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, a video link) 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.
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.
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 breeding. The Plant Genome 2:2.
Bernardo, R.*, and J. Yu. 2007. Prospects
for genomewide selection for quantitative traits in maize. Crop 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 maize. Genome 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 mapping. Heredity 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 types. Genetics 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 mapping. The Plant Genome 2:63-77.
Yu, J., J.B. Holland, M.D. McMullen, and E.S. Buckler*. 2008. Genetic design and
statistical power of nested association mapping in maize. Genetics 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
relatedness. Nature Genetics 38:203-208.
[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 cereals. Nature 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
Tannin1. PNAS 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*.
diversities in rice starch biosynthesis lead to a diverse array of rice eating
and cooking qualities. PNAS 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 time. Science 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 systems. Nucleic
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
boundary. Molecular Biology and Evolution 28:1901–1911.