Jianming Yu

Associate Professor

Office: 1569 AGRON
Phone: (515) 294-2757

Jianming Yu is associate professor in Quantitative Genetics and Pioneer Distinguished Chair in Maize Breeding in the Department of Agronomy, Iowa State University. The focus of Yu’s program is to address significant questions in plant breeding by combining cutting-edge genomic technologies and quantitative genetics theories. All members of this research program conduct empirical experiments in plant breeding and genetics and contribute to summer and winter nursery work, and many of them also carry out computer simulations or bioinformatics research to generalize their specific findings to a broad context. Yu teaches a graduate student class, AGRON 621 - Advanced Plant Breeding, each Spring semester. Guiding questions addressed by this program include: 

  • How can we improve the current plant breeding methods to make better use of genetic resources and high throughput genotyping and phenotyping technologies? 
  • How can we leverage genetic design, experimental design, and optimization thinking to plan out our research?
  • How can we efficiently identify genes underlying quantitative traits so that the resulting empirical findings can guide our research in plant breeding?

Yu's research integrates knowledge in Plant Breeding, Quantitative Genetics, Genomics, Molecular Genetics, and Statistics, and has the ultimate goal of developing and implementing new strategies and methods in trait dissection and crop improvement. Current research includes Genome-Wide Association Studies (GWAS) with diverse germplasm or multiple designed mapping populations (such as Nested Association Mapping, NAM; or meta-QTL analysis), Genomic Selection (GS; or Genome-Wide Selection GWS) to efficiently integrate high throughput genotyping into various breeding processes, Gene Cloning for traits with agronomic and domestication importance, Genotype-by-Environment Interaction (GEI) and Epistasis dissection to causal polymorphic sites, Genome and Chromosome Size Evolution across taxonomic groups, and Genome-Wide Base Composition changes and underlying principles. Here is a list of news releases about our research.

(YouTube) Genomic Selection: Historical Context, Technical Details, Empirical Findings, and Perspectives

Dr. Yu is a faculty member of three Graduate Programs: Plant Breeding and Genetics (PB&G) in Agronomy, Interdepartmental Genetics and Genomics (IG2), and Interdepartmental Plant Biology (IPB). 

Homepage: Quantitative Genetics and Maize Breeding; Publication: Google Scholar & ORCiD.

Selected Publications:

[Breeding Strategy]

Yu, X., X. Li, T. Guo, C. Zhu, Y. Wu, S.E. Mitchell, K.L. Roozeboom, D. Wang, M.L. Wang, G.A. Pederson, T.T. Tesso, P.S. Schnable, R. Bernardo, and J. Yu*. 2016. Genomic prediction contributing to a promising global strategy to turbocharge gene banks. Nature Plants 2:16150.

Yu, J.* 2009. Realizing the potential of ultrahigh throughput genomic technologies in plant breedingThe Plant Genome 2:2.

Bernardo, R.*, and J. Yu. 2007. Prospects for genomewide selection for quantitative traits in maizeCrop Science 47:1082-1090.

[Complex Trait Dissection]

Li, Xin, Xianran Li, E. Fridman, T.T. Tesso, and J. Yu*. 2015. Dissecting repulsion linkage in the dwarfing gene Dw3 region for sorghum plant height provides insights into heterosis. PNAS 112:11823-11828.

Li, X., C. Zhu, C.-T. Yeh, W. Wu, K. Petsch, E. Takacs, F. Tian, G. Bai, E.S. Buckler, G.J. Muehlbauer, M.C.P. Timmermans, M.J. Scanlon, P.S. Schnable* and J. Yu*. 2012. Genic and non-genic contributions to natural variation of quantitative traits in maizeGenome Research 22:2436-2444.

Zhu, C., X. Li, and J. Yu* 2011. Integrating rare-variant testing, function prediction, and gene network in composite resequencing-based genome-wide association studies (CR-GWAS)G3 1:233-243.

Sun, G., C. Zhu, S. Yang, W. Song, M. H. Kramer, H.-P. Piepho, and J. Yu*. 2010. Variation explained in mixed model association mappingHeredity 105:333-340.

