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WGCNA Identifies a Comprehensive and Dynamic Gene Co-Expression Network That Associates with Smut Resistance in Sugarcane

文献类型： 外文期刊

作者： Wu, Qibin 1 ; Pan, Yong-Bao 2 ; Su, Yachun 1 ; Zou, Wenhui 1 ; Xu, Fu 1 ; Sun, Tingting 1 ; Grisham, Michael P. 2 ; Yang, Shaolin 1 ; Xu, Liping 1 ; Que, Youxiong 1 ;

作者机构： 1.Fujian Agr & Forestry Univ, Natl Engn Res Ctr Sugarcane, Minist Agr & Rural Affairs, Key Lab Sugarcane Biol & Genet Breeding, Fuzhou 350002, Peoples R China

2.USDA ARS, Southeast Area, Sugarcane Res Unit, Houma, LA 70360 USA

3.Yunnan Acad Agr Sci, Sugarcane Res Inst, Yunnan Key Lab Sugarcane Genet Improvement, Kaiyuan 661600, Peoples R China

关键词： sugarcane; smut resistance; gene co-expression network; hub genes; WGCNA

期刊名称：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES （ 影响因子：6.208； 五年影响因子：6.628 ）

ISSN：

年卷期： 2022 年 23 卷 18 期

页码：

收录情况： SCI

摘要： Sugarcane smut is a major fungal disease caused by Sporisorium scitamineum, which seriously reduces the yield and quality of sugarcane. In this study, 36 transcriptome data were collected from two sugarcane genotypes, YT93-159 (resistant) and ROC22 (susceptible) upon S. scitamineum infection. Data analysis revealed 20,273 (12,659 up-regulated and 7614 down-regulated) and 11,897 (7806 up-regulated and 4091 down-regulated) differentially expressed genes (DEGs) in YT93-159 and ROC22, respectively. A co-expression network was then constructed by weighted gene co-expression network analysis (WGCNA), which identified 5010 DEGs in 15 co-expressed gene modules. Four of the 15 modules, namely, Skyblue, Salmon, Darkorange, and Grey60, were significantly associated with smut resistance. The GO and KEGG enrichment analyses indicated that the DEGs involving in these four modules could be enriched in stress-related metabolic pathways, such as MAPK and hormone signal transduction, plant-pathogen interaction, amino acid metabolism, glutathione metabolism, and flavonoid, and phenylpropanoid biosynthesis. In total, 38 hub genes, including six from the Skyblue module, four from the Salmon module, 12 from the Darkorange module, and 16 from the Grey60 module, were screened as candidate hub genes by calculating gene connectivity in the corresponding network. Only 30 hub genes were amplifiable with RT-qPCR, of which 27 were up-regulated upon S. scitamineum infection. The results were consistent with the trend of gene expression in RNA-Seq, suggesting their positive roles in smut resistance. Interestingly, the expression levels of AOX, Cyb5, and LAC were higher in ROC22 than in YT93-159, indicating these three genes may act as negative regulators in response to S. scitamineum infection. This study revealed the transcriptome dynamics in sugarcane challenged by S. scitamineum infection and provided gene targets for smut resistance breeding in sugarcane.

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