Global Transcriptomic Analyses Provide New Insight into the Molecular Mechanisms of Endocarp Formation and Development in Iron Walnut (<i>Juglans sigillata</i> Dode)
Iron walnut (<i>Juglans sigillata</i> Dode) is a native species in southwestern China that exhibits variation in both fruit morphology and shell thickness. However, the underlying molecular processes controlling hardened endocarp development in walnut has not yet been reported. Here, we...
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MDPI AG
2023-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/7/6543 |
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| author | Anmin Yu Hanyu Zou Ping Li Xiaowei Yao Jiayu Guo Rui Sun Gaosheng Wang Xueliang Xi Aizhong Liu |
| author_facet | Anmin Yu Hanyu Zou Ping Li Xiaowei Yao Jiayu Guo Rui Sun Gaosheng Wang Xueliang Xi Aizhong Liu |
| author_sort | Anmin Yu |
| collection | DOAJ |
| description | Iron walnut (<i>Juglans sigillata</i> Dode) is a native species in southwestern China that exhibits variation in both fruit morphology and shell thickness. However, the underlying molecular processes controlling hardened endocarp development in walnut has not yet been reported. Here, we generated transcriptional profiles of iron walnut endocarp at three developmental stages using “Dapao”, the most common commercial variety. Using pairwise comparisons between these three stages, a total of 8555 non-redundant differentially expressed genes (DEGs) were identified, and more than one-half of the total DEGs exhibited significant differential expression in stage I as compared with stage II or stage III, suggesting that the first stage may ultimately determine the final characteristics of the mature walnut shell. Furthermore, in the clustering analysis of the above DEGs, 3682, 2349, and 2388 genes exhibited the highest expression in stages I, II, and III, respectively. GO enrichment analysis demonstrated that the major transcriptional variation among the three developmental stages was caused by differences in cell growth, plant hormones, metabolic process, and phenylpropanoid metabolism. Namely, using the tissue-specific expression analysis and a gene co-expression network, we identified MADS-box transcription factor JsiFBP2 and bHLH transcription factor JsibHLH94 as candidate regulators of endocarp formation in the early stage, and JsiNAC56 and JsiMYB78 might play key roles in regulating the lignification process of endocarp in the late stage. This study provides useful information for further research to dissect the molecular mechanisms governing the shell formation and development of iron walnut. |
| first_indexed | 2024-03-11T05:35:06Z |
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| language | English |
| last_indexed | 2024-03-11T05:35:06Z |
| publishDate | 2023-03-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-a2671359363545f0aa4f03f3e6a198cd2023-11-17T16:52:35ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-03-01247654310.3390/ijms24076543Global Transcriptomic Analyses Provide New Insight into the Molecular Mechanisms of Endocarp Formation and Development in Iron Walnut (<i>Juglans sigillata</i> Dode)Anmin Yu0Hanyu Zou1Ping Li2Xiaowei Yao3Jiayu Guo4Rui Sun5Gaosheng Wang6Xueliang Xi7Aizhong Liu8Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaYunnan Academy of Forestry and Grassland, Kunming 650201, ChinaYunnan Academy of Forestry and Grassland, Kunming 650201, ChinaKey Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaIron walnut (<i>Juglans sigillata</i> Dode) is a native species in southwestern China that exhibits variation in both fruit morphology and shell thickness. However, the underlying molecular processes controlling hardened endocarp development in walnut has not yet been reported. Here, we generated transcriptional profiles of iron walnut endocarp at three developmental stages using “Dapao”, the most common commercial variety. Using pairwise comparisons between these three stages, a total of 8555 non-redundant differentially expressed genes (DEGs) were identified, and more than one-half of the total DEGs exhibited significant differential expression in stage I as compared with stage II or stage III, suggesting that the first stage may ultimately determine the final characteristics of the mature walnut shell. Furthermore, in the clustering analysis of the above DEGs, 3682, 2349, and 2388 genes exhibited the highest expression in stages I, II, and III, respectively. GO enrichment analysis demonstrated that the major transcriptional variation among the three developmental stages was caused by differences in cell growth, plant hormones, metabolic process, and phenylpropanoid metabolism. Namely, using the tissue-specific expression analysis and a gene co-expression network, we identified MADS-box transcription factor JsiFBP2 and bHLH transcription factor JsibHLH94 as candidate regulators of endocarp formation in the early stage, and JsiNAC56 and JsiMYB78 might play key roles in regulating the lignification process of endocarp in the late stage. This study provides useful information for further research to dissect the molecular mechanisms governing the shell formation and development of iron walnut.https://www.mdpi.com/1422-0067/24/7/6543endocarpformationlignificationiron walnutRNA-seq |
| spellingShingle | Anmin Yu Hanyu Zou Ping Li Xiaowei Yao Jiayu Guo Rui Sun Gaosheng Wang Xueliang Xi Aizhong Liu Global Transcriptomic Analyses Provide New Insight into the Molecular Mechanisms of Endocarp Formation and Development in Iron Walnut (<i>Juglans sigillata</i> Dode) International Journal of Molecular Sciences endocarp formation lignification iron walnut RNA-seq |
| title | Global Transcriptomic Analyses Provide New Insight into the Molecular Mechanisms of Endocarp Formation and Development in Iron Walnut (<i>Juglans sigillata</i> Dode) |
| title_full | Global Transcriptomic Analyses Provide New Insight into the Molecular Mechanisms of Endocarp Formation and Development in Iron Walnut (<i>Juglans sigillata</i> Dode) |
| title_fullStr | Global Transcriptomic Analyses Provide New Insight into the Molecular Mechanisms of Endocarp Formation and Development in Iron Walnut (<i>Juglans sigillata</i> Dode) |
| title_full_unstemmed | Global Transcriptomic Analyses Provide New Insight into the Molecular Mechanisms of Endocarp Formation and Development in Iron Walnut (<i>Juglans sigillata</i> Dode) |
| title_short | Global Transcriptomic Analyses Provide New Insight into the Molecular Mechanisms of Endocarp Formation and Development in Iron Walnut (<i>Juglans sigillata</i> Dode) |
| title_sort | global transcriptomic analyses provide new insight into the molecular mechanisms of endocarp formation and development in iron walnut i juglans sigillata i dode |
| topic | endocarp formation lignification iron walnut RNA-seq |
| url | https://www.mdpi.com/1422-0067/24/7/6543 |
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