1569 Agronomy, 716 Farm House Ln
1569 Agronomy, 716 Farm House Ln
Jianming Yu is Professor 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 quantitative genetics by combining cutting-edge genomic technologies and maize breeding. All members of this research program conduct empirical experiments in genetics and breeding 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 leverage design thinking, genetic design, and experimental design to plan out our research?
- How can we efficiently identify genes underlying quantitative traits so that the resulting empirical findings can help answer fundamental questions?
- How should we design the current plant breeding methods to make better use of genetic resources and high throughput genotyping and phenotyping technologies?
Yu’s research integrates knowledge in quantitative genetics, genomics, plant breeding, molecular genetics, and statistics, and has the ultimate goal of developing and implementing new strategies and methods in complex trait dissection and crop improvement. Current research includes Phenotypic Plasticity and Reaction Norm of complex traits across multiple crops, 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) 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.
Yu was elected as a Fellow of the American Association for the Advancement of Science (AAAS) in 2018.
- News and Views article from Nature Plants: When bitter is better (2019)
- AAAS honors seven Iowa State researchers for distinguished work (2018)
- News and Views article from Nature Plants, Plant breeding: Effective use of genetic diversity, Editorial from Nature Plants, Technologies to boost breeding
- News and Views article from Nature Genetics, One gene’s shattering effects
- Dzievit, M.J., T. Guo, X. Li, and J. Yu*. 2021. Comprehensive analytical and empirical evaluation of genomic prediction across diverse accessions in maize. Plant Genome 14:e20160.
- Yu, X., S. Leiboff, X. Li, T. Guo, N. Ronning, X. Zhang, G.J. Muehlbauer, M.C.P. Timmermans, P.S. Schnable, M.J. Scanlon, and J. Yu*. 2020. Genomic prediction of maize micro-phenotypes provides insights for optimizing selection and mining diversity. Plant Biotechnology Journal 18:2456-2465.
- Guo, T., X. Yu, X. Li, H. Zhang, C. Zhu, S. Flint-Garcia, M.D. McMullen, J.B. Holland, S.J. Szalman, R.J. Wisser, and J. Yu*. 2019. Optimal designs for genomic selection in hybrid crops. Molecular Plant 12:390-401.
- 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. 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]
- Qi, M., T. Guo, X. Li*, and J. Yu*. 2021. Phenotypic plasticity in plant height shaped by interaction between genetic loci and diurnal temperature range. New Phytologist 233:1768-1779.
- Wang, J., X. Li, T. Guo, M.J. Dzievit, X. Yu, P. Liu, K.P. Price, and J. Yu*. 2021. Genetic dissection of seasonal vegetation index dynamics in maize through aerial based high-throughput phenotyping. Plant Genome 14:e20155.
- Li, X., T. Guo, J. Wang, W.A. Bekele, S. Sukumaran, A.E. Vanous, J.P. McNellie, L. Tibbs Cortes, M.S. Lopes, K. Lamkey, M.E. Westgate, J. McKay, S.V. Archontoulis, M.P. Reynolds, N.A. Tinker, P.S. Schnable, and J. Yu*. 2021. An integrated framework reinstating the environmental dimension for GWAS and genomic selection in crops. Molecular Plant 14:874-887.
- Tibbs Cortes, L., Z. Zhang, and J. Yu*. 2021. Status and prospects of genome-wide association studies in plants. Plant Genome 14:e20077.
- Guo, T., Q. Mu, J. Wang, A.E. Vanous, A. Onogi, H. Iwata, X. Li*, and J. Yu*. 2020. Dynamic effects of interacting genes underlying rice flowering-time phenotypic plasticity and global adaptation. Genome Research 30:673-683.
- Wu, Yuye, T. Guo, Q. Mu, J. Wang, Xin. Li, Yun Wu, B. Tian, M.L. Wang, G. Bai, R. Perumal, H.N. Trick, S.R. Bean, I.M. Dweikat, M.R. Tuinstra, G. Morris, T.T. Tesso, J. Yu*, and Xianran Li*. 2019. Allelochemicals targeted to balance competing selections in African agroecosystems. Nature Plants 5:1229-1236.
- Dzievit, M.J., X. Li, and J. Yu*. 2019. Dissection of leaf angle variation in maize through genetic mapping and meta-analysis. Plant Genome 12:180024.
- McNellie, J.P., J. Chen*, X. Li, and J. Yu*. 2018. Genetic mapping of foliar and tassel heat stress tolerance in maize. Crop Science 58:2484-2493.
- Li. Xin, T. Guo, Q. Mu, Xianran Li*, and J. Yu*. 2018. Genomic and environmental determinants and their interplay underlying phenotypic plasticity. PNAS 115:6679-6684.
- Sukumaran, S., Xin Li, Xianran Li, C. Zhu, G. Bai, R. Perumal, M.R. Tuinstra, P.V.V. Prasad, S.E. Mitchell, T.T. Tesso, and J. Yu*. 2016. QTL mapping for grain yield, flowering time, and stay-green traits in sorghum using genotyping-by-sequencing markers. Crop Science 56:1429-1442.
- 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.
- Sukumaran, S., W. Xiang, S.R. Bean, J.F. Pedersen, S. Kresovich, M.R. Tuinstra, T.T. Tesso, M.T. Hamblin, and J. Yu*. 2012. Association mapping for grain quality in a diverse sorghum collection. Plant Genome 5:126-135.
- 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., 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]
- Char, S.N., J. Wei, Q. Mu, X. Li, Z. Zhang, J. Yu, and B. Yang*. 2020. An Agrobacterium-delivered CRISPR/Cas9 system for targeted mutagenesis in sorghum. Plant Biotechnology Journal 18:319-321.
- Su, Z., A. Bernardo, B. Tian, H. Chen, S. Wang, H. Ma, S. Cai, D. Liu, D. Zhang, T. Li, H. Trick, P. St. Amand, J. Yu, Z. Zhang, and G. Bai*. 2019. A deletion mutation in TaHRC confers Fhb1 resistance to Fusarium head blight in wheat. Nature Genetics 51:1099–1105.
- Leiboff, S., X. Li, H. Alvis, N. Todt, J. Yang, X. Li, X. Yu, G.J. Muehlbauer, M.C.P. Timmermans, J. Yu, P.S. Schnable, and M.J. Scanlon*. 2015. Genetic control of morphometric diversity in the maize shoot apical meristem. Nature Communications 6:8974.
- 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*. 2009. Allelic 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]
- Wang, J., X. Li*, K.D. Kim, M.J. Scanlon, S.A. Jackson, N.M. Springer, and J. Yu*. 2019. Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean. Genome Biology 20:74.
- 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.