Photosynthesis is the process by which plants utilize solar energy to convert CO2 and H2O into carbohydrates and releases O2. Via this process, plants are the ultimate source of all of our food and all of fossil fuels, and have the potential to play a critical role in producing renewable energy resources and in mitigating climate change. My group is focusing on developing next generation computational models and algorithms to identify new approaches to adapt photosynthesis to meet societal needs and to improve photosynthesis beyond the accomplishments of evolution. Specifically, we are working on two projects, representing two different approaches with the shared goal of engineering higher photosynthetic energy conversion efficiency, i.e., optimizing existing C3 photosynthetic systems (the ePlant project) and engineering C4 photosynthetic pathway into C3 crops (the C4 rice project).
Research Areas
Photosynthesis, systems biology, crop yield, breeding, molecular breeding, synthetic biology, rice
Experience
Education and Work Experiences:
1999-2004, PHD, University of Illinois at Urbana Champaign
2004-2006, Postdoctoral Scientist, University of Illinois at Urbana Champaign
2006-2008, Research Assistant Professor, University of Illinois at Urbana Champaign
2008-2017, CAS-MPG Partner Institute for Computational Biology
2017-present, Shanghai Institute of Plant Physiology and Ecology, CAS
Publications
1. Yu Wang, Qingfeng Song, Deepak Jaiswal, de Souza Amanda, Stephen P Long, Xin-Guang Zhu (2017) Development of a three-dimensional ray-tracing model of sugarcane canopy photosynthesis and its application in assessing impacts of varied row spacing. BioEnery Research （Accepted）.
2. Tian-Gen Chang and Xin-Guang Zhu (2017) Source sink interaction: a century old concept under the light of modern molecular systems biology. Journal of Experimental Botany (Accepted).
3. Xin-Guang Zhu, Martin Parry, Yonglong Lu, Matthew Heard, Guangguo Ying, Simon Vaughan, Jianbo Shen, Alan Jenkins, Yunpeng Wang, Silvia Lacorte, Tingping Ouyang, Francisco Pedrero Salcedo, Jun Niu, John Quinton, Chunling Luo, Fusuo Zhang, Gan Zhang, Achim Dobermann, William Davies, Kevin Jones, and David Tyfield. Building the new international science of the agri-food-water-environment nexus. Ecosystem Health and Sustainability (Accepted).
4. Jiajia Xu, Yuanyuan Li, Yaling Wang, Xinyu Liu, Xin-Guang Zhu. Altered expression profiles of microRNA families during de-etiolation of maize and rice leaves. BMC Research Notes (Accepted).
5. Jemaa Essemine, Yi Xiao, Hualing Mi, Xin-Guang Zhu. Cyclic electron flow may provide some protection against PSII photoinhbition in rice (Oryza sativa L.) leaves under heat stress. Journal of Plant Physiology (Accepted).
6. Xin Wang, Wei Liu, Changpeng Xin, Yi Zheng, Yanbing Cheng, Su Sun, Runze Li, Xin-Guang Zhu, Susie Y Dai, Peter M Rentzepis, Joshua S Yuan. Enhanced limonene production in cyanobacteria reveals photosynthesis limitations. PNAS 113:14225-14230.
7. Shuyue Wang, Danny Tholen, Xin-Guang Zhu (2016) C4 photosynthesis in C3 rice: a theoretical analysis of biochemical and anatomical factors. Plant Cell and Environment 40(1): 80-94.
8. Yi Xiao, Danny Tholen, Xin-Guang Zhu (2016) The influence of leaf anatomy on the internal light environment and photosynthetic electron transport rate. Journal of Experimental Botany 67(21): 6021-6035.
9. Guangyong Zheng, Yaochen Xu, Xiujun Zhang, Zhi-Ping Liu, Zhuo Wang, Luonan Chen, and Xin-Guang Zhu (2016) CMIP: a software package capable of reconstructing gene regulatory networks using genome-scale data with parallel computing strategy. BMC Bioinformatics 17(17): 137-144.
