Transcriptome-based Identification of Key Genes Involved in Drought Stress Response in Flax

doi:10.7668/hbnxb.20196084

Abstract

Abstract:

In order to uncover key genes involved in flax's response to drought stress and elucidate the underlying molecular mechanisms,thereby providing theoretical support for breeding drought-resistant varieties.Using roots of the drought-resistant flax cultivar Tianya 13 as experimental material,drought stress was simulated with different concentrations(5%,10%,20%,30%)of polyethylene glycol(PEG).Based on the analysis of physiological indicators such as root length,root thickness,and dry/fresh weight ratio,20% PEG was identified as the optimal stress concentration,under which the above indicators were significantly reduced by 31.63%,30.50%,and 13.39 percentage points,respectively,compared to the control.Subsequently,Illumina transcriptome sequencing was performed on roots subjected to drought stress at different time points(8,16,24 h),identifying 5 428,5 304,and 3 603 differentially expressed genes(DEGs)at each time point,respectively.KEGG enrichment analysis revealed that these DEGs were significantly enriched in key pathways such as carbohydrate metabolism(12 genes),betaine biosynthesis(4 genes),and the antioxidant defense system(36 genes).qRT-PCR validation of selected DEGs confirmed expression trends consistent with the RNA-seq results,verifying data reliability.This study systematically reveals,that flax enhances drought tolerance through the coordinated regulation of osmotic adjustment substance(e.g.,betaine)synthesis,energy metabolism reprogramming(carbohydrate metabolism),and reactive oxygen species scavenging mechanisms.It provides important theoretical foundations and candidate gene resources for molecular design breeding in flax.

Key words: Flax, Drought stress, Transcriptomics, Drought resistance genes

CLC Number:

S188
S565

HE Li, FU Dandan, DOU Chenxi, WANG Na, LI Jun. Transcriptome-based Identification of Key Genes Involved in Drought Stress Response in Flax[J]. Acta Agriculturae Boreali-Sinica, 2026, 41(4): 99-111. doi: 10.7668/hbnxb.20196084.

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URL: http://www.hbnxb.net/EN/10.7668/hbnxb.20196084

http://www.hbnxb.net/EN/Y2026/V41/I4/99

Figures/Tables 12

Tab.1 Assessment of the quality associated with 12 samples

样本名称 Sample name	原始序列数 Raw reads	过滤后序列数 Clean reads	过滤后碱基/Gb Clean bases	错误率/% Error rate	Q20/%	Q30/%	GC 含量/% GC content
CK_1	11763638	11585163	0.58	0.01	98.29	96.23	48.99
CK_2	12186381	11994323	0.60	0.01	98.27	96.19	49.65
CK_3	12066987	11844725	0.60	0.01	98.07	96.11	49.21
TY8 h_1	10575274	10392565	0.52	0.01	98.10	95.81	49.41
TY8 h_2	10807289	10703269	0.54	0.01	98.28	96.21	49.44
TY8 h_3	10617452	10604433	0.53	0.01	98.16	96.02	49.42
TY16 h_1	11176167	11071109	0.55	0.01	98.28	96.21	49.75
TY16 h_2	10278785	10169417	0.51	0.01	98.03	95.60	49.72
TY16 h_3	10843682	10665422	0.51	0.01	98.03	95.60	49.74
TY24 h_1	11987425	11817837	0.59	0.01	98.42	96.53	49.45
TY24 h_2	10456025	10401224	0.52	0.01	99.08	98.19	49.27
TY24 h_3	10823044	10772827	0.55	0.01	99.22	97.45	49.36

