
		2373	GO: 0043226	CC	细胞器Organelle	0.202	6.33E-43
		2366	GO: 0043229	CC	细胞内细胞器Intracellular organelle	0.202	7.62E-43
		2214	GO: 0043227	CC	膜结合细胞器Membrane-bounded organelle	0.204	7.62E-43
	2207	GO: 0043231	CC	细胞膜内细胞器Intracellular membrane-bounded organelle	0.204	1.55E-42

Table 3

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References 70

[1]	BARTHWAL-DATTA M.. Food security in Asia: Challenges, policies and implications. London: International Institute for Strategic Studies, 2017
[2]	张家秀. 浅谈我国优质稻米产业的现状及其发展. 粮食加工, 2008, 33(3): 49-50, 60.
	ZHANG J X. On the present situation and development of high-quality rice industry in China. Grain Processing, 2008, 33(3): 49-50, 60. (in Chinese)
[3]	宋群, 韦柳利, 王增澔, 陈海鹏, 孙艳春. 粮食储藏环境对储粮害虫影响的研究进展. 中国农学通报, 2024, 40(11): 127-133. doi: 10.11924/j.issn.1000-6850.casb2023-0813
	SONG Q, WEI L L, WANG Z H, CHEN H P, SUN Y C. Effects of grain storage environment on stored grain pests: Research progress. Chinese Agricultural Science Bulletin, 2024, 40(11): 127-133. (in Chinese) doi: 10.11924/j.issn.1000-6850.casb2023-0813
[4]	XIE C, MAO X Z, HUANG J J, DING Y, WU J M, DONG S, KONG L, GAO G, LI C Y, WEI L P. KOBAS 2.0: A web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Research, 2011, 39(suppl_2): W316-W322.
[5]	LIN C J, LI C Y, LIN S K, YANG F H, HUANG J J, LIU Y H, LUR H S. Influence of high temperature during grain filling on the accumulation of storage proteins and grain quality in rice (Oryza sativa L.). Journal of Agricultural and Food Chemistry, 2010, 58(19): 10545-10552.
[6]	周显青, 张玉荣, 赵秋红, 周展明, 卞科, 钟丽玉. 稻谷新陈度的研究(四): 稻谷储藏过程中挥发性物质的变化及其与新陈度的关系. 粮食与饲料工业, 2005(2): 1-3.
	ZHOU X Q, ZHANG Y R, ZHAO Q H, ZHOU Z M, BIAN K, ZHONG L Y. Study on the freshness of paddy (IV): The change of volatile matters during rice storage and its relation with the freshness and aging of rice. Cereal & Feed Industry, 2005(2): 1-3. (in Chinese)
[7]	WANG Q, ZHANG D, ZHAO L Y, LIU J L, SHANG B, YANG W Q, DUAN X L, SUN H. Metabolomic analysis reveals insights into deterioration of rice quality during storage. Foods, 2022, 11(12): 1729.
[8]	HU H, LI S P, PAN D J, WANG K J, QIU M M, QIU Z Z, LIU X Q, ZHANG J J. The variation of rice quality and relevant starch structure during long-term storage. Agriculture, 2022, 12(8): 1211.
[9]	ZHU D W, SHAO Y F, FANG C Y, LI M, YU Y H, QIN Y B. Effect of storage time on chemical compositions, physiological and cooking quality characteristics of different rice types. Journal of the Science of Food and Agriculture, 2023, 103(4): 2077-2087.
[10]	ZHAO C J, XIE J Q, LI L, CAO C J. Comparative transcriptomic analysis in paddy rice under storage and identification of differentially regulated genes in response to high temperature and humidity. Journal of Agricultural and Food Chemistry, 2017, 65(37): 8145-8153. doi: 10.1021/acs.jafc.7b03901 pmid: 28846395
[11]	WANG Y B, WANG Y F, LIU X, ZHOU J Q, DENG H B, ZHANG G L, XIAO Y H, TANG W B. WGCNA analysis identifies the hub genes related to heat stress in seedling of rice (Oryza sativa L.). Genes, 2022, 13(6): 1020.
[12]	许惠滨. 转反义LOX-3基因水稻的耐储藏分子机制研究[D]. 福州: 福建农林大学, 2013.
