Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress
The indica ecotypes, IR64, an elite drought-susceptible variety adapted to irrigated ecosystem, and Apo (IR55423-01 or NSIC RC9), a moderate drought-tolerant upland genotype together with their hybrid (IR64 × Apo) were exposed to non- and water-stress conditions. By sequencing (RNA-seq) these genoty...
| Autores principales: | , , , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2021
|
| Acceso en línea: | https://hdl.handle.net/10568/164236 |
| _version_ | 1855527810351759360 |
|---|---|
| author | Ereful, Nelzo C. Laurena, Antonio Liu, Li-Yu Kao, Shu-Min Tsai, Eric Greenland, Andy Powell, Wayne Mackay, Ian Leung, Hei |
| author_browse | Ereful, Nelzo C. Greenland, Andy Kao, Shu-Min Laurena, Antonio Leung, Hei Liu, Li-Yu Mackay, Ian Powell, Wayne Tsai, Eric |
| author_facet | Ereful, Nelzo C. Laurena, Antonio Liu, Li-Yu Kao, Shu-Min Tsai, Eric Greenland, Andy Powell, Wayne Mackay, Ian Leung, Hei |
| author_sort | Ereful, Nelzo C. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The indica ecotypes, IR64, an elite drought-susceptible variety adapted to irrigated ecosystem, and Apo (IR55423-01 or NSIC RC9), a moderate drought-tolerant upland genotype together with their hybrid (IR64 × Apo) were exposed to non- and water-stress conditions. By sequencing (RNA-seq) these genotypes, we were able to map genes diverging in cis and/or trans factors. Under non-stress condition, cis dominantly explains (11.2%) regulatory differences, followed by trans (8.9%). Further analysis showed that water-limiting condition largely affects trans and cis + trans factors. On the molecular level, cis and/or trans regulatory divergence explains their genotypic differences and differential drought response. Between the two parental genotypes, Apo appears to exhibit more photosynthetic efficiency even under water-limiting condition and is ascribed to trans. Statistical analyses showed that regulatory divergence is significantly influenced by environmental conditions. Likewise, the mode of parental expression inheritance which drives heterosis (HET) is significantly affected by environmental conditions indicating the malleability of heterosis to external factors. Further analysis revealed that the HET class, dominance, was significantly enriched under water-stress condition. We also identified allelic imbalance switching in which several genes prefer IR64- (or Apo-) specific allele under non-stress condition but switched to Apo- (or IR64-) specific allele when exposed to water-stress condition. |
| format | Journal Article |
| id | CGSpace164236 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1642362024-12-19T14:12:48Z Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress Ereful, Nelzo C. Laurena, Antonio Liu, Li-Yu Kao, Shu-Min Tsai, Eric Greenland, Andy Powell, Wayne Mackay, Ian Leung, Hei The indica ecotypes, IR64, an elite drought-susceptible variety adapted to irrigated ecosystem, and Apo (IR55423-01 or NSIC RC9), a moderate drought-tolerant upland genotype together with their hybrid (IR64 × Apo) were exposed to non- and water-stress conditions. By sequencing (RNA-seq) these genotypes, we were able to map genes diverging in cis and/or trans factors. Under non-stress condition, cis dominantly explains (11.2%) regulatory differences, followed by trans (8.9%). Further analysis showed that water-limiting condition largely affects trans and cis + trans factors. On the molecular level, cis and/or trans regulatory divergence explains their genotypic differences and differential drought response. Between the two parental genotypes, Apo appears to exhibit more photosynthetic efficiency even under water-limiting condition and is ascribed to trans. Statistical analyses showed that regulatory divergence is significantly influenced by environmental conditions. Likewise, the mode of parental expression inheritance which drives heterosis (HET) is significantly affected by environmental conditions indicating the malleability of heterosis to external factors. Further analysis revealed that the HET class, dominance, was significantly enriched under water-stress condition. We also identified allelic imbalance switching in which several genes prefer IR64- (or Apo-) specific allele under non-stress condition but switched to Apo- (or IR64-) specific allele when exposed to water-stress condition. 2021-06-29 2024-12-19T12:53:37Z 2024-12-19T12:53:37Z Journal Article https://hdl.handle.net/10568/164236 en Open Access Springer Ereful, Nelzo C.; Laurena, Antonio; Liu, Li-Yu; Kao, Shu-Min; Tsai, Eric; Greenland, Andy; Powell, Wayne; Mackay, Ian and Leung, Hei. 2021. Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress. Sci Rep, Volume 11, no. 1 |
| spellingShingle | Ereful, Nelzo C. Laurena, Antonio Liu, Li-Yu Kao, Shu-Min Tsai, Eric Greenland, Andy Powell, Wayne Mackay, Ian Leung, Hei Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress |
| title | Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress |
| title_full | Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress |
| title_fullStr | Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress |
| title_full_unstemmed | Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress |
| title_short | Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress |
| title_sort | unraveling regulatory divergence heterotic malleability and allelic imbalance switching in rice due to drought stress |
| url | https://hdl.handle.net/10568/164236 |
| work_keys_str_mv | AT erefulnelzoc unravelingregulatorydivergenceheteroticmalleabilityandallelicimbalanceswitchinginriceduetodroughtstress AT laurenaantonio unravelingregulatorydivergenceheteroticmalleabilityandallelicimbalanceswitchinginriceduetodroughtstress AT liuliyu unravelingregulatorydivergenceheteroticmalleabilityandallelicimbalanceswitchinginriceduetodroughtstress AT kaoshumin unravelingregulatorydivergenceheteroticmalleabilityandallelicimbalanceswitchinginriceduetodroughtstress AT tsaieric unravelingregulatorydivergenceheteroticmalleabilityandallelicimbalanceswitchinginriceduetodroughtstress AT greenlandandy unravelingregulatorydivergenceheteroticmalleabilityandallelicimbalanceswitchinginriceduetodroughtstress AT powellwayne unravelingregulatorydivergenceheteroticmalleabilityandallelicimbalanceswitchinginriceduetodroughtstress AT mackayian unravelingregulatorydivergenceheteroticmalleabilityandallelicimbalanceswitchinginriceduetodroughtstress AT leunghei unravelingregulatorydivergenceheteroticmalleabilityandallelicimbalanceswitchinginriceduetodroughtstress |