Journal of Agricultural Science and Technology ›› 2023, Vol. 25 ›› Issue (10): 22-34.DOI: 10.13304/j.nykjdb.2023.0108
• BIOTECHNOLOGY & LIFE SCIENCE • Previous Articles Next Articles
Hui ZHANG1,2(), Yueyue WANG2,3, Bo ZHAO2,3, Liling ZHANG3, Qianru QIE3, Yuanhuai HAN2,3, Xukai LI1,2(
)
Received:
2023-02-17
Accepted:
2023-06-14
Online:
2023-10-15
Published:
2023-10-27
Contact:
Xukai LI
张会1,2(), 王越越2,3, 赵波2,3, 张丽玲3, 郄倩茹3, 韩渊怀2,3, 李旭凯1,2(
)
通讯作者:
李旭凯
作者简介:
张会 E-mail:huizhang@sxau.edu.cn;
基金资助:
CLC Number:
Hui ZHANG, Yueyue WANG, Bo ZHAO, Liling ZHANG, Qianru QIE, Yuanhuai HAN, Xukai LI. Identification of Co-expression Genes Related to Cold Stress in Foxtail Millet by WGCNA[J]. Journal of Agricultural Science and Technology, 2023, 25(10): 22-34.
张会, 王越越, 赵波, 张丽玲, 郄倩茹, 韩渊怀, 李旭凯. 基于WGCNA的谷子苗期冷胁迫应答基因网络构建与核心因子发掘[J]. 中国农业科技导报, 2023, 25(10): 22-34.
基因 Gene | 上游引物 Forward primer (5’-3’) | 下游引物 Reverse primer (5’-3’) |
---|---|---|
Actin | TGCTCAGTGGAGGCTCAACA | CCAGACACTGTACTTGCGCTC |
Si2g38970 | GCCGGATGTTCTGGTGGTAT | CCTTGAAACTGCGTTCACCG |
Si3g02940 | TATACCGCACCAGCGATGAC | TCCTTTGGGACCTGATTGCC |
Si3g08050 | CTCCGACACCGACTCATTCT | AAGAAGATGACCGACACCCG |
Si5g36480 | CAGCATCCCCAGAGAGCAAA | GCACCTTGGGAACTGTGTCT |
Si6g03220 | GAGCATCGTGCTGTCAGAGG | CGTTGGGTCCAGGAACAGAT |
Si9g50340 | CCTCACAGACATGCCCATCG | TCGACATCGACTCAGTTGCC |
Table 1 RT-qPCR primer sequence
基因 Gene | 上游引物 Forward primer (5’-3’) | 下游引物 Reverse primer (5’-3’) |
---|---|---|
Actin | TGCTCAGTGGAGGCTCAACA | CCAGACACTGTACTTGCGCTC |
Si2g38970 | GCCGGATGTTCTGGTGGTAT | CCTTGAAACTGCGTTCACCG |
Si3g02940 | TATACCGCACCAGCGATGAC | TCCTTTGGGACCTGATTGCC |
Si3g08050 | CTCCGACACCGACTCATTCT | AAGAAGATGACCGACACCCG |
Si5g36480 | CAGCATCCCCAGAGAGCAAA | GCACCTTGGGAACTGTGTCT |
Si6g03220 | GAGCATCGTGCTGTCAGAGG | CGTTGGGTCCAGGAACAGAT |
Si9g50340 | CCTCACAGACATGCCCATCG | TCGACATCGACTCAGTTGCC |
Fig. 1 Gene cluster dendrogram and module detectingA: Clustering of genes based on the topological overlap; B: Dynamic tree cut represents the module divided according to the expression of each gene, colors represent modules; C: Merged dynamic is the result of merging similar modules according to the dynamic tree cut
Fig. 2 Analysis of differentially expressed genes in foxtail millet under cold stressA: Venn diagram of number of the differentially expressed genes among 6 different cold stress conditions; B: Number of the differentially expressed genes in 6 different cold stress conditions; C:Number of the differentially expressed genes that are unique or shared under 6 different cold stress conditions,1~6 in the X-axis mean the frequency of the differentially expressed genes among 6 different cold stress conditions
