Research interests:
Zhiwu Zhang received his first PhD in Genetics & Breeding from Northeast Agriculture University (China) and the second PhD in Statistical Genetics from Michigan State University (USA). Dr. Zhang has long-term experience to develop statistical methods for mapping genes underlying complex traits and make genetic prediction at individual level. His research has resulted in many publications in high profile journals, such as Nature Genetics, Science and Plant Cell. He and his coleagues developed a statistical tool for association analysis by using mixed linear model in software TASSEL, which is widely used in the world for Quantitative trait loci (QTL) mapping. Its corresponding paper in Bioinformatics has received nearly a hundred citations. His interest of implementation to solve practical problems covered several species, including maize, rice, cattle, dog and human. Currently his major research aims are 1) to improve statistical power for association analysis to allow the reduction of false positives for QTL finding and 2) to use ancient and recent linkage disequilibrium simultaneously so that genes with low frequency or having confounding effect with population structure could be identified.
Publications (*Coresponding authors):
34. Gang Guo, Zhengkui Zhou, Yachun Wang, Keyan Zhao, Lan Zhu, George Lust, Linda Hunter, Junya Li, Jody Sandler, Rory Todhunter, and Zhiwu Zhang* Canine Hip Dysplasia is Predictable by Genotyping. Osteoarthritis and Cartilage. 2011 (19) 420-429
33. Friedenberg SG, Zhu L, Zhang Z, Foels WB, Schweitzer PA, Wang W, Fisher PJ, Dykes NL, Corey E, Vernier-Singer M, Jung SW, Sheng X, Hunter LS, McDonough SP, Lust G, Bliss SP, Krotscheck U, Gunn TM, Todhunter RJ., Evaluation of a fibrillin 2 gene haplotype associated with hip dysplasia and incipient osteoarthritis in dogs. Am J Vet Res. 2011 (72):530-40
32. Zhengkui Zhou, Xihui Sheng, Zhiwu Zhang*, Keyan Zhao, Lan Zhu, Gang Guo,Steve Friedenberg, Linda Hunter, Wendy Vandenberg-Foels, William Hornbuckle, Ursula Krotscheck, Elizabeth Corey, Sydney Moise, Nathan Dykes, Junya Li, Shangzhong Xu, Lixin Du, Yachun Wang, Jody Sandler, Gregory Acland, George Lust, Rory Todhunter. Differential Genetic Regulation of Canine Hip Dysplasia and Osteoarthritis, PLoS ONE 5(10): e13219. doi:10.1371/journal.pone.0013219.
31. Yali Hou, Yachun Wang, George Lust, Lan Zhu, Zhiwu Zhang*, Rory J. Todhunter. Retrospective Analysis for Genetic Improvement of Hip Joints of Cohort Labrador Retrievers in the United States: 1970–2007. PLoS One, 2010 5(2): e9410
30. Zhiwu Zhang*, Elhan Ersoz, Chao-Qiang Lai, Rory J Todhunter, Hemant K Tiwari, Michael A Gore, Peter J Bradbury, Jianming Yu, Donna K Arnett, Jose M Ordovas, & Edward S Buckler, Adaptation of Mixed Linear Model for Genome-Wide Association Studies, Nature Genetics 2010 42: 355-360.
29. Tim L. Setter, Jianbing Yan, Marilyn Warburton, Jean-Marcel Ribaut, Yunbi Xu, Mark Sawkins, Edward S. Buckler, Zhiwu Zhang, Michael A. Gore. Polymorphisms in Genes that Affect Abscisic Acid Levels in Maize Floral Tissues During Drought. The Journal of Experimental Botany, 2010, doi:10.1093/jxb/erq308.
28. Nengyi Zhang, Yves Gibon, Amit Gur, Charles Chen, Nicholas Lepak, Melanie Höhne, Zhiwu Zhang, Dallas Kroon, Hendrik Tschoep, Mark Stitt, and Edward Buckler. Fine Quantitative Trait Loci Mapping of Carbon and Nitrogen Metabolism Enzyme Activities and Seedling Biomass in the Intermated Maize IBM Mapping Population. Plant Physiology, 2010 (154) 1753-1765
27. Xuehui Huang, Tao Sang, Qiang Zhao, Xinhua Wei, Qi Feng, Yan Zhao, Canyang Li, Chuanrang Zhu, Tingting Lu, Zhiwu Zhang, Meng Li, Danlin Fan, Yunli Guo, Ahong Wang, Lu Wang, Liuwei Deng, Wenjun Li, Yiqi Lu, Qijun Weng, Kunyan Liu, Tao Huang, Taoying Zhou, Yufeng Jing, Wei Li, Lei Zhang, Edward S. Buckler, Qian Qian, Qifa Zhang, Jiayang Li and Bin Han. Genome-wide association studies of 14 agronomic traits in rice landraces, Nature Genetics 2010 (42) 961–967.
