Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars

DOI

https://doi.org/10.6084/m9.figshare.c.6763727

Dataset

Kang Tang (Creator)
Lin Li (Creator)
Bowen Zhang (Creator)
Wei ZhangArthritis Research Canada Vancouver British Columbia Canada; Department of Rehabilitation Medicine, West China Hospital Sichuan University Chengdu Sichuan China; Rehabilitation Medicine Key Laboratory of Sichuan Province, West China Hospital Sichuan University Chengdu Sichuan China, Department of Orthopedics, Renmin Hospital, Wuhan University, Wuhan 430060, People's Republic of China., Guangzhou & Chinese Academy of Sciences, Jiangsu Academy of Agricultural Sciences, Oregon State Univ, Oregon University System, Oregon State University, Forest Biodivers Res Network, Forest Ecosyst & Soc, ShenZhen People’s Hospital, Shanghai Cancer Institute, The First Affiliated Hospital, Dalian Medical University, Dalian, China, CAS - Northwest Institute of Eco-Environment and Resources, Hebei North University, Xuzhou Medical College, Chinese Academy of Medical Sciences & Peking Union Medical College, Sun Yat Sen Univ, Sun Yat Sen University, Sch Life Sci, Tianjin Key Laboratory of Molecular Optoelectronic Sciences Collaborative Innovation Center of Chemical Science and Engineering Tianjin University Tianjin 300072 China, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China., Univ Hawaii Manoa, University of Hawaii Manoa, University of Hawaii System, Hawaii Inst Geophys & Planetol, Northwestern Univ, Northwestern University, Huazhong Agricultural University, First Affiliated Hospital of Wannan Medical College, School of Electronic Science and Engineering, University of Electronic Science and Technology of China (UESTC), Chengdu, China, Hainan University, Southeast Univ, Southeast University - China, Sch Transportat, Yangtze University, National Clinical Research Center for Digestive Diseases, Tianjin Medical University Eye Hospital, Hunan Agricultural University, Shandong Tumor Hospital, Shandong Provincial Hospital, Second Affiliated Hospital of Chongqing Medical University, Centre for Health Evaluation and Outcome Sciences, Affiliated Hospital of North Sichuan Medical College, Department of Epidemiology, School of Public Health, Air Force Medical University, Xi’an, China; Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Air Force Medical University, Xi’an, China, Northwest University for Nationalities, Southern Medical University, North West Agriculture and Forestry University, Second Military Medical University, Chongqing Technology and Business University, College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China., Center for Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China., Zhejiang Univ, Zhejiang University, Inst Informat & Commun Engn, Second Hospital of Hebei Medical University, Shanghai Jiao Tong Univ, Shanghai Jiao Tong University, Sch Mech Engn, Affiliated Hospital of Xuzhou Medical College, Tsinghua Univ, Tsinghua University, Dept Phys, Tsinghua Ctr Astrophys, Bruyère Research Institute, East China Jiaotong University, Fudan University Shanghai Cancer Center, Arthritis Research Canada Vancouver British Columbia Canada; Department of Physical Therapy University of British Columbia Vancouver British Columbia Canada, Southern University of Science and Technology, Jinan Univ, Jinan University, Coll Pharm, Guangdong Prov Key Lab Pharmacodynam Constituents, Dian Diagnostics (China), Capital Med Univ, Capital Medical University, Henan Provincial People's Hospital, Xiamen Univ, Xiamen University, Coll Chem & Chem Engn, Dept Chem & Biochem Engn, Honghe University, Affiliated Hospital of Zunyi Medical College, Geography & Environment Loughborough University Loughborough UK; Department of Ecology and Environmental Science Umeå University Umeå Sweden, First Affiliated Hospital of Soochow University, Central South University, School of Cyber Science and Engineering, Wuhan University, Wuhan 430072 China, Suzhou Research Institute of Wuhan University, Suzhou 215123 China, Jiangsu Province Hospital, Univ Chinese Acad Sci, Chinese Academy of Sciences, University of Chinese Academy of Sciences, CAS, Kansas State Univ, Kansas State University, Wenzhou Medical University, Nanjing Tech University, Peking University Shenzhen Hospital, State Key Laboratory of Powder Metallurgy, Central South University, Changsha, 410083, China; Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, 410011, China, Shanghai Changzheng Hospital, Chinese Academy of Agricultural Sciences, Shandong Academy of Agricultural Sciences, First Affiliated Hospital of GuangXi Medical University, Beijing Academy of Agricultural and