Tab.2 qRT-PCR primer sequences for 16 DEGs

基因编号 Gene ID	上游引物(5'—3') Forward primer(5'—3')	下游引物(5'—3') Reverse primer(5'—3')
SDH1	GGCGAACTTCATGTTTGCG	CGCAAACATGAATTCGCC
PetF	TCTGATCATGGCAAAGTCAACA	TAACTGTCCCCCCAGTTAAAGA
TYR	CTACGACATCGATGTCGC	GCGACATCGATGTCGTAG
fumB	TCTTGGCAGCAATTCGCA	TGCGAATTGCTGCCAAGA
5GT	CGTACTGCAACTTCGACA	TGTCGAAGTTGCAGTACG
CCD32	GAACAAGGTCGGCGAAAT	TAAACTGGCCGTTGGTCC
SUCD1	GGTCAGCGACTATCAAGCTG	CAGCTTGATAGTCGCTGACC
APX4	AGGACCATGTACGAATAGATGA	CTTAGGTAACACCACCTCTT
GST4	TCTACTATGGTTAAGATGA	TCATCTTAACCATAGTAGA
bHLH63	GCGTGGCTTCTCTCTGTG	CGCACGATGCCAGAACC
SOD-Mn	CCTGGTTGCCAATCAGGC	GCCTGATTGGCAACCAGG
ERF71	GGAAGCTGTCCAATGGAAT	GGGCATCGACCATCTAGGTA
WRKY49	AGGACCATGTACGAATGATA	CTAAGGTAACACCATCTCAT
CDOPA-O	ACTTCTATGGCCTACTCGAG	TGAAGATACCGGATGAGCTC
CHI1	TGTCATCATGGCAAGTCACT	ATCTGTCCCCAGTTATACA
PetE	CTCACTCCGAACCTGTCTT	AAGACAGGTTCGGAGTGAG

Fig.1 Effects of different concentrations of PEG on root length,root thickness,root dry to fresh weight ratio of Tianya 13 seedlings Different lowercase letters are significantly different(P<0.05).The same as Fig.8.

Fig.2 DEGs in roots at different time points following drought stress A.Venn plots of TY8 h vs CK,TY16 h vs CK,and TY24 h vs CK DEGs under 20% PEG treatment,with 0 h as control(CK);B.Expression profiles of DEGs in Flax root system after drought stress at 8,16,24 h were plotted by using heatmap;C—J.Analysis of different temporal expression patterns of DEGs in Flax root system after drought stress by using STEM software.Different temporal expression patterns of DEGs in the root system.Each expression profile was represented using a different graphical representation.Data were normalised using log₂ with a false discovery rate(FDR)<0.05.