26. Zhiwu Zhang*, Edward S. Buckler, Terry M. Casstevens and Peter J. Bradbury. Software engineering the mixed model for genome-wide association studies on large samples. Briefings in Bioinformatics 2009 10(6):664-675
25. Zhiwu Zhang, Changxi Li, Rory J. Todhunter, George Lust, Laksiri Goonewardene and Zhiquan Wang. 2009. An Algorithm to Sort Complex Pedigrees Chronologically without Birthdates. Journal of Animal and Veterinary Advances 8 (1): 177-182
24. Zhiwu Zhang, Lan Zhu, Jody Sandler, Steve Friedenberg, Jill Egelhoff, Alma J. Williams, Nathan L. Dykes, William Hornbuckle, Ursula Krotscheck, N. Sydney Moise, George Lust, Rory J. Todhunter. 2009, Heritabilities, Genetic Correlations, and Breeding Values of Four Traits Collectively Defining Hip Dysplasia. American Journal of Veterinary Research 70(4):483-92.
23. Buckler, E. S.; Holland, J. B.; Bradbury, P. J.; Acharya, C. B.; Brown, P. J.; Browne, C.; Ersoz, E.; Flint-Garcia, S.; Garcia, A.; Glaubitz, J. C.; Goodman, M. M.; Harjes, C.; Guill, K.; Kroon, D. E.; Larsson, S.; Lepak, N. K.; Li, H.; Mitchell, S. E.; Pressoir, G.; Peiffer, J. A.; Rosas, M. O.; Rocheford, T. R.; Romay, M. C.; Romero, S.; Salvo, S.; Sanchez Villeda, H.; da Silva, H. S.; Sun, Q.; Tian, F.; Upadyayula, N.; Ware, D.; Yates, H.; Yu, J.; Zhang, Z.; Kresovich, S.; McMullen, M. D. The genetic architecture of maize flowering time. Science 325, 714-8 (2009).
22. Myles, S.; Peiffer, J.; Brown, P. J.; Ersoz, E. S.; Zhang, Z.; Costich, D. E.; Buckler, E. S. Association Mapping: Critical Considerations Shift from Genotyping to Experimental Design. Plant Cell 21, 2194-202 (2009).
21. Jianming Yu, Zhiwu Zhang, Chengsong Zhu, Dindo A. Tabanao, Gael Pressoir, Mitchell R. Tuinstra, Stephen Kresovich, Rory J. Todhunter, Edward S. Buckler. 2009. Simulation Appraisal of the Adequacy of Number of Background Markers for Relationship Estimation in Association Mapping. Plant Genome, (2) 63-77
20. Mateescu RG, Burton-Wurster NI, Tsai K, Phavaphutanon J, Zhang Z, Murphy KE, Lust G, Todhunter RJ.. 2008. Identification of quantitative trait loci for osteoarthritis of hip joints in dogs. American Journal of Veterinary Research, 69(10):1294-300.
19. Zhu L, Zhang Z, Feng F, Schweitzer P, Phavaphutanon J, Vernier-Singer M, Corey E, Friedenberg S, Mateescu R, Williams A, Lust G, Acland G, Todhunter R. 2008. Single nucleotide polymorphisms refine QTL intervals for hip joint laxity in dogs. Animal Genetics. 39(2):141-6.
18. Liu, T., Rory J Todhunter, Song Wu, Wei Hou, Raluca Mateescu, Zhiwu Zhang, Nancy I Burton-Wurster, Gregory M Acland, George Lust, Rongling Wu. 2007. A random model for mapping imprinted quantitative trait loci in a structured pedigree: An implication for mapping canine hip dysplasia. Genomics. 90 (2): 276-284.