10. Jiajia Xu, Andrea Bräutigam, Yuanyuan Li, Andreas P. M. Weber and Xin-Guang Zhu (2016) Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation. Journal of Experimental Botany 67: 5105-5117.
11. Qing-Feng Song, Dairui Chen, Stephen P Long, Xin-Guang Zhu (2016) A user-friendly means to scale from the biochemistry of photosynthesis to whole crop canopies and production in time and space - development of Java WIMOVAC. Plant Cell and Environment 40: 51-55.
12. Zehong Ding, Yang Zhang, Yi Xiao, Fangfang Liu, Minghui Wang, Xin-Guang Zhu, Peng Liu, Qi Sun, Wenquan Wang, Ming Peng, Tom Brutnell, Pinghua Li (2016) Transcriptome response of cassava leaves under natural shade. Scientific Reports (doi: 10.1038/srep31673).
13. Michael Hodges, Younès Dellero, Olivier Keech, Marco Betti, Agepati S. Raghavendra, Rowan Sage, Xin-Guang Zhu, Douglas K. Allen, Andreas P.M. Weber (2016) Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network. Journal of Experimental Botany 67: 3015-3026.
14. Jemaa Essemine, Mingnan Qu, Hualing Mi and Xin-Guang Zhu (2016) Response of chloroplast NAD(P)H dehydrogenase-mediated cyclic electron flow to a shortage or lack in ferredoxin-quinone oxidoreductase-dependent pathway in rice following short-term heat stress. Frontiers in Plant Science 7: 383 doi: 10.3389/fpls.2016.00383.
15. Mingnan Qu, Saber Hamdani, Wenzhen Li, Shimei Wang, Jiuyou Tang, Zhuo Chen, Qingfeng Song, Ming Li, Honglong Zhao, Tiangen Chang, Chengcai Chu and Xin-Guang Zhu (2016) Rapid stomatal response to fluctuating light: an under-explored mechanism to improve drought tolerance in rice. Functional Plant Biology 43: 727-738.
16. Chensi Cao, Jiajia Xu, Guangyong Zheng, Xin-Guang Zhu (2016) Evidence for the role of transposons in the recruitment of cis-regulatory motifs during the evolution of C4 photosynthesis. BMC Genomics 17:201.
17. Qing-Feng Song, Han Xiao, Xianglin Xiao, Xin-Guang Zhu (2016) A new canopy photosynthesis and transpiration measurement system (CAPTS) for canopy gas exchange research. Agricultural and Forest Meteorology 217:101-107.
18. Qing-Feng Song, Chengcai Chu, Martin Parry, Xin-Guang Zhu (2016) Genetics based dynamic systems model of canopy photosynthesis: the key to improve light and resource use efficiencies for crops. Food and Energy Security, doi: 10.1002/fes3.74.
19. Xiurong Jiao, Kirsten Kørup, Mathias Andersen, Erik Sacks, Xin-Guang Zhu, Poul Lærke, Uffe Jørgensen (2016) Can Miscanthus C4 photosynthesis compete with festulolium C3 photosynthesis in a temperate climate? GCB Bioenergy 9: 18-30.
20. Yimin Tao, Mingzhu Lyv, Xin-Guang Zhu (2016) Transcriptome comparisons shed light on the pre-condition and potential barrier for C4 photosynthesis evolution in eudicots. Plant Molecular Biology 91: 193-209.
21. Shuoqi Chang, Tiangen Chang, Qingfeng Song, Xin-Guang Zhu*, Qiyun Deng* (2016) Photosynthetic and agronomic traits of an elite hybrid rice Y-Liang-You 900 with a record-high yield. Field Crops Research 187: 49-57.
22. Yuan Fang*, Mingju Lyu*, Leng BY, Xin-Guang Zhu, Baoshan Wang (2016) The transcriptome of NaCl-treated Limonium bicolor leaves reveals the genes controlling salt secretion of salt gland. Plant Molecular Biology 91: 241-256.