Fig.3 GO and KEGG analysis of DEGs under drought stress A,B,and C are bar charts showing the GO enrichment of DEGs for the comparisons 8 h vs CK,16 h vs CK,and 24 h vs CK,respectively.The vertical axis represents the enriched GO terms,and the horizontal axis represents the number of DEGs within each term.*.Significantly enriched.A:1.Metabolic process;2.Biological regulation;3.Organic substance metabolic process;4.Biosynthetic process;5.Cellular biosynthetic process;6.Oxidation-reduction process;7.Organic nitrogen compound biosynthetic process;8.Cellular nitrogen compound biosynthetic process;9.Organic substance metabolic process;10.Organic nitrogen compound metabolic process;11.Single-organism metabolic process;12.Amide biosynthetic process;13.Transcription,DNA-templated;14.Cellular metabolic process;15.Primary metabolic process;16.Peptide biosynthetic process;17.Cellular amide metabolic process;18.Peptide metabolic process;19.Macromolecule biosynthetic process;20.Cellular macromolecule biosynthetic process;21.Cellular process;22.Ribosome;23.Ribonucleoprotein complex;24.Non-membrane-bounded organelle;25.Intracellular non-membrane-bounded organelle;26.Cytoplasm;27.Structural constituent of ribosome;28.Oxidoreductase activity;29.Structural molecule activity;30.Sequence-specific DNA binding.B:1.Oxidation-reduction process;2.Carbohydrate caetabolic process;3.Potassium ion transport;4.Intracellular carbohydrate metabolic process;5.Metabolic process;6.Single-organism metabolic process;7.Metal ion transport;8.Biological process;9.Polysaccharide metabolic process;10.Cell projection organization;11.Carbohydrate catabolic process;12.Quinone metabolic process;13.Quinone biosynthetic process;14.Disaccharide biosynthetic process;15.Cell projection part;16.ATP synthase complex;17.Cell-type specific flagellum part;18.Oxidoreductase activity;19.Hydrolase activity;20.Hydrolase activity,hydrolyzing O-glycosyl compounds;21.Phosphotransferase activity;22.Amylase activity;23.Molecular function;24.ATPase activity,coupled;25.Antagonist activity;26.Transition metal ion binding;27.Beta-amylase activity;28.ATP synthase;29.Catalytic activity;30.Actin monomer binding.C:1.Oxidation-reduction process;2.Single-organism metabolic process;3.Single-organism process;4.Carbohydrate metabolic process;5.Carbohydrate catabolic process;6.Purine nucleoside triphosphate metabolic process;7.Nucleoside triphosphate metabolic process;8.Purine ribonucleoside triphosphate metabolic process;9.Biological process;10.Quinone metabolic process;11.Quinone biosynthetic process;12.Nucleoside monophosphate metabolic process;13.ATP metabolic process;14.Ribonucleoside triphosphate metabolic process;15.Potassium ion transport;16.Polysaccharide metabolic process;17.Purine nucleoside monophosphate metabolic process;18.Purine ribonucleoside monophosphate metabolic process;19.External encapsulating structure;20.Oxidoreductase activity;21.Heme binding;22.Phosphoglycerate mutase activity;23.Tetrapyrrole binding;24.Hydrolase activity,hydrolyzing O-glycosyl compounds;25.Copper ion binding;26.2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity;27.Hydrolase activity;28.Proton-transporting ATPase complex;29.Iron ion binding;30.ATPase activity.D,E,and F are scatter plots showing the KEGG enrichment of DEGs for the comparisons 8 h vs CK,16 h vs CK,and 24 h vs CK,respectively.The size of the dots indicates the number of differentially expressed genes in that pathway,and the color of the dots corresponds to different Q-value ranges.D:1.Metabolism;2.Terpenoid backbone biosynthesis;3.Stilbenoid,diarylheptanoid and gingerol biosynthesis;4.Starch and sucrose metabolism;5.Sphingolipid metabolism;6.Ribosome;7.Phenylpropanoid biosynthesis;8.Phenylalanine metabolism;9.Metabolic pathways;10.Glutathione metabolism;11.Glucosinolate biosynthesis;12.Flavonoid biosynthesis;13.Fatty acid degradation;14.Diterpenoid biosynthesis;15.Degradation of aromatic compounds;16.Cysteine and methionine metabolism;17.Circadian rhythm-plant;18.Brassinosteroid biosynthesis;19.Biosynthesis of secondary metabolites;20.alpha-Linolenic acid metabolism.E:1.Vitamin B6 metabolism;2.Ubiquinone and other terpenoid-quinone biosynthesis;3.Peroxisome;4.Biosynthesis of alkaloids derived from ornithine,lysine and nicotinic acid;5.Thiamine metabolism;6.Starch and sucrose metabolism;7.Protein processing in endoplasmic reticulum;8.Photosynthesis-antenna proteins;9.Phenylalanine metabolism;10.Pentose and glucuronate interconversions;11.Betalain biosynthesis;12.Glucosinolate biosynthesis;13.Flavonoid biosynthesis;14.Diterpenoid biosynthesis;15.Cysteine and methionine metabolism;16.Circadian rhythm-plant;17.Carbon fixation in photosynthetic organisms;18.Biosynthesis of secondary metabolites;19.beta-Alanine metabolism;20.alpha-Linolenic acid metabolism.F:1.Ubiquinone and other terpenoid-quinone biosynthesis;2.Tyrosine metabolism;3.Biosynthesis of alkaloids derived from ornithine,lysine and nicotinic acid;4.Starch and sucrose metabolism;5.Protein processing in endoplasmic reticulum;6.Betalain biosynthesis;7.Phenylpropanoid biosynthesis;8.Phenylalanine metabolism;9.Pentose and glucuronate interconversions;10.Isoquinoline alkaloid biosynthesis;11.Ascorbate and aldarate metabolism;12.Glucosinolate biosynthesis;13.Flavonoid biosynthesis;14.Diterpenoid biosynthesis;15.Cysteine and methionine metabolism;16.Circadian rhythm-plant;17.Carbon fixation in photosynthetic organisms;18.Peroxisome;19.Arginine and proline metabolism;20.alpha-Linolenic acid metabolism.

