生物技术通报 ›› 2023, Vol. 39 ›› Issue (12): 148-157.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0819
收稿日期:
2023-08-20
出版日期:
2023-12-26
发布日期:
2024-01-11
通讯作者:
谢洋,女,博士,副教授,研究方向:蔬菜栽培生理及分子生物学;E-mail: xieyangly123@163.com基金资助:
XIE Yang(), ZHOU Guo-yan, SU Hang, XING Yu-meng, YAN Li-ying
Received:
2023-08-20
Published:
2023-12-26
Online:
2024-01-11
摘要:
干旱是影响黄瓜生长发育并导致产量降低最为普遍的非生物胁迫因素之一。为解析黄瓜干旱胁迫响应分子作用机制,以抗旱型旱黄瓜‘KS33’与敏感型旱黄瓜‘KS30’为试材,利用PEG模拟干旱对种子进行处理,选取发芽前期和发芽后期进行转录组测序。结果表明,发芽前期是抗旱基因挖掘的重要时期,其中,抗旱型材料发芽前期PEG模拟干旱诱导较对照(DT1_TvsDT1_CK)鉴定到727个上调和345个下调差异基因,敏感型材料发芽前期PEG模拟干旱诱导较对照(DS1_TvsDS1_CK)鉴定到1 226个上调和111个下调差异基因;KEGG富集联合分析鉴定到富集于亚油酸代谢(csv00591)、戊糖、葡萄糖醛酸转换(csv00040)、苯丙素的生物合成(csv00940)和植物激素信号转导(csv04075)通路上的20个抗旱关键候选基因。关联SNP变异位点信息及RT-qPCR分析验证,最终筛选出抗旱基因CsaV3_4G023820、CsaV3_2G006420及2个相关SNP分子标记。
谢洋, 周国彦, 苏航, 邢雨蒙, 闫立英. PEG模拟干旱条件下黄瓜种子发芽前后转录组分析[J]. 生物技术通报, 2023, 39(12): 148-157.
XIE Yang, ZHOU Guo-yan, SU Hang, XING Yu-meng, YAN Li-ying. Transcriptome Analysis of Cucumber Seeds Early and Late Germination Under PEG Drought Simulation[J]. Biotechnology Bulletin, 2023, 39(12): 148-157.
图1 PEG模拟干旱诱导下旱黄瓜种子萌发特征 A、C:发芽前期芽长,比例尺为5 mm;B、D:发芽后期芽长+根长,比例尺为2 cm。*代表在P<0.05水平下差异显著,**代表在P<0.01水平下差异显著
Fig. 1 Seed germination characteristics of dry cucumber under PEG drought simulation A, C: Bud length at the early germination stage, scale=5 mm. B, D: Bud length + root length at the late germination stage, scale=2 cm. * significant difference at P<0.05, ** significant difference at P<0.01
样本 Sample | 原始reads Raw reads | 干净reads Clean reads | 错误率 Error rate | Q20/% | GC比率 GC pct/% |
---|---|---|---|---|---|
DT1_CK | 44 400 920 | 43 834 726 | 0.03 | 97.20 | 44.66 |
DT1_T | 39 592 606 | 39 021 166 | 0.03 | 97.58 | 44.43 |
DS1_CK | 41 022 958 | 40 686 226 | 0.03 | 97.10 | 44.02 |
DS1_T | 42 691 442 | 42 269 126 | 0.03 | 97.30 | 44.04 |
DT2_CK | 41 340 818 | 40 790 806 | 0.03 | 97.13 | 43.72 |
DT2_T | 44 591 656 | 43 820 724 | 0.03 | 97.23 | 43.71 |
DS2_CK | 42 263 290 | 41 550 102 | 0.03 | 97.34 | 43.66 |
DS2_T | 43 966 094 | 43 058 866 | 0.03 | 97.22 | 43.81 |
表1 样本测序数据质量汇总
Table 1 Quality summary of samples sequencing data
样本 Sample | 原始reads Raw reads | 干净reads Clean reads | 错误率 Error rate | Q20/% | GC比率 GC pct/% |
---|---|---|---|---|---|
DT1_CK | 44 400 920 | 43 834 726 | 0.03 | 97.20 | 44.66 |
DT1_T | 39 592 606 | 39 021 166 | 0.03 | 97.58 | 44.43 |
DS1_CK | 41 022 958 | 40 686 226 | 0.03 | 97.10 | 44.02 |
DS1_T | 42 691 442 | 42 269 126 | 0.03 | 97.30 | 44.04 |
DT2_CK | 41 340 818 | 40 790 806 | 0.03 | 97.13 | 43.72 |
DT2_T | 44 591 656 | 43 820 724 | 0.03 | 97.23 | 43.71 |
