University of Kentucky College of Agriculture

Hongyan Zhu



Directions to University of Kentucky, Lexington, KYUniversity of Kentucky, PSS
Campus LocationPlant Science Building
1405 Veterans Drive (Office:301B)
Lexington, KY 40546-0312
Phone(859) 257-3647
Fax(859) 257-7125


Plant Genetics and Genomics


Ph.D., Genetics, Texas A&M University, College Station, Texas, 2001

M.S., Genetics, Kansas State University, Manhattan, Kansas, 1997

M.S., Statistics and Quantitative Genetics, Yangzhou University, Yangzhou, China, 1991

B.S., Agronomy, Yangzhou University, Yangzhou, China, 1988


2009-present, Associate Professor, Department of Plant and Soil Sciences, University of Kentucky

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

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

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

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

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

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

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


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.



This person page last updated on 2014-06-20


    PLS615 - Advanced Plant Genetics and Genomics; Credits - 3
    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. Prereq: Introductory courses in genetics and biochemistry. .
    Instructors: Hongyan Zhu

Research/Teaching Publications

    Refereed Journal Articles

    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
    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: 691-700.
    Yang S, Tang F, Zhu H 2014. Alternative splicing in plant immunity. International Journal of Molecular Sciences 15:10424
    Chen C, Zhu H. 2013. Are common symbiosis genes required for endophytic rice-rhizobial interactions? Plant Signal & Behavior 8(9):e25453
    Gao M, Zhu H. 2013. Fine mapping of a major quantitative trait locus that regulates pod shattering in soybean. Molecular Breeding 32:485-491
    Tang F, Yang S, Gao M, Zhu H. 2013. Alternative splicing is required for RCT1-mediated disease resistance in Medicago truncatula. Plant Molecular Biology 82:367-374
    Yang S, Tang F, Caixeta ET, Zhu H. 2013. Epigenetic regulation of a powdery mildew resistance gene in Medicago truncatula. Molecular Plant 6:2000-2003
    Wang D, Yang S, Tang F, Zhu H. 2012. Symbiosis specificity in the legume-rhizobial mutualism. Cellular Microbiology 14:334-342.
    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. Theor Appl Genet. 120:1415-1441
    Yang S, Tang F, Gao M, Krishnan HB, Zhu H. 2010. R gene-controlled host specificity in the legume-rhizobia symbiosis. Proc. Natl. Acad. Sci. USA 107(43):18735-40
    Chen C, Fan C, Gao M, and 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 149:306-317.
    Ameline-Torregrosa C, Wang B, O'Bleness M, Deshpande S, Zhu H, Roe B, Young ND, Cannon B. 2008. Identification and characterization of NBS-LRR genes in the model plant Medicago truncatula. Plant Physiology 146: 5-21
    Ane J-M, Zhu H, Frugoli J. 2008. Recent advances in Medicago truncatula genomics. International Journal of Plant Genomics doi: 10.1155/2008/256597
    Chen C, Ane 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: 311-315
    Dhandaydham M, Charles L, Zhu H, Starr JL, Huguet T, Cook DR, Prosperi JM, 2008. Characterization of Root-Knot Nematode Resistance in Medicago truncatula. J Nematol. 40:46-54
    Yang S, Gao M, Xu C, Gao J, Deshpande S, Lin S, Roe BA, Zhu H. 2008. Alfalfa benefits from Medicago truncatula: the RCT1 gene from M. truncatula confers broad-spectrum resistance to anthracnose in alfalfa. Proc Natl Acad Sci USA. 105(34):12164-9.
    Chen, C., M. Gao, J. Liu, and H. Zhu. 2007. Fungal symbiosis in rice requires an ortholog of a legume common symbiosis gene encoding a Ca2+/calmodulin-dependent protein kinase. Plant Physiology 145:1619-1628.
    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 116:45-52
    Zhu H, Riely B, Burns NJ, and Ane JM 2006. Tracing non-legume orthologs of legume genes required for nodulation and arbuscular mycorrhizal symbioses. Genetics, 172:2491-2499
    Zhu H, Choi HK, Cook DR and Shoemaker RC 2005. Bridging model and crop legumes through comparative genomics. Plant Physiology 137: 1189-1196
    Choi HK, Mun JH, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND and Cook DR 2004. Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA, 101:15289-15294
    Zhu H, Kim DJ, Baek JM, Choi HK, Ellis L, Kuester H, McCombie WR, Peng HM and Cook, DR 2003. Syntenic relationships between Medicago truncatula and Arabidopsis thaliana reveal extensive divergence of genome organization. Plant Physiology, 131: 1018-1026
    Cannon SB, Zhu H, Baumgarten AM, Spangler R, May G, Cook DR and Young ND 2002. Diversity, distribution, and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies. J Mol Evol, 54: 548-562
    Zhu H, Cannon S, Young ND and Cook DR 2002. Phylogeny and genomic organization of the TIR and non-TIR NBS-LRR resistance gene family in Medicago truncatula. MPMI, 15:529-539
    Cook DR, Kim D, Zhu H and Uribe P 2000. Plant-pathogen interactions in Medicago truncatula. Grain Legumes Magazine, 28: 20.
    Zhu H, Briceņo G, Dovel R, Hayes PM, Liu BH, Liu CT and Ullrich SE 1999. Molecular breeding for grain yield in barley: an evaluation of QTL effects in a spring barley cross. Theor Appl Genet, 98: 772-779
    Zhu H, Gilchrist L, Hayes P, Kleinhofs A, Kudrna D, Liu Z, Prom L, Steffenson B, Toojinda T and Vivar H 1999. Does function follow form? Principal QTLs for Fusarium head blight (FHB) resistance are coincident with QTLs for inflorescence traits and plant height in a doubled-haploid population of barley. Theor Appl Genet, 99: 1221-1232.
    Zhu H, Muthukrishnan S, Krishnaveni S, Wilde G, Jeoung J-M and Liang GH 1998. Biolistic transformation of sorghum using a rice chitinase gene. Journal of Genetics & Breeding, 52: 243-252
    Mo H, Huang Z and Zhu H 1997. Statistical methods for genetic analysis of seed traits in diallel cross designs. Journal of Jiangsu Agricultural College, 18: 25-30.
    Zhu, H., Mo, H. and Huang, Z. 1995. Genetic analysis of grain protein and gum content in barley (H. vulgare L.). Journal of Jiangsu Agricultural College, 16: 39-46.