基因 Gene | 水稻同源基因 Homologous gene in rice | 功能注释 Function annotation | 拟南芥同源基因 Homologous gene in Arabidopsis thaliana | 功能注释 Function annotation |
---|---|---|---|---|
Si2g38970 | LOC_Os07g42650 | 保守假蛋白 Conserved hypothetical protein | At4g33980 | 冷调控基因28 Cold-regulate gene 28 |
Si3g01950 | LOC_Os04g58710 | 4-香豆酸-Co-A连接酶类蛋白 4-coumarate-Co-A ligase (4CL) like protein | At1g77230 | 四肽重复类超家族蛋白 Tetratricopeptide repeat (TPR)-like superfamily protein |
Si3g02940 | LOC_Os04g57550 | 多胺氧化酶,种子萌发 Polyamine oxidase (PAO2), seed germination | At2g43020 | 多肽氧化酶2 Polyamine oxidase 2, ATPAO2 |
Si3g08050 | LOC_Os05g11810 | 类赤霉素2-β-双加氧酶 Similar to gibberellin 2-beta-dioxygenase | At1g30040 | 赤霉素2-氧化酶 Gibberellin 2-oxidase |
Si5g36480 | LOC_Os01g60600 | WRKY 转录因子 WRKY transcription factor | At5g22570 | WRKY DNA 结合蛋白38 WRKY DNA-binding protein 38 |
Si5g39150 | LOC_Os05g37060 | R-R型MYB类转录因子 R-R-type MYB-like transcription factor | At5g67420 | 含LOB结构域的蛋白37 LOB-domain-containing protein 37 |
Si6g03220 | LOC_Os04g52090 | APETALA 2 类转录因子 APETALA-2-like transcription factor | At5g44210 | ERF 结构域蛋白9 ERF domain protein- 9 |
Si7g06300 | LOC_Os04g23550 | 螺旋-环-螺旋转录激活因子 Basic helix-loop-helix (bHLH) transcription activator | At4g16430 | bHLH DNA 结合超家族蛋白 bHLH DNA-binding superfamily protein |
Si9g50340 | LOC_Os07g42370 | 含TIFY结构域蛋白 TIFY domain containing protein | At1g74950 | TIFY结构域/发散CCT基序家族蛋白 TIFY domain/divergent CCT motif family protein |
Table 2 Differentially expressed genes under 6 cold stress conditions in foxtail millet
基因 Gene | 水稻同源基因 Homologous gene in rice | 功能注释 Function annotation | 拟南芥同源基因 Homologous gene in Arabidopsis thaliana | 功能注释 Function annotation |
---|---|---|---|---|
Si2g38970 | LOC_Os07g42650 | 保守假蛋白 Conserved hypothetical protein | At4g33980 | 冷调控基因28 Cold-regulate gene 28 |
Si3g01950 | LOC_Os04g58710 | 4-香豆酸-Co-A连接酶类蛋白 4-coumarate-Co-A ligase (4CL) like protein | At1g77230 | 四肽重复类超家族蛋白 Tetratricopeptide repeat (TPR)-like superfamily protein |
Si3g02940 | LOC_Os04g57550 | 多胺氧化酶,种子萌发 Polyamine oxidase (PAO2), seed germination | At2g43020 | 多肽氧化酶2 Polyamine oxidase 2, ATPAO2 |
Si3g08050 | LOC_Os05g11810 | 类赤霉素2-β-双加氧酶 Similar to gibberellin 2-beta-dioxygenase | At1g30040 | 赤霉素2-氧化酶 Gibberellin 2-oxidase |
Si5g36480 | LOC_Os01g60600 | WRKY 转录因子 WRKY transcription factor | At5g22570 | WRKY DNA 结合蛋白38 WRKY DNA-binding protein 38 |
Si5g39150 | LOC_Os05g37060 | R-R型MYB类转录因子 R-R-type MYB-like transcription factor | At5g67420 | 含LOB结构域的蛋白37 LOB-domain-containing protein 37 |
Si6g03220 | LOC_Os04g52090 | APETALA 2 类转录因子 APETALA-2-like transcription factor | At5g44210 | ERF 结构域蛋白9 ERF domain protein- 9 |
