Scientia Agricultura Sinica ›› 2020, Vol. 53 ›› Issue (16): 3280-3293.doi: 10.3864/j.issn.0578-1752.2020.16.007

• PLANT PROTECTION • Previous Articles     Next Articles

Identification of Co-Expression Genes Related to Endogenous Abscisic Acid in Response to the Stress of Sclerospora graminicola by WGCNA in Foxtail Millet

CHANG GuoRong(),LI RenJian,ZHANG Qi,ZHANG YuMing,HAN YuanHuai,ZHANG BaoJun()   

  1. College of Plant Protection, Shanxi Agricultural University, Taigu 030801, Shanxi
  • Received:2020-02-17 Accepted:2020-03-04 Online:2020-08-16 Published:2020-08-27
  • Contact: BaoJun ZHANG E-mail:1064382617@qq.com;zhangbj992@163.com

Abstract:

【Objective】Abscisic acid (ABA), as a stress hormone, plays an important role in plant growth and development, biological and abiotic stresses. The ABA receptor protein PYR/PYL/PCAR and SNF1-related protein kinase (SnRK2) are important regulatory factors that mediate ABA signaling. The objective of this study is to predict the regulatory roles of ABA and the key genes in its signaling pathway in foxtail millet (Setaria italica) downy mildew caused by Sclerospora graminicola, and to provide a reference for the research of endogenous ABA in S. italica in response to the infection of S. graminicola.【Method】S. italica variety Jingu 21 infected by S. graminicola was used for transcriptome sequencing and ABA content measurement, and the PYL and SnRK2 family genes in the ABA signaling pathway were identified and analyzed based on the whole genome sequence of S. italica. A weighted gene co-expression network analysis (WGCNA) was constructed using the transcriptome, and it was associated with the content of host endogenous ABA in the context of S. graminicola infection to predict the key genes in the interaction between S. italica and S. graminicola regulated by ABA and the PYL and SnRK2 genes in its downstream signaling. The candidate genes were validated by qRT-PCR.【Result】There were 11 PYL and 11 SnRK2 family genes in S. italica, which were relatively conservative in the Gramineae, and ABA responsive elements were predicted in the promoters of PYL and SnRK2 family genes. The endogenous ABA in the host accumulated at the first and second stages after S. graminicola infection, and its content (22.50 and 18.08 ng·mL-1, respectively) was significantly higher than that of the control group. However, the content of ABA decreased at the third, fourth, and fifth stages, which was lower than that of the control group. For the WGCNA, a total of 34 gene co-expression modules were constructed by using 18 535 genes. The MEpaleturquoise and MEbrown modules were predicted as the core candidate modules through the association analysis of ABA content and PYL, SnRK2 family genes. GO function enrichment and module key gene mining revealed that one PYL family gene (Seita.1G030500), two SnRK2 family genes (Seita.2G394500 and Seita.3G03200), and three core genes (Seita.4G105600, Seita.6G218100, and Seita.9G138400) might be involved in the interaction between S. italica and S. graminicola during the regulation of ABA and its signal transduction. After comparing three predicted core genes with the reference genes in Oryza sativa and Arabidopsis thaliana databases, Seita.4G105600 was identified as the transducin/WD40 repeat-like superfamily protein, Seita.6G218100 as the WRKY57 transcription factor, and Seita.9G138400 as the TIFY transcription factor. qRT-PCR analysis showed that Seita.2G394500, Seita.4G105600, and Seita.6G218100 genes were up-regulated at the early stage of S. graminicola infection.【Conclusion】The ABA accumulates in S. italica infected by S. graminicola. One PYL family gene, two SnRK2 family genes, two transcription factor genes, and one WD40 family protein gene were predicted as the key genes related to the response to S. graminicola infection. qRT-PCR results showed that one SnRK2 gene, one WD40 family protein gene, and one WRKY57 transcription factor gene may play an important role in the response of ABA in S. italica to the infection of S. graminicola.

Key words: foxtail millet (Setaria italica), abscisic acid, Sclerospora graminicola, PYL, SnRK2, weighted gene co-expression network analysis (WGCNA)

Table 1

The basic information of PYL and SnRK2 gene family members in S. italica"

类型
Type
基因编号
Gene ID
染色体
Chromosome
基因组位置
Genomic location
氨基酸长度
Amino
acid (aa)
等电点
pI
分子量
Molecular weight (kD)
总平均疏水指数
Average of hydropathicity
PYL Seita.1G013900 1 1185261-1188981 211 5.92 23.67 -0.393
Seita.1G030500 1 2860241-2862675 201 5.97 21.72 -0.338
Seita.3G072600 3 4600680-4602575 193 4.39 20.38 -0.011
Seita.3G076200 3 4851939-4854302 205 5.91 22.16 -0.233
Seita.3G207900 3 16201030-16202684 204 8.88 21.58 -0.132
Seita.4G239500 4 36338582-36339202 206 6.71 22.14 -0.220
Seita.5G140800 5 12377439-12378609 206 5.25 21.84 -0.101
Seita.5G302400 5 35644268-35645327 175 4.93 18.81 -0.210
Seita.5G369100 5 40592575-40593198 207 6.75 22.70 -0.252
Seita.9G311900 9 36003871-36005478 207 5.24 22.13 -0.195
Seita.9G437300 9 48993016-48994206 220 6.58 22.92 0.036
SnRK2 Seita.1G190000 1 27251818-27256180 454 8.49 51.77 -0.605
Seita.2G394500 2 45956776-45961725 339 5.30 38.47 -0.177
Seita.3G003200 3 157270-159276 380 5.99 43.11 -0.547
Seita.3G230400 3 19092668-19097929 360 5.68 41.77 -0.546
Seita.3G369900 3 47387035-47389674 374 4.94 41.46 -0.224
Seita.5G395400 5 42440116-42444731 362 6.06 42.33 -0.619
Seita.7G100500 7 20312278-20317276 358 6.00 40.98 -0.558
Seita.9G318200 9 36623246-36626468 333 5.48 37.93 -0.467
Seita.9G079800 9 4716246-4721220 366 4.81 41.48 -0.308
Seita.9G169200 9 11473484-11476494 362 4.73 40.73 -0.283
Seita.9G379000 9 43841287-43845704 344 5.10 39.13 -0.238