17. Hays, L., Zhang, Z. Mateescu, R. G. Lust, G. Burton-Wurster, N. I. Todhunter, R. J.. 2007. Quantitative genetics of secondary hip joint osteoarthritis in a Labrador Retriever-Greyhound pedigree. American Journal of Veterinary Research. 68 (1): 35-41.
16. Zhang, Z., P. J. Bradbury, D. E. Kroon, T.M. Casstevens, Y. Ram-doss, and E. S. Buckler, TASSEL: Software for Association Mapping of Complex Traits in Diverse Samples. 2007. Bioinformatics 20: 2839-2840.
15. Zhang Z, R. J. Todhunter, E. S. Buckler, and L. D. Van Vleck. Technical note: Use of marker-based relationships with multiple-trait derivative-free restricted maximal likelihood. J Anim Sci, 2007, 85: 881-885.
14. Zhang Z, Michal JJ, Gaskins CT, Jiang Z. The bovine fatty acid binding protein 4 gene is significantly associated with marbling and subcutaneous fat depth in Wagyu x Limousin F2 crosses. Animal Genetics, 2006, 37 (4) 400-402.
13. Todhunter RJ, Mateescu R, Lust G, Burton-Wurster NI, Dykes NL, Bliss SP, Williams AJ, Vernier-Singer M, Corey E, Harjes C, Quaas RL, Zhang Z, Gilbert RO, Volkman D, Casella G, Wu R, Acland GM., Quantitative trait loci for hip dysplasia in a cross-breed canine pedigree. Mamm Genome. 2005;16(9):720-30.
12. Mateescu RG, Zhang Z, Tsai K, Phavaphutanon J, Burton-Wurster NI, Lust G, Quaas R, Murphy K, Acland GM, Todhunter RJ, Analysis Of Allele Fidelity, Polymorphic Information Content, And Density Of Microsatellites: In a Genome Wide Screening for Hip Dysplasia in A Cross Breed Pedigree. Journal of Heredity 2005 96(7):847-853.
11. Dikeman ME, Pollak EJ, Zhang Z, Moser DW, Gill CA, Dressler EA, Phenotypic ranges and relationships among carcass and meat palatability traits for fourteen cattle breeds, and heritabilities and expected progeny differences for Warner-Bratzler shear force in three beef cattle breeds. J. Anim. Sci. 2005. 83:2461–2467
10. Sun B, Chen,Y, Xu S, Zhang Z. Effect of the Simmental as the sire line on linear type traits in crossbreeding with Mongolian cattle. Acta Veterinaria et Zootechnica Sinica. (in Chinese with English abstract) 1998. 29(3):221-224.
9. Meng, AM, Qi SZ, Yu RL, Wang RX, Cai YH, Jiao SX, Xin CY, Z. Zhang. Analysis of DNA Fingerprints of Fengjing Pig and Xian Pig. Hereditas, (in Chinese with English abstract) 1995,17:19-22.
8. Zhang Z, Sheng ZL. Research on the mathematical model of systemic conserving livestock genetic resources and its application. Acta Veterinaria et Zootechnica Sinica (in Chinese with English abstract) 1994. 25(4) 306-310.
7. Zhang Z, Yu RL, Wang RX, Fang ZM, Zheng YM. Estimates of gene effects and effective gene number on litter size pig. Acta Genetica Sinica. (in Chinese with English abstract) 1994, 21(4) 275-280.
6. Zhang Z. Decision support system of grading local pigs conserved, Application of Computer in Agriculture, (in Chinese with English abstract) 1993, 2,27‑30.
5. Zhang Z. Statistical Model for the Standardized Trainability, Journal of Chinese Simmental, (in Chinese with English abstract) 1993, 1 18-37-39.
4. Zhang Z. Research on the pattern of Eco breeding for livestock, Eco‑Agriculture Research, (in Chinese with English abstract) 1993, 3, 48‑51.
3. Zhang Z, Sheng ZL, Feng WQ. Strategies and schemes for conserving genetic resources of Chinese pigs, Chinese J. of Animal Science, (in Chinese) 1993, (29)5, 5‑7.
2. Zhang Z. Iterative method for calculating inbreeding and kinship coefficients, Journal of Northeast Agricultural University, (in Chinese with English abstract) 1991, 22(3) 231-235.
1. Zhang Z, Cai YH, Jin XX. Group mating model with quadratic program and its application in minimizing inbreeding, Chinese J. of Animal and Veterinary Science, (in Chinese with English abstract) 1991, 22(1) 49‑56.
