Exploring drought-responsive crucial genes in Sorghum
Summary: Drought severely affects global food production. Sorghum is a typical drought-resistant model crop. Based on RNA-seq data for Sorghum with multiple time points and the gray correlation coefficient, this paper firstly selects candidate genes via mean variance test and constructs weighted gen...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-11-01
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| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004222016194 |
| _version_ | 1811197049363759104 |
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| author | Yilin Bi Pei Wang |
| author_facet | Yilin Bi Pei Wang |
| author_sort | Yilin Bi |
| collection | DOAJ |
| description | Summary: Drought severely affects global food production. Sorghum is a typical drought-resistant model crop. Based on RNA-seq data for Sorghum with multiple time points and the gray correlation coefficient, this paper firstly selects candidate genes via mean variance test and constructs weighted gene differential co-expression networks (WGDCNs); then, based on guilt-by-rewiring principle, the WGDCNs and the hidden Markov random field model, drought-responsive crucial genes are identified for five developmental stages respectively. Enrichment and sequence alignment analysis reveal that the screened genes may play critical functional roles in drought responsiveness. A multilayer differential co-expression network for the screened genes reveals that Sorghum is very sensitive to pre-flowering drought. Furthermore, a crucial gene regulatory module is established, which regulates drought responsiveness via plant hormone signal transduction, MAPK cascades, and transcriptional regulations. The proposed method can well excavate crucial genes through RNA-seq data, which have implications in breeding of new varieties with improved drought tolerance. |
| first_indexed | 2024-04-12T01:09:36Z |
| format | Article |
| id | doaj.art-1df9ce435805415f8adbd3c46c9bbbc8 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-04-12T01:09:36Z |
| publishDate | 2022-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-1df9ce435805415f8adbd3c46c9bbbc82022-12-22T03:54:09ZengElsevieriScience2589-00422022-11-012511105347Exploring drought-responsive crucial genes in SorghumYilin Bi0Pei Wang1School of Mathematics and Statistics, Henan University, Kaifeng 475004, ChinaSchool of Mathematics and Statistics, Henan University, Kaifeng 475004, China; Center for Applied Mathematics of Henan Province, Henan University, Kaifeng 475004, China; Corresponding authorSummary: Drought severely affects global food production. Sorghum is a typical drought-resistant model crop. Based on RNA-seq data for Sorghum with multiple time points and the gray correlation coefficient, this paper firstly selects candidate genes via mean variance test and constructs weighted gene differential co-expression networks (WGDCNs); then, based on guilt-by-rewiring principle, the WGDCNs and the hidden Markov random field model, drought-responsive crucial genes are identified for five developmental stages respectively. Enrichment and sequence alignment analysis reveal that the screened genes may play critical functional roles in drought responsiveness. A multilayer differential co-expression network for the screened genes reveals that Sorghum is very sensitive to pre-flowering drought. Furthermore, a crucial gene regulatory module is established, which regulates drought responsiveness via plant hormone signal transduction, MAPK cascades, and transcriptional regulations. The proposed method can well excavate crucial genes through RNA-seq data, which have implications in breeding of new varieties with improved drought tolerance.http://www.sciencedirect.com/science/article/pii/S2589004222016194Natural resourcesGeneticsPlant biologyAgricultural science |
| spellingShingle | Yilin Bi Pei Wang Exploring drought-responsive crucial genes in Sorghum iScience Natural resources Genetics Plant biology Agricultural science |
| title | Exploring drought-responsive crucial genes in Sorghum |
| title_full | Exploring drought-responsive crucial genes in Sorghum |
| title_fullStr | Exploring drought-responsive crucial genes in Sorghum |
| title_full_unstemmed | Exploring drought-responsive crucial genes in Sorghum |
| title_short | Exploring drought-responsive crucial genes in Sorghum |
| title_sort | exploring drought responsive crucial genes in sorghum |
| topic | Natural resources Genetics Plant biology Agricultural science |
| url | http://www.sciencedirect.com/science/article/pii/S2589004222016194 |
| work_keys_str_mv | AT yilinbi exploringdroughtresponsivecrucialgenesinsorghum AT peiwang exploringdroughtresponsivecrucialgenesinsorghum |