	XU H B. Molecular mechanism research on rice seed longevity with antisense LOX-3 gene[D]. Fuzhou: Fujian Agriculture and Forestry University, 2013. (in Chinese)
[13]	MA L, ZHU F G, LI Z W, ZHANG J F, LI X, DONG J L, WANG T. TALEN-based mutagenesis of lipoxygenase LOX3 enhances the storage tolerance of rice (Oryza sativa) seeds. PLoS ONE, 2015, 10(12): e0143877.
[14]	LIVAK K J, SCHMITTGEN T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2^-ΔΔCT method. Methods, 2001, 25(4): 402-408.
[15]	KARLOWSKI W M, HIRSCH A M. The over-expression of an alfalfa RING-H2 gene induces pleiotropic effects on plant growth and development. Plant Molecular Biology, 2003, 52(1): 121-133.
[16]	XU R Q, QUINN LI Q. A RING-H2 zinc-finger protein gene RIE1 is essential for seed development in Arabidopsis. Plant Molecular Biology, 2003, 53(1): 37-50.
[17]	BI Y, WANG H, YUAN X, YAN Y Q, LI D Y, SONG F M. The NAC transcription factor ONAC083 negatively regulates rice immunity against Magnaporthe oryzae by directly activating transcription of the RING-H2 gene OsRFPH2-6. Journal of Integrative Plant Biology, 2023, 65(3): 854-875.
[18]	LI Y L, QIN P, SUN A L, XIAO W J, CHEN F L, HE Y, YU K Y, LI Y, ZHANG M, GUO X H. Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.). BMC Genomics, 2022, 23(1): 696.
[19]	TIAN M M, LOU L J, LIU L J, YU F F, ZHAO Q Z, ZHANG H W, WU Y R, TANG S Y, XIA R, ZHU B G, SERINO G, XIE Q. The RING finger E3 ligase STRF1 is involved in membrane trafficking and modulates salt-stress response in Arabidopsis thaliana. The Plant Journal, 2015, 82(1): 81-92.
[20]	THANGASAMY S, CHEN P W, LAI M H, CHEN J, JAUH G Y. Rice LGD1 containing RNA binding activity affects growth and development through alternative promoters. The Plant Journal, 2012, 71(2): 288-302. doi: 10.1111/j.1365-313X.2012.04989.x pmid: 22409537
[21]	SHIMADA T L, SHIMADA T, TAKAHASHI H, FUKAO Y, HARA-NISHIMURA I. A novel role for oleosins in freezing tolerance of oilseeds in Arabidopsis thaliana. The Plant Journal, 2008, 55(5): 798-809.
[22]	MIQUEL M, TRIGUI G, D’ANDRÉA S, KELEMEN Z, BAUD S, BERGER A, DERUYFFELAERE C, TRUBUIL A, LEPINIEC L, DUBREUCQ B. Specialization of oleosins in oil body dynamics during seed development in Arabidopsis seeds. Plant Physiology, 2014, 164(4): 1866-1878.
[23]	WANG X S, ZHU H B, JIN G L, LIU H L, WU W R, ZHU J. Genome-scale identification and analysis of LEA genes in rice (Oryza sativa L.). Plant Science, 2007, 172(2): 414-420.
[24]	WANG H, NIU Q W, WU H W, LIU J, YE J, YU N, CHUA N H. Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits. The Plant Journal, 2015, 84(2): 404-416. doi: 10.1111/tpj.13018 pmid: 26387578
[25]	SUN J Q, WANG W N, ZHENG H Q. ROOT HAIR DEFECTIVE3 is a receptor for selective autophagy of the endoplasmic reticulum in Arabidopsis. Frontiers in Plant Science, 2022, 13: 817251.
[26]	SIMONINI S, BEMER M, BENCIVENGA S, GAGLIARDINI V, PIRES N D, DESVOYES B, VAN DER GRAAFF E, GUTIERREZ C, GROSSNIKLAUS U. The Polycomb group protein MEDEA controls cell proliferation and embryonic patterning in Arabidopsis. Developmental Cell, 2021, 56(13): 1945-1960.
[27]	ZHAO H, YIN C C, MA B, CHEN S Y, ZHANG J S. Ethylene signaling in rice and Arabidopsis: New regulators and mechanisms. Journal of Integrative Plant Biology, 2021, 63(1): 102-125.
