Fei Lu

 

To speed up breeding cycle and further improve crop varieties, we are trying to understand the genetics of agronomic traits, especially the complex traits (e.g. yield, heterosis, drought tolerance, resistance, etc.). We use quantitative genetic and statistical genomic approaches to answer the following questions:

 

1) What loci are controlling the traits?

2) What is the effect distribution among these loci?

3) What is the casual variant in each locus?

4) What variants interact with environments differently?

5) How to apply the knowledge obtained from 1-4 efficiently to accelerate breeding?

 

Our research goal is to enhance the genomic selection and/or develop a new system for breeding by efficiently using genomic editing technologies.

 

 

Quantitative traits are important for crop improvement, but difficult to work with, because 1) hundreds to thousands of loci controlling the traits; 2) each locus has small effect. The challenge is to identify thousands of loci and accurately estimate their effects together, which generally requires a large sample size in GWAS. However, due to the much higher cost for collecting phenotypes (compared with human genetic studies), it is not feasible to build a population of 1 million plants to estimate these small effects. There has to be another route to dissect complex trait, which needs to be creative, efficient, and cost-effective.

 

 

We use functional genome prediction approach to pinpoint trait controlling variants and estimate their effect. By using evolution (nature’s experiment of one billion years), decomposing complex traits to molecular level, combining with field trials and high-throughput sequencing, utilizing the power of optimization and machine learning approaches, we predict causal variants underneath important agronomic traits. The successful development of functional genome prediction approach will tremendously expand the application of genomic editing technologies in crops.

 

 

Please visit https://plantgeneticslab.github.io/home/

 

EMPLOYMENT
Institute of genetics and developmental biology, Chinese Academy of Sciences	Beijing, China
CAS-JIC Centre of Excellence for Plant and Microbial Sciences	Beijing, China
2017-Present   Group Leader
Institute for genomic diversity, Cornell University	Ithaca, NY, US
2014-2017        Research Associate
Institute for genomic diversity, Cornell University	Ithaca, NY, US
2010-2014        Post-doctoral Associate
EDUCATION
Institute of genetics and developmental biology, Chinese Academy of Sciences	Beijing, China
2005-2010        Ph.D.
College of Life Science, Northwest A&F University	Shaanxi, China
2003-2005        M.S.
1999-2003       B.S.

 

 

Xuebo Zhao^#, Yafei Guo^#, Lipeng Kang, Aoyue Bi, Daxing Xu, Zhiliang Zhang, Zhang Jijin, Xiaohan Yang, Jun Xu, Song Xu, Xinyue Song, Ming Zhang, Yiwen Li, Philip Kear, Jing Wang, Changbin Yin, Zhiyong Liu, Xiangdong Fu, Fei Lu*. Population genomics unravels the Holocene history of Triticum-Aegilops species. bioRxiv. (2022). doi:10.1101/2022.04.07.487499

 

Zhiliang Zhang^#, Jijin Zhang^#, Lipeng Kang, Xuebing Qiu, Beirui Niu, Aoyue Bi, Xuebo Zhao, Daxing Xu, Jing Wang, Changbin Yin, Xiangdong Fu, Fei Lu*. Genotyping of structural variation using PacBio high-fidelity sequencing. bioRxiv. (2022). doi:10.1101/2021.10.28.466362

 

Xiaofei Yang, Haopeng Yu, Wenqing Sun, Ling Ding, Ji Li, Jitender Cheema, Ricardo Ramirez-Gonzalez, Xuebo Zhao, Azahara C. Martín, Fei Lu, Bao Liu, Cristobal Uauy, Yiliang Ding & Huakun Zhang. Wheat in vivo RNA structure landscape reveals a prevalent role of RNA structure in modulating translational subgenome expression asymmetry. Genome Biology. (2021). doi:https://doi.org/10.1186/s13059-021-02549-y

 

Zhang, X.*, Zhu, Y., Kremling, K.A.G., Romay, M.C., Bukowski, R., Sun, Q., Gao, S., Buckler, E.S., Lu, F.*. Genome？wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. Theor. Appl. Genet.. (2021). doi:10.1007/s00122-021-03965-1

 

Wang J#, Xu J#, Yang X#, Xu S, Zhang M, Lu F*. Boosting the power of transcriptomics by developing an efficient gene expression profiling approach. Plant Biotechnol J. (2021). doi:10.1111/PBI.13706

