Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids
Abstract Background In diverse plant taxa, whole-genome duplication (WGD) events are major sources of phenotypic novelty. Studies of gene expression in synthetic polyploids have shown immediate expression and functional partitioning of duplicated genes among different tissues. Many studies of the ti...
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BMC
2018-10-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-5150-7 |
| _version_ | 1828917795391275008 |
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| author | Long Zhao Lei Han Chaoxia Xiao Xiuyun Lin Chunming Xu Chunwu Yang |
| author_facet | Long Zhao Lei Han Chaoxia Xiao Xiuyun Lin Chunming Xu Chunwu Yang |
| author_sort | Long Zhao |
| collection | DOAJ |
| description | Abstract Background In diverse plant taxa, whole-genome duplication (WGD) events are major sources of phenotypic novelty. Studies of gene expression in synthetic polyploids have shown immediate expression and functional partitioning of duplicated genes among different tissues. Many studies of the tissue-specific homeolog expression partitioning have focused on allopolyploids that have very different parental genomes, while few studies have focused on autopolyploids or allopolyploids that have similar parental genomes. Results In this study, we used a set of reciprocal F1 hybrids and synthetic tetraploids constructed from subspecies (japonica and indica) of Asian rice (Oryza sativa L.) as a model to gain insights into the expression partitioning of homeologs among tissues in a developmental context. We assayed the tissue-specific silencing (TSS) of the parental homeologs of 30 key genes in the hybrids and tetraploids relative to the in vitro “hybrids” (parental mixes) using Sequenom MassARRAY. We found that the parental mix and synthetic tetraploids had higher frequencies of homeolog TSS than the F1, revealing an instantaneous role of WGD on homeolog expression partitioning. Conclusions Our observations contradicted those of previous studies in which newly formed allopolyploids had a low TSS frequency, similar to that of F1 hybrids, suggesting that the impact of WGD on homeolog expression requires a longer time to manifest. In addition, we found that the TSS frequency in the tetraploids varied at different growth stages and that roots had a much higher frequency of TSS than leaves, which indicated that developmental and metabolic traits may influence the expression states of duplicated genes in newly formed plant polyploids. |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T20:57:52Z |
| publishDate | 2018-10-01 |
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| series | BMC Genomics |
| spelling | doaj.art-1ad89fb2f1944ddaa41c83452aa7d7bd2022-12-21T23:31:40ZengBMCBMC Genomics1471-21642018-10-0119111010.1186/s12864-018-5150-7Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploidsLong Zhao0Lei Han1Chaoxia Xiao2Xiuyun Lin3Chunming Xu4Chunwu Yang5Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal UniversityKey laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal UniversityKey laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal UniversityKey laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal UniversityKey laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal UniversityKey laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal UniversityAbstract Background In diverse plant taxa, whole-genome duplication (WGD) events are major sources of phenotypic novelty. Studies of gene expression in synthetic polyploids have shown immediate expression and functional partitioning of duplicated genes among different tissues. Many studies of the tissue-specific homeolog expression partitioning have focused on allopolyploids that have very different parental genomes, while few studies have focused on autopolyploids or allopolyploids that have similar parental genomes. Results In this study, we used a set of reciprocal F1 hybrids and synthetic tetraploids constructed from subspecies (japonica and indica) of Asian rice (Oryza sativa L.) as a model to gain insights into the expression partitioning of homeologs among tissues in a developmental context. We assayed the tissue-specific silencing (TSS) of the parental homeologs of 30 key genes in the hybrids and tetraploids relative to the in vitro “hybrids” (parental mixes) using Sequenom MassARRAY. We found that the parental mix and synthetic tetraploids had higher frequencies of homeolog TSS than the F1, revealing an instantaneous role of WGD on homeolog expression partitioning. Conclusions Our observations contradicted those of previous studies in which newly formed allopolyploids had a low TSS frequency, similar to that of F1 hybrids, suggesting that the impact of WGD on homeolog expression requires a longer time to manifest. In addition, we found that the TSS frequency in the tetraploids varied at different growth stages and that roots had a much higher frequency of TSS than leaves, which indicated that developmental and metabolic traits may influence the expression states of duplicated genes in newly formed plant polyploids.http://link.springer.com/article/10.1186/s12864-018-5150-7RiceWhole-genome duplicationHomeologous expressionDevelopmentTissue-specific silence |
| spellingShingle | Long Zhao Lei Han Chaoxia Xiao Xiuyun Lin Chunming Xu Chunwu Yang Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids BMC Genomics Rice Whole-genome duplication Homeologous expression Development Tissue-specific silence |
| title | Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids |
| title_full | Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids |
| title_fullStr | Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids |
| title_full_unstemmed | Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids |
| title_short | Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids |
| title_sort | rapid and pervasive development and tissue specific homeolog expression partitioning in newly formed inter subspecific rice segmental allotetraploids |
| topic | Rice Whole-genome duplication Homeologous expression Development Tissue-specific silence |
| url | http://link.springer.com/article/10.1186/s12864-018-5150-7 |
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