23. Justin McGrith, Amy M. Betzelberger, Shaowen Wang, Eric Shook, Xin-Guang Zhu, Steve P Long, Elizebeth A Ainsworth (2015) An analysis of ozone damage to historical maize and soybean yields in the United States. PNAS 112:14390-5.
24. Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang M-L, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo H-B, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen L-Y, Shirley N, Lin Y-R, Liu L-Y, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X-G, Yang X, Smith JAC, Cushman JC, Paull RE, Yu Q (2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genetetics 47: 1435-1442.
25. Xin-Guang Zhu, Jonathan P. Lynch, David S. LeBauer, Andrew J. Millar, Mark Stitt, Stephen P. Long (2015). Plants in silico: why, why now and what?--an integrative platform for plant systems biology research. Plant Cell and Environment 39:1049-1057.
26. Donald R. Ort, Sabeeha S. Merchant, Jean Alric, Alice Barkan, Robert E. Blankenship, Ralph Bock, Roberta Croce, Maureen R. Hanson, Julian Hibberd, Derek L. Lindstrom, Stephen P. Long, Thomas A. Moore, James Moroney, Krishna K. Niyogi, Martin Parry, Pamela Peralta-Yahya, Roger Prince, Kevin Redding, Martin Spalding, Klaas van Wijk, Wim F.J. Vermaas, Susanne von Caemmerer, Andreas Weber, Todd Yeates, Joshua Yuan, Xin-Guang Zhu (2015) Redesigning photosynthesis to sustainably meet global food and bioenergy demand. PNAS 112:8529-36.
27. Ming-Ju Amy Lyu, Udo Gowik, Steve Kelly, Sarah Covshoff, Julia Mallmann, Peter Westhoff, Julian M. Hibberd, Matt Stata, Rowan F. Sage, Haorong Lu, Xiaofeng Wei, Gane Ka-Shu Wong, Xin-Guang Zhu (2015) RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications. BMC Evolutionary Biology 15:116.
28. Chengzhen Liang, Guangyong Zheng, Wenzhen Li, Yiqin Wang, Bin Hu, Hongru Wang, Hongkai Wu, Yangwen Qian, Xin-Guang Zhu, Duan Xian Tan, Shou-Yi Chen and Chengcai Chu (2015) Melatonin delays leaf senescence and enhances salt stress tolerance in rice. Journal of Pineal Research 59: 91-101.
29. Johannes Anton Hofberger, Aldana M. Ramirez, Xin-Guang Zhu, Harro J. Bouwmeester, Robertus C. Schuurink, Eric Schranz (2015) Large-scale evolutionary analysis of genes and supergene clusters from terpenoid modular pathways provides insights into metabolic diversification in flowering plants. PLOS One 10(6):e0128808. doi: 10.1371/journal.pone.0128808. 19(1):43-51.
30. Stephen P. Long, Amy Marshall-Colon, Xin-Guang Zhu (2015) Meeting the global food demand of the future by engineering crop photosynthesis and yield potential. Cell 161: 56-66.
31. Fang Yuan, Ming-Ju Lv, Bingying Leng, Guangyong Zheng, Zhongtao Feng, Pinghua Li, Xin-Guang Zhu, Baoshan Wang (2015) Comparative transcriptome analysis of developmental stages of the Limonium bicolor leaf generates insights into salt gland differentiation. Plant Cell and Environment 38:1637-1657.
32. Changpeng Xin, Danny Tholen, Xin-Guang Zhu (2015) The benefit of photorespiratory bypass – How can they work? Plant Physiology 167: 574-585.
33. Saber Hamdani, Mingnan Qu, Chang-Peng Xin, Chengcai Chu, Govindjee, Xin-Guang Zhu (2015) Variations between the photosynthetic properties of elite and landrace Chinese rice cultivars revealed by simultaneous measurements of 820 nm transmission signal and chlorophyll a fluorescence induction. Journal of Plant Physiology 177: 128-138.
34. Chunyun Jiang, Jiajia Mercedes Xu, Changpeng Xin, Danny Tholen, Hui Zhang, Xin-Guang Zhu*, Yanxiu Zhao* (2014) Increased expression of mitochondria-localized carbonic anhydrase activity resulted in an increased biomass accumulation in Arabidopsis thaliana. Journal of Plant Biology 57: 366-374.
