Hongyan Zhu

Hongyan Zhu

Portrait of Hongyan Zhu

Hongyan Zhu


301B Plant Sciences Building 1405 Veterans Drive Lexington, KY 40546-0312

Last Revised: Mar 19th, 2024

Professional Biography

Areas of Interest: Plant Genetics and Genomics

The Zhu laboratory studies pathogenic and symbiotic plant-microbe interactions, with a special focus on legumes. His lab has engineered alfalfa for resistance to anthracnose disease using the gene cloned from the model legume Medicago truncatula. Research projects involving root symbioses include 1) functional analysis of non-legume orthologs of legume genes required for nodulation and mycorrhizal symbioses, 2) cloning and characterization of soybean and Medicago genes that control nodulation specificity, and 3) identification and cloning of Medicago genes that govern strain-specific nitrogen fixation and regulate natural variation in nitrogen fixation efficiency. He and his colleagues (as well as others) have shown that non-legumes, such as rice and maize, possess the orthologs of all cloned genes required for root nodule symbiosis in legumes, and these non-legume genes have equivalent functions to their legume counterparts. Zhu also led the isolation of two soybean genes Rj2 and Rfg1 that control cultivar-specific nodulation, and showed that legume plants use disease resistance (R) genes to choose their symbiotic partners. This latter finding reveals a common recognition mechanism underlying symbiotic and pathogenic host-bacteria interactions and indicates that establishment of a root nodule nitrogen fixing symbiosis requires the evasion of plant immune responses triggered by rhizobial effectors or microbe-associated molecular patterns (MAMPs). Despite recent advances in our understanding of the signaling pathways leading to root nodule development, the molecular mechanisms underlying natural variation in nitrogen fixation efficiency/specificity are completely unknown. Thus, the Zhu lab also attempts to elucidate the complexity of this important, but currently overlooked, aspect of the legume-rhizobia symbiosis using genetic, genomic, and molecular approaches, with an ultimate goal of developing novel strategies to enhance the agronomic potential of biological nitrogen fixation.


Professor, Plant Genetics and Genomics, Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky, 2015-present

Associate Professor, Plant Genetics and Genomics, Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky, 2009-2015

Assistant Professor, Plant Genetics and Genomics, Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky, 2004-2009

Postdoctoral Research Associate, Department of Plant Pathology, University of California, Davis, California, 2002-2004

Graduate Research Assistant, Department of Plant Pathology and Genetics Program, Texas A&M University, College Station, Texas, 1998-2001

Graduate Research Assistant, Department of Crop and Soil Sciences and Genetics Program, Oregon State University, Corvallis, Oregon, 1997-1998

Graduate Research Assistant, Department of Agronomy and Genetics Program, Kansas State University, Manhattan, Kansas, 1995-1997

Assistant Wheat Breeder, Nanjing Agricultural Institute, Nanjing, China, 1991-1994

Graduate Research Assistant, Department of Agronomy, Yangzhou University, Yangzhou, China, 1988-1991