[28]	HUANG S Z, MA Z M, HU L J, HUANG K, ZHANG M X, ZHANG S H, JIANG W Z, WU T, DU X L. Involvement of rice transcription factor OsERF19 in response to ABA and salt stress responses. Plant Physiology and Biochemistry, 2021, 167: 22-30. doi: 10.1016/j.plaphy.2021.07.027 pmid: 34329842
[29]	JUNG S E, BANG S W, KIM S H, SEO J S, YOON H B, KIM Y S, KIM J K. Overexpression of OsERF83, a vascular tissue-specific transcription factor gene, confers drought tolerance in rice. International Journal of Molecular Sciences, 2021, 22(14): 7656.
[30]	HSIEH Y S Y, KAO M R, TUCKER M R. The knowns and unknowns of callose biosynthesis in terrestrial plants. Carbohydrate Research, 2024, 538: 109103.
[31]	WANG B, ANDARGIE M, FANG R Q. The function and biosynthesis of callose in high plants. Heliyon, 2022, 8(4): e09248.
[32]	LOCHER K P. Mechanistic diversity in ATP-binding cassette (ABC) transporters. Nature Structural & Molecular Biology, 2016, 23(6): 487-493.
[33]	TAYLOR N L. Targets of stress-induced oxidative damage in plant mitochondria and their impact on cell carbon/nitrogen metabolism. Journal of Experimental Botany, 2003, 55(394): 1-10.
[34]	DVOŘÁKOVÁ-HOLÁ K, MATUŠKOVÁ A, KUBALA M, OTYEPKA M, KUČERA T, VEČEŘ J, HEŘMAN P, PARKHOMENKO N, KUTEJOVA E, JANATA J. Glycine-rich loop of mitochondrial processing peptidase α-subunit is responsible for substrate recognition by a mechanism analogous to mitochondrial receptor Tom20. Journal of Molecular Biology, 2010, 396(5): 1197-1210.
[35]	NAGAO Y, KITADA S, KOJIMA K, TOH H, KUHARA S, OGISHIMA T, ITO A. Glycine-rich region of mitochondrial processing peptidase α-subunit is essential for binding and cleavage of the precursor proteins. Journal of Biological Chemistry, 2000, 275(44): 34552-34556.
[36]	VINSON V. How ribosomes are made. Science, 2020, 369(6510): 1443.
[37]	GONZÁLEZ B, VERA P. Folate metabolism interferes with plant immunity through 1C methionine synthase-directed genome-wide DNA methylation enhancement. Molecular Plant, 2019, 12(9): 1227-1242. doi: S1674-2052(19)30163-7 pmid: 31077872
[38]	HE L, HUANG H, BRADAI M, ZHAO C, YOU Y, MA J, ZHAO L, LOZANO-DURÁN R, ZHU J K. DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development. Nature Communications, 2022, 13: 1335.
[39]	LÓPEZ SÁNCHEZ A, STASSEN J H M, FURCI L, SMITH L M, TON J. The role of DNA (de)methylation in immune responsiveness of Arabidopsis. The Plant Journal, 2016, 88(3): 361-374.
[40]	ZHOU H R, ZHANG F F, MA Z Y, HUANG H W, JIANG L, CAI T, ZHU J K, ZHANG C, HE X J. Folate polyglutamylation is involved in chromatin silencing by maintaining global DNA methylation and histone H3K9 dimethylation in Arabidopsis. The Plant Cell, 2013, 25(7): 2545-2559.
[41]	FAN D M, HU B, LIN L F, HUANG L L, WANG M F, ZHAO J X, ZHANG H. Rice protein radicals: Growth and stability under microwave treatment. RSC Advances, 2016, 6(100): 97825-97831.
[42]	NANDI S, SEN-MANDI S, SINHA T P. Active oxygen and their scavengers in rice seeds (Oryza sativacv. IET 4094) aged under tropical environmental conditions. Seed Science Research, 1997, 7(3): 253-260.
[43]	WANG R L, XIAO L, YANG L S, LU Q. Oxidative stress with the damage of scavenging system: A mechanism for the nutrients loss in rice seeds during post-harvest storage. CyTA - Journal of Food, 2019, 17(1): 260-271.
[44]	BURGE S, KELLY E, LONSDALE D, MUTOWO-MUELLENET P, MCANULLA C, MITCHELL A, SANGRADOR-VEGAS A, YONG S Y, MULDER N, HUNTER S. Manual GO annotation of predictive protein signatures: The InterPro approach to GO curation. Database, 2012, 2012: bar068.
