Expression Quantitative Trait Locus of Wood Formation-Related Genes in <i>Salix suchowensis</i>
Shrub willows are widely planted for landscaping, soil remediation, and biomass production, due to their rapid growth rates. Identification of regulatory genes in wood formation would provide clues for genetic engineering of willows for improved growth traits on marginal lands. Here, we conducted an...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-12-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/25/1/247 |
| _version_ | 1797358757629394944 |
|---|---|
| author | Li Chen Liyan Liu Guo Yang Xiaoping Li Xiaogang Dai Liangjiao Xue Tongming Yin |
| author_facet | Li Chen Liyan Liu Guo Yang Xiaoping Li Xiaogang Dai Liangjiao Xue Tongming Yin |
| author_sort | Li Chen |
| collection | DOAJ |
| description | Shrub willows are widely planted for landscaping, soil remediation, and biomass production, due to their rapid growth rates. Identification of regulatory genes in wood formation would provide clues for genetic engineering of willows for improved growth traits on marginal lands. Here, we conducted an expression quantitative trait locus (eQTL) analysis, using a full sibling F<sub>1</sub> population of <i>Salix suchowensis</i>, to explore the genetic mechanisms underlying wood formation. Based on variants identified from simplified genome sequencing and gene expression data from RNA sequencing, 16,487 eQTL blocks controlling 5505 genes were identified, including 2148 cis-eQTLs and 16,480 trans-eQTLs. eQTL hotspots were identified, based on eQTL frequency in genomic windows, revealing one hotspot controlling genes involved in wood formation regulation. Regulatory networks were further constructed, resulting in the identification of key regulatory genes, including three transcription factors (<i>JAZ1</i>, <i>HAT22</i>, <i>MYB36</i>) and <i>CLV1</i>, <i>BAM1</i>, <i>CYCB2;4</i>, <i>CDKB2;1</i>, associated with the proliferation and differentiation activity of cambium cells. The enrichment of genes in plant hormone pathways indicates their critical roles in the regulation of wood formation. Our analyses provide a significant groundwork for a comprehensive understanding of the regulatory network of wood formation in <i>S</i>. <i>suchowensis</i>. |
| first_indexed | 2024-03-08T15:05:44Z |
| format | Article |
| id | doaj.art-d541ee7c664b4c6f990357fb34b6c524 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-08T15:05:44Z |
| publishDate | 2023-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-d541ee7c664b4c6f990357fb34b6c5242024-01-10T14:58:46ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-12-0125124710.3390/ijms25010247Expression Quantitative Trait Locus of Wood Formation-Related Genes in <i>Salix suchowensis</i>Li Chen0Liyan Liu1Guo Yang2Xiaoping Li3Xiaogang Dai4Liangjiao Xue5Tongming Yin6State Key Laboratory of Tree Genetics and Breeding, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, ChinaShrub willows are widely planted for landscaping, soil remediation, and biomass production, due to their rapid growth rates. Identification of regulatory genes in wood formation would provide clues for genetic engineering of willows for improved growth traits on marginal lands. Here, we conducted an expression quantitative trait locus (eQTL) analysis, using a full sibling F<sub>1</sub> population of <i>Salix suchowensis</i>, to explore the genetic mechanisms underlying wood formation. Based on variants identified from simplified genome sequencing and gene expression data from RNA sequencing, 16,487 eQTL blocks controlling 5505 genes were identified, including 2148 cis-eQTLs and 16,480 trans-eQTLs. eQTL hotspots were identified, based on eQTL frequency in genomic windows, revealing one hotspot controlling genes involved in wood formation regulation. Regulatory networks were further constructed, resulting in the identification of key regulatory genes, including three transcription factors (<i>JAZ1</i>, <i>HAT22</i>, <i>MYB36</i>) and <i>CLV1</i>, <i>BAM1</i>, <i>CYCB2;4</i>, <i>CDKB2;1</i>, associated with the proliferation and differentiation activity of cambium cells. The enrichment of genes in plant hormone pathways indicates their critical roles in the regulation of wood formation. Our analyses provide a significant groundwork for a comprehensive understanding of the regulatory network of wood formation in <i>S</i>. <i>suchowensis</i>.https://www.mdpi.com/1422-0067/25/1/247<i>Salix suchowensis</i>eQTLwood formationregulatory networks |
| spellingShingle | Li Chen Liyan Liu Guo Yang Xiaoping Li Xiaogang Dai Liangjiao Xue Tongming Yin Expression Quantitative Trait Locus of Wood Formation-Related Genes in <i>Salix suchowensis</i> International Journal of Molecular Sciences <i>Salix suchowensis</i> eQTL wood formation regulatory networks |
| title | Expression Quantitative Trait Locus of Wood Formation-Related Genes in <i>Salix suchowensis</i> |
| title_full | Expression Quantitative Trait Locus of Wood Formation-Related Genes in <i>Salix suchowensis</i> |
| title_fullStr | Expression Quantitative Trait Locus of Wood Formation-Related Genes in <i>Salix suchowensis</i> |
| title_full_unstemmed | Expression Quantitative Trait Locus of Wood Formation-Related Genes in <i>Salix suchowensis</i> |
| title_short | Expression Quantitative Trait Locus of Wood Formation-Related Genes in <i>Salix suchowensis</i> |
| title_sort | expression quantitative trait locus of wood formation related genes in i salix suchowensis i |
| topic | <i>Salix suchowensis</i> eQTL wood formation regulatory networks |
| url | https://www.mdpi.com/1422-0067/25/1/247 |
| work_keys_str_mv | AT lichen expressionquantitativetraitlocusofwoodformationrelatedgenesinisalixsuchowensisi AT liyanliu expressionquantitativetraitlocusofwoodformationrelatedgenesinisalixsuchowensisi AT guoyang expressionquantitativetraitlocusofwoodformationrelatedgenesinisalixsuchowensisi AT xiaopingli expressionquantitativetraitlocusofwoodformationrelatedgenesinisalixsuchowensisi AT xiaogangdai expressionquantitativetraitlocusofwoodformationrelatedgenesinisalixsuchowensisi AT liangjiaoxue expressionquantitativetraitlocusofwoodformationrelatedgenesinisalixsuchowensisi AT tongmingyin expressionquantitativetraitlocusofwoodformationrelatedgenesinisalixsuchowensisi |