Recent Publications

  1. Yang S, Wang Q, Fedorova E, Liu J, Qin Q, Zheng Q, Price PA, Pan H, Wang D, Griffitts JS, Bisseling T, Zhu H (2017) Microsymbiont discrimination mediated by a host-secreted peptide in Medicago truncatula. Proceedings of the National Academy of Sciences USA 114 : 6848
  2. Wang Q, Yang S, Liu J, Terecskei K, Ábrahám E, Gombár A, Domonkos Á, Szűcs A, Körmöczi P, Wang T, Fodor L, Mao L, Fei Z, Kondorosi É, Kaló P, Kereszt A, Zhu H (2017) Host-secreted antimicrobial peptide enforces symbiotic selectivity in Medicago truncatula. Proceedings of the National Academy of Sciences USA 114: 6854
  3. Fan Y, Liu J, Lyu S, Wang Q, Yang S, Zhu H (2017) The soybean Rfg1 gene restricts nodulation by Sinorhizobium fredii USDA193. Frontiers in Plant Science doi: 10.3389/fpls.2017.01548
  4. Zheng Q, Liu J, Goff B, Dinkins R, Zhu H (2016) Genetic manipulation of miR156 for improvement of biomass production and forage quality in red clover. Crop Science 56: 1-7
  5. Tang F, Yang S, Zhu H (2016) Functional analysis of alternative transcripts of the soybean Rj2 gene that restricts nodulation with specific rhizobial strains. Plant Biology doi: 10.1111/plb.12442
  6. Tang F, Yang S, Liu J, Zhu H (2016) Rj4, a gene controlling nodulation specificity in soybeans, encodes a thaumatin-Like protein but not the one previously reported. Plant Physiology 170:26-32
  7. Liu J, Yang S, Zheng Q, Zhu H (2014) Identification of a dominant gene in Medicago truncatula that restricts nodulation by Sinorhizobium meliloti strain Rm41. BMC Plant Biology 14:167
  8. Yang S, Tang F, Zhu H (2014) Alternative splicing in plant immunity. International Journal of Molecular Sciences 15:10424
  9. Tang F, Yang S, Liu J, Gao M, Zhu H (2014) Fine mapping of the Rj4 locus, a gene controlling nodulation specificity in soybean. Molecular Breeding 33:691
  10. Chen C, Zhu H (2013) Are common symbiosis genes required for endophytic rice-rhizobial interactions? Plant Signal & Behavior 8(9): e25453
  11. Yang S, Tang F, Caixeta ET, Zhu H (2013) Epigenetic regulation of a powdery mildew resistance gene in Medicago truncatula. Molecular Plant 6:2000
  12. Tang F, Yang S, Gao M, Zhu H (2013) Alternative splicing is required for RCT1-mediated disease resistance in Medicago truncatula. Plant Molecular Biology 82:367
  13. Gao M, Zhu H (2013) Fine mapping of a major quantitative trait locus that regulates pod shattering in soybean. Molecular Breeding 32:485
  14. Wang D*, Yang S, Tang F, Zhu H (2012) Symbiosis specificity in the legume-rhizobial mutualism. Cellular Microbiology 14:334
  15. Nayak SN, Zhu H, Varghese N, Datta S, Choi HK, Horres R, Jüngling R, Singh J, Kishor PB, Sivaramakrishnan S, Hoisington DA, Kahl G, Winter P, Cook DR, Varshney RK (2010) Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. Theoretical and Applied Genetics 120:1415
  16. Yang S, Tang F, Gao M, Krishnan HB, Zhu H (2010) R gene-controlled host specificity in the legume-rhizobia symbiosis. Proceedings of the National Academy of Sciences USA 107:18735
  17. Chen C, Fan C, Gao M, Zhu H (2009) Antiquity and function of CASTOR and POLLUX, the twin ion channel-encoding genes key to the evolution of root symbioses in plants. Plant Physiology 149:306
  18. Dhandaydham M, Charles L, Zhu H, Starr JL, Huguet T, Cook DR, Prosperi JM, Opperman C (2008) Characterization of Root-Knot Nematode Resistance in Medicago truncatula. The Journal of Nematology 40:46
  19. Yang S, Gao M, Xu C, Gao J, Deshpande S, Lin S, Roe B, Zhu H (2008) Alfalfa benefits from Medicago truncatula: The RCT1 gene from M. truncatula confers broad-spectrum resistance to anthracnose in alfalfa. Proceedings of the National Academy of Sciences USA 105:12164
  20. Chen C, Ané J-M, Zhu H (2008) Os-IPD3, an ortholog of the Medicago truncatula DMI3 interacting protein IPD3, is required for mycorrhizal symbiosis in rice. New Phytologist 180:311
  21. Ané JM, ZhuH, FrugoliJ (2008) Recent advances in Medicago truncatula genomics. International Journal of Plant Genomics doi: 10.1155/2008/256597
  22. Ameline-Torregrosa C, Wang BB, O'Bleness MS, Deshpande S, Zhu H, Roe B, Young ND, Cannon SB (2008) Identification and characterization of NBS-LRR genes in the model plant Medicago truncatula. Plant Physiology 146:5
  23. Chen C, Gao M, Liu J, Zhu H (2007) Fungal symbiosis in rice requires an ortholog of a legume common symbiosis gene encoding a Ca2+/calmodulin-dependent protein kinase. Plant Physiology 145:1619
  24. Yang S, Gao M, Deshpande S, Lin S, Roe B, Zhu H (2007) Genetic and physical localization of an anthracnose resistance gene in Medicago truncatula. Theoretical and Applied Genetics 116:45


Ph.D., Genetics, Texas A&M University, 2001
M.S., Genetics, Kansas State University, 1997
M.S., Statistics and Quantitative Genetics, Yangzhou University, 1991
B.S., Agronomy, Yangzhou University, 1988

Course Instruction

PLS 615: Advanced Plant Genetics and Genomics (3)
Course Description: Genomics is reshaping the life sciences, providing high-throughput tools to decipher function of individual genes and to characterize their regulation and interactions. This course will introduce graduate students to most recent advances in the area of plant genetics and genomics. The topics will include structural and functional analysis of plant genomes, genome evolution, application of genomics tools to crop improvement, and basic concepts of bioinformatics.

Contact Information

Rebecca McCulley, Ph.D.
Department Chair

105 Plant Sciences Building Lexington, KY 40546-0312

(859) 257-5020