DS2_CK | 42 263 290 | 41 550 102 | 0.03 | 97.34 | 43.66 |
DS2_T | 43 966 094 | 43 058 866 | 0.03 | 97.22 | 43.81 |
KEGG ID | 基因ID Gene ID | RPKM值 RPKM value | 基因描述 Gene description | |||||
---|---|---|---|---|---|---|---|---|
DT1_T | DT1_CK | log2FC | DS1_T | DS1_CK | log2FC | |||
csv00591 | CsaV3_4G023820 | 2 660.909 | 177.544 | 3.905 | 8 268.943 | 3.90E+02 | 4.406 | 亚油酸13S -脂氧合酶2-1 Linoleate 13S-lipoxygenase 2-1 |
CsaV3_2G006420 | 20.813 | 1.39E-17 | 7.391 | 2 200.098 | 7.36E+01 | 4.899 | 亚油酸9S -脂氧合酶4 Linoleate 9S-lipoxygenase 4 | |
CsaV3_4G023810 | 9.458 | 1.39E-17 | 6.263 | 282.605 | 46.658 | 2.595 | 亚油酸13S -脂氧合酶2-1 Linoleate 13S-lipoxygenase 2-1 | |
csv00040 | CsaV3_2G025090 | 223.315 | 7.402 | 4.893 | 1 319.479 | 129.599 | 3.347 | 果胶裂解酶5 Pectate lyase 5 |
CsaV3_3G011280 | 101.247 | 9.516 | 3.395 | 670.348 | 58.062 | 3.527 | 果胶裂解酶8 Pectate lyase 8 | |
CsaV3_3G028700 | 459.883 | 80.320 | 2.516 | 1 844.185 | 193.879 | 3.249 | 果胶裂解酶8 Pectate lyase 8 | |
CsaV3_2G014800 | 34.061 | 7.402 | 2.184 | 506.377 | 1.24E+01 | 5.333 | 果胶甲基酯酶11 Pectin methylesterase 11, PME11 | |
csv00940 | CsaV3_1G042480 | 4329.184 | 54.957 | 6.296 | 34 647.010 | 1 795.690 | 4.270 | β-葡糖苷酶12 Beta-glucosidase 12 |
CsaV3_6G006890 | 294.286 | 26.424 | 3.471 | 1 065.807 | 1.39E-17 | 13.059 | 过氧化物酶61 Peroxidase 61 | |
CsaV3_3G030410 | 80.427 | 19.027 | 2.073 | 217.017 | 31.106 | 2.798 | 4-香豆酸-辅酶a连接酶异构体 4-coumarate--CoA ligase isoform 7,4CL7 | |
CsaV3_2G035150 | 14.190 | 1.39E-17 | 6.842 | 658.773 | 9.334 | 6.122 | 氧化物酶39 Peroxidase 39,ATP19a | |
CsaV3_2G009070 | 36.900 | 7.402 | 2.299 | 54.975 | 3.113 | 4.090 | 细胞色素P450 Cytochrome P450,CYP73A100 | |
CsaV3_6G039690 | 17.028 | 2.118 | 2.938 | 42.436 | 4.150 | 3.317 | 苯丙氨酸氨裂合酶 Phenylalanine ammonia-lyase | |
csv04075 | CsaV3_2G013210 | 45.416 | 1.39E-17 | 8.511 | 2 138.368 | 17.628 | 6.913 | 激素响应蛋白 Auxin-responsive protein, IAA14 |
CsaV3_5G023170 | 65.288 | 5.289 | 3.596 | 652.022 | 81.907 | 2.991 | 生长素转运蛋白3 Auxin transporter-like protein 3 | |
CsaV3_6G007970 | 7.566 | 4.86E+01 | -2.663 | 87.770 | 5.187 | 4.049 | 激素响应蛋白 Auxin responsive protein | |
CsaV3_7G027610 | 423.925 | 67.639 | 2.646 | 548.817 | 99.533 | 2.462 | 吲哚-3-乙酸诱导蛋白 Indole-3-acetic acid-induced protein, ARG13 | |
CsaV3_1G030250 | 20.813 | 1.062 | 4.148 | 64.621 | 5.187 | 3.608 | EIN3结合F-box蛋白 EIN3-binding F-box protein 2 | |
CsaV3_2G004130 | 719.161 | 75.036 | 3.259 | 1 417.861 | 305.850 | 2.212 | 吲哚-3-乙酸诱导蛋白 Indole-3-acetic acid-induced protein, ARG13 | |
CsaV3_3G005590 | 17.975 | 1.39E-17 | 7.180 | 42.436 | 2.0767 | 4.275 | 吲哚-3-乙酸-氨基合成酶Indole-3-acetic acid-amido synthetase, GH3.6 |
