WGCNA identifies a comprehensive and dynamic gene co-expression network that associates with smut resistance in sugarcane

Authors: WU, QIBIN - Fujian Agriculture And Forest University; Pan, Yong-Bao; SU, YACHUN - Fujian Agriculture And Forest University; ZOU, WENHUI - Fujian Agriculture And Forest University; XU, FU - Fujian Agriculture And Forest University; YANG, SHAOLIN - Fujian Agriculture And Forest University; GRISHAM, MICHAEL - Retired ARS Employee; SUN, TINGTING - Yunnan Academy Of Agriculture Sciences; XU, LIPING - Fujian Agriculture And Forest University; QUE, YOUXIONG - Fujian Agriculture And Forest University

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/13/2022
Publication Date: 9/15/2022
Citation: Wu, Q., Pan, Y.-B., Su, Y., Zou, W., Xu, F., Yang, S., Grisham, M.P., Sun, T., Xu, L., Que, Y. 2022. WGCNA identifies a comprehensive and dynamic gene co-expression network that associates with smut resistance in sugarcane. International Journal of Molecular Sciences. 23:1-23. https://doi.org/10.3390/ijms231810770.
DOI: https://doi.org/10.3390/ijms231810770

Interpretive Summary: Smut is a major fungal disease that seriously reduces the yield and quality of sugarcane. Growing smut-resistant varieties is the most economical and effective way to manage this disease. However, it takes about 12 years to breed a new sugarcane variety for commercial production by traditional method due to its complex genetic background and smut resistance is determined by multiple genes. The purpose of this study is to discover key genes that associate with smut resistance in sugarcane. Plants of two varieties, YT93-159 (resistant) and ROC22 (susceptible), were infected with the fungal pathogen. Infected buds were collected at 0, 1, 2, 3, 4, and 5 days post-infection with three replications. Total RNA were extracted from the buds and subject to RNA-sequencing to produce a total of 36 large sets of data. Follow-up data analysis discovered numerous differentially expressed genes (DEGs) from YT93-159 (20,273 DEGs) and ROC22 (11,897 DEGs). A co-expression network was then constructed by weight gene co-expression network analysis (WGCNA) that identified 5,010 DEGs in 15 co-expressed gene modules. Four of the 15 modules were significantly associated with smut resistance and the DEGs in these four modules had been enriched in several stress-related metabolic pathways, Further data mining discovered 38 genes that displayed large gene connectivity values in the corresponding network, but only 30 genes could be amplified with PCR. PCR results indicated that 27 genes were up-regulated in plants of YT93-159, suggesting their positive roles in smut resistance. Interestingly, the other three genes had a higher level of expression in ROC22 than YT93-159, indicating that these three genes may be negative regulators in response to smut infection. The results of this study benefit further understanding of the molecular mechanism of smut resistance and provide a new gene resource for future smut resistance breeding in sugarcane.

Technical Abstract: 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 7,614 down-regulated) and 11,897 (7,806 up-regulated and 4,091 down-regulated) differentially expressed genes (DEGs) in YT93-159 and ROC22, respectively. A co-expression network was then constructed by weight gene co-expression network analysis (WGCNA), which identified 5,010 DEGs in 15 co-expressed gene modules. Four of the 15 modules, namely, Skyblue, Salmon, Darkorange, and Grey60, were significantly associated with smut resistance. 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 6 from Skyblue module, 4 from Salmon module, 12 from Darkorange module, and 16 from 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.