 

Yuanying Peng*, Honghai Yan, Laichun Guo, Cao Deng, Lipeng Kang, Chunlong Wang, Pingping Zhou, Kaiquan Yu, Xiaolong Dong, Jun Zhao, Yun Peng, Xiaomeng Liu, Di Deng, Yinghong Xu, Ying Li, Qiantao Jiang, Yan Li, Liming Wei, Jirui Wang, Jian Ma, Ming Hao, Wei Li, Houyang Kang, Youliang Zheng, Yuming Wei, F. Lu*, Changzhong Ren*. Reference genome assemblies reveal the origin and evolution of allohexaploid oat. Research Square. (2021). doi:10.21203/rs.3.rs-664692/v1

 

X. Zhao, X. Fu, C. Yin*, F. Lu*. Wheat Speciation and Adaptation: Perspectives from Reticulate Evolution. aBiotech. (2021). doi:10.1007/s42994-021-00047-0

 

X. Zhao, X. Fu, C. Yin*, F. Lu*. Wheat Speciation and Adaptation: Perspectives from Reticulate Evolution. Preprints. (2021). 2021040559

 

Y. Zhou^#, X. Zhao^#, Y. Li, J. Xu, A. Bi, L. Kang, D. Xu, H. Chen, Y. Wang, Y. Wang, S. Liu, C. Jiao, H. Lu, J. Wang, C. Yin, Y. Jiao*, F. Lu*.  Triticum population sequencing provides insights into wheat adaptation. Nature Genetics. (2020). doi:10.1038/s41588-020-00722-w

 

Y. Zhou^#, X. Zhao^#, Y. Li, J. Xu, A. Bi, L. Kang, H. Chen, Y. Wang, Y. Wang, S. Liu, C. Jiao, H. Lu, J. Wang, C. Yin, Y. Jiao*, F. Lu*.  Convergence within divergence: insights of wheat adaptation from Triticum population sequencing. bioRxiv. (2020). doi:10.1101/2020.03.21.001362

 

Chunzhi Zhang, Pei Wang, Die Tang, Zhongmin Yang, Fei Lu, Jianjian Qi, Nilesh R. Tawari, Yi Shang, Canhui Li & Sanwen Huang .TThe genetic basis of inbreeding depression in potato. Nature Genetics. (2019). doi:10.1038/s41588-018-0319-1

 

Springer Nathan M., Anderson Sarah N., Andorf Carson M., Ahern Kevin R., Bai Fang, Barad Omer, Barbazuk W. Brad, Bass Hank W., Baruch Kobi, Ben-Zvi Gil, Buckler Edward S., Bukowski Robert, Campbell Michael S., Cannon Ethalinda K. S., Chomet Paul, Dawe R. Kelly, Davenport Ruth, Dooner Hugo K., Du Limei He, Du Chunguang, Easterling Katherine A., Gault Christine, Guan Jiahn-Chou, Hunter Charles T., Jander Georg, Jiao Yinping, Koch Karen E., Kol Guy, K？llner Tobias G., Kudo Toru, Li Qing, Lu Fei, Mayfield-Jones Dustin, Mei Wenbin, McCarty Donald R., Noshay Jaclyn M., Portwood John L., Ronen Gil, Settles A. Mark, Shem-Tov Doron, Shi Jinghua, Soifer, Ilya, Stein Joshua C., Stitzer Michelle C., Suzuki Masaharu, Vera Daniel L., Vollbrecht Erik, Vrebalov Julia T., Ware Doreen, Wei Sharon, Wimalanathan, Kokulapalan, Woodhouse Margaret R., Xiong Wenwei, Brutnell Thomas P.The maize W22 genome provides a foundation for functional genomics and transposon biology. Nature Genetics. (2018). doi:10.1038/s41588-018-0158-0 

 

Sun Silong, Zhou Yingsi, Chen Jian, Shi Junpeng, Zhao Haiming, Zhao Hainan, Song Weibin, Zhang Mei, Cui Yang, Dong Xiaomei, Liu Han, Ma Xuxu, Jiao Yinping, Wang Bo, Wei Xuehong, Stein Joshua C., Glaubitz Jeff C., Lu Fei, Yu Guoliang, Liang Chengzhi, Fengler Kevin, Li Bailin, Rafalski Antoni, Schnable Patrick S., Ware Doreen H., Buckler Edward S., Lai Jinsheng. Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nature Genetics. (2018). doi:10.1038/s41588-018-0182