[45]	IVANOVA A, GILL-HILLE M, HUANG S B, BRANCA R M, KMIEC B, TEIXEIRA P F, LEHTIÖ J, WHELAN J, MURCHA M W. A mitochondrial LYR protein is required for complex I assembly. Plant Physiology, 2019, 181(4): 1632-1650. doi: 10.1104/pp.19.00822 pmid: 31601645
[46]	WANG L K, QIAO H. New insights in transcriptional regulation of the ethylene response in Arabidopsis. Frontiers in Plant Science, 2019, 10: 790.
[47]	XIONG F, YU X R, ZHOU L, WANG Z, WANG F, XIONG A S. Structural development of aleurone and its function in common wheat. Molecular Biology Reports, 2013, 40(12): 6785-6792. doi: 10.1007/s11033-013-2795-9 pmid: 24057188
[48]	ZHANG W T, SUN J, ZHAO G X, WANG J G, LIU H L, ZHENG H L, ZHAO H W, ZOU D T. Association analysis of the glutelin synthesis genes GluA and GluB1 in a Japonica rice collection. Molecular Breeding, 2017, 37(10): 129.
[49]	MORITA R, KUSABA M, IIDA S, NISHIO T, NISHIMURA M. Knockout of glutelin genes which form a tandem array with a high level of homology in rice by gamma irradiation. Genes & Genetic Systems, 2007, 82(4): 321-327.
[50]	BLAUTH S L, KIM K N, KLUCINEC J, SHANNON J C, THOMPSON D, GUILTINAN M. Identification of Mutator insertional mutants of starch-branching enzyme1 (sbe1) in Zea mays L. Plant Molecular Biology, 2002, 48(3): 287-297.
[51]	FUJITA N, YOSHIDA M, KONDO T, SAITO K, UTSUMI Y, TOKUNAGA T, NISHI A, SATOH H, PARK J H, JANE J L, MIYAO A, HIROCHIKA H, NAKAMURA Y. Characterization of SSIIIa- deficient mutants of rice: The function of SSIIIa and pleiotropic effects by SSIIIa deficiency in the rice endosperm. Plant Physiology, 2007, 144(4): 2009-2023.
[52]	REVILLA P, GARZÓN R, ROSELL C M, MALVAR R A. Effects of high amylopectin (waxy1) and high-quality protein (opaque2) maize mutants in agronomic performance and bakery quality. Journal of Cereal Science, 2019, 89: 102796.
[53]	TALUKDER Z A, CHHABRA R, BASU S, GAIN N, MISHRA S J, KUMAR A, ZUNJARE R U, MUTHUSAMY V, HOSSAIN F. High amylopectin in waxy maize synergistically affects seed germination and seedling vigour over traditional maize genotypes. Journal of Applied Genetics, 2025, 66(2): 267-278.
[54]	HELMER N, WOLF S, STOCK G. Energy transport and its function in heptahelical transmembrane proteins. The Journal of Physical Chemistry B, 2022, 126(43): 8735-8746.
[55]	VINSON V. A pathway for helical membrane proteins. Science, 2019, 366(6469): 1090.
[56]	WANG Q C, JIANG M Q, ISUPOV M N, CHEN Y Y, LITTLECHILD J A, SUN L F, WU X L, WANG Q, YANG W D, CHEN L F, LI Q, WU Y K. The crystal structure of Arabidopsis BON1 provides insights into the copine protein family. The Plant Journal, 2020, 103(3): 1215-1232.
[57]	HARTL F U. Heat shock proteins in protein folding and membrane translocation. Seminars in Immunology, 1991, 3(1):5-16. pmid: 1680013
[58]	UNGELENK S, MOAYED F, HO C T, GROUSL T, SCHARF A, MASHAGHI A, TANS S, MAYER M P, MOGK A, BUKAU B. Small heat shock proteins sequester misfolding proteins in near-native conformation for cellular protection and efficient refolding. Nature Communications, 2016, 7: 13673. doi: 10.1038/ncomms13673 pmid: 27901028
[59]	ZAMORA-BRISEÑO J A, DE JIMÉNEZ E S. A LEA 4 protein up-regulated by ABA is involved in drought response in maize roots. Molecular Biology Reports, 2016, 43(4): 221-228.
