Genetic analysis for the grain number heterosis of a super-hybrid rice WFYT025 combination using RNA-Seq
Abstract Background Despite the great contributions of utilizing heterosis to crop productivity worldwide, the molecular mechanism of heterosis remains largely unexplored. Thus, the present research is focused on the grain number heterosis of a widely used late-cropping indica super hybrid rice comb...
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| Format: | Article |
| Language: | English |
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SpringerOpen
2018-06-01
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| Series: | Rice |
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| Online Access: | http://link.springer.com/article/10.1186/s12284-018-0229-y |
| _version_ | 1818195742634803200 |
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| author | Liang Chen Jianmin Bian Shilai Shi Jianfeng Yu Hira Khanzada Ghulam Mustafa Wassan Changlan Zhu Xin Luo Shan Tong Xiaorong Yang Xiaosong Peng Shuang Yong Qiuying Yu Xiaopeng He Junru Fu Xiaorong Chen Lifang Hu Linjuan Ouyang Haohua He |
| author_facet | Liang Chen Jianmin Bian Shilai Shi Jianfeng Yu Hira Khanzada Ghulam Mustafa Wassan Changlan Zhu Xin Luo Shan Tong Xiaorong Yang Xiaosong Peng Shuang Yong Qiuying Yu Xiaopeng He Junru Fu Xiaorong Chen Lifang Hu Linjuan Ouyang Haohua He |
| author_sort | Liang Chen |
| collection | DOAJ |
| description | Abstract Background Despite the great contributions of utilizing heterosis to crop productivity worldwide, the molecular mechanism of heterosis remains largely unexplored. Thus, the present research is focused on the grain number heterosis of a widely used late-cropping indica super hybrid rice combination in China using a high-throughput next-generation RNA-seq strategy. Results Here, we obtained 872 million clean reads, and at least one read could maps 27,917 transcripts out of 35,679 annotations. Transcript differential expression analysis revealed a total of 5910 differentially expressed genes (DGHP) between super-hybrid rice Wufengyou T025 (WFYT025) and its parents were identified in the young panicles. Out of the 5910 DGHP, 63.1% had a genetic action mode of over-dominance, 17.3% had a complete-dominance action, 15.6% had a partial-dominance action and 4.0% had an additive action. DGHP were significantly enriched in carotenoid biosynthesis, diterpenoid biosynthesis and plant hormone signal transduction pathways, with the key genes involved in the three pathways being up-regulated in the hybrid. By comparing the DGHP enriched in the KEGG pathway with QTLs associated with grain number, several DGHP were located on the same chromosomal segment with some of these grain number QTLs. Conclusion Through young panicle development transcriptome analysis, we conclude that the over-dominant effect is probably the major contributor to the grain number heterosis of WFYT025. The DGHP sharing the same location with grain number QTLs could be considered a candidate gene and provide valuable targets for the cloning and functional analysis of these grain number QTLs. |
| first_indexed | 2024-12-12T01:23:01Z |
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| id | doaj.art-b010ea4314264e0b8680b3975ca3433b |
| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-12-12T01:23:01Z |
| publishDate | 2018-06-01 |
| publisher | SpringerOpen |
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| series | Rice |
| spelling | doaj.art-b010ea4314264e0b8680b3975ca3433b2022-12-22T00:43:10ZengSpringerOpenRice1939-84251939-84332018-06-0111111310.1186/s12284-018-0229-yGenetic analysis for the grain number heterosis of a super-hybrid rice WFYT025 combination using RNA-SeqLiang Chen0Jianmin Bian1Shilai Shi2Jianfeng Yu3Hira Khanzada4Ghulam Mustafa Wassan5Changlan Zhu6Xin Luo7Shan Tong8Xiaorong Yang9Xiaosong Peng10Shuang Yong11Qiuying Yu12Xiaopeng He13Junru Fu14Xiaorong Chen15Lifang Hu16Linjuan Ouyang17Haohua He18Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural UniversityAbstract Background Despite the great contributions of utilizing heterosis to crop productivity worldwide, the molecular mechanism of heterosis remains largely unexplored. Thus, the present research is focused on the grain number heterosis of a widely used late-cropping indica super hybrid rice combination in China using a high-throughput next-generation RNA-seq strategy. Results Here, we obtained 872 million clean reads, and at least one read could maps 27,917 transcripts out of 35,679 annotations. Transcript differential expression analysis revealed a total of 5910 differentially expressed genes (DGHP) between super-hybrid rice Wufengyou T025 (WFYT025) and its parents were identified in the young panicles. Out of the 5910 DGHP, 63.1% had a genetic action mode of over-dominance, 17.3% had a complete-dominance action, 15.6% had a partial-dominance action and 4.0% had an additive action. DGHP were significantly enriched in carotenoid biosynthesis, diterpenoid biosynthesis and plant hormone signal transduction pathways, with the key genes involved in the three pathways being up-regulated in the hybrid. By comparing the DGHP enriched in the KEGG pathway with QTLs associated with grain number, several DGHP were located on the same chromosomal segment with some of these grain number QTLs. Conclusion Through young panicle development transcriptome analysis, we conclude that the over-dominant effect is probably the major contributor to the grain number heterosis of WFYT025. The DGHP sharing the same location with grain number QTLs could be considered a candidate gene and provide valuable targets for the cloning and functional analysis of these grain number QTLs.http://link.springer.com/article/10.1186/s12284-018-0229-yRiceSuper-hybrid RiceHeterosisGrain numberRNA-seq |
| spellingShingle | Liang Chen Jianmin Bian Shilai Shi Jianfeng Yu Hira Khanzada Ghulam Mustafa Wassan Changlan Zhu Xin Luo Shan Tong Xiaorong Yang Xiaosong Peng Shuang Yong Qiuying Yu Xiaopeng He Junru Fu Xiaorong Chen Lifang Hu Linjuan Ouyang Haohua He Genetic analysis for the grain number heterosis of a super-hybrid rice WFYT025 combination using RNA-Seq Rice Rice Super-hybrid Rice Heterosis Grain number RNA-seq |
| title | Genetic analysis for the grain number heterosis of a super-hybrid rice WFYT025 combination using RNA-Seq |
| title_full | Genetic analysis for the grain number heterosis of a super-hybrid rice WFYT025 combination using RNA-Seq |
| title_fullStr | Genetic analysis for the grain number heterosis of a super-hybrid rice WFYT025 combination using RNA-Seq |
| title_full_unstemmed | Genetic analysis for the grain number heterosis of a super-hybrid rice WFYT025 combination using RNA-Seq |
| title_short | Genetic analysis for the grain number heterosis of a super-hybrid rice WFYT025 combination using RNA-Seq |
| title_sort | genetic analysis for the grain number heterosis of a super hybrid rice wfyt025 combination using rna seq |
| topic | Rice Super-hybrid Rice Heterosis Grain number RNA-seq |
| url | http://link.springer.com/article/10.1186/s12284-018-0229-y |
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