35. Jindong Sun, Zhaozhong Feng, Andrew Leakey, Xin-Guang Zhu, Carl J Bernacchi, Donald R Ort (2014) In-consistency of mesophyll conductance estimate causes the inconsistency for the estimates of maximum rate of Rubisco carboxylation among the linear, rectangular and non-rectangular hyperbola biochemical models of leaf photosynthesis - a case study of CO2 enrichment and leaf aging effects in soybean. Plant Science 226: 49-60.
36. Taiyu Chen, Xin-Guang Zhu, Yongjun Lin (2014) Major alterations in transcript profiles between C3–C4 and C4 photosynthesis of an amphibious species Eleocharis baldwinii. Plant Molecular Biology 86: 93-110.
37. Lin Wang, Angelika Czedik-Eysenberg, Rachel A. Mertz, Yaqing Si, Takayuki Tohge, Adriano Nunes-Nesi, Stephanie Arrivault, Lauren K. Dedow, Douglas W. Bryant, Wen Zhou, Jiajia Xu, Sarit Weissmann, Anthony Studer, Pinghua Li, Cankui Zhang, Therese LaRue, Ying Shao, Zehong Ding, Qi Sun, Rohan V. Patel, Robert Turgeon, Xin-Guang Zhu, Nicholas J. Provart, Todd C. Mockler, Alisdair R. Fernie, Mark Stitt, Peng Liu, Thomas P. Brutnell (2014) Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice. Nature Biotechnology 32: 1158-1165.
38. Xianbin Yu, Guangyong Zheng, Lanlan Shan, Guofeng Meng, Martin Vingron, Qi Liu, Xin-Guang Zhu (2014) Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana. Frontiers in Plant Sciences. doi: 10.3389/fpls.2014.00273.
39. Yi-Bo Chen, Tian-Cong Lu, Hong-Xia Wang, Jie Shen, Tian-Tian Bu, Qing Chao, Zhi-Fang Gao, Xin-Guang Zhu, Yue-Feng Wang, Bai-Chen Wang (2014) Posttranslational modification of maize chloroplast pyruvate orthophosphate dikinase reveals the precise regulatory mechanism of its enzyme activity. Plant Physiology 165: 534-549.
40. Yuanyuan Li, Jiajia Xu, Noor UI Haq, Hui Zhang, Xin-Guang Zhu (2014) Was low CO2 a driving force of C4 evolution? Arabidopsis responses to long-term low CO2 stress. Journal of Experimental Botany 65: 3657-67.
Conferences
（2）Redesigning crops for increased yield and resource use efficeincy 2015-10-23
（3）Changchun. Molecular mechanisms of C4 evolution 2015-10-09
（4）Development of a generic crop growth and development model to support biomass crop breeding 2015-09-07
（5）Modeling photosynthesis at cell and tissue levels. 2015-06-15
（6）The role of low CO2 during evolution of C4 photosynthesis 2015-06-01
（7）Modelling of sink-source partitioning 2015-03-06
（8）The role of low CO2 during the evolution of C4 photosynthesis 2015-01-10
（9）ePlant: a modeling framework to support engineering crops for improved water and radiation use efficiencies 2014-11-04
（10）Reclassficiation of C4 photosynthesis in Nature 2014-08-15
（11）Rationale design of photosynthetic metabolism for increased efficiency 2014-07-02
（12）Rationale design of photosynthetic metabolism for increased efficiency. 2014-06-21
（13）Special features of C4 photosynthesis in Setaria viridis. 2014-03-10
Students
已指导学生
信长朋 01 61369
王玉 01 61369
余贤斌 01 61369
田野 02 61369
宋青峰 01 61369
陶一敏 01 61369
徐佳佳 01 61369
吕明菊 01 61369
肖怡 01 61369
曹晨思 02 61369
现指导学生
王书月 01 67854
常天根 01 67854
赵洪龙 01 19174
赵永耀 02 19174