Effect of the B chromosome-located long non-coding RNAs on gene expression in maize
Using artificial chromosomes in maize breeding allows for site-specific integration of multigene stacks, effectively overcoming the limitations of conventional transgenic approaches. The maize B chromosome, which is dispensable and highly heterochromatic, has minimal impact on phenotypes at low copy...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-02-01
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| Series: | Crop Design |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2772899424000405 |
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| author | Xin Liu Wenjie Yue Shiqi Lin Yuxian Yang Tong Chen Xiaowen Shi |
| author_facet | Xin Liu Wenjie Yue Shiqi Lin Yuxian Yang Tong Chen Xiaowen Shi |
| author_sort | Xin Liu |
| collection | DOAJ |
| description | Using artificial chromosomes in maize breeding allows for site-specific integration of multigene stacks, effectively overcoming the limitations of conventional transgenic approaches. The maize B chromosome, which is dispensable and highly heterochromatic, has minimal impact on phenotypes at low copy numbers, making it a promising platform for engineering artificial chromosomes. However, recent studies have demonstrated that the maize B chromosome can impact gene expression and recombination on the A chromosome. Understanding the genetic characteristics of the B chromosomes and their impact on gene expression is essential for their application in artificial chromosome construction. Despite advancements in elucidating how the B chromosome affects A chromosome expression, the role of long non-coding RNAs (lncRNAs) in this context remains unclear. In this study, we analyzed the RNA-seq data from leaf tissue of plants with 0–7 B chromosomes, identifying a total of 1614 lncRNAs, including 1516 A chromosome-located and 98 B chromosome-located lncRNAs, 72 of which are specific to the B chromosome. While A-located lncRNAs show greater dependence on the mere presence of the B chromosome, the expression of B-located lncRNAs is significantly affected by the number of B chromosomes present. Regulatory networks constructed in this study suggest that B-located lncRNAs may drive the differential expression of A chromosome-located transcription factors and genes associated with circadian rhythm regulation, indicating their regulatory role in A chromosome gene expression. |
| format | Article |
| id | doaj-art-123bd3bab2654f3db993c42582a90162 |
| institution | Kabale University |
| issn | 2772-8994 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Crop Design |
| spelling | doaj-art-123bd3bab2654f3db993c42582a901622025-01-24T04:46:04ZengElsevierCrop Design2772-89942025-02-0141100091Effect of the B chromosome-located long non-coding RNAs on gene expression in maizeXin Liu0Wenjie Yue1Shiqi Lin2Yuxian Yang3Tong Chen4Xiaowen Shi5College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, ChinaCollege of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, ChinaCollege of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, ChinaCollege of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, ChinaCollege of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, ChinaCorresponding author.; College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, ChinaUsing artificial chromosomes in maize breeding allows for site-specific integration of multigene stacks, effectively overcoming the limitations of conventional transgenic approaches. The maize B chromosome, which is dispensable and highly heterochromatic, has minimal impact on phenotypes at low copy numbers, making it a promising platform for engineering artificial chromosomes. However, recent studies have demonstrated that the maize B chromosome can impact gene expression and recombination on the A chromosome. Understanding the genetic characteristics of the B chromosomes and their impact on gene expression is essential for their application in artificial chromosome construction. Despite advancements in elucidating how the B chromosome affects A chromosome expression, the role of long non-coding RNAs (lncRNAs) in this context remains unclear. In this study, we analyzed the RNA-seq data from leaf tissue of plants with 0–7 B chromosomes, identifying a total of 1614 lncRNAs, including 1516 A chromosome-located and 98 B chromosome-located lncRNAs, 72 of which are specific to the B chromosome. While A-located lncRNAs show greater dependence on the mere presence of the B chromosome, the expression of B-located lncRNAs is significantly affected by the number of B chromosomes present. Regulatory networks constructed in this study suggest that B-located lncRNAs may drive the differential expression of A chromosome-located transcription factors and genes associated with circadian rhythm regulation, indicating their regulatory role in A chromosome gene expression.http://www.sciencedirect.com/science/article/pii/S2772899424000405B chromosomeMaizelncRNAsRegulatory networkDosage effect |
| spellingShingle | Xin Liu Wenjie Yue Shiqi Lin Yuxian Yang Tong Chen Xiaowen Shi Effect of the B chromosome-located long non-coding RNAs on gene expression in maize Crop Design B chromosome Maize lncRNAs Regulatory network Dosage effect |
| title | Effect of the B chromosome-located long non-coding RNAs on gene expression in maize |
| title_full | Effect of the B chromosome-located long non-coding RNAs on gene expression in maize |
| title_fullStr | Effect of the B chromosome-located long non-coding RNAs on gene expression in maize |
| title_full_unstemmed | Effect of the B chromosome-located long non-coding RNAs on gene expression in maize |
| title_short | Effect of the B chromosome-located long non-coding RNAs on gene expression in maize |
| title_sort | effect of the b chromosome located long non coding rnas on gene expression in maize |
| topic | B chromosome Maize lncRNAs Regulatory network Dosage effect |
| url | http://www.sciencedirect.com/science/article/pii/S2772899424000405 |
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