Genome Research
Abstract
Ribosomal repeats occupy 5% of a plant genome, yet there has been little study of their diversity in the modern age of genomics. Ribosomal copy number and expression variations present an opportunity to tap a novel source of diversity. In the present study, we estimated the ribosomal DNA copy (rDNA) number and ribosomal RNA (rRNA) expression for a population of maize inbred lines, and investigated the potential role of rDNA and rRNA dosage in regulating global gene expression. Extensive variations were found in both ribosomal DNA copy number and ribosomal RNA expression among maize inbred lines. However, rRNA abundance was not consistent with the copy number of the rDNA. We have not found that the rDNA gene dosage has regulatory role in gene expression; however, thousands of genes are identified to be co-regulated with rRNA expression, including genes participating in ribosome biogenesis and other functionally relevant pathways. We further investigated the potential roles of copy number and the expression level of rDNA on agronomic traits, and found that both correlated with flowering time, but through different regulatory mechanisms. This comprehensive analysis suggested that rRNA expression variation is a valuable source of functional diversity that affects gene expression variation and field-based phenotypic changes.
| 论文编号: | DOI:10.1101/gr.229716.117 |
| 论文题目: | Co-regulation of Ribosomal RNA with Hundreds of Ggenes Contributes to Phenotypic Variations |
| 英文论文题目: | Co-regulation of Ribosomal RNA with Hundreds of Ggenes Contributes to Phenotypic Variations |
| 第一作者: | Bo Li, Karl Kremling, Penghao Wu, Robert Bukowski, Maria Romay, En Xie, Edward Buckler, and Mingsheng Chen |
| 英文第一作者: | Bo Li, Karl Kremling, Penghao Wu, Robert Bukowski, Maria Romay, En Xie, Edward Buckler, and Mingsheng Chen |
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| 发表年度: | 2018-09-04 |
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| 摘要: | Ribosomal repeats occupy 5% of a plant genome, yet there has been little study of their diversity in the modern age of genomics. Ribosomal copy number and expression variations present an opportunity to tap a novel source of diversity. In the present study, we estimated the ribosomal DNA copy (rDNA) number and ribosomal RNA (rRNA) expression for a population of maize inbred lines, and investigated the potential role of rDNA and rRNA dosage in regulating global gene expression. Extensive variations were found in both ribosomal DNA copy number and ribosomal RNA expression among maize inbred lines. However, rRNA abundance was not consistent with the copy number of the rDNA. We have not found that the rDNA gene dosage has regulatory role in gene expression; however, thousands of genes are identified to be co-regulated with rRNA expression, including genes participating in ribosome biogenesis and other functionally relevant pathways. We further investigated the potential roles of copy number and the expression level of rDNA on agronomic traits, and found that both correlated with flowering time, but through different regulatory mechanisms. This comprehensive analysis suggested that rRNA expression variation is a valuable source of functional diversity that affects gene expression variation and field-based phenotypic changes. |
| 英文摘要: | Ribosomal repeats occupy 5% of a plant genome, yet there has been little study of their diversity in the modern age of genomics. Ribosomal copy number and expression variations present an opportunity to tap a novel source of diversity. In the present study, we estimated the ribosomal DNA copy (rDNA) number and ribosomal RNA (rRNA) expression for a population of maize inbred lines, and investigated the potential role of rDNA and rRNA dosage in regulating global gene expression. Extensive variations were found in both ribosomal DNA copy number and ribosomal RNA expression among maize inbred lines. However, rRNA abundance was not consistent with the copy number of the rDNA. We have not found that the rDNA gene dosage has regulatory role in gene expression; however, thousands of genes are identified to be co-regulated with rRNA expression, including genes participating in ribosome biogenesis and other functionally relevant pathways. We further investigated the potential roles of copy number and the expression level of rDNA on agronomic traits, and found that both correlated with flowering time, but through different regulatory mechanisms. This comprehensive analysis suggested that rRNA expression variation is a valuable source of functional diversity that affects gene expression variation and field-based phenotypic changes. |
| 刊物名称: | Genome Research |
| 英文刊物名称: | Genome Research |
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| 其它备注: | Bo Li, Karl Kremling, Penghao Wu, Robert Bukowski, Maria Romay, En Xie, Edward Buckler, and Mingsheng Chen. Co-regulation of Ribosomal RNA with Hundreds of Ggenes Contributes to Phenotypic Variations. Genome Research. DOI:10.1101/gr.229716.117 |
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