 

Karl A. G. Kremling, Shu-Yun Chen, Mei-Hsiu Su, Nicholas K. Lepak, M. Cinta Romay, Kelly L. Swarts, Fei Lu, Anne Lorant, Peter J. Bradbury & Edward S. Buckler. (2018). Dysregulation of expression correlates with rare-allele burden and fitness loss in maize. Nature. doi:10.1038/nature25966

 

Punna Ramu*, Williams Esuma, Robert Kawuki, Ismail Y Rabbi, Chiedozie Egesi, Jessen V Bredeson, Rebecca S Bart, Janu Verma, Edward S Buckler, Fei Lu*. (2017). Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation. Nature Genetics. doi: 10.1038/ng.3845

 

Punna Ramu*, Williams Esuma, Robert Kawuki, Ismail Y Rabbi, Chiedozie Egesi, Jessen V Bredeson, Rebecca S Bart, Janu Verma, Edward S Buckler, Fei Lu*. (2016). Cassava HapMap: Managing genetic load in a clonal crop species. bioRxiv. doi: http://dx.doi.org/10.1101/077123

 

Candice N. Hirsch, Cory D. Hirsch, Alex B. Brohammer, Megan J. Bowman, Ilya Soifer, Omer Barad, Doron Shem-Tov, Kobi Baruch, Fei Lu, Alvaro G. Hernandez, Christopher J. Fields, Chris L. Wright, Klaus Koehler, Nathan Springer, Edward Buckler, C. Robin Buell, Natalia de Leon, Shawn M. Kaeppler, Kevin L. Childs, Mark Mikel. (2016). Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. The Plant Cell. doi:10.1105/tpc.16.00353

 

Williams Esuma, Liezel Herselman, Maryke Tine Labuschagne, Punna Ramu, Fei Lu, Yona Baguma, Edward S. Buckler, Robert Sezi Kawuki. (2016). Genome-wide association mapping of provitamin A carotenoid content in cassava. Euphytica. DOI: 10.1007/s10681-016-1772-5

 

Li, Y., Li, C., Bradbury, P. J., Liu, X., Lu, F., Romay, M. C., Glaubitz, J. C., Wu, X., Peng, B., Shi, Y., Song, Y., Zhang, D., Buckler, E. S., Zhang, Z., Li, Y. and Wang, T. (2016), Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population. Plant J. doi:10.1111/tpj.13174

 

Fei Lu*, Maria C Romay, Jeff C Glaubitz, Peter J Bradbury, Rob J Elshire, Tianyu Wang, Yu Li, Yongxiang Li, Kassa Semagn, Xuecai Zhang, Alvaro G. Hernandez, Mark A. Mikel, Ilya Soifer, Omer Barad, Edward S Buckler*. (2015) High-resolution genetic mapping of maize pan-genome sequence anchors. Nature Communications. DOI:10.1038/ncomms7914

 

Guillaume P. Ramstein, Alexander E. Lipka, Fei Lu, Denise E. Costich, Jerome H. Cherney, Edward S. Buckler and Michael D. Casler. (2015) Genome-Wide Association Study Based on Multiple Imputation with Low-Depth Sequencing Data: Application to Biofuel Traits in Reed Canarygrass. G3: Genes | Genomes | Genetics. DOI: 10.1534/g3.115.017533

 

Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES. (2014) TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline. PLoS ONE 9(2): e90346.

 

Lipka AE, Lu F, Cherney JH, Buckler ES, Casler MD, and Costich DE (2014). “Accelerating the switchgrass (Panicum virgatum L.) breeding cycle using genomic selecting approaches”. PLoS ONE 9(11), e112227.

 

Lu F, Lipka AE, Elshire RJ, Glaubitz JC, Cherney JH, Casler MD, Buckler ES, Costich DE. (2013) Switchgrass genomic diversity, ploidy and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genetics 9(1):e1003215.