Fig.4 DEGs are involved in carbohydrate metabolism process under drought stress The squares.Expression of DEGs,where the left side represents the expression of DEGs in the 8 h vs CK comparison group;the middle represents the expression of DEGs in the 16 h vs CK comparison group;and the right side represents the expression of DEGs in the 24 h vs CK comparison group.

Fig.5 Analysis of DEGs related to betaine synthesis in flax under drought stress Circles.Metabolites regulated under drought stress;Rectangles.Genes regulated by drought stress(where red indicates up-regulation;blue indicates down-regulation);The three squares.Expression levels of each gene under the conditions of 8,16,and 24 h respectively.

Fig.6 Linear relationship graph of key genes in betaine biosynthesis pathway and betaine content at different times

Fig.7 Clustered heatmaps of antioxidant molecules and GPX candidate genes at four different time points(0,8,16,24 h) After centralised correction,the value of log₂(TPM+1)indicates the expression level,where genes with similar expression patterns are clustered.

Fig.8 Validation of 16 drought stress-responsive DEGs in flax by qRT-PCR Actin was used as an internal reference gene;Y-axis indicates normalised expression of DEGs after log₂ transformation.

Tab.3 Validation of RNA-seq and qPCR results

基因编码 Gene ID	基因 Gene	FPKM (CK)	FPKM (8)	FPKM (16)	FPKM (24)	8 h vs CK	16 h vs 8 h	24 h vs 16 h
Lus_GLEAN_10000016	SDH1	56.45	103.03	121.24	149.64	上调	上调	上调
Lus_GLEAN_10000033	PetF	23.04	62.73	48.53	89.61	上调	下调	上调
Lus_GLEAN_10000019	TYR	65.49	176.98	40.55	107.64	上调	下调	上调
Lus_GLEAN_10000160	fumB	65.55	72.99	43.88	56.11	上调	上调	下调
Lus_GLEAN_10000376	5GT	100.87	120.66	140.77	24.55	上调	上调	下调
Lus_GLEAN_10000519	CCD32	169.77	122.92	78.98	44.32	下调	下调	下调
Lus_GLEAN_10000561	SUCD1	44.21	78.76	42.44	44.89	上调	下调	下调
Lus_GLEAN_10000711	APX4	56.67	180.88	66.43	69.21	上调	下调	下调
Lus_GLEAN_10000842	GST4	124.32	98.76	134.67	34.55	下调	上调	下调
Lus_GLEAN_10000666	bHLH63	29.88	54.44	87.66	40.98	上调	上调	下调
Lus_GLEAN_10001270	SOD-Mn	38.54	98.87	66.23	60.98	上调	下调	下调
Lus_GLEAN_10001140	ERF71	30.45	56.66	90.34	112.32	上调	上调	上调
Lus_GLEAN_10001414	WRKY49	58.65	26.54	79.45	38.45	下调	上调	下调
Lus_GLEAN_10000945	CDOPA-O	47.66	53.66	62.67	91.77	上调	上调	上调
Lus_GLEAN_10001332	CHI1	24.34	39.67	53.44	75.44	上调	上调	上调
Lus_GLEAN_10001514	PetE	46.45	92.03	111.24	150.64	上调	上调	上调

Fig.9 Expression levels of 16 key genes in aerial and subterranean part

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