Transcriptome Analysis of Rice Bud Stage in Response to Cadmium Stress

doi:10.7668/hbnxb.20193136

Abstract

Abstract:

In order to study the reasons for the differences of different types of rice under cadmium stress,it used the cadmium sensitive indica rice restorer line Changhui 891(CH891)and the cadmium tolerant japonica rice variety 02428 as materials,and selected the buds after seed germination,which were continuously treated with cadmium for 3 days and not treated with cadmium for RNA-Seq analysis using high-throughput Illumina HiSeq 4000 sequencing technology.A total of 539 524 490 valid read were obtained,the comparison rate with the reference genome was between 94.81% and 96.82%,and the GC content was above 49%.Through comparative analysis,a total of 7 204 differentially expressed genes(DEGs)were detected,among which 849 genes were specifically expressed in CH891(SCR3),676 genes were specifically expressed in 02428(RCR3),and 770 genes were expressed in both varieties(CCR3),but the expression level was different.The analysis of enrichment pathways of KEGG and GO showed that isoflavone biosynthesis,inositol phosphate metabolism,flavonoid biosynthesis and anthocyanin biosynthesis were significantly enriched in SCR3.Ribosome,regulation of autophagy and insulin resistance pathways were significantly enriched in RCR3.Alpha-linolenic acid metabolism,phagosome,limonene and pinene degradation and fatty acid degradation pathways were significantly enriched in CCR3.The results showed that after Cd treatment,the secondary metabolic process was mainly enriched in CH891,and the protein metabolism was mainly enriched in 02428.In conclusion,the metabolic pathways of CH891 and 02428 were different after Cd treatment,and the molecular mechanism controlling these metabolic pathways might be the main reason for the differences of cadmium stress in different rice varieties.

Key words: Indica rice, Japonica rice, Cadmium stress, Transcriptome, Differential expression

WANG Yanning, HUANG Tao, WU Guangliang, HUANG Shiying, ZHONG Qi, WANG Peng, YANG Mengmeng, LI Caijing, CHENG Qin, HE Haohua, JIN Wei, GUO Ling, BIAN Jianmin. Transcriptome Analysis of Rice Bud Stage in Response to Cadmium Stress[J]. Acta Agriculturae Boreali-Sinica, 2022, 37(5): 25-35. doi: 10.7668/hbnxb.20193136.

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URL: http://www.hbnxb.net/EN/10.7668/hbnxb.20193136

http://www.hbnxb.net/EN/Y2022/V37/I5/25

Figures/Tables 13

Tab.1 The sequences for qRT-PCR primers

基因名称 Gene name	正向引物(5'—3') F-primer(5'—3')	反向引物(5'—3') R-primer(5'—3')
LOC_Os03g08470	CTGGAGTTCGACCCGTTCAT	TCGAAGCTCCACAGGTTGAC
LOC_Os04g39880	CACCTCAGGCGTTGGAAGAT	AGGCCAGTTGCATAGCCATT
LOC_Os09g36700	TGCCATTGCTGCCAAAGATG	GGACAGGGAAGAGTTGGTGG
LOC_Os10g40720	CAGGTGGATCTCATGGAGGC	GAAAGAACGGTAGACGGCCA
LOC_Os02g02400	GGACGAGGAGGTGGACTACT	TGCTTGTGTATCGTCGCCTT
LOC_Os04g33830	TTTCCGCAGGACTGGCTTAG	GAGAAGAAGAGCCCCGTGAG
LOC_Os06g21590	ATGGAGAAGGACCCCGAGAA	ACGCAGAAACCCACAAAAGC
LOC_Os09g31430	TGAGGGCGCCTACAAAGAAG	GGAGAACCGGAAAGCATCCA
LOC_Os01g18744	CGATTCCCTGTTCGTCTCCG	TGAACGGGTAGTACGCGAAG
LOC_Os06g13280	GTTGGGGAGAGGAGGATTGC	CAGACCCGACCACCGTATTT
LOC_Os03g03600	CAAGCAGATGCCGTACAAGC	TCCTCGAACGTCTTGAGCAC
LOC_Os08g06110	GAGGGTCGTCTGGCTTTTGA	ACCGTCACCGTGGTTACTTC

Fig.1 CH891 and 02428 performance under different treatment conditions A.Control treatment;B.Cadmium treatment;C.Seedling height;Different lowercase letters indicate that the seedling height of the treatment group is significantly different from that of the control group(P<0.05).