Forestry Sciences, Shandong University, Qingdao, Shandong 266237, China, Bioprocessing Technology Institute, Shanghai Sixth People's Hospital, Guangdong Provincial Center for Disease Control and Prevention, First Affiliated Hospital of Jinan University, First Affiliated Hospital of Zhengzhou University, Beijing Tian Tan Hospital, First Affiliated Hospital of Nanchang University, First Affiliated Hospital of Harbin Medical University, Nanjing Medical University, Qingdao Institute of Bioenergy and Bioprocess Technology, Huazhong University of Science and Technology, Tongji University, Xi'an Medical University, Peking Univ, Peking University, Sch Earth & Space Sci, Miami Univ, Miami University, Dept Biol, Shandong University of Finance and Economics, Anhui Academy of Agricultural Sciences, Fudan Univ, Fudan University, Sch Informat Sci & Technol, Urology Department Peking University People's Hospital Beijing China, First Affiliated Hospital of Chongqing Medical University, Chongqing University of Posts and Telecommunications, Second Affiliated Hospital of Zhejiang University, Minzu University of China, Xinjiang Medical University, Center for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dow Street, Dundee DD1 5EH, Scotland, U.K., Guangdong Provincial People's Hospital, Beihang University, Hubei Academy of Agricultural Sciences, Third Hospital of Hebei Medical University, Second Affiliated Hospital of Soochow University, Heilongjiang Provincial Academy of Agricultural Sciences, Hebei Agricultural University, University of Electronic Science and Technology of China, Chengdu, China, Xinjiang Agricultural University, Guangdong Medical College (Creator)
Ningbo Zeng (Creator)
Hao ZhangShanghai Children's Medical Center, Urology Department The Affiliated Qingdao Central Hospital of Qingdao University, The Second Affiliated Hospital of Medical College of Qingdao University Qingdao Shandong China, The First Affiliated Hospital, Dalian Medical University, Dalian, China, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China., First Affiliated Hospital of Harbin Medical University, Center for Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China., Chongqing Medical University, Zhongnan Hospital of Wuhan University, Shanghai Jiao Tong Univ, Shanghai Jiao Tong University, Sch Mech Engn, Heilongjiang Provincial Hospital, Ruian People's Hospital, Jinan Univ, Jinan University, Coll Pharm, Guangdong Prov Key Lab Pharmacodynam Constituents, Nanjing Medical University, Univ Arizona, University of Arizona, Henan Normal University, Zhejiang Univ, Zhejiang University, Inst Informat & Commun Engn, Ocean University of China, Nanchang University, Shandong University, Qingdao, Shandong 266237, China, Changhai Hospital, Jiangsu Province Hospital, Jilin University, Jiangnan University, Nanyang Technol Univ, Nanyang Technological University, Nanyang Technological University & National Institute of Education (NIE) Singapore, Sch Mat Sci & Engn, Guangzhou & Chinese Academy of Sciences, Second Affiliated Hospital of Harbin Medical University, Chinese Academy of Medical Sciences & Peking Union Medical College, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Huazhong University of Science and Technology, Hubei Academy of Agricultural Sciences, China agricultural University, Second Affiliated Hospital of Nanjing Medical University, Yunnan Academy of Agricultural Sciences, Department of Cardiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China, Hunan Agricultural University, Guangdong University of Petrochemical Technology, Northwestern Polytechnical University Xian, Shanghai Stomatological Hospital, Fudan Univ, Fudan University, Sch Informat Sci & Technol, South China University of Technology, Beijing Anzhen Hospital, Dalian University of Technology, Arthritis Research Canada Vancouver British Columbia Canada; Department of Rehabilitation Medicine, West China Hospital Sichuan University Chengdu Sichuan China; Rehabilitation Medicine Key Laboratory of Sichuan Province, West China Hospital Sichuan University Chengdu Sichuan China, Guangdong Pharmaceutical University, McGill Univ, McGill University, McGill Sch Environm, Harvard Univ, Harvard University, Dept Phys, Cornell Univ, Cornell University, Kavli Inst Cornell, Univ Victoria, University of Victoria, Dept Phys & Astron, Wenzhou Medical University, Univ Chinese Acad Sci, Chinese Academy of Sciences, University of Chinese Academy of Sciences, CAS (Creator)
Dengwang Liu (Creator)
Zinan Luo (Creator)

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.

Date made available	2023
Publisher	Figshare

Contact person

rdm@lancaster.ac.uk

Research

DOI