Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (<i>Oryza sativa</i> L.)
Heterosis is a common biological phenomenon that is useful for breeding superior lines. Using heterosis to increase the yield and quality of crops is one of the main achievements of modern agricultural science. In this study, we analysed the transcriptome and metabolome of two three-line hybrid rice...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-10-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/21/12934 |
| _version_ | 1797468046050197504 |
|---|---|
| author | Dahu Zhou Xinyi Zhou Changhui Sun Guoping Tang Lin Liu Le Chen Haohua He Qiangqiang Xiong |
| author_facet | Dahu Zhou Xinyi Zhou Changhui Sun Guoping Tang Lin Liu Le Chen Haohua He Qiangqiang Xiong |
| author_sort | Dahu Zhou |
| collection | DOAJ |
| description | Heterosis is a common biological phenomenon that is useful for breeding superior lines. Using heterosis to increase the yield and quality of crops is one of the main achievements of modern agricultural science. In this study, we analysed the transcriptome and metabolome of two three-line hybrid rice varieties, Taiyou 871 (TY871), and Taiyou 398 (TY398) and the parental grain endosperm using RNA-seq (three biological repeats per variety) and untargeted metabolomic (six biological repeats per variety) methods. TY871 and TY398 showed specific heterosis in yield and quality. Transcriptome analysis of the hybrids revealed 638 to 4059 differentially expressed genes in the grain when compared to the parents. Metabolome analysis of the hybrids revealed 657 to 3714 differential grain metabolites when compared to the parents. The honeydew1 and grey60 module core genes <i>Os04g0350700</i> and <i>Os05g0154700</i> are involved in the regulation of awn development, grain size, and grain number, as well as the regulation of grain length and plant height, respectively. Rice grain length may be an important indicator for improving the quality of three-line hybrid rice. In addition, the rice quality-related metabolite NEG_M341T662 was highly connected to the module core genes <i>Os06g0254300</i> and <i>Os03g0168100</i>. The functions of <i>Os06g0254300</i> and <i>Os03g0168100</i> are EF-hand calcium binding protein and late embroideries absolute protein repeat containing protein, respectively. These genes may play a role in the formation of rice quality. We constructed a gene and metabolite coexpression network, which provides a scientific basis for the utilization of heterosis in producing high-yield and high-quality hybrid rice. |
| first_indexed | 2024-03-09T19:01:57Z |
| format | Article |
| id | doaj.art-c8bfa9995a954c5b89e735e76f5bca43 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T19:01:57Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-c8bfa9995a954c5b89e735e76f5bca432023-11-24T05:00:00ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-10-0123211293410.3390/ijms232112934Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (<i>Oryza sativa</i> L.)Dahu Zhou0Xinyi Zhou1Changhui Sun2Guoping Tang3Lin Liu4Le Chen5Haohua He6Qiangqiang Xiong7Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, ChinaKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, ChinaJiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaJiangxi Academy of Agricultural Sciences Rice Research Institute, Nanchang 330200, ChinaKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, ChinaJiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, ChinaJiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaHeterosis is a common biological phenomenon that is useful for breeding superior lines. Using heterosis to increase the yield and quality of crops is one of the main achievements of modern agricultural science. In this study, we analysed the transcriptome and metabolome of two three-line hybrid rice varieties, Taiyou 871 (TY871), and Taiyou 398 (TY398) and the parental grain endosperm using RNA-seq (three biological repeats per variety) and untargeted metabolomic (six biological repeats per variety) methods. TY871 and TY398 showed specific heterosis in yield and quality. Transcriptome analysis of the hybrids revealed 638 to 4059 differentially expressed genes in the grain when compared to the parents. Metabolome analysis of the hybrids revealed 657 to 3714 differential grain metabolites when compared to the parents. The honeydew1 and grey60 module core genes <i>Os04g0350700</i> and <i>Os05g0154700</i> are involved in the regulation of awn development, grain size, and grain number, as well as the regulation of grain length and plant height, respectively. Rice grain length may be an important indicator for improving the quality of three-line hybrid rice. In addition, the rice quality-related metabolite NEG_M341T662 was highly connected to the module core genes <i>Os06g0254300</i> and <i>Os03g0168100</i>. The functions of <i>Os06g0254300</i> and <i>Os03g0168100</i> are EF-hand calcium binding protein and late embroideries absolute protein repeat containing protein, respectively. These genes may play a role in the formation of rice quality. We constructed a gene and metabolite coexpression network, which provides a scientific basis for the utilization of heterosis in producing high-yield and high-quality hybrid rice.https://www.mdpi.com/1422-0067/23/21/12934heterosistranscriptomemetabolomehybrid riceWGCNA |
| spellingShingle | Dahu Zhou Xinyi Zhou Changhui Sun Guoping Tang Lin Liu Le Chen Haohua He Qiangqiang Xiong Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (<i>Oryza sativa</i> L.) International Journal of Molecular Sciences heterosis transcriptome metabolome hybrid rice WGCNA |
| title | Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (<i>Oryza sativa</i> L.) |
| title_full | Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (<i>Oryza sativa</i> L.) |
| title_fullStr | Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (<i>Oryza sativa</i> L.) |
| title_full_unstemmed | Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (<i>Oryza sativa</i> L.) |
| title_short | Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (<i>Oryza sativa</i> L.) |
| title_sort | transcriptome and metabolome analysis provides insights into the heterosis of yield and quality traits in two hybrid rice varieties i oryza sativa i l |
| topic | heterosis transcriptome metabolome hybrid rice WGCNA |
| url | https://www.mdpi.com/1422-0067/23/21/12934 |
| work_keys_str_mv | AT dahuzhou transcriptomeandmetabolomeanalysisprovidesinsightsintotheheterosisofyieldandqualitytraitsintwohybridricevarietiesioryzasativail AT xinyizhou transcriptomeandmetabolomeanalysisprovidesinsightsintotheheterosisofyieldandqualitytraitsintwohybridricevarietiesioryzasativail AT changhuisun transcriptomeandmetabolomeanalysisprovidesinsightsintotheheterosisofyieldandqualitytraitsintwohybridricevarietiesioryzasativail AT guopingtang transcriptomeandmetabolomeanalysisprovidesinsightsintotheheterosisofyieldandqualitytraitsintwohybridricevarietiesioryzasativail AT linliu transcriptomeandmetabolomeanalysisprovidesinsightsintotheheterosisofyieldandqualitytraitsintwohybridricevarietiesioryzasativail AT lechen transcriptomeandmetabolomeanalysisprovidesinsightsintotheheterosisofyieldandqualitytraitsintwohybridricevarietiesioryzasativail AT haohuahe transcriptomeandmetabolomeanalysisprovidesinsightsintotheheterosisofyieldandqualitytraitsintwohybridricevarietiesioryzasativail AT qiangqiangxiong transcriptomeandmetabolomeanalysisprovidesinsightsintotheheterosisofyieldandqualitytraitsintwohybridricevarietiesioryzasativail |