Rice Improvement by Molecular Design

Team Name: Rice Improvement by Molecular Design

Research Focus: The team research hasthree major aspects: (1) traits of interest including tolerances to abiotic stresses, resistances to biotic stresses and traits related to high yield potential and heterosis; (2)functional genomics of complex traits which includes discovery and functional characterization of genetic and molecular networks underlying abiotic/biotic stress tolerances; cloning and functional analysis of important genes/QTLs affecting abiotic stress tolerances and important agronomic traits, and genetic/molecular dissection of the interaction between rice and its pathogens; and (3)trait improvement and cultivar development by molecular design, including development of large numbers of trait-specific introgression line (IL) sets in elite rice genetic backgrounds as the platform, genetic and molecular characterization of complex traits by high throughput SNP genotyping and genome re-sequencing of parental and breeding materials, establishment of phenotypic, genetic, molecular databases of the developed IL sets and breeding materials, development of efficient analytical tools for discovering genes/QTLs and genetic networks underlying target traits in molecular breeding materials, and development/application of theories, tools andtechnologies for trait improvement and cultivar development by molecular design.

Research Objectives:(1) to establish a permanentinformation and material platforms for rice molecular design and molecular breeding by deep analyses of the genome sequences of 3,000 rice core germplasmaccessions and molecular characterization of large numbers of trait specific introgression lines; (2) to perform large scale identification and mining of genes/QTL/alleles and genetic networks underlying important rice traits using trait specific ILs, SNP genotyping and genome sequencing information; (3) todevelop theories and methodology for improving complex traits by molecular design,QTL pyramiding and molecular recurrent selection; and (4) to develop new green super ricecultivars that have high yield potential and resistances to multiple abiotic/biotic stresses usingmolecular design and genomics-based technologies.

Team Chief Scientist: Dr. FU Bin-ying

Education Background

Dr. FU Binying received his Bachelor Degree of Biology from Wuhan University (1987) and Ph.D of Plant Genetics from College of Life Sciences at Wuhan University (2000).

Research Area

Dr. FU Binying is a rice molecular scientist with experience in the field of crop molecular breeding and functional genomics. He currently leads the rice molecular research including gene discovery and function identification of abiotic stress tolerance in rice. He is also involved in molecular dissection of epigenetic mechanisms of abiotic stress tolerance in rice.

Position/Employment

2003-Present, Professor, Institute of Crop Sciences, Chinese Academy of Agriculture Science, Beijing 100081, China

2000-2003, Postdoctoral Fellowship/Project Scientist, PBGB, International Rice Research Institute, Philippines

1993-2002, Lecturer, College of Life Sciences, Wuhan University, Wuhan, China 1987-1992, Assistant Teacher, Institute of Genetics, Wuhan University, China

Current Research Projects

1. Inheritance and Molecular Mechanism of Epigenetic Trait for Drought Tolerance in Rice (PI), National Nature Science Foundation of China (2012-2016)

2. Genetics and Molecular Mechanism of Rhizome Development in Oryza longistaminata, NSFC Yunnan Joint Project (2014-2017)

3. Functional Characterization and Molecular Network Dissection of the Transcription Factor OsDRAP1 Conferring Abiotic Stress Tolerance in Rice (PI), National Nature Science Foundation of China (2016-2019)

4. Green Super Rice for Resource Poor farmers of Asia and Africa” –Phase II (Lead by Dr. Zhikang Li) funded by the Bill and Melinda Gates Foundation (2016-2018)

Recent Publications

1. Wensheng Wang^#, Xiuqin Zhao^#, Min Li^#, Liyu Huang, Jianlong Xu, Fan Zhang, Yanru Cui, Binying Fu*, and Zhikang Li*. 2016. Complex molecular mechanisms underlying seedling salt tolerance in rice (Oryza sativa L.) revealed by comparative transcriptome and metabolomic profiling. Journal of Experimental Botany, 67(1):405-19.

