Hongyan Zhu

Hongyan Zhu

Professor

hzhu4@uky.edu
Phone (859) 257-3647
Fax (859) 257-7125

University of Kentucky, PSS
Plant Science Building
1405 Veterans Drive (Office:301B) Lexington KY 40546-0312

Professional Profile

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

Specialty

Plant Genetics and Genomics

Research Interests

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.

Education

  • 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

Courses Taught

PLS 615 Advanced Plant Genetics and Genomics (3 credits)

Genomics is reshaping the life sciences by providing high-throughput tools to decipher the functions of individual genes and to characterize their regulation and interactions. The last decade has seen tremendous development of genomic resources and technologies in major crops and their models. The intelligent use of these resources and technological innovations will advance our understanding of genome function, allow for prediction of phenotype from genotype, and thus enhance our ability to improve crop production. This course will introduce graduate students to the major contemporary areas of genomics, including, but not limited to, genome mapping, genome sequencing, genome annotation, genome-wide association analysis, marker-assisted selection in plant breeding, genome-wide transcriptional profiling, high throughput forward and reverse genetics, DNA methylation and epigenetics, quantitative trait locus analysis, and the basic bioinformatics tools.

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. Yang S, Tang F, Zhu H (2014) Alternative splicing in plant immunity. International Journal of Molecular Sciences 15:10424
  6. 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
  7. Chen C, Zhu H (2013) Are common symbiosis genes required for endophytic rice-rhizobial interactions? Plant Signal & Behavior 8(9): e25453
  8. Yang S, Tang F, Caixeta ET, Zhu H (2013) Epigenetic regulation of a powdery mildew resistance gene in Medicago truncatula. Molecular Plant 6:2000
  9. 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
  10. Gao M, Zhu H (2013) Fine mapping of a major quantitative trait locus that regulates pod shattering in soybean. Molecular Breeding 32:485
  11. Wang D*, Yang S, Tang F, Zhu H (2012) Symbiosis specificity in the legume-rhizobial mutualism. Cellular Microbiology 14:334
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. Ané JM, ZhuH, FrugoliJ (2008) Recent advances in Medicago truncatula genomics. International Journal of Plant Genomics doi: 10.1155/2008/256597
  19. 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
  20. 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
  21. 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
  22. Zhu H, Riely B, Burns NJ, Ané JM (2006) Tracing non-legume orthologs of legume genes required for nodulation and arbuscular mycorrhizal symbioses.  Genetics 172:2491
  23. Zhu H, Choi HK, Cook DR, Shoemaker RC (2005) Bridging model and crop legumes through comparative genomics.  Plant Physiology 137:1189
  24. Choi HK, Mun JH, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR (2004) Estimating genome conservation between crop and model legume species. Proceedings of the National Academy of Sciences USA 101:15289-15294
  25. Zhu H, Kim DJ, Baek JM, Choi HK, Ellis L, Kuester H, McCombie WR, Peng HM, Cook DR (2003) Syntenic relationships between Medicago truncatula and Arabidopsis thaliana reveal extensive divergence of genome organization. Plant Physiology 131: 1018-1026
  26. Zhu H, Cannon S, Young ND, Cook DR (2002) Phylogeny and genomic organization of the TIR and non-TIR NBS-LRR resistance gene family in Medicago truncatula. Molecular Plant-Microbe Interactions 15:529-539
  27. Cannon SB, ZhuH, Baumgarten AM, Spangler R, May G, Cook DR, Young ND (2002) Diversity, distribution, and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies.  Journal of Molecular Evolution 54: 548-562
  28. Cook DR, Kim D, Zhu H, Uribe P (2000) Plant-pathogen interactions in Medicago truncatula. Grain Legumes Magazine 28: 20
  29. Zhu H, Gilchrist L, Hayes P, Kleinhofs A, Kudrna D, Liu Z, Prom L, Steffenson B, Toojinda T, 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.  Theoretical and Applied Genetics 99: 1221-1232
  30. Zhu H, Briceño G, Dovel R, Hayes PM, Liu BH, Liu CT, Ullrich SE (1999) Molecular breeding for grain yield in barley: an evaluation of QTL effects in a spring barley cross. Theoretical and Applied Genetics 98: 772-779
  31. Zhu H, Muthukrishnan S, Krishnaveni S, Wilde G, Jeoung J-M, Liang GH (1998) Biolistic transformation of sorghum using a rice chitinase gene.  Journal of Genetics & Breeding 52: 243-252
  32. Mo H, Huang Z, Zhu H (1997) Statistical methods for genetic analysis of seed traits in diallel cross designs. Journal of Jiangsu Agricultural College 18: 25-30
  33. Zhu H, Mo H, Huang Z (1995) Genetic analysis of grain protein and gum content in barley (H. vulgare L.). Journal of Jiangsu Agricultural College 16: 39-46