Tab.2 Sequencing data statistics and mapped ratios to the reference genome

样本 Sample	原始测序读长 Raw read	原始测序数据/G Raw base	有效测序读长 Vaild read	有效数据/G Valid base	有效读长占比/% Valid ratio	Q20/%	Q30/%	GC含量/% GC content	匹配读长 Mapped reads	唯一匹配读长 Unique Mapped reads
CK_02428_A	45 696 550	6.85	45 295 626	6.79	99.12	99.75	97.20	51.0	43 662 999(96.40%)	29 723 198(65.62%)
CK_02428_B	43 930 280	6.59	43 488 498	6.52	98.99	99.73	97.14	49.0	41 938 316(96.44%)	32 091 614(73.79%)
CK_02428_C	47 475 320	7.12	47 064 332	7.06	99.13	99.71	97.09	50.0	45 444 073(96.56%)	34 732 722(73.80%)
Cd_02428_A	45 814 010	6.87	45 396 612	6.81	99.09	99.62	96.82	50.0	43 807 260(96.50%)	33 435 746(73.65%)
Cd_02428_B	38 458 390	5.77	38 150 196	5.72	99.20	99.74	97.21	50.0	36 936 246(96.82%)	28 311 301(74.21%)
Cd_02428_C	43 063 576	6.46	42 676 692	6.40	99.10	99.70	96.94	49.5	41 266 571(96.70%)	31 487 488(73.78%)
CK_CH891_A	46 690 704	7.00	46 101 030	6.92	98.74	99.74	97.36	49.5	43 707 017(94.81%)	29 993 285(65.06%)
CK_CH891_B	57 839 194	8.68	56 921 950	8.54	98.41	99.75	97.56	50.0	53 993 658(94.86%)	35 354 036(62.11%)
CK_CH891_C	40 120 618	6.02	39 672 946	5.95	98.88	99.74	97.44	50.0	37 650 255(94.90%)	26 731 113(67.38%)
Cd_CH891_A	50 374 398	7.56	49 926 492	7.49	99.11	99.76	97.37	51.0	47 493 447(95.13%)	34 023 070(68.15%)
Cd_CH891_B	41 353 200	6.20	40 980 030	6.15	99.10	99.73	97.21	50.0	38 855 388(94.82%)	27 810 209(67.86%)
Cd_CH891_C	44 193 960	6.63	43 850 086	6.58	99.22	99.72	97.27	51.0	41 624 578(94.92%)	29 506 145(67.29%)

Fig.2 DEGs in all comparison groups A,B,C and D.Volcano plot;E.The number of up and down-regulated DEGs.

Fig.3 Comparison of differentially expressed gene transcriptome and qRT-PCR results

Fig.4 Venn diagrams for DEGs in the four comparison groups

Tab.3 Classification of three categories of DEGs

分类 Categories	亚组 Subgroups	差异表达基因数 Number of DEGs
SCR3	仅Cd3_CH891vs.CK3_CH891、	715
	Cd3_CH891vs.CK3_CH891、Cd3_CH891vs.Cd3_02428	134
RCR3	仅Cd3_02428vs.CK3_02428、	565
	Cd3_02428vs.CK3_02428、Cd3_CH891vs.Cd3_02428	111
CCR3	仅Cd3_CH891vs.Cd3_02428	506
	Cd3_CH891vs.CK3_CH891、Cd3_02428vs.CK3_02428、	253
	Cd3_CH891vs.CK3_CH891、Cd3_02428vs.CK3_02428、	11
	Cd3_CH891vs.Cd3_02428