 

Abhijit Sanyal^#, Ammiraju S.S.Jetty^#, Fei Lu^#, Yeisoo Yu Teri Rambo, Jennifer Currie, Kristi Kollura, Hye-Ran Kim, Jinfeng Chen, Jianxin Ma, Phillip San Miguel, Mingsheng Chen, Rod A. Wing and Scott A. Jackson. (2010). Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in sorghum. MOL BIOL EVOL. DOI:10.1093/molbev/msq133

 

Jetty S.S. Ammiraju, Chuanzhu Fan, Yeisoo Yu, Xiang Song, Karen A. Cranston, Ana Clara Pontaroli, Fei Lu, Abhijit Sanyal, Ning Jiang, Teri Rambo, Jennifer Currie, Kristi Collura, Jayson Talag, Jeffrey L. Bennetzen, Mingsheng Chen, Scott Jackson, Rod A. Wing. (2010). Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza. The Plant Journal. DOI: 10.1111/j.1365-313X.2010.04251.x

 

Lu, F. ^#, Ammiraju, J. S. ^#, Sanyal, A. ^#, Zhang, S. ^#, Song, R., Chen, J. ^#, Li, G., Sui, Y., Song, X., Cheng, Z., de Oliveira, A. C., Bennetzen, J. L.,Jackson, S., Wing, R. A., and Chen, M. (2009). Comparative sequence analysis of the MONOCULM1 orthologous regions in fourteen Oryza genomes. Proc Natl Acad Sci USA. 106(6):2071-6.

 

Ammiraju, J. S. ^#, Lu, F ^#., Sanyal, A. ^#, Yu, Y., Song, X., Jiang, N., Pontaroli, A. C., Rambo, T., Currie, J., Collura, K., Talag, J., Fan, C., Goicoechea, J. L., Zuccolo, A., Chen, J., Bennetzen, J. L., Chen, M., Jackson, S., and Wing, R. A. (2008). Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set. The Plant Cell 10.1105/tpc.1108.063727

 

Lukas A. Mueller, René Klein Lankhorst, Steven D. Tanksley, James J. Giovannoni, Ruth White, Julia Vrebalov, Zhangjun Fei, Joyce van Eck, Robert Buels, Adri A. Mills, Naama Menda, Isaak Y. Tecle, Aureliano Bombarely, Stephen Stack, Suzanne M. Royer, Song-Bin Chang, Lindsay A. Shearer, Byung Dong Kim, Sung-Hwan Jo, Cheol-Goo Hur, Doil Choi, Chang-Bao Li, Jiuhai Zhao, Hongling Jiang, Yu Geng, Yuanyuan Dai, Huajie Fan, Jinfeng Chen, Fei Lu, et al. (2009). A Snapshot of the Emerging Tomato Genome Sequence. The Plant Genome. 10.3835/plantgenome2008.08.0005: 78-92

 

Li C-B, Zhao JH, Jiang HL, Geng Y, Dai YY, Fan HJ,  Zhang DF, Chen JF, Lu F, Shi JF, Sun SH, Chen JJ, Yan XH, Lu C, Chen MS, Cheng ZK, Ling HQ, Wang Y, Xue YB, Li C. (2008). A snapshot of the Chinese SOL Project. Journal of Genomics and Genetics. 35: 387-390

 

Chen JF, Lu F, Chen SS, Tao SH. Significant positive correlation between the recombination rate and GC content in the human pseudoautosomal region. Genome (2006) 49:413–419.

 

Fei Lu FastCall 2. (2021).

Superfast variant calling and genotyping software for whole genome shotgun (WGS) data.

 

Fei Lu. Toolkits Integrated for Genetic and Evolutionary Research (TIGER). (2020).

Java-based code packages and tools developed in the lab to conduct efficient analysis on genetics and evolution.

 

Fei Lu. FastCall. (2016).

Super-fast variant caller for whole genome shotgun (WGS) sequencing data. It works for diploid species, including both inbreds and outcrossers.

 

Fei Lu, Jeff Glaubitz, Terry Casstevens, Qi Sun, Robert Bukowski, Katie Hyma, Ed Buckler. TASSEL 5.0 Pan-genome Atlas (PanA) pipeline. (2014).

PanA combines genetic mapping and machine learning to produces millions of genetic anchor for the genome of a species.

 

Fei Lu, Jeff Glaubitz, James Harriman, Terry Casstevens, Rob Elshire. TASSEL 3.0 Universal Network Enabled Analysis Kit (UNEAK) pipeline. (2012).

A reference genome free SNP calling pipeline.