Fig. 1

Phylogenetic tree of PYL and SnRK2 family genes in S. italic Each color covered gene is a kind of gene with close relationship"

Fig. 2

Functions of promoter cis-acting elements in PYL and SnRK2 family genes in S. italic Each color block in the figure represents the response element corresponding to the legend, and the position of each block represents the position on the starter"

Fig. 3

Determination of abscisic acid content"

Fig. 4

Determination of soft threshold and construction of co-expression network A:Different colors represent the built network modules, cluster dendrogram indicates hierarchical clustering of different samples, and each sample corresponds to a color of the module;B:The vertical coordinate on the left represents the index of the network model, the right represents the mean connectivity, and the horizontal coordinate represents the soft threshold of the network, the red line indicates the best soft threshold selected"

Fig. 5

Identification of key modules A:The heat map of co-expression module related to the content of abscisic acid;B:Relativity of module to the content of abscisic acid;C:The distribution of PYL and SnRK2 family genes in the module, the inner circle sector represents the proportion of family genes belonging to the module in the total number of genes, and the outer sector represents the number of family genes belonging to the module"

Table 2

GO enrichments of network modules"

类型 Type 基因编号 Gene ID GO富集 GO term P-value
MEpaleturquoise GO:0000775 染色体、着丝粒区域Chromosome, centromeric region 0.02291
GO:0008135 翻译因子活性、核酸结合位点Translation factor activity, nucleic acid binding 0.03575
GO:0006075 1-3-beta-D-葡聚糖生物合成过程 1-3-beta-D-glucan biosynthetic process 0.0002
GO:2000112 调控细胞大分子生物合成过程Regulation of cellular macromolecule biosynthetic process 0.0015
GO:0051552 类黄酮代谢过程Flavone metabolic process 0.0249
GO:0051553 类黄酮生物合成过程Flavone biosynthetic process 0.0249
GO:0055074 钙离子平衡Calcium ion homeostasis 0.0249
GO:0016780 磷酸转移酶活性,用于其他取代磷酸基Phosphotransferase activity, for other substituted phosphate groups 0.02825
MEbrown GO:0003995 脂酰CoA脱氢酶活性Acyl-CoA dehydrogenase activity 0.001849608
GO:0051171 调节氮化合物代谢过程Regulation of nitrogen compound metabolic process 1.95E-05
GO:0009755 激素介导的信号通路Hormone-mediated signaling pathway 7.67E-05
GO:0071383 细胞对类固醇激素刺激的反应Cellular response to steroid hormone stimulus 8.79E-04
GO:0009725 激素响应Response to hormone 0.002160987
GO:0009742 油菜素类内酯介导的信号通路Brassinosteroid mediated signaling pathway 0.002538882
GO:0002376 免疫系统的过程Immune system process 0.003433683
GO:0043207 对外界生物刺激的反应Response to external biotic stimulus 0.018615083
GO:0009873 乙烯激活的信号通路Ethylene-activated signaling pathway 0.018737534
GO:0009607 生物刺激反应Response to biotic stimulus 0.019137736
GO:0080134 应激反应的调节Regulation of response to stress 0.019394085
GO:0006631 脂肪酸代谢过程Fatty acid metabolic process 0.022668677
GO:0009744 蔗糖响应Response to sucrose 0.023618658
GO:0044038 细胞壁大分子生物合成过程Cell wall macromolecule biosynthetic process 0.033696381
GO:0009620 响应真菌Response to fungus 0.043398934

Fig. 6

Gene co-expression network of the MEpaleturquoise module and PYL, SnRK2 family genes in MEbrown module The size of the midpoint in the figure indicates the weight of the gene in the network. The red in figure A indicates the core gene. In figure B, the red indicates the gene with higher weight value, the blue indicates the gene with medium weight value, and the green indicates the gene with lower weight value"

Table 3

Functional annotation of modular hub genes"

候选基因
Candidate gene
水稻同源基因
Homologous genes in O. sativa
基因功能
Gene function
拟南芥同源基因
Homologous genes in A. thaliana
基因功能
Gene function
Seita.4G105600 LOC_Os06g33480 包含蛋白质的WD结构域、G-beta重复结构域
WD domain, G-beta repeat domain containing protein
AT1G24130 转导蛋白/WD40重复超家族蛋白
Transduction/WD40 repeat-like superfamily protein
Seita.6G218100 LOC_Os12g01180 WRKY57转录因子
WRKY57 transcription factors
AT5G46780 包含VQ基序的蛋白
VQ motif-containing protein
Seita.9G138400 LOC_Os06g36670 TIFY 转录因子
TIYF transcription factors
AT1G51600 TIFY2A转录因子
TIYF2A transcription factors

Fig. 7

Gene expression pattern and correlation analysis of PYL and SnRK2 families A:The expression heat map of PYL and SnRK2 family genes in the transcriptome;B:The systematic heat map of correlation between PYL and SnRK2 family genes and abscisic acid content in the transcriptome"

Fig. 8

Changes in gene expression at different stages"

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