Fig.5 The GO enrichment of differentially expressed genes in SCR3 1.Biological process;2.Regulation of transcription,DNA-templated;3.Transcription,DNA-templated;4.Protein phosphorylation;5.Metabolic process;6.Response to wounding;7.Oxidation-reduction reaction;8.Response to abscisic acid;9.Response to brassinosteroid;10.Lipid transport;11.Response to hypoxia;12.Protein ubiquitination;13.Proteasome-mediated ubiquitination-dependent catabolic process;14.Response to cold;15.Multicellular organism development;16.Embryo development ending in seed dormancy;17.Leaf development;18.Response to light stimulation reaction;19.Protein folding;20.Flavonold glucuronidation;21.Exocytosis;22.Secondary metabolic biosynthesis;23.Defense response;24.Response to gibberellin;25.Methylation;26.Nucleus;27.Integral component of membrane;28.Plasma membrane;29.Cytoplasm;30.Extracellular region;31.Cytosol;32.Chloroplast;33.Membrane;34.Golgi apparatus;35.Mitochondrion;36.Cell wall;37.Plant-type cell wall;38.Endoplasmic reticulum;39.Anchored components of plasma membrane;40.Plasmodesmata;41.Molecular function;42.RNA binding;43.Transcription factor activity,sequence-specific DNA binding;44.Metal ion binding;45.Protein binding;46.ATP binding;47.Carboxylic ester hydrolase;48.Protein serine/threonine kinase activity;49.Zinc ion binding;50.Hydrolase activity.

Fig.6 The KEGG enrichment of differentially expressed genes in SCR3 1.Alpha-Linolenic acid metabolism;2.Terpenoid backbone biosynthesis;3.Steroid biosynthesis;4.Starch and sucrose metabolism;5.Sesquiterpenoid and triterpenoid biosynthesis;6.Regulation of autophagy;7.RNA polymerase;8.RNA degradation;9.Pyrimidine metabolism;10.Porphyrin and chlorophyll metabolism;11.Plant hormone signal transduction;12.Photosynthesis;13.Phosphatidylinositol signaling system;14.Phenylpropanoid biosynthesis;15.Phenylalanine,tyrosine and tryptophan biosynthesis;16.Pentose phosphate pathway;17.N-Glycan biosynthesis;18.Isoflavonoid biosynthesis;19.Inositol phosphate metabolism;20.Glycosylphosphatidylinositol(GPI)-anchor biosynthesis;21.Glucosinolate biosynthesis;22.Flavonoid biosynthesis;23.Ether lipid metabolism;24.Diterpenoid biosynthesis;25.Cutin,suberine and wax biosynthesis;26.Carotenoids;27.Carbon fixation in photosynthetic organisms;28.Biosynthesis;29.Base excision repair;30.Anthocyanin biosynthesis.

Fig.7 The GO enrichment of differentially expressed genes in RCR3 1.Biological process;2.Regulation of transcription,DNA-template;3.Transcription,DNA-template;4.Oxidation-reduction reaction;5.Defense response;6.Protein phosphorylation;7.Cell wall organization;8.Response to abscisic acid;9.Response to wounding;10.Response to salt stress;11.Proteolysis;12.Multicellular organism development;13.Undimensional cell growth;14.Response to oxidative stress;15.Response to cold;16.Strigolactone biosynthetic process;17.Response to jasmonic acid;18.Proteasome-mediated ubiquitination-dependent catabolic process;19.Signal transduction;20.Lipid transport;21.Flavonoid biosynthetic process;22.Response to Karikin;23.Plant-type cell wall modification involved in multidimensional cell growth;24.Protein transport;25.Vesicle docking involved in exocytosis;26.Nucleus;27.Plasma membrane;28.Integral component of membrane;29.Extracellular region ;30.Cytoplasm;31.Mitochondria;32.Membrane;33.Chloroplast;34.Cytosol;35.Plasmodesmata;36.Cell wall;37.Cellular components;38.Vacuole;39.Plant-type cell wall;40.Intracellular membrane-bounded organelle;41.Molecular function;42.Transcription factor activity,sequence-specific DNA binding;43.Protein binding;44.DNA binding;45.Protein serine/Threonine kinase activity;46.ATP binding;47.Metal ion binding;48.Kinase activity;49.Structural constituent of ribosome;50.Zinc ion binding.

