Genome-wide gene/genome dosage imbalance regulates gene expressions in synthetic Brassica napus and derivatives (AC, AAC, CCA, CCAA)
Gene/genome dosage balance is an essential evolutionary mechanism for organisms to ensure a normal function, but the underlying causes of dosage-imbalance regulation remain poorly understood. Herein, the serial Brassica hybrids/polyploids (AC, AAC, CCA, CCAA) with different copies of A and C subgeno...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2016-09-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01432/full |
| _version_ | 1819053363106414592 |
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| author | Chen Tan Qi Pan Cheng Cui Yi Xiang Xianhong Ge Zaiyun Li |
| author_facet | Chen Tan Qi Pan Cheng Cui Yi Xiang Xianhong Ge Zaiyun Li |
| author_sort | Chen Tan |
| collection | DOAJ |
| description | Gene/genome dosage balance is an essential evolutionary mechanism for organisms to ensure a normal function, but the underlying causes of dosage-imbalance regulation remain poorly understood. Herein, the serial Brassica hybrids/polyploids (AC, AAC, CCA, CCAA) with different copies of A and C subgenomes from the same two parents of B. rapa and B. oleracea were synthesized to investigate the effects of genome dosages on gene expressions and interactions by using RNA-Seq. The expression changes of A- and C-subgenome genes were consistent with dosage alterations. Dosage-dependent and -independent genes were grouped according to the correlations between dosage variations and gene expressions. Expression levels of dosage-dependent genes were strongly correlated with dosage changes and mainly contributed to dosage effects, while those of dosage-independent genes gave weak correlations with dosage variations and mostly facilitated dosage compensation. More protein–protein interactions were detected for dosage-independent genes than dosage-dependent ones, as predicted by the dosage balance hypothesis. Dosage-dependent genes more likely impacted the expressions by trans effects, whereas dosage-independent genes preferred to play by cis effects. Furthermore, dosage-dependent genes were mainly associated with the basic biological processes to maintain the stability of the growth and development, while dosage-independent genes were more enriched in the stress response related processes to accelerate adaptation. The present comprehensive analysis of gene expression dependent/independent on dosage alterations in Brassica polyploids provided new insights into gene/genome dosage-imbalance regulation of gene expressions. |
| first_indexed | 2024-12-21T12:34:32Z |
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| id | doaj.art-77e8f663559d4c23b185c81d7c01fe4a |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-21T12:34:32Z |
| publishDate | 2016-09-01 |
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| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-77e8f663559d4c23b185c81d7c01fe4a2022-12-21T19:03:57ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2016-09-01710.3389/fpls.2016.01432211522Genome-wide gene/genome dosage imbalance regulates gene expressions in synthetic Brassica napus and derivatives (AC, AAC, CCA, CCAA)Chen Tan0Qi Pan1Cheng Cui2Yi Xiang3Xianhong Ge4Zaiyun Li5National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. ChinaNational Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. ChinaCrop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, P. R. ChinaNational Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. ChinaNational Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. ChinaNational Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. ChinaGene/genome dosage balance is an essential evolutionary mechanism for organisms to ensure a normal function, but the underlying causes of dosage-imbalance regulation remain poorly understood. Herein, the serial Brassica hybrids/polyploids (AC, AAC, CCA, CCAA) with different copies of A and C subgenomes from the same two parents of B. rapa and B. oleracea were synthesized to investigate the effects of genome dosages on gene expressions and interactions by using RNA-Seq. The expression changes of A- and C-subgenome genes were consistent with dosage alterations. Dosage-dependent and -independent genes were grouped according to the correlations between dosage variations and gene expressions. Expression levels of dosage-dependent genes were strongly correlated with dosage changes and mainly contributed to dosage effects, while those of dosage-independent genes gave weak correlations with dosage variations and mostly facilitated dosage compensation. More protein–protein interactions were detected for dosage-independent genes than dosage-dependent ones, as predicted by the dosage balance hypothesis. Dosage-dependent genes more likely impacted the expressions by trans effects, whereas dosage-independent genes preferred to play by cis effects. Furthermore, dosage-dependent genes were mainly associated with the basic biological processes to maintain the stability of the growth and development, while dosage-independent genes were more enriched in the stress response related processes to accelerate adaptation. The present comprehensive analysis of gene expression dependent/independent on dosage alterations in Brassica polyploids provided new insights into gene/genome dosage-imbalance regulation of gene expressions.http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01432/fullBrassicaGene Expressionpolyploidsdosage imbalancecis / trans effects |
| spellingShingle | Chen Tan Qi Pan Cheng Cui Yi Xiang Xianhong Ge Zaiyun Li Genome-wide gene/genome dosage imbalance regulates gene expressions in synthetic Brassica napus and derivatives (AC, AAC, CCA, CCAA) Frontiers in Plant Science Brassica Gene Expression polyploids dosage imbalance cis / trans effects |
| title | Genome-wide gene/genome dosage imbalance regulates gene expressions in synthetic Brassica napus and derivatives (AC, AAC, CCA, CCAA) |
| title_full | Genome-wide gene/genome dosage imbalance regulates gene expressions in synthetic Brassica napus and derivatives (AC, AAC, CCA, CCAA) |
| title_fullStr | Genome-wide gene/genome dosage imbalance regulates gene expressions in synthetic Brassica napus and derivatives (AC, AAC, CCA, CCAA) |
| title_full_unstemmed | Genome-wide gene/genome dosage imbalance regulates gene expressions in synthetic Brassica napus and derivatives (AC, AAC, CCA, CCAA) |
| title_short | Genome-wide gene/genome dosage imbalance regulates gene expressions in synthetic Brassica napus and derivatives (AC, AAC, CCA, CCAA) |
| title_sort | genome wide gene genome dosage imbalance regulates gene expressions in synthetic brassica napus and derivatives ac aac cca ccaa |
| topic | Brassica Gene Expression polyploids dosage imbalance cis / trans effects |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01432/full |
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