Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars
Abstract Background Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed bet...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-07-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09436-9 |
| _version_ | 1797769626969440256 |
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| author | Kang Tang Lin Li Bowen Zhang Wei Zhang Ningbo Zeng Hao Zhang Dengwang Liu Zinan Luo |
| author_facet | Kang Tang Lin Li Bowen Zhang Wei Zhang Ningbo Zeng Hao Zhang Dengwang Liu Zinan Luo |
| author_sort | Kang Tang |
| collection | DOAJ |
| description | Abstract Background Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. Results In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. Conclusion The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency. |
| first_indexed | 2024-03-12T21:11:44Z |
| format | Article |
| id | doaj.art-3b7ee3b9fbf34fe4afb7db7565c4ee9b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-12T21:11:44Z |
| publishDate | 2023-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-3b7ee3b9fbf34fe4afb7db7565c4ee9b2023-07-30T11:08:36ZengBMCBMC Genomics1471-21642023-07-0124111610.1186/s12864-023-09436-9Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivarsKang Tang0Lin Li1Bowen Zhang2Wei Zhang3Ningbo Zeng4Hao Zhang5Dengwang Liu6Zinan Luo7College of Agriculture, Hunan Agricultural UniversityCollege of Agriculture, Hunan Agricultural UniversityCollege of Agriculture, Hunan Agricultural UniversityCollege of Plant Protection, Hunan Agricultural UniversityCollege of Agriculture, Hunan Agricultural UniversityCollege of Agriculture, Hunan Agricultural UniversityCollege of Agriculture, Hunan Agricultural UniversityCollege of Agriculture, Hunan Agricultural UniversityAbstract Background Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. Results In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. Conclusion The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency.https://doi.org/10.1186/s12864-023-09436-9PeanutTranscriptomeWeighted gene co-expression network analysis (WGCNA)Differentially expressed genes (DEGs)Hub genes |
| spellingShingle | Kang Tang Lin Li Bowen Zhang Wei Zhang Ningbo Zeng Hao Zhang Dengwang Liu Zinan Luo Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars BMC Genomics Peanut Transcriptome Weighted gene co-expression network analysis (WGCNA) Differentially expressed genes (DEGs) Hub genes |
| title | Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars |
| title_full | Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars |
| title_fullStr | Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars |
| title_full_unstemmed | Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars |
| title_short | Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars |
| title_sort | gene co expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars |
| topic | Peanut Transcriptome Weighted gene co-expression network analysis (WGCNA) Differentially expressed genes (DEGs) Hub genes |
| url | https://doi.org/10.1186/s12864-023-09436-9 |
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