[60]	ZHAO W, YAO F, ZHANG M C, JING T, ZHANG S, HOU L, ZOU X Y. The potential roles of the G1LEA and G3LEA proteins in early embryo development and in response to low temperature and high salinity in Artemia sinica. PLoS ONE, 2016, 11(9): e0162272.
[61]	KIKUCHI S, SATOH K, NAGATA T, KAWAGASHIRA N, DOI K, KISHIMOTO N, YAZAKI J, ISHIKAWA M, YAMADA H, OOKA H, NAGATA T, et al. Collection, mapping, and annotation of over 28, 000 cDNA clones from Japonica rice. Science, 2003, 301(5631): 376-379.
[62]	LIAN J H, NELSON R, LEHNER R. Carboxylesterases in lipid metabolism: From mouse to human. Protein & Cell, 2018, 9(2): 178-195.
[63]	DONG X, SHAO J, WU X Y, DONG J L, TANG P A. Lipidomic profiling reveals the protective mechanism of nitrogen-controlled atmosphere on brown rice quality during storage. Food Chemistry, 2025, 473: 143081.
[64]	GUO Z W, KUNDU S Y. Recent research progress in glycosylphosphatidylinositol-anchored protein biosynthesis, chemical/ chemoenzymatic synthesis, and interaction with the cell membrane. Current Opinion in Chemical Biology, 2024, 78: 102421.
[65]	AZE A, ZHOU J C, COSTA A, COSTANZO V. DNA replication and homologous recombination factors: Acting together to maintain genome stability. Chromosoma, 2013, 122(5): 401-413. doi: 10.1007/s00412-013-0411-3 pmid: 23584157
[66]	KOENIG A M, LIU B, HU J P. Visualizing the dynamics of plant energy organelles. Biochemical Society Transactions, 2023, 51(6): 2029-2040. doi: 10.1042/BST20221093 pmid: 37975429
[67]	MAJERUS P W, CONNOLLY T M, DECKMYN H, ROSS T S, BROSS T E, ISHII H, BANSAL V S, WILSON D B. The metabolism of phosphoinositide-derived messenger molecules. Science, 1986, 234(4783): 1519-1526. pmid: 3024320
[68]	RANCOUR D M, DICKEY C E, PARK S, BEDNAREK S Y. Characterization of AtCDC48. evidence for multiple membrane fusion mechanisms at the plane of cell division in plants. Plant Physiology, 2002, 130(3): 1241-1253.
[69]	HU Y, ZHONG R Q, MORRISON W H, YE Z H. The Arabidopsis RHD3 gene is required for cell wall biosynthesis and actin organization. Planta, 2003, 217(6): 912-921.
[70]	WANG H Y, LEE M M, SCHIEFELBEIN J W. Regulation of the cell expansion gene RHD3 during Arabidopsis development. Plant Physiology, 2002, 129(2): 638-649.

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基因 Genes	基因ID Gene ID	引物序列 Primer sequences（5′-3′)	产物大小 Amplicon size (bp)
EF-la	Os03g0177400	F: AGACCACCAAGTACTACTGCAC	540
EF-la	Os03g0177400	R: CCACCAATCTTGTACACATCC	540
Actin	Os04g0177600	F: AGACTACATACAACTCCATCAT	80
Actin	Os04g0177600	R: CACCACTGAGAACGATGT	80
OsEMF2a	Os04g0162100	F: ACTGCGTATTGTAAGGCTAA	268
OsEMF2a	Os04g0162100	R: CCGATGGCTATTATCAACTTC	268
-	Os12g0467200	F: ATGATGGTGAGGACGATTG	144
-	Os12g0467200	R: AGAAGATGTTGGAAGAAGCA	144
LGD1	Os09g0502100	F: GATGCCTCAGTGAACAATAG	238
LGD1	Os09g0502100	R: TAGTGCCTTCGGTCTCTT	238
-	Os02g0618250	F: GAATCTCCTCTCGGTGTTC	134
-	Os02g0618250	R: TACTTTGGTGCTGGCTTT	134
-	Os01g0212700	F: ACGGTGAGAAGCCAAGAA	144
-	Os01g0212700	R: GGTAGACGAGGAAGGAGAG	144