表2 KEGG显著富集的差异基因分析
Table 2 Differential gene analysis of KEGG enrichment
KEGG ID | 基因ID Gene ID | RPKM值 RPKM value | 基因描述 Gene description | |||||
---|---|---|---|---|---|---|---|---|
DT1_T | DT1_CK | log2FC | DS1_T | DS1_CK | log2FC | |||
csv00591 | CsaV3_4G023820 | 2 660.909 | 177.544 | 3.905 | 8 268.943 | 3.90E+02 | 4.406 | 亚油酸13S -脂氧合酶2-1 Linoleate 13S-lipoxygenase 2-1 |
CsaV3_2G006420 | 20.813 | 1.39E-17 | 7.391 | 2 200.098 | 7.36E+01 | 4.899 | 亚油酸9S -脂氧合酶4 Linoleate 9S-lipoxygenase 4 | |
CsaV3_4G023810 | 9.458 | 1.39E-17 | 6.263 | 282.605 | 46.658 | 2.595 | 亚油酸13S -脂氧合酶2-1 Linoleate 13S-lipoxygenase 2-1 | |
csv00040 | CsaV3_2G025090 | 223.315 | 7.402 | 4.893 | 1 319.479 | 129.599 | 3.347 | 果胶裂解酶5 Pectate lyase 5 |
CsaV3_3G011280 | 101.247 | 9.516 | 3.395 | 670.348 | 58.062 | 3.527 | 果胶裂解酶8 Pectate lyase 8 | |
CsaV3_3G028700 | 459.883 | 80.320 | 2.516 | 1 844.185 | 193.879 | 3.249 | 果胶裂解酶8 Pectate lyase 8 | |
CsaV3_2G014800 | 34.061 | 7.402 | 2.184 | 506.377 | 1.24E+01 | 5.333 | 果胶甲基酯酶11 Pectin methylesterase 11, PME11 | |
csv00940 | CsaV3_1G042480 | 4329.184 | 54.957 | 6.296 | 34 647.010 | 1 795.690 | 4.270 | β-葡糖苷酶12 Beta-glucosidase 12 |
CsaV3_6G006890 | 294.286 | 26.424 | 3.471 | 1 065.807 | 1.39E-17 | 13.059 | 过氧化物酶61 Peroxidase 61 | |
CsaV3_3G030410 | 80.427 | 19.027 | 2.073 | 217.017 | 31.106 | 2.798 | 4-香豆酸-辅酶a连接酶异构体 4-coumarate--CoA ligase isoform 7,4CL7 | |
CsaV3_2G035150 | 14.190 | 1.39E-17 | 6.842 | 658.773 | 9.334 | 6.122 | 氧化物酶39 Peroxidase 39,ATP19a | |
CsaV3_2G009070 | 36.900 | 7.402 | 2.299 | 54.975 | 3.113 | 4.090 | 细胞色素P450 Cytochrome P450,CYP73A100 | |
CsaV3_6G039690 | 17.028 | 2.118 | 2.938 | 42.436 | 4.150 | 3.317 | 苯丙氨酸氨裂合酶 Phenylalanine ammonia-lyase | |
csv04075 | CsaV3_2G013210 | 45.416 | 1.39E-17 | 8.511 | 2 138.368 | 17.628 | 6.913 | 激素响应蛋白 Auxin-responsive protein, IAA14 |
CsaV3_5G023170 | 65.288 | 5.289 | 3.596 | 652.022 | 81.907 | 2.991 | 生长素转运蛋白3 Auxin transporter-like protein 3 | |
CsaV3_6G007970 | 7.566 | 4.86E+01 | -2.663 | 87.770 | 5.187 | 4.049 | 激素响应蛋白 Auxin responsive protein | |
CsaV3_7G027610 | 423.925 | 67.639 | 2.646 | 548.817 | 99.533 | 2.462 | 吲哚-3-乙酸诱导蛋白 Indole-3-acetic acid-induced protein, ARG13 | |
CsaV3_1G030250 | 20.813 | 1.062 | 4.148 | 64.621 | 5.187 | 3.608 | EIN3结合F-box蛋白 EIN3-binding F-box protein 2 | |
CsaV3_2G004130 | 719.161 | 75.036 | 3.259 | 1 417.861 | 305.850 | 2.212 | 吲哚-3-乙酸诱导蛋白 Indole-3-acetic acid-induced protein, ARG13 | |
CsaV3_3G005590 | 17.975 | 1.39E-17 | 7.180 | 42.436 | 2.0767 | 4.275 | 吲哚-3-乙酸-氨基合成酶Indole-3-acetic acid-amido synthetase, GH3.6 |
