Screening of Candidate Genes Resistant to Maize Head Smut Based on RNA-seq and WGCNA

ZHANG Xiliang; ZHANG Changhui; SHEN Tao; WANG Hanlei; ZHANG Xiaomei; QIU Hongbo; LI Leixin

doi:10.15933/j.cnki.1004-3268.2026.04.002

Abstract：Using the resistant inbred line T32 and two susceptible inbred lines HuangC and Jiao 51 as experimental materials,we performed treatments with and without inoculation of Sporisorium reilianum.Samples were collected for high-throughput sequencing(RNA-seq)to screen differentially expressed genes(DEGs).Based on the FPKM expression matrix of all samples,weighted gene co-expression network analysis(WGCNA)was conducted after data processing to construct a weighted gene co-expression network and identify modules significantly positively correlated with the disease resistance phenotype.Module-trait cross hub candidate genes were screened by both module membership and gene significance,and then were intersected with the identified DEGs.The overlapping genes were subjected to KEGG pathway and GO term enrichment analysis.Combined with literature reviews,final disease resistance candidate genes were selected,to provide a theoretical basis for molecular disease resistance breeding.The results showed that high-quality 154 Gb data were obtained by RNA-seq,experimental reproducibility was good,and data was reliable.Differential expression analysis of genes revealed 10 563 DEGs(4 822 up-regulated genes,5 741 down-regulated genes)in T32 inoculation vs HuangC inoculation group(YTA vs YHA),10 808 DEGs(5 698 up-regulated genes,5 110 down-regulated genes)were selected in T32 inoculation vs Jiao 51 inoculation group(YTA vs YJA),and 1 335 DEGs(588 up-regulated genes,747 down-regulated genes)in T32 inoculation vs T32 non-inoculation group(YTB vs YTA),respectively.KEGG pathway enrichment analysis indicated that these DEGs were significantly enriched in carbon metabolism,biosynthesis of amino acids,phenylpropanoid biosynthesis,and MAPK signaling-plant pathway and so on.WGCNA showed that two modules(brown and turquoise)were positively correlated with disease resistance,and 2 787 module-trait cross hub candidate genes were screened.Among these,906 genes were enriched in KEGG pathways,primarily involved in carbon metabolism,biosynthesis of amino acids,cysteine and methionine metabolism.Thirty-five intersection genes of module-trait hub candidate genes with DEGs were obtained,16 of which obtained annotations in the NCBI database.KEGG pathway analysis of the above 35 genes showed that eight genes were enriched in pathways like metabolic pathway and plant hormone signal transduction,GO analysis revealed that six genes were enriched in protein dimerization activity,including five genes encoding transcription factors(three MADS,one bZIP and one bHLH)and one gene encoding auxin-responsive protein IAA24.Finally,ten disease resistance candidate genes were comprehensively selected,including two directly related to disease resistance[LOC100283065 and LOC100280308(TLP1)],three genes involved in auxin and flavonoid metabolism[LOC100284018(CHI),LOC100273383 and LOC100280600(IAA24)],and five genes encoding transcription factors(three MADS,one bZIP and one bHLH)].