Fig.8 The KEGG enrichment of differentially expressed genes in RCR3 1.mRNA surveillance pathway;2.Beta-Alanine metabolism;3.Zeatin biosynthesis;4.Valine,leucine and isoleucine degradation;5.SNARE interactions in vesicular transport;6.Ribosome;7.Regulation of autophagy;8.Propanoate metabolism;9.Plant-pathogen interaction;10.Plant hormone signal transduction;11.Phenylpropanoid biosynthesis;12.Phenylalanine,tyrosine and tryptophan biosynthesis;13.Pentose phosphate pathway;14.Oxidative phosphorylation;15.Other types of O-glycan biosynthesis;16.Other glycan degradation;17.N-glycan biosynthesis;18.Insulin resistance;19.Glycosylphosphatidylinositol(GPI)-anchor biosynthesis;20.Glycolysis/Gluconeogenesis;21.Fructose and mannose metabolism;22.Diterpenoid biosynthesis;23.Cutin,suberine and wax biosynthesis;24.Citrate cycle(TCA cycle);25.Carotenoid biosynthesis;26.Carbon metabolism;27.Base excision repair;28.Ascorbate and aldarate metabolism;29.Arginine and proline metabolism;30.Anthocyanin biosynthesis.

Fig.9 The GO enrichment of differentially expressed genes in CCR3 1.Regulation of transcription,DNA-template;2.Biological process;3.Transcription,DNA-template;4.Response to wounding;5.Protein ubiquitination;6.Oxidation-reduction reaction;7.Response to cold;8.Response to abscisic acid;9.Response to salicylic acid;10.Oligopeptide transport;11.Defense response;12.Response to oxidative stress;13.Fatty acid biosynthetic process;14.Response water dehydration;15.Protelysis involved in cellular protein catabolic process;16.Response to light stimulus;17.Undimensional cell growth;18.Acetylen-activated signaling pathway;19.Gibberellic acid mediated signaling transduction;20.Secondary metabolic biosynthesis;21.Salt stress reaction;22.Chitin reaction;23.Regulating the defense response;24.Other organic reactions;25.Lignin biosynthetic process;26.Nuclus;27.Cytoplasm;28.Integral component of membrane;29.Plasma membrane;30.Membrane;31.Chloroplast;32.Intracellular;33.Extracellular region;34.Mitochondria;35.Anchored components of plasma membrane;36.Cytosol;37.Golgi apparatus;38.Plastid;39.Chloroplast stroma;40.Cell wall;41.Transcription factor activity,sequence-specific DNA binding;42.Molecular function;43.Protein binding;44.DNA binding;45.Zinc ion binding;46.Sequence-specific DNA binding;47.Transporter activity;48.Transferase activity,transferring glycoayl groups;49.Ubiquitin-protein transferase activity;50.Transcription regulatory region DNA binding.

Fig.10 The KEGG enrichment of differentially expressed genes in CCR3 1.Alpha-Linolenic acid metabolism;2.Valine,leucine and isoleucine degradation;3.Stilbenoid,diarylheptanoid and gingerol biosynthesis;4.Plant-pathogen interaction;5.Phagosome;6.Peroxisome;7.Nicotinate and nicotinamide metabolism;8.N-Glycan biosynthesis;9.Lysine degradation;10.Linoleic acid metabolism;11.Limonene and pinene degradation;12.Isoflavonoid biosynthesis;13.Glycophospholipid biosynthesis-globo series;14.Glycophospholipid biosynthesis-ganglio series;15.Glycolysis/Gluconeogenesis;16.Glycine,serine and threonine metabolism;17.Glycerophospholipid metabolism;18.Galactose metabolism;19.Fatty acid elongation;20.Fatty acid degradation;21.Fatty acid biosynthesis;22.Diterpenoid biosynthesis;23.Cutin,suberine and wax biosythesis;24.Citrate cycle(TCA cycle);25.Circadian rhythm-plant;26.Carbon metabolism;27.Brassinosteroid biosynthesis;28.Arginine biosynthesis;29.Aminoacyl-tRNA biosynthesis;30.Alanine,aspartate and glutamate metabolism.

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