低温胁迫条件下大豆萌发期转录组分析

doi:10.7668/hbnxb.20195302

摘要/Abstract

摘要：

大豆萌发阶段遭受低温胁迫会对产量造成巨大影响。为挖掘大豆萌发期低温胁迫响应相关基因,探究大豆萌发期耐低温的生物学过程,对8个萌发期低温耐性存在显著差异材料萌发3 d的种子进行了转录组测序。筛选耐低温材料与低温敏感材料间差异表达基因(DEGs),并对差异表达基因进行GO富集分析、KEGG富集分析和转录因子分析。在15个低温耐性差异对比组中筛选到231个共有差异表达基因,其中159个DEGs在冷敏感大豆中表达上调,72个DEGs在冷敏感大豆中表达下调。GO富集分析结果显示,DEGs主要集中在细胞过程(GO:0009987)、代谢过程(GO:0008152)、生物调节过程(GO:0065007)、对刺激的反应(GO:0050896)、结合(GO:0005488)、转运蛋白活性(GO:0005215)和转录调节剂活性(GO:0140110)等生物学过程。KEGG富集通路分析发现,DEGs主要富集在淀粉和蔗糖代谢通路(ko00500)。参与种子发育的基因Glyma.03G144400、Glyma.19G147200、Glyma.10G027600、Glyma.10G247500、Glyma.20G147600,参与代谢反应的基因Glyma.05G004300、Glyma.17G086400和编码谷胱甘肽氧化酶的基因Glyma.01G219400均在冷敏感材料中上调。在231个差异表达基因中共鉴定出15个转录因子,属于MYB、AP2/ERF、NAC等转录因子家族。说明大豆通过调节多种生物学过程、物质代谢和信号传导来应对萌发期低温胁迫。

关键词: 大豆, 萌发期, 低温胁迫, 转录组, 候选基因

Abstract:

The soybean germination stage is greatly affected by low-temperature stress,which can have a significant impact on yield.In order to explore genes related to the response of soybean germination to low-temperature stress and investigate the biological processes underlying soybean germination tolerance to cold,this study conducted transcriptome sequencing on seeds germinating for three days from eight materials showing significant differences in low-temperature tolerance during germination.Differential expressed genes (DEGs) between materials tolerant and sensitive to low temperatures were identified and subjected to GO enrichment analysis,KEGG pathway enrichment analysis,and transcription factor analysis.Among 231 DEGs identified in 15 contrasting groups of low-temperature tolerance,159 DEGs were up-regulated and 72 DEGs were down-regulated in cold-sensitive soybeans.GO enrichment analysis revealed that DEGs were mainly involved in biological processes such as cellular processes (GO:0009987),metabolic processes (GO:0008152),biological regulation (GO:0065007),response to stimulus (GO:0050896),binding (GO:0005488),transporter activity (GO:0005215),and transcription regulator activity (GO:0140110).KEGG pathway enrichment analysis indicated that DEGs were significantly enriched in starch and sucrose metabolism pathways (ko00500).Genes involved in seed development (Glyma.03G144400, Glyma.19G147200,Glyma.10G027600,Glyma.10G247500,Glyma.20G147600),metabolic reactions (Glyma.05G004300,Glyma.17G086400),and genes encoding glutathione oxidase (Glyma.01G219400) were up-regulated in cold-sensitive materials.Fifteen transcription factors from families such as MYB,AP2/ERF,and NAC were identified among the 231 differentially expressed genes,suggesting that soybeans respond to low-temperature stress during germination by regulating various biological processes,metabolic pathways,and signal transduction pathways.

Key words: Soybean, Germination stage, Low temperature stress, Transcriptome, Candidate gene

中图分类号:

S565.1

陈玥含, 魏玉, 冯燕, 赵丽, 闫龙, 杨庆, 刘智. 低温胁迫条件下大豆萌发期转录组分析[J]. 华北农学报, 2025, 40(6): 11-20. doi: 10.7668/hbnxb.20195302.

