Allele-Specific Transcriptional Regulation of Shoot Regeneration in Hybrid Poplar
Plant tissue regeneration is a key process for genetic transformation and genome editing. The exploration of regulatory mechanisms in plant regeneration would improve regeneration efficiency. In comparison to some model plants, the genomic heterozygosity is much higher in forest trees, increasing th...
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| Format: | Article |
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MDPI AG
2023-11-01
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| Series: | Forests |
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| Online Access: | https://www.mdpi.com/1999-4907/14/11/2195 |
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| author | Xiawei Ding Chengjin Wen Ganggui Yang Ying Guo Liangjiao Xue |
| author_facet | Xiawei Ding Chengjin Wen Ganggui Yang Ying Guo Liangjiao Xue |
| author_sort | Xiawei Ding |
| collection | DOAJ |
| description | Plant tissue regeneration is a key process for genetic transformation and genome editing. The exploration of regulatory mechanisms in plant regeneration would improve regeneration efficiency. In comparison to some model plants, the genomic heterozygosity is much higher in forest trees, increasing the complexity of transcriptional regulation. Here, we report the allele-specific transcriptional analysis in hybrid poplar 84K (<i>Populus alba</i> × <i>P. tremula</i> var. <i>glandulosa</i> cv. 84K) during the shoot regeneration process. Firstly, 180 regeneration-related genes (REGs) and 2446 REG-homologous genes (REGHs) were identified in hybrid poplar. The expression patterns of REGs exhibited that about half of them were positively correlated between poplar and <i>Arabidopsis</i> at the locus level. The expression levels of REGHs vary among the gene family at different stages during callus and shoot induction. Among the gene clusters with similar expression patterns, the distribution of gene families in poplar and <i>Arabidopsis</i> also exhibits large variations. At the allele level, most of the allele pairs of REGs were positively correlated in expression. The expression patterns of genes in auxin synthesis, transport, and signaling pathways agree with the general patterns. Due to the presence/absence of variations between two subgenomes, two <i>YUC</i> alleles and two <i>IAA</i> alleles are present only in one subgenome, and the expression patterns of the two alleles are greatly different. Our analysis indicates the conservativeness and diversity of transcriptional regulation during shoot regeneration in poplar and <i>Arabidopsis</i>. The complexity in allele expression contributed by heterozygosity suggests the importance of genotyping in the screening of explants for plant regeneration. |
| first_indexed | 2024-03-09T16:49:27Z |
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| institution | Directory Open Access Journal |
| issn | 1999-4907 |
| language | English |
| last_indexed | 2024-03-09T16:49:27Z |
| publishDate | 2023-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Forests |
| spelling | doaj.art-ff31a280ace3489cb308933b717e283b2023-11-24T14:42:39ZengMDPI AGForests1999-49072023-11-011411219510.3390/f14112195Allele-Specific Transcriptional Regulation of Shoot Regeneration in Hybrid PoplarXiawei Ding0Chengjin Wen1Ganggui Yang2Ying Guo3Liangjiao Xue4State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, ChinaPlant tissue regeneration is a key process for genetic transformation and genome editing. The exploration of regulatory mechanisms in plant regeneration would improve regeneration efficiency. In comparison to some model plants, the genomic heterozygosity is much higher in forest trees, increasing the complexity of transcriptional regulation. Here, we report the allele-specific transcriptional analysis in hybrid poplar 84K (<i>Populus alba</i> × <i>P. tremula</i> var. <i>glandulosa</i> cv. 84K) during the shoot regeneration process. Firstly, 180 regeneration-related genes (REGs) and 2446 REG-homologous genes (REGHs) were identified in hybrid poplar. The expression patterns of REGs exhibited that about half of them were positively correlated between poplar and <i>Arabidopsis</i> at the locus level. The expression levels of REGHs vary among the gene family at different stages during callus and shoot induction. Among the gene clusters with similar expression patterns, the distribution of gene families in poplar and <i>Arabidopsis</i> also exhibits large variations. At the allele level, most of the allele pairs of REGs were positively correlated in expression. The expression patterns of genes in auxin synthesis, transport, and signaling pathways agree with the general patterns. Due to the presence/absence of variations between two subgenomes, two <i>YUC</i> alleles and two <i>IAA</i> alleles are present only in one subgenome, and the expression patterns of the two alleles are greatly different. Our analysis indicates the conservativeness and diversity of transcriptional regulation during shoot regeneration in poplar and <i>Arabidopsis</i>. The complexity in allele expression contributed by heterozygosity suggests the importance of genotyping in the screening of explants for plant regeneration.https://www.mdpi.com/1999-4907/14/11/2195shoot regenerationhybrid poplarallele specifictranscriptomegenomic variation |
| spellingShingle | Xiawei Ding Chengjin Wen Ganggui Yang Ying Guo Liangjiao Xue Allele-Specific Transcriptional Regulation of Shoot Regeneration in Hybrid Poplar Forests shoot regeneration hybrid poplar allele specific transcriptome genomic variation |
| title | Allele-Specific Transcriptional Regulation of Shoot Regeneration in Hybrid Poplar |
| title_full | Allele-Specific Transcriptional Regulation of Shoot Regeneration in Hybrid Poplar |
| title_fullStr | Allele-Specific Transcriptional Regulation of Shoot Regeneration in Hybrid Poplar |
| title_full_unstemmed | Allele-Specific Transcriptional Regulation of Shoot Regeneration in Hybrid Poplar |
| title_short | Allele-Specific Transcriptional Regulation of Shoot Regeneration in Hybrid Poplar |
| title_sort | allele specific transcriptional regulation of shoot regeneration in hybrid poplar |
| topic | shoot regeneration hybrid poplar allele specific transcriptome genomic variation |
| url | https://www.mdpi.com/1999-4907/14/11/2195 |
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