Transcriptomic analysis of genes in soybean in response to Peronospora manshurica infection
Abstract Background Soybean downy mildew (SDM), caused by Peronospora manshurica (Pm), is a major fungal disease in soybean. To date, little is known regarding the defense mechanism at molecular level and how soybean plants response to Pm infection. In this study, differential gene expression in SDM...
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| Format: | Article |
| Language: | English |
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BMC
2018-05-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-018-4741-7 |
| _version_ | 1811201382046236672 |
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| author | Hang Dong Shuangfeng Shi Chong Zhang Sihui Zhu Mei Li Jie Tan Yue Yu Liping Lin Shirong Jia Xujing Wang Yuanhua Wu Yuhui Liu |
| author_facet | Hang Dong Shuangfeng Shi Chong Zhang Sihui Zhu Mei Li Jie Tan Yue Yu Liping Lin Shirong Jia Xujing Wang Yuanhua Wu Yuhui Liu |
| author_sort | Hang Dong |
| collection | DOAJ |
| description | Abstract Background Soybean downy mildew (SDM), caused by Peronospora manshurica (Pm), is a major fungal disease in soybean. To date, little is known regarding the defense mechanism at molecular level and how soybean plants response to Pm infection. In this study, differential gene expression in SDM-resistant (HR) and SDM-susceptible (HS) genotype was analyzed by RNA-seq to identify differentially expressed genes (DEGs) following Pm infection. Results Of a total of 55,017 genes mapped to the soybean reference genome sequences, 2581 DEGs were identified. Clustering analysis of DEGs revealed that these genes could be grouped into 8 clusters with distinct expression patterns. Functional annotation based on gene ontology (GO) and KEGG analysis indicated they involved in diverse metabolism pathways. Of particular interest were the detected DEGs participating in SA/ROS and JA signalling transduction and plant/pathogen interaction. Conclusion Totally, 52 DEGs with P value < 0.001 and log2 fold change > 2 or < − 2 upon fungal inoculation were identified, suggesting they were SDM defense responsive genes. These findings have paved way in further functional characterization of candidate genes and subsequently can be used in breeding of elite soybean varieties with better SDM-resistance. |
| first_indexed | 2024-04-12T02:21:03Z |
| format | Article |
| id | doaj.art-577c575d8ae34787b1d69ed206e95e8b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-12T02:21:03Z |
| publishDate | 2018-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-577c575d8ae34787b1d69ed206e95e8b2022-12-22T03:52:07ZengBMCBMC Genomics1471-21642018-05-0119111310.1186/s12864-018-4741-7Transcriptomic analysis of genes in soybean in response to Peronospora manshurica infectionHang Dong0Shuangfeng Shi1Chong Zhang2Sihui Zhu3Mei Li4Jie Tan5Yue Yu6Liping Lin7Shirong Jia8Xujing Wang9Yuanhua Wu10Yuhui Liu11Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBiotechnology Research Institute, Chinese Academy of Agricultural SciencesCollege of Plant Protection, Shenyang Agricultural UniversityBiotechnology Research Institute, Chinese Academy of Agricultural SciencesBiotechnology Research Institute, Chinese Academy of Agricultural SciencesBiotechnology Research Institute, Chinese Academy of Agricultural SciencesSchool of Biotechnology, East China University of Science and TechnologyBiotechnology Research Institute, Chinese Academy of Agricultural SciencesBiotechnology Research Institute, Chinese Academy of Agricultural SciencesBiotechnology Research Institute, Chinese Academy of Agricultural SciencesCollege of Plant Protection, Shenyang Agricultural UniversityBiotechnology Research Institute, Chinese Academy of Agricultural SciencesAbstract Background Soybean downy mildew (SDM), caused by Peronospora manshurica (Pm), is a major fungal disease in soybean. To date, little is known regarding the defense mechanism at molecular level and how soybean plants response to Pm infection. In this study, differential gene expression in SDM-resistant (HR) and SDM-susceptible (HS) genotype was analyzed by RNA-seq to identify differentially expressed genes (DEGs) following Pm infection. Results Of a total of 55,017 genes mapped to the soybean reference genome sequences, 2581 DEGs were identified. Clustering analysis of DEGs revealed that these genes could be grouped into 8 clusters with distinct expression patterns. Functional annotation based on gene ontology (GO) and KEGG analysis indicated they involved in diverse metabolism pathways. Of particular interest were the detected DEGs participating in SA/ROS and JA signalling transduction and plant/pathogen interaction. Conclusion Totally, 52 DEGs with P value < 0.001 and log2 fold change > 2 or < − 2 upon fungal inoculation were identified, suggesting they were SDM defense responsive genes. These findings have paved way in further functional characterization of candidate genes and subsequently can be used in breeding of elite soybean varieties with better SDM-resistance.http://link.springer.com/article/10.1186/s12864-018-4741-7Soybean downy mildewRNA-seq analysisDifferentially expressed genesTranscription factorsDisease resistanceSoybean |
| spellingShingle | Hang Dong Shuangfeng Shi Chong Zhang Sihui Zhu Mei Li Jie Tan Yue Yu Liping Lin Shirong Jia Xujing Wang Yuanhua Wu Yuhui Liu Transcriptomic analysis of genes in soybean in response to Peronospora manshurica infection BMC Genomics Soybean downy mildew RNA-seq analysis Differentially expressed genes Transcription factors Disease resistance Soybean |
| title | Transcriptomic analysis of genes in soybean in response to Peronospora manshurica infection |
| title_full | Transcriptomic analysis of genes in soybean in response to Peronospora manshurica infection |
| title_fullStr | Transcriptomic analysis of genes in soybean in response to Peronospora manshurica infection |
| title_full_unstemmed | Transcriptomic analysis of genes in soybean in response to Peronospora manshurica infection |
| title_short | Transcriptomic analysis of genes in soybean in response to Peronospora manshurica infection |
| title_sort | transcriptomic analysis of genes in soybean in response to peronospora manshurica infection |
| topic | Soybean downy mildew RNA-seq analysis Differentially expressed genes Transcription factors Disease resistance Soybean |
| url | http://link.springer.com/article/10.1186/s12864-018-4741-7 |
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