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.
- 相关文献
作者其他论文 更多>>
-
Comprehensive high-throughput sequencing, evolutionary and functional analyses reveal the conservation and diversification of miR166s in regulating pleiotropic traits between rapeseed and Arabidopsis
作者:Zhang, Liyuan;Chen, Si;Yang, Ziyan;Xu, Jinxiong;Sun, Tingting;Kong, Xizeng;Qu, Cunmin;Li, Jiana;Zhang, Liyuan;Lu, Kun;Zhang, Chao;Yang, Bo;Kang, Lin
关键词:High -throughput sequencing; Pleiotropic traits; MiR166/HD-Zip III; Functional research; Rapeseed and Arabidopsis
-
Integrating GWAS, RNA-Seq and functional analysis revealed that BnaA02.SE mediates silique elongation by affecting cell proliferation and expansion in Brassica napus
作者:Zhang, Liyuan;Li, Xiaodong;Chen, Si;Xiang, Sirou;Sun, Tingting;Yang, Ziyan;Kong, Xizeng;Qu, Cunmin;Li, Jiana;Yang, Bo;Zhang, Chao;Lu, Kun
关键词:Brassica napus; silique elongation; GWAS; transcriptome analysis; BnaA02.SE; functional research
-
Structure characteristics of mutation sites in two waxy alleles from Yunnan waxy maize (Zea mays L. var. certaina Kulesh) landraces
作者:Sun, Tingting;Wu, Xiaoyang
关键词:
-
Study on the origin of Asian cultivated rice based on 15 domestication regions
作者:Sun, Tingting;Lu, Hongwei;Wang, Kejian;Sun, Tingting
关键词:Cultivated rice; Domestication; Wild populations; Gene pool; Phylogenetic tree
-
Characterization and Functional Implications of the Nonexpressor of Pathogenesis-Related Genes 1 (NPR1) in Saccharum
作者:Zang, Shoujian;Qin, Liqian;Zhao, Zhennan;Zhang, Jing;Zou, Wenhui;Wang, Dongjiao;Feng, Aoyin;Yang, Shaolin;Que, Youxiong;Su, Yachun;Yang, Shaolin;Que, Youxiong;Su, Yachun
关键词:sugarcane; NPR1-like gene; genome-wide analysis; expression profile; defense response
-
Phenotypic and Molecular Characterization of a Core Collection of Saccharum spontaneum L. in China
作者:Xu, Chao-hua;Liu, Xin-long;Burner, David M.;Abbas, Zaheer;Elgamal, Ibrahim Soliman;Lu, Xin;Su, Huo-sheng;Pan, Yong-Bao
关键词:Genetic diversity; Phenotypic diversity; SSR; Sugarcane
-
Genome-Wide Analysis of the Trehalose-6-Phosphate Synthase (TPS) Gene Family and Expression Profiling of ScTPS Genes in Sugarcane
作者:Hu, Xin;Wu, Zhuan-Di;Luo, Zheng-Ying;Burner, David M.;Wu, Cai-Wen;Pan, Yong-Bao
关键词:comprehensive analysis; expression profiling; Saccharum; trehalose-6-phosphate synthase