2. Xiuqin Zhao, Guilian Zhang, Yun Wang, Fan Zhang, Wensheng Wang, Wenhao Zhang, Binying Fu*, Jianlong Xu*, Zhikang Li. 2015. Metabolic profiling and physiological analysis of a novel rice introgression line with broad leaf size. PLoS ONE, 10(12): e0145646.

3. Wensheng Wang, Fei Huang, Qiao Qin, Xiuqin Zhao, Zhikang Li, and Binying Fu*. 2015. Comparative analysis of DNA methylation changes in two rice genotypes under salt stress and subsequent recovery. Biochemical and Biophysical Research Communications 465: 790-796.

4. Yesheng Zhang^#, Shilai Zhang^#, Hui Liu^#, Binying Fu^#, Lijuan Li, Min Xie, Yue Song, Xin Li, Jing Cai, Wenting Wan, Ling Kui, Hui Huang, Jun Lyu, Yang Dong, Wensheng Wang, Liyu Huang, Jing Zhang, Qinzhong Yang, Qinli Shan, Qiong Li, Wangqi Huang, Dayun Tao, Muhua Wang, Mingsheng Chen, Yeisoo Yu, Rod A. Wing, Wen Wang, and Fengyi Hu. 2015. Genome and comparative transcriptomics of African wild rice Oryza longistaminata provide insights into molecular mechanism of rhizomatousness and self-incompatibility. Molecular Plant 8:1683–1686.

5. Wensheng Wang^#, Binying Fu^#, Jauhar Ali^#, Jianlong Xu, Yongming Gao, Tianqing Zheng, Fan Zhang, and Zhikang Li*. 2015. Genome-wide responses to selection and genetic networks underlying submergence tolerance in rice. The Plant Genome 8(2): 1-13.

6. Liyu Huang, Fan Zhang, Qiao Qin, Wensheng Wang, Ting Zhang, Binying Fu*. 2015. Identification and validation of root-specific promoters in rice. Journal of Integrative Agriculture 14(1): 1–10

7. Liyu Huang^#, Fan Zhang^#, Fan Zhang, Wensheng Wang, Yongli Zhou*, Binying Fu* and Zhikang Li. 2014. Comparative transcriptome sequencing of tolerant rice introgression line and its parents in response to drought stress. BMC Genomics 15:1026.

8. Xiuqin Zhao^#, Wensheng Wang^#, Fan Zhang, Jianli Deng, Zhikang Li, Binying Fu*. 2014. Comparative metabolite profiling of two rice genotypes with contrasting salt stress tolerance at the seedling stage. PLoS ONE 9(9): e108020.

9. Ting Zhang^#, Xiuqin Zhao^#, Wensheng Wang, Liyu Huang, Xiaoyue Liu, Ying Zong, Linghua Zhu, Daichang Yang, Binying Fu*, Zhikang Li*. 2014. Deep transcriptome sequencing of rhizome and aerial-shoot in Sorghum propinquum. Plant Molecular Biology 84(3): 315–327. DOI: 10.1007/s11103-013-0135-z 

10. Xiuqin Zhao, Wensheng Wang, Fan Zhang, Ting Zhang, Wen Zhao, Binying Fu*, Zhikang Li*. 2013. Temporal profiling of primary metabolites under chilling stress and its association with seedling chilling tolerance of rice (Oryza sativa L.). Rice 6(1):23

11. Ting Zhang, Xiuqin Zhao, Liyu Huang, Xiaoyue Liu, Ying Zong, Linghua Zhu, Daichang Yang *, Binying Fu*. 2013. Tissue-specific transcriptomic profiling of Sorghum propinquum using a rice genome array. PLoS ONE 8(3):e60202.

12. Fan Zhang^#, Liyu Huang^#, Wensheng Wang, Xiuqin Zhao, Linghua Zhu, Binying Fu* and Zhikang Li*. 2012. Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background. BMC Genomics 13:461.