-	Os01g0342800	F: GAGAACTTCGTCAACTACC	105
-	Os01g0342800	R: GATCGAGTACTTGGAGAGG	105
OsCDAP3	Os07g0162900	F: CGTCTCGTCTCGTCTCAT	135
OsCDAP3	Os07g0162900	R: GGCGATGGATGGATGGAT
-	Os06g0563300	F: ATGAGGCGTCAGATTGTAA	178
-	Os06g0563300	R: CAGCACATGCGATAGAATT	178
OsLTP1.4	Os05g0477900	F: TGTTGGTTCTGGACTTCTG	170
OsLTP1.4	Os05g0477900	R: GATCGGACAAGCACACTT	170
OsC3H27	Os04g0394300	F: CCACAGCCATCTTCTTCC	152
OsC3H27	Os04g0394300	R: TTGGTGTCAGGAGGTAATG	152
OsS40-6	Os04g0413900	F: CCAGATGGTAAGGCAACAA	114
OsS40-6	Os04g0413900	R: CTCACAGTAATATCACACTCAC	114
OsLEA32	Os03g0747500	F: GACGAGGACAGGATCAAG	115
OsLEA32	Os03g0747500	R: ACACCATCCAAGGTTAGC	115

分类 Category	类型 Term type	GO ID GO编号	描述 Description	基因ID Gene ID	基因名 Gene name	功能注释 Gene description
上调 Up-regulate	MF	GO: 0003700	DNA 结合转录因子的活性 DNA-binding transcription factor activity	Os03g0183300	OsERF064	致病相关转录因子和含ERF结构域的蛋白质 Pathogenesis-related transcriptional factor and ERF domain containing protein
				Os01g0313300	OsERF068	类似EREBP-3蛋白（片段） Similar to EREBP-3 protein (Fragment)
				Os01g0657400	OsERF054	类似乙烯反应转录因子5（乙烯反应元件结合因子5） Similar to Ethylene-responsive transcription factor 5 (Ethylene-responsive element binding factor 5)
				Os05g0497300	OsERF074	类似乙烯反应因子2 Similar to Ethylene response factor 2
下调 Down-regulate	MF	GO: 0140657	ATP 依赖性活动 ATP-dependent activity	Os01g0533800	OsGSL4	保守假定性蛋白质 Conserved hypothetical protein
				Os06g0113150	OsGSL1	与 GSL8（GLUCAN SYNTHASE-LIKE 8）相似；1,3-β-葡聚糖合成酶/转移酶，转移糖基 Similar to GSL8 (GLUCAN SYNTHASE-LIKE 8); 1,3-beta-glucan synthase/ transferase, transferring glycosyl groups
				Os02g0832400	OsGSL7	与Callose synthase 1催化亚基相似 Similar to Callose synthase 1 catalytic subunit
				Os06g0728902	OsGSL6	类似预测蛋白质 Similar to predicted protein
	CC	GO: 0098797	质膜蛋白复合体 Plasma membrane protein complex	Os06g0158900	OsABCC15	类似耐多药相关蛋白3 Similar to Multidrug-resistance associated protein 3
				Os06g0184700	OsABCC12	保守假定性蛋白质 Hypothetical conserved gene
				Os03g0859500	OsABCG7	含ABC转运体类结构域的蛋白质 ABC transporter-like domain containing protein

模块 Module	基因数 Number	通路编号 Pathway ID	描述 Description	富集因子 Rich factor	P值 P value	P校正值 P-adjust
Brown	25	map03010	核糖体Ribosome	0.0568182	3.80E-06	0.0002773
Brown	5	map00790	叶酸的生物合成Folate biosynthesis	0.1250000	0.0012465	0.0454974
Black	12	map04141	内质网中的蛋白质加工 Protein processing in endoplasmic reticulum	0.0384615	5.04E-05	0.0028206
Blue	20	map00500	淀粉和蔗糖代谢 Starch and sucrose metabolism	0.0716846	6.45E-05	0.0056143
Turquoise	19	map00563	糖基磷脂酰肌醇（GPI）锚生物合成 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis	0.5428571	1.64E-06	0.0001957
	28	map03440	同源重组Homologous recombination	0.3589744	0.0001526	0.0090771
	43	map03013	核细胞质运输Nucleocytoplasmic transport	0.2885906	0.0009115	0.0180778
	32	map00562	肌醇磷酸盐代谢 Inositol phosphate metabolism	0.3137255	0.0008698	0.0207011

Construction of a Differential Gene Expression and Quality Regulation Network in Stored Rice Grain Using WGCNA

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