Si7g06300 | LOC_Os04g23550 | 螺旋-环-螺旋转录激活因子 Basic helix-loop-helix (bHLH) transcription activator | At4g16430 | bHLH DNA 结合超家族蛋白 bHLH DNA-binding superfamily protein |
Si9g50340 | LOC_Os07g42370 | 含TIFY结构域蛋白 TIFY domain containing protein | At1g74950 | TIFY结构域/发散CCT基序家族蛋白 TIFY domain/divergent CCT motif family protein |
Fig. 3 Expression patterns of differentially expressed genesA: Expression patterns of the 9 differentially expressed genes in ‘Yugu 1’ among 6 cold stress conditions; B: Expression patterns of the 9 differentially expressed genes in mutant xiaomi during 11 developmental stages
Fig. 5 Co-expression network of genes relative to cold stress in 3 modulesA: Darkturquoise module; B: Turquoise module; C: Blue module. The red diamond indicates the core gene that is both annotated to the transcription factor and belongs to the network and red circle indicates the annotated core genes, the purple circle indicates the annotated candidate genes and the purple diamond represents annotated candidate gene transcription factors, the green circle indicates transcription factors associated with motif analysis, the green diamond represents annotated candidate gene transcription factors and binding motif analysis transcription factors, the green triangle represents both transcription factors that bind to motif analysis and core genes
模块 Module | 基因名称 Gene name | 水稻Rice | 拟南芥Arabidopsis thaliana | |||
---|---|---|---|---|---|---|
同源基因 Homologous gene | 功能注释 Function annotation | 同源基因 Homologous gene | 功能注释 Function annotation | |||
Darkturquoise | Si3g17990 (TCP) | LOC_Os07g05720 | TCP 家族转录因子 TCP family transcription factor | At1g30210 | TCP 家族24 TCP family 24 | |
Si7g22390 | LOC_Os04g49510 | CAMK-CAMK27钙/钙调素依赖性蛋白激酶 CAMK_CAMK_like.27-CAMK includes calcium/calmodulin depedent protein kinases | At2g17290 | 钙依赖性蛋白激酶家族蛋白 Calcium-dependent protein kinase family protein | ||
Si9g50120 | LOC_Os03g08570 | 胺氧化酶,含黄素,含结构域蛋白 Amine oxidase, flavin-containing, domain containing protein | At4g14210 | 八氢番茄红素脱氢酶3 Phytoene desaturase 3 | ||
Si1g03360 | LOC_Os01g10840 | CGMC_GSK.2-CGMC 激酶 CGMC_GSK.2-CGMC includes CDA, MAPK, GSK3, and CLKC kinases | At1g06390 | GSK3/SHAGGY 类蛋白激酶1 GSK3/SHAGGY-like protein kinase 1 | ||
Turquoise | Si4g02480 (ERF) | LOC_Os09g35010 | 脱水反应元件结合蛋白 Dehydration-responsive element-binding protein | At5g51990 | 核碱、核苷、核苷酸和核酸代谢过程 Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | |
Si2g28390 (ERF) | LOC_Os09g35030 | 脱水反应元件结合蛋白 Dehydration-responsive element-binding protein | — | — | ||
Si7g18940 (ERF) | LOC_Os09g20350 | 乙烯应答转录因子 Ethylene-responsive transcription factor | — | — | ||
Si3g13090 | LOC_Os05g50710 | 晚期胚胎蛋白 Late embryogenesis abundant protein | At2g46140 | 晚期胚胎蛋白 Late embryogenesis abundant protein | ||
