Transcriptome Analysis of Germinating Soybeans under Low Temperature Stress

doi:10.7668/hbnxb.20195302

Abstract

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

CLC Number:

S565.1

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.

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References 33

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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

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

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

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

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

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