CHEN Yuehan, WEI Yu, FENG Yan, ZHAO Li, YAN Long, YANG Qing, LIU Zhi. Transcriptome Analysis of Germinating Soybeans under Low Temperature Stress[J]. Acta Agriculturae Boreali-Sinica, 2025, 40(6): 11-20. doi: 10.7668/hbnxb.20195302.

http://www.hbnxb.net/CN/Y2025/V40/I6/11

图/表 12

表1 实时荧光定量引物

Tab.1 qRT-PCR primers

基因名称 Gene name	正向引物(5'—3') Forward primer(5'—3')	反向引物(5'—3') Reverse primer(5'—3')
Glyma.01G156600	TGGAAGAACCTCTTATCGAAGGC	GTTTGGTCTTGTGGATCTGAACG
Glyma.02G047200	TGAACCAGTTCTTCGGGTACAG	CGTGAATTCCCATTTTGTGCCT
Glyma.05G033400	TCATTGCACTTACAACCGCAAG	CATAGATCCGCCTCCTCTCAAC
Glyma.05G198000	CAGAGGCGAAAGATTGCTTGAC	ACTGACCACCGATGAAACCATC
Glyma.09G072200	GCAAACACCCTTAAATCCGC	CTGTTGCGCTCTCTGTTGAG
Glyma.11G208700	TCAACAACACACAGAAGGGGT	ACAGAAGAAGATGTCGAGGAAGA
Glyma.13G092500	GGCGACAATCAAGACTCCG	AATCCTTATCCCTGCCGCTC
Glyma.17G086400	GTCAGGCCCAGGAAACAGTC	TGCTACGCTTTCTTTGTGGG
Glyma.19G227800	CCTGATAAGGTTCAATGGCCCT	CAAAAGAAGTGGGCTTGGTGAG
Glyma.02G304500	GCTTCTTCGCGTTCATCGAAT	GACCGATTTTTGGTGCGAATG
Glyma.10G262900	CCCTTCTTTGGCTCCTCTTCTT	GCTGAGAACTTTGTTGAGGCTG
Glyma.13G328600	GTTGGGGTGGAAGGAGTACG	TTGAATCCCCGGTATGCACC
Glyma.14G137100	GAACGGTAAGCAGAAGAAACGG	ACATTGTCAAACTCTTTCGGCG
Glyma.16G058100	AATGAGTTTTGCTGCCTTGACC	TGAAGGGTTGATGTTTCTGCCT
ACTIN	CGGTGGTTCTATCTTGGCATC	GTCTTTCGCTTCAATAACCCTA

图1 8个大豆品种3 ℃萌发表型不同字母表示0.05水平差异显著。图8同。

Fig.1 The germination phenotype of eight soybean varieties under 3 ℃ Different letters indicate a significant differential level of 0.05.The same as Fig.8.

