Comparative transcriptome analysis of elite 'ROC' sugarcane parents for exploring genes involved in Sporisorium scitamineum infection by using Illumina-and SMRT-based RNA-seq

• Published in: Zuo wu xue bao Vol. 49; no. 9; p. 2412
• Main Authors: Hu, Xin, Luo, Zheng-Ying, Li, Chun-Jia, Wu, Zhuan-Di, Li, Xu-Juan, Liu, Xin-Long
• Format: Journal Article
• Language: Chinese
• Published: Beijing Chinese Academy of Agricultural Sciences (CAAS) 01.01.2023
• Subjects: Alternative splicing; Biosynthesis; Disease resistance; Exploitation; Gene expression; Genes; Infections; Isoforms; Linoleic acid; MAP kinase; Metabolism; Open reading frames; Parents & parenting; Plant diseases; Plant immunity; Resistance factors; Ribonucleic acid; RNA; Signal transduction; Simple sequence repeats; Smut; Sporisorium scitamineum; Sucrose; Sugarcane; Transcription factors; Transcriptomes
• ISSN: 0496-3490

Sugarcane smut, caused by the fungus Sporisorium scitamineum, is the most challenging disease of sugarcane, causing significant losses in cane yield. There is a dearth of information on smut resistance mechanism in elite parents for the development of smut-resistant varieties. In the present study, we adopted joint Illumina-and Single Molecule Real-Time（SMRT）-based RNA-seq analysis to identify transcript expression in an smut-resistant and-susceptible parents（ROC25 and ROC22） infected with S. scitamineum. A total of 79,885 high-quality transcripts was obtained, including 60,115 open reading frames, 3692 alternate splicing isoforms, 1799 long non-coding RNAs, 29,139 simple sequence repeats, and 7794 transcription factors. About 92.72% of the total transcripts were annotated, which should have increased the available data amount for transcriptome profile analysis.There were 2033 and 9716 differentially expressed transcripts（DETs） in ROC22 and ROC25, respectively. The analyses of GO and KEGG enrichment showed th