图6 SNP变异位点统计分析 A:变异位点区域;B:变异位点功能;C:变异位点影响
Fig. 6 Statistical analysis of SNP variation sites A: Variation site region. B: Function of variation site. C: Influence of variation sites
基因ID Gene ID | 数据库 Database | 染色体CHROM | 位置POS/bp | 参考碱基EF | 实际碱基ALT | 质量QUAL | 测序深度DP | 基因型GT |
---|---|---|---|---|---|---|---|---|
CsaV3_4G023820 | DS1-CK | chr.4 | 13 866 362 | C | G | 30.60 | 11 | 0/1 |
DS1-T | chr.4 | 13 866 362 | C | G | 4 177.60 | 234 | 0/1 | |
CsaV3_2G006420 | DS1-CK | chr.2 | 3 052 439 | C | T | 254.60 | 11 | 0/1 |
DS1-T | chr.2 | 3 052 439 | C | T | 852.60 | 194 | 0/1 | |
CsaV3_2G025090 | DT1-CK | chr.2 | 17 299 201 | G | A | 353.02 | 10 | 0/1 |
DT1-T | chr.2 | 17 301 308 | A | T | 6 787.03 | 176 | 0/1 | |
chr.2 | 17 303 282 | G | C | 879.03 | 24 | 0/1 | ||
chr.2 | 17 305 064 | T | C | 347.00 | 12 | 0/1 | ||
chr.2 | 17 305 060 | T | C | 347.00 | 12 | 0/1 |
表3 SNP变异位点与差异基因整合分析
Table 3 Integration analysis of SNP variation sites and differential genes
基因ID Gene ID | 数据库 Database | 染色体CHROM | 位置POS/bp | 参考碱基EF | 实际碱基ALT | 质量QUAL | 测序深度DP | 基因型GT |
---|---|---|---|---|---|---|---|---|
CsaV3_4G023820 | DS1-CK | chr.4 | 13 866 362 | C | G | 30.60 | 11 | 0/1 |
DS1-T | chr.4 | 13 866 362 | C | G | 4 177.60 | 234 | 0/1 | |
CsaV3_2G006420 | DS1-CK | chr.2 | 3 052 439 | C | T | 254.60 | 11 | 0/1 |
DS1-T | chr.2 | 3 052 439 | C | T | 852.60 | 194 | 0/1 | |
CsaV3_2G025090 | DT1-CK | chr.2 | 17 299 201 | G | A | 353.02 | 10 | 0/1 |
DT1-T | chr.2 | 17 301 308 | A | T | 6 787.03 | 176 | 0/1 | |
chr.2 | 17 303 282 | G | C | 879.03 | 24 | 0/1 | ||
chr.2 | 17 305 064 | T | C | 347.00 | 12 | 0/1 | ||
chr.2 | 17 305 060 | T | C | 347.00 | 12 | 0/1 |
基因ID Gene ID | 序列Sequence(5'-3') |
---|---|
Actin-F | ATTGTTCTCAGTGGTGGTTCTAC |
Actin-R | CCTTTGAGATCCACATCTGCT |
CsaV3_4G023820-F | ACTGCTGTCAACTTCATT |
CsaV3_4G023820-R | TTGGTCATAGTCCTCTGT |
CsaV3_2G006420-F | CCTCTAATCATTCGTCGTCTT |
CsaV3_2G006420-R | GTCTTCTTCGGTAATCTTGCTA |
CsaV3_2G025090-F | GGTTGATTGATGCGATTC |
CsaV3_2G025090-R | ATGTTCTTATCTTGAGTATAGGA |
表4 SNP变异位点与差异基因整合分析
Table 4 Integration analysis of SNP variation sites and differential genes
基因ID Gene ID | 序列Sequence(5'-3') |
---|---|
Actin-F | ATTGTTCTCAGTGGTGGTTCTAC |
Actin-R | CCTTTGAGATCCACATCTGCT |
CsaV3_4G023820-F | ACTGCTGTCAACTTCATT |
CsaV3_4G023820-R | TTGGTCATAGTCCTCTGT |
CsaV3_2G006420-F | CCTCTAATCATTCGTCGTCTT |
CsaV3_2G006420-R | GTCTTCTTCGGTAATCTTGCTA |
CsaV3_2G025090-F | GGTTGATTGATGCGATTC |
CsaV3_2G025090-R | ATGTTCTTATCTTGAGTATAGGA |
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