表2 测序数据统计和与参考基因组序列比对分析

Tab.2 Statistics of sequencing data and comparison with reference genome

样品 Samples	重复 Repetition	有效数据数量 Number of clean reads	有效数据中 GC的比例/% GC content of clean reads	质量值≥30的碱基所占的比例/% Proportion of bases with quality value≥30	对比率/% Mapping ratio	比对到唯一位置的 reads比例/% Unique mapping ratio
东农50(A)	1	24 650 287	43.72	94.26	96.74	94.89
Dongnong 50	2	20 950 410	43.92	94.13	96.83	94.86
	3	22 233 726	43.80	93.83	96.65	94.58
极早黄(B)	1	21 248 987	43.49	93.90	96.97	95.02
Jizaohuang	2	21 501 014	43.82	93.93	96.90	94.92
	3	21 662 600	43.89	93.78	96.86	94.94
Maple arrow(C)	1	21 802 230	43.48	93.64	96.58	94.64
	2	21 954 698	43.98	93.90	96.75	94.62
	3	25 070 441	43.64	94.64	97.04	95.21
Glacier(D)	1	21 543 756	43.65	93.57	96.73	94.85
	2	21 916 615	43.85	93.45	96.82	94.85
	3	21 790 509	43.96	95.14	97.07	95.05
黑河49(E)	1	21 553 334	44.18	95.06	96.61	94.48
Heihe 49	2	22 492 989	44.28	94.28	96.71	94.45
	3	21 351 606	44.37	94.92	97.05	95.00
黑交92-1495(F)	1	21 675 089	44.40	94.61	96.37	94.02
Heijiao 92-1495	2	21 238 175	44.94	95.48	96.39	94.01
	3	21 468 307	44.04	94.73	96.89	94.67
呼辐8012(G)	1	21 163 014	44.64	94.93	95.72	92.52
Hufu 8012	2	21 632 882	44.32	94.76	96.64	94.30
	3	21 509 034	44.51	94.99	95.23	91.71
黑河10(H)	1	24 621 454	44.89	93.99	93.65	90.00
Heihe 10	2	21 367 135	45.10	95.12	94.44	91.31
	3	21 253 268	44.48	94.92	96.26	93.66

图2 24个样品聚类和主成分分析 A'.样品聚类分析;B'.主成分分析。A—H.东农50、极早黄、Maple arrow、Glacier、黑河49、黑交92-1495、呼辐8012、黑河10;1—3.一个材料的3个重复样本。表3、图3,4,7同。

Fig.2 Cluster and principal component analysis of 24 samples A'.Sample cluster analysis;B'.Principal component analysis.A—H.Dongnong 50,Jizaohuang,Maple arrow, Glacier,Heihe 49,Heijiao 92-1495,Hufu 8012,Heihe 10;1—3.Three replicates of a single material.The same as Tab.3,Fig.3,4,7.

表3 耐低温大豆与低温敏感大豆不同对比组的差异表达基因

Tab.3 Differentially expressed genes in different comparison groups of low-temperature tolerant soybean and low-temperature sensitive soybean

对比组 Comparative group	差异表达基因 Differentially expressed genes	上调基因 Up-regulated genes	下调基因 Down-regulated genes	对比组 Comparative group	差异表达基因 Differentially expressed genes	上调基因 Up-regulated genes	下调基因 Down-regulated genes
A vs F	5 880	2 975	2 905	C vs H	4 997	3 346	1 651
A vs G	4 075	2 275	1 800	D vs F	2 330	1 573	1 657
A vs H	7 788	4 479	3 309	D vs G	2 284	1 277	1 007
B vs F	3 693	1 940	1 753	D vs H	2 284	1 277	1 007
B vs G	2 727	1 627	1 100	E vs F	2 135	1 036	1 099
B vs H	6 112	3 904	2 280	E vs G	1 710	968	742
C vs F	4 292	2 385	1 907	E vs H	3 587	2 212	1 375
C vs G	2 359	1 474	885

图3 差异表达基因的Upset图图中仅显示DEGs数量前15的对比组合。

Fig.3 Upset plot of differentially expressed genes The figure only shows the comparative combination of the top 15 DEGs quantities.

图4 差异表达基因的表达热图

Fig.4 Heatmap of differentially expressed genes

图5 231个DEGs的GO功能富集 1.细胞过程;2.代谢过程;3.生物调节;4.对刺激的反应;5.定位;6.多细胞有机体过程;7.发育过程;8.信号传导;9.复制;10.生殖过程;11.解毒;12.多生物过程;13.移动;14.细胞解剖实体;15.细胞内;16.含蛋白质组合物;17.结合;18.催化活性;19.转运活性;20.转录调节活性;21.分子转导活性;22.抗氧化活性;23.营养储存库活性。

Fig.5 GO functional enrichment of 231 DEGs 1.Cellular process;2.Metabolic process;3.Biological regulation;4.Response to stimulus;5.Localization;6.Multicellular organismal process;7.Developmental process;8.Signaling;9.Reproduction;10.Reproductive process;11.Detoxification;12.Multi-organism process;13.Locomotion;14.Cellular anatomical entity;15.Intracellular;16.Protein-containing complex;17.Binding;18.Catalytic activity;19.Transporter activity;20.Transcription regulator activity;21.Molecular transducer activity;22.Antioxidant activity;23.Nutrient reservoir activity.