Blue | Si4g17730 (bZIP) | LOC_Os06g45140 | 含bZIP转录因子结构域的 蛋白 bZIP transcription factor domain containing protein | — | — | |
Si2g39810 (bHLH) | LOC_Os07g43530 | 螺旋-环-螺旋DNA结合蛋白 Helix-loop-helix DNA-binding domain containing protein | — | — | ||
Si5g13680 (WRKY) | LOC_Os02g08440 | WRKY71转录因子 WRKY71 transcription factor | At1g80840 | 病原体诱导转录因子,体外结合 W-box 序列 Pathogen-induced transcription factor. Binds W-box sequences in vitro | ||
Si9g43500 | LOC_Os03g17690 | 抗坏血酸过氧化物酶1 Ascorbate peroxidase 1 | At1g07890 | 抗坏血酸过氧化物酶1 Ascorbate peroxidase 1 |
Table 3 Functional annotation of hub genes relative to cold stress in 3 modules
模块 Module | 基因名称 Gene name | 水稻Rice | 拟南芥Arabidopsis thaliana | |||
---|---|---|---|---|---|---|
同源基因 Homologous gene | 功能注释 Function annotation | 同源基因 Homologous gene | 功能注释 Function annotation | |||
Darkturquoise | Si3g17990 (TCP) | LOC_Os07g05720 | TCP 家族转录因子 TCP family transcription factor | At1g30210 | TCP 家族24 TCP family 24 | |
Si7g22390 | LOC_Os04g49510 | CAMK-CAMK27钙/钙调素依赖性蛋白激酶 CAMK_CAMK_like.27-CAMK includes calcium/calmodulin depedent protein kinases | At2g17290 | 钙依赖性蛋白激酶家族蛋白 Calcium-dependent protein kinase family protein | ||
Si9g50120 | LOC_Os03g08570 | 胺氧化酶,含黄素,含结构域蛋白 Amine oxidase, flavin-containing, domain containing protein | At4g14210 | 八氢番茄红素脱氢酶3 Phytoene desaturase 3 | ||
Si1g03360 | LOC_Os01g10840 | CGMC_GSK.2-CGMC 激酶 CGMC_GSK.2-CGMC includes CDA, MAPK, GSK3, and CLKC kinases | At1g06390 | GSK3/SHAGGY 类蛋白激酶1 GSK3/SHAGGY-like protein kinase 1 | ||
Turquoise | Si4g02480 (ERF) | LOC_Os09g35010 | 脱水反应元件结合蛋白 Dehydration-responsive element-binding protein | At5g51990 | 核碱、核苷、核苷酸和核酸代谢过程 Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | |
Si2g28390 (ERF) | LOC_Os09g35030 | 脱水反应元件结合蛋白 Dehydration-responsive element-binding protein | — | — | ||
Si7g18940 (ERF) | LOC_Os09g20350 | 乙烯应答转录因子 Ethylene-responsive transcription factor | — | — | ||
Si3g13090 | LOC_Os05g50710 | 晚期胚胎蛋白 Late embryogenesis abundant protein | At2g46140 | 晚期胚胎蛋白 Late embryogenesis abundant protein | ||
Blue | Si4g17730 (bZIP) | LOC_Os06g45140 | 含bZIP转录因子结构域的 蛋白 bZIP transcription factor domain containing protein | — | — | |
Si2g39810 (bHLH) | LOC_Os07g43530 | 螺旋-环-螺旋DNA结合蛋白 Helix-loop-helix DNA-binding domain containing protein | — | — | ||
Si5g13680 (WRKY) | LOC_Os02g08440 | WRKY71转录因子 WRKY71 transcription factor | At1g80840 | 病原体诱导转录因子,体外结合 W-box 序列 Pathogen-induced transcription factor. Binds W-box sequences in vitro | ||
Si9g43500 | LOC_Os03g17690 | 抗坏血酸过氧化物酶1 Ascorbate peroxidase 1 | At1g07890 | 抗坏血酸过氧化物酶1 Ascorbate peroxidase 1 |
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