Genome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea
Hybrids are extensively used in agriculture to deliver an increase in yield, yet the molecular basis of heterosis is not well understood. Global DNA methylation analysis, transcriptome analysis and small RNA profiling were aimed to understand the epigenetic effect of the changes in gene expression l...
| Autores principales: | , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Wiley
2020
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/164550 |
| _version_ | 1855527323559788544 |
|---|---|
| author | Sinha, Pallavi Singh, Vikas K. Saxena, Rachit K. Kale, Sandip M. Li, Yuqi Garg, Vanika Meifang, Tang Khan, Aamir W. Kim, Kyung Do Chitikineni, Annapurna Saxena, K.B. Sameer Kumar, C.V. Liu, Xin Xu, Xun Jackson, Scott Powell, Wayne Nevo, Eviatar Searle, Iain R. Lodha, Mukesh Varshney, Rajeev K. |
| author_browse | Chitikineni, Annapurna Garg, Vanika Jackson, Scott Kale, Sandip M. Khan, Aamir W. Kim, Kyung Do Li, Yuqi Liu, Xin Lodha, Mukesh Meifang, Tang Nevo, Eviatar Powell, Wayne Sameer Kumar, C.V. Saxena, K.B. Saxena, Rachit K. Searle, Iain R. Singh, Vikas K. Sinha, Pallavi Varshney, Rajeev K. Xu, Xun |
| author_facet | Sinha, Pallavi Singh, Vikas K. Saxena, Rachit K. Kale, Sandip M. Li, Yuqi Garg, Vanika Meifang, Tang Khan, Aamir W. Kim, Kyung Do Chitikineni, Annapurna Saxena, K.B. Sameer Kumar, C.V. Liu, Xin Xu, Xun Jackson, Scott Powell, Wayne Nevo, Eviatar Searle, Iain R. Lodha, Mukesh Varshney, Rajeev K. |
| author_sort | Sinha, Pallavi |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Hybrids are extensively used in agriculture to deliver an increase in yield, yet the molecular basis of heterosis is not well understood. Global DNA methylation analysis, transcriptome analysis and small RNA profiling were aimed to understand the epigenetic effect of the changes in gene expression level in the two hybrids and their parental lines. Increased DNA methylation was observed in both the hybrids as compared to their parents. This increased DNA methylation in hybrids showed that majority of the 24‐nt siRNA clusters had higher expression in hybrids than the parents. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) responsive hybrid‐MPV DEGs were significantly altered in both the hybrids in comparison to MPV. DEGs associated with plant immunity and growth were overexpressed whereas DEGs associated with basal defence level were repressed. This antagonistic patterns of gene expression might contribute to the greater growth of the hybrids. It was also noticed that some common as well as unique changes in the regulatory pathways were associated with heterotic growth in both the hybrids. Approximately 70% and 67% of down‐regulated hybrid‐MPV DEGs were found to be differentially methylated in ICPH 2671 and ICPH 2740 hybrid, respectively. This reflected the association of epigenetic regulation in altered gene expressions. Our findings also revealed that miRNAs might play important roles in hybrid vigour in both the hybrids by regulating their target genes, especially in controlling plant growth and development, defence and stress response pathways. The above finding provides an insight into the molecular mechanism of pigeonpea heterosis. |
| format | Journal Article |
| id | CGSpace164550 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace1645502025-12-08T09:54:28Z Genome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea Sinha, Pallavi Singh, Vikas K. Saxena, Rachit K. Kale, Sandip M. Li, Yuqi Garg, Vanika Meifang, Tang Khan, Aamir W. Kim, Kyung Do Chitikineni, Annapurna Saxena, K.B. Sameer Kumar, C.V. Liu, Xin Xu, Xun Jackson, Scott Powell, Wayne Nevo, Eviatar Searle, Iain R. Lodha, Mukesh Varshney, Rajeev K. agronomy crop science biotechnology plant science Hybrids are extensively used in agriculture to deliver an increase in yield, yet the molecular basis of heterosis is not well understood. Global DNA methylation analysis, transcriptome analysis and small RNA profiling were aimed to understand the epigenetic effect of the changes in gene expression level in the two hybrids and their parental lines. Increased DNA methylation was observed in both the hybrids as compared to their parents. This increased DNA methylation in hybrids showed that majority of the 24‐nt siRNA clusters had higher expression in hybrids than the parents. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) responsive hybrid‐MPV DEGs were significantly altered in both the hybrids in comparison to MPV. DEGs associated with plant immunity and growth were overexpressed whereas DEGs associated with basal defence level were repressed. This antagonistic patterns of gene expression might contribute to the greater growth of the hybrids. It was also noticed that some common as well as unique changes in the regulatory pathways were associated with heterotic growth in both the hybrids. Approximately 70% and 67% of down‐regulated hybrid‐MPV DEGs were found to be differentially methylated in ICPH 2671 and ICPH 2740 hybrid, respectively. This reflected the association of epigenetic regulation in altered gene expressions. Our findings also revealed that miRNAs might play important roles in hybrid vigour in both the hybrids by regulating their target genes, especially in controlling plant growth and development, defence and stress response pathways. The above finding provides an insight into the molecular mechanism of pigeonpea heterosis. 2020-08 2024-12-19T12:54:01Z 2024-12-19T12:54:01Z Journal Article https://hdl.handle.net/10568/164550 en Open Access Wiley Sinha, Pallavi; Singh, Vikas K.; Saxena, Rachit K.; Kale, Sandip M.; Li, Yuqi; Garg, Vanika; Meifang, Tang; Khan, Aamir W.; Kim, Kyung Do; Chitikineni, Annapurna; Saxena, K. B.; Sameer Kumar, C. V.; Liu, Xin; Xu, Xun; Jackson, Scott; Powell, Wayne; Nevo, Eviatar; Searle, Iain R.; Lodha, Mukesh and Varshney, Rajeev K. 2020. Genome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea. Plant Biotechnology Journal, Volume 18 no. 8 p. 1697-1710 |
| spellingShingle | agronomy crop science biotechnology plant science Sinha, Pallavi Singh, Vikas K. Saxena, Rachit K. Kale, Sandip M. Li, Yuqi Garg, Vanika Meifang, Tang Khan, Aamir W. Kim, Kyung Do Chitikineni, Annapurna Saxena, K.B. Sameer Kumar, C.V. Liu, Xin Xu, Xun Jackson, Scott Powell, Wayne Nevo, Eviatar Searle, Iain R. Lodha, Mukesh Varshney, Rajeev K. Genome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea |
| title | Genome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea |
| title_full | Genome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea |
| title_fullStr | Genome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea |
| title_full_unstemmed | Genome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea |
| title_short | Genome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea |
| title_sort | genome wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea |
| topic | agronomy crop science biotechnology plant science |
| url | https://hdl.handle.net/10568/164550 |
| work_keys_str_mv | AT sinhapallavi genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT singhvikask genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT saxenarachitk genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT kalesandipm genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT liyuqi genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT gargvanika genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT meifangtang genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT khanaamirw genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT kimkyungdo genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT chitikineniannapurna genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT saxenakb genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT sameerkumarcv genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT liuxin genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT xuxun genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT jacksonscott genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT powellwayne genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT nevoeviatar genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT searleiainr genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT lodhamukesh genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea AT varshneyrajeevk genomewideanalysisofepigeneticandtranscriptionalchangesassociatedwithheterosisinpigeonpea |