title: Dual transcriptome analysis reveals insights into the response to Rice black-streaked dwarf virus in maize.
abstract: Maize rough dwarf disease (MRDD) is a viral infection that results in heavy yield losses in maize worldwide, particularly in the summer maize-growing regions of China. MRDD is caused by the Rice black-streaked dwarf virus (RBSDV). In the present study, analyses of microRNAs (miRNAs), the degradome, and transcriptome sequences were used to elucidate the RBSDV-responsive pathway(s) in maize. Genomic analysis indicated that the expression of three non-conserved and 28 conserved miRNAs, representing 17 known miRNA families and 14 novel miRNAs, were significantly altered in response to RBSDV when maize was inoculated at the V3 (third leaf) stage. A total of 99 target transcripts from 48 genes of 10 known miRNAs were found to be responsive to RBSDV infection. The annotations of these target genes include a SQUAMOSA promoter binding (SPB) protein, a P450 reductase, an oxidoreductase, and a ubiquitin-related gene, among others. Characterization of the entire transcriptome suggested that a total of 28 and 1085 differentially expressed genes (DEGs) were detected at 1.5 and 3.0 d, respectively, after artificial inoculation with RBSDV. The expression patterns of cell wall- and chloroplast-related genes, and disease resistance- and stress-related genes changed significantly in response to RBSDV infection. The negatively regulated genes GRMZM2G069316 and GRMZM2G031169, which are the target genes for miR169i-p5 and miR8155, were identified as a nucleolin and a NAD(P)-binding Rossmann-fold superfamily protein in maize, respectively. The gene ontology term GO:0003824, including GRMZM2G031169 and other 51 DEGs, was designated as responsive to RBSDV.
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang Province 150030, China.
authors: Yu
authors: Y
authors: Zhou
authors: College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang Province 150030, China.
authors: Zhennan
authors: Z
authors: Xu
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China.
authors: Canxing
authors: C
authors: Duan
authors: Jiangsu Academy of Agricultural Sciences, Zhongling Street, Xuanwu District, Nanjing, Jiangsu Province 210014, China.
authors: Yanping
authors: Y
authors: Chen
authors: Jiangsu Academy of Agricultural Sciences, Zhongling Street, Xuanwu District, Nanjing, Jiangsu Province 210014, China.
authors: Qingchang
authors: Q
authors: Meng
authors: Jiangsu Academy of Agricultural Sciences, Zhongling Street, Xuanwu District, Nanjing, Jiangsu Province 210014, China.
authors: Jirong
authors: J
authors: Wu
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China.
authors: Zhuanfang
authors: Z
authors: Hao
authors: College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang Province 150030, China.
authors: Zhenhua
authors: Z
authors: Wang
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China.
authors: Mingshun
authors: M
authors: Li
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China.
authors: Hongjun
authors: H
authors: Yong
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China.
authors: Degui
authors: D
authors: Zhang
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China.
authors: Shihuang
authors: S
authors: Zhang
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China Lixinhai@caas.cn wengjianfeng@caas.cn.
authors: Jianfeng
authors: J
authors: Weng
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China Lixinhai@caas.cn wengjianfeng@caas.cn.
authors: Xinhai
authors: X
authors: Li
mesh_terms: D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000502:physiology; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D010935:Plant Diseases / Q000821:virology*; D060888:Real-Time Polymerase Chain Reaction; D012087:Reoviridae / Q000502:physiology*; D017422:Sequence Analysis, DNA; D003313:Zea mays / Q000235:genetics / Q000378:metabolism / Q000821:virology*
chemical_list: D035683:MicroRNAs
keywords: Degradome; Rice black-streaked dwarf virus; maize; miRNA; transcriptome; virus-response.