图6 231个DEGs的KEGG富集通路 1.淀粉和蔗糖代谢;2.谷胱甘肽代谢;3.丙氨酸、天门冬氨酸和谷氨酸代谢;4.玉米素生物合成;5.内质网中的蛋白质加工;6.硒化合物的代谢;7.一个叶酸的碳池;8.类固醇生物合成;9.糖基磷脂酰肌醇(GPI)锚定蛋白合成;10.花生四烯酸代谢;11.硫胺素新陈代谢;12.半胱氨酸和蛋氨酸代谢;13.真核生物中的核糖体生物发生;14.角质、木犀素和蜡生物合成;15.甘油酯代谢;16.β-丙氨酸代谢;17.植物激素信号转导;18.错配修复;19.脂肪酸延长;20.植物-病原体互作。气泡图中点的大小表示富集在这些通路中的基因数量,点的颜色表示 P 值。图中仅展示了排名前20的KEGG pathway。

Fig.6 KEGG enrichment pathways for 231 DEGs 1.Starch and sucrose metabolism;2.Glutathione metabolism;3.Alanine,aspartate and glutamate metabolism;4.Zeatin biosynthesis;5.Protein processing in endoplasmic reticulum;6.Selenocompound metabolism;7.One carbon pool by folate;8.Steroid biosynthesis;9.Glycosylphosphatidylinositol (GPI)-anchor biosynthesis;10.Arachidonic acid metabolism;11.Thiamine metabolism;12.Cysteine and methionine metabolism;13.Ribosome biogenesis in eukaryotes;14.Cutin,suberine and wax biosynthesis;15.Glycerolipid metabolism;16.β-Alanine metabolism;17.Plant hormone signal transduction;18.Mismatch repair;19.Fatty acid degradation;20.Plant-pathogen interaction.The size of the dots in the bubble chart indicated the number of genes enriched in these pathways,and the color of the dots indicated the P value.The figure only shows the top 20 KEGG pathways.

表4 差异表达基因中转录因子的类型和所属家族

Tab.4 Types and families of transcription factors in differentially expressed genes

基因号 Gene ID	转录因子家族 TF family
Glyma.01G038600	MYB-related
Glyma.03G247100	bZIP
Glyma.04G150500	GRAS
Glyma.05G033400	E2F-DP
Glyma.07G066100	MYB-related
Glyma.08G092400	BBR-BPC
Glyma.09G072200	B3-ARF
Glyma.10G063200	PLATZ
Glyma.13G279900	NAC
Glyma.14G152700	NAC
Glyma.15G110300	WRKY
Glyma.17G167100	MYB-related
Glyma.17G240100	AP2/ERF
Glyma.18G018200	AP2/ERF
Glyma.20G247500	C3H

图7 15个转录因子编码基因在耐低温材料和低温敏感材料中的表达模式

Fig.7 Expression patterns of 15 transcription factor encoding genes in low-temperature tolerant and low-temperature sensitive materials

图8 14个DEGs的荧光定量PCR结果柱状图中浅绿色背景表示转录组数据中在冷敏感材料上调表达的基因,浅黄色背景表示转录组数据中在冷敏感材料下调表达的基因。

Fig.8 The quantitative PCR results of 14 DEGs In the bar chart,the light green background represents genes that are upregulated in cold-sensitive materials according to transcriptome data, while the light yellow background represents genes that are downregulated in cold-sensitive materials according to transcriptome data.

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