13. Ting Zhang, Xiuqin Zhao, Wensheng Wang, Yajiao Pan, Liyu Huang, Xiaoyue Liu, Ying Zong, Linghua Zhu, Daichang Yang*, Binying Fu*. 2012. Comparative transcriptome profiling of chilling stress responsiveness in two contrasting rice genotypes. PLoS ONE 7(8): e43274.

14. Xiuqin Zhao, Ting Zhang, Liyu Huang, Huimin Wu, Fengyi Hu, Fan Zhang, Linghua Zhu and Binying Fu*. 2012. Comparative metabolite profiling and hormone analysis of perennial and annual Rice. Journal of Plant Biology 55:73-80.

15. Ting Zhang, Lijuan Li, Fengyi Hu, Xiuqin Zhao, Binying Fu* and Daichang Yang*. 2012. Analysis of ESTs from a normalized cDNA library of the rhizome tip of Oryza longistaminata.  Journal of Plant Biology 55:33–42.

16. Yajiao Pan, Wensheng Wang, Xiuqin Zhao, Linghua Zhu, Binying Fu* and Zhikang Li. 2011. DNA methylation alterations of rice in response to cold stress. Plant Omics Journal 4(7):364-369.

17. Wensheng Wang, Xiuqin Zhao, Yajiao Pan, Linghua Zhu, Binying Fu*, Zhikang Li. 2011. DNA methylation changes detected by methylation-sensitive amplified polymorphism in two contrasting rice genotypes under salt stress. Journal of Genetics and Genomics 38(9): 419-424.

18. Di Wang, Yajiao Pan, Xiuqin Zhao, Linghua Zhu, Binying Fu*, Zhikang Li*. 2011. Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice.  BMC Genomics 12: 149.

19. Fengyi Hu, Di Wang, Ting Zhang, Xiuqin Zhao, Tianqing Zheng, Fan Zhan,  Dayun Tao, Linghua Zhu, Binying Fu*, Zhi-Kang Li*. 2011. Identification of rhizome-specific genes by genome-wide differential expression analysis in Oryza longistaminata. BMC Plant Biology 11:18.

20. Wensheng Wang, Yajiao Pan, Xiuqin Zhao, D. Dwivedi, Linghua Zhu, J. Ali, Binying Fu* and Zhikang Li*. 2011. Drought induced site specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.). Journal of Experimental Botany 62(6):1951–1960.

21. Yongli Zhou, Meirong Xu, Mingfu Zhao, Xuewen Xie, Linghua Zhu, Binying Fu*, Zhikang Li*. 2010. Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. Oryzicola. BMC Genomics 11:78.

22. Binying Fu, Jianhua Xiong, Linghua Zhu, Xiuqin Zhao, Huaxue Xu, Yongming Gao, Yangsheng Li, Jianlong Xu, Zhikang Li*. 2007. Identification of functional candidate genes for drought tolerance in rice. MGG 278(6):599-609.

23. Sanhong Liu^#, Binying Fu^#, Huaxue Xu, Linghua Zhu, Huqu Zhai, Zhikang Li. 2007. Cell death in response to osmotic and salt stresses in two rice (Oryza sativa L.) ecotypes. Plant Science 172: 897–902.

24. Ying Zong, Liyu Huang, Ting Zhang, Qiao Qin, Wensheng Wang, Xiuqin Zhao, Fengyi Hu, Binying Fu*, Zhikang Li. 2014. Differential microRNA expression between shoots and rhizomes in Oryza longistaminata using high-throughput RNA sequencing. The Crop Journal 2:102-109. DOI: 10.1016/j.cj.2014.03.005

Team Members: LI Zhi-kang, GAO Yong-ming, ZHOU Yong-li, HU Feng-yi, ZHAO Xiu-qin, ZHENG Tian-qing, ZHANG Fan, WANG Wen-sheng, WANG Chun-chao.