Zhang, Z.*, E. Ersoz, C.-Q. Lai, R.J. Todhunter, H.K. Tiwari, M.A. Gore, P.J. Bradbury, J. Yu, D.K. Arnett, J.M. Ordovas, and E.S. Buckler. 2010. Mixed linear model approach adapted for genome-wide association studies. Nature Genetics 42:355-360.

Zhu, C., and J. Yu*. 2009. Nonmetric multidimensional scaling corrects for populationstructure in association mapping with different sample typesGenetics 182:875-888.

Yu, J.*, Z. Zhang, C. Zhu, D. Tabanao, G. Pressoir, M.R. Tuinstra, S. Kresovich, R.J. Todhunter, and E.S. Buckler. 2009. Simulation appraisal of the adequacy of number of background markers for relationship estimation in association mappingThe Plant Genome 2:63-77.

Zhu, C., M. Gore, E.S. Buckler, and J. Yu*. 2008. Status and prospects of association mapping in plants. The Plant Genome 1:5-20.

Yu, J., J.B. Holland, M.D. McMullen, and E.S. Buckler*. 2008. Genetic design and statistical power of nested association mapping in maizeGenetics 138:539-551.

Yu, J., G. Pressoir, W.H. Briggs, I. Vroh Bi, M. Yamasaki, J.F. Doebley, M.D. McMullen, B.S. Gaut, D. Nielsen, J.B. Holland, S. Kresovich, and E.S. Buckler*. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatednessNature Genetics 38:203-208.

Yu, J., and E.S. Buckler*. 2006. Genetic association mapping and genome organization of maize. Current Opinion in Biotechnology 17:155-160

[Genes and Genetics]

Lin, Z., X. Li, L.M. Shannon, C.-T. Yeh, M.L. Wang, G. Bai, Z. Peng, J. Li, H.N. Trick, T.E. Clemente, J. Doebley, P.S. Schnable, M.R. Tuinstra, T.T. Tesso, F. White, and J. Yu*. 2012. Parallel domestication of the Shattering1 genes in cerealsNature Genetics 44:720–724.

Wu, Y., X. Li, W. Xiang, C. Zhu, Z. Lin, Y. Wu, J. Li, S. Pandravada, D.D. Ridder, G. Bai, M.L. Wang, H.N. Trick, S.R. Bean, M.R. Tuinstra, T.T. Tesso, and J. Yu*. 2012. Presence of tannins in sorghum grains is conditioned by different natural alleles of Tannin1PNAS 109:10281-10286.

Wisser, R.J.*, J.M. Kolkman, M.E. Patzoldt, J.B. Holland, J. Yu, M. Krakowskyc, R.J. Nelson, and P.J. Balint-Kurti. 2011. Multivariate analysis of maize disease resistances suggests a pleiotropic genetic basis and implicates a glutathione S-transferase gene. PNAS 108:7339-7344.

Tian, Z., Q. Qian, Q. Liu, M. Yan, X. Liu, C. Yan, G. Liu, Z. Gao, S. Tang, D. Zeng, Y. Wang, J. Yu*, M. Gu*, and J. Li*. 2009. Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualitiesPNAS 106:21760-21765.

Buckler, E.S.*, J.B. Holland*, ..., J. Yu, Z. Zhang, S. Kresovich*, and M.M. Mullen* 2009. The genetic architecture of maize flowering timeScience 325:714-718.

[Genomes and Chromosomes]

Li, X., M.J. Scanlon, and J. Yu*. 2015. Evolutionary patterns of DNA base composition and correlation to polymorphisms in DNA repair systemsNucleic Acids Research 43:3614-3625.

Li, X., C. Zhu, Z. Lin, Y. Wu, D. Zhang, G. Bai, W. Song, J. Ma, G.J. Muehlbauer, M.J. Scanlon, M. Zhang*, and J. Yu*. 2011.  Chromosome size in diploid eukaryotic species centers on the average length with a conserved boundaryMolecular Biology and Evolution 28:1901–1911.