Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Digital gene expression analysis of early root infection of Sporisorium reilianum f.sp.zeae in maize based on susceptible and resistant lines

ABSTRACT: The maize smut fungus, Sporisorium reilianum f. sp. zeae, which is an important biotrophic pathogen responsible for extensive crop losses, infects maize by invading the root during the early seedling stage. In order to investigate disease-resistance mechanisms at this early seedling stage, digital gene expression (DGE) analysis, which applies a dual-enzyme approach (DpnII and NlaIII), was used to identify the transcriptional changes in roots of Huangzao4 (susceptible) and Mo17 (resistant) after inoculation with teliospores of S. reilianum. Before and after inoculation, pathogenesis-related genes were differentially regulated and enzymes involved in controlling reactive oxygen species (ROS) levels showed different activity between Huangzao4 and Mo17, which can potentially lead to changes in the growth of S. reilianum and ROS production in maize. Moreover, lignin depositions of roots were also changed differentially during root colonization of hyphae between Huangzao4 and Mo17. These results suggest that the interplays between S. reilianum and maize during the early infection stage involve many interesting transcriptional and physiological changes, which offer several novel insights for understanding the mechanisms of resistance to the fungal infection. Examination of control stage (ck), post-inoculation stage1 (P1) and post-inoculation stage2 (P2) in Huangzao4 (susceptible) and Mo17 (resistant)

ORGANISM(S): Zea mays

SUBMITTER: shaopeng zhang

PROVIDER: E-GEOD-40952 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Digital gene expression analysis of early root infection resistance to Sporisorium reilianum f. sp. zeae in maize.

Zhang Shaopeng S Xiao Yannong Y Zhao Jiuran J Wang Fengge F Zheng Yonglian Y

Molecular genetics and genomics : MGG 20121130 1-2

The maize smut fungus, Sporisorium reilianum f. sp. zeae, which is an important biotrophic pathogen responsible for extensive crop losses, can infect maize by invading the root during the early seedling stage. In order to investigate disease-resistance mechanisms at this early seedling stage, digital gene expression analysis, which applies a dual-enzyme approach, was used to identify the transcriptional changes in the roots of Huangzao4 (susceptible) and Mo17 (resistant) after root inoculation w ...[more]

PMID: 23196693

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Project description:Genome-wide expression signatures detect specific perturbations in developmental programs and contribute to functional resolution of key regulatory networks. In maize (Zea mays) inflorescences, mutations in the RAMOSA (RA) genes affect determinacy of axillary meristems and thus alter branching patterns, an important agronomic trait. In this work, we developed and tested a framework for analysis of tag-based, digital gene expression (DGE) profiles using Illumina’s high-throughput sequencing technology and the newly-assembled B73 maize reference genome. We also used a mutation in the RA3 gene to identify putative expression signatures specific to stem cell fate in determinacy of axillary meristems. The RA3 gene encodes a trehalose-6-phosphate-phosphatase and may act at the interface between developmental and metabolic processes. Deep sequencing of DGE libraries, representing three biological replicate ear samples from wild-type and ra3 plants, generated 27 million 20-21nt reads with frequencies spanning four orders of magnitude. Unique sequence tags were anchored to 3´-ends of individual transcripts by DpnII and NlaIII digests, which were multiplexed during sequencing. We mapped 86% of non-redundant signature tags to the maize genome, which associated with 37,117 working gene models and un-annotated regions of expression. 66% of maize genes were detected at ? nine reads in immature maize ears. We used comparative genomics to leverage existing information from Arabidopsis and rice in functional analyses of differentially expressed maize genes. Results from this study provide a basis for analysis of short-read expression data in maize and resolved specific expression signatures that will help define mechanisms of action for the RA3 gene. 3' tag-based DGE libraries were generated using Illumina 1G technology. Libraries were prepared from 2mm ear samples and represent: 3 biological replicates of wild-type B73, 3 biological replicates of ramosa3 (ra3) mutants, and 1 technical replicate of a ra3 sample. Each sample was sequenced in a single lane of a flow cell. Each lane includes library preparations from both DpnII and NlaIII digests for that sample. Sequences from DpnII digests start with GATC and those from NlaIII digests start with ATG.

Dataset Information

Digital gene expression analysis of early root infection of Sporisorium reilianum f.sp.zeae in maize based on susceptible and resistant lines

Publications

Digital gene expression analysis of early root infection resistance to Sporisorium reilianum f. sp. zeae in maize.

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