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 plant breeding. He is internationally recognized as a go-to person in the intersection of quantitative genetics, genetics, genomics, plant breeding, and statistics. Yu obtained his B.S. from Northwest A&F University in 1994, M.S. from Kansas State University in 2000, and Ph.D. from University of Minnesota in 2003. He was a postdoctoral research associate at University of Minnesota from 2003 to 2004, and at Cornell University from 2004 to 2006. Yu worked at Kansas State University as Assistant Professor and then Associate Professor from 2006 to 2012 and moved to Iowa State University in 2013.
(Note: All significant contributions listed here were only possible because of the collaboration with many intelligent and dedicated scientists.)
Complex Trait Dissection
- Developed an integrated framework for gene discovery underlying phenotypic plasticity and performance prediction across environments (PNAS 115:6679-6683, Genome Research 30:673-683, Molecular Plant 14:874-887, New Phytologist 233:1768-1779, Journal of Experimental Botany 2023). This general framework facilitates biologically informed dissection of complex traits, enhanced performance prediction in breeding for future climates, and coordinated efforts to enrich our understanding of mechanisms underlying phenotypic variation.
- Uncovered a complete case of heterosis due to pseudo-overdominance (PNAS 112:11823-11828). While the pseudo-overdominance hypothesis (dominance with repulsion linkage) for heterosis has been proposed for a long time, clearly delineated cases are scarce in the literature.
- Quantified genic and nongenic contributions to quantitative trait variation in maize (Genome Research 22:2436-2444). This paper was the first attempt to answer the fundamental question about contributions of different genomic regions to quantitative traits in plants.
- Outlined the nested association mapping (NAM) strategy (Genetics 138:539-551), the approach that has been replicated in multiple crops to combine the strengths of linkage mapping using populations derived from bi-parental crosses and linkage disequilibrium mapping using diverse accessions. NAM strategy, combining the advantages of linkage analysis and association mapping, provided a high-resolution and cost-effective approach to dissecting the genetic architecture of complex traits.
- Developed the unified mixed model framework for genome-wide association studies (GWAS) (Nature Genetics 38:203-208), the standard method framework for complex trait dissection that is widely adopted in plant and human genetics. This research solved a long-standing scientific problem in genome-wide association analysis – too many false positive signals than expected from the analysis with simple methods due to the complex genetic relationship among individuals used in GWAS.
- Developed several optimal training set design methods for genomic selection in hybrid crops (Molecular Plant 12:390-401). Identifying the superior hybrids among the immense number of possible combinations of parental inbreds is a long-standing challenge. By viewing plant breeding as a process of genetic space exploration, data mining and design thinking would help reshape the next generation breeding programs.
- Prototyped a comprehensive strategy based on genomic selection and other relevant technologies to mine the natural heritage stored in numerous gene banks (Nature Plants 2:16150, Plant Biotechnology Journal 18:2456-2465). Turbocharging genebanks through genomic prediction repurposes the phenotyping process as training data collection so that data generated can be better used to generate prediction models to iteratively enhance the prediction power to guide the exploration of genetic space represented by the accessions in the genebanks.
- Pioneered genomic selection (GS) research in crops (Crop Science 47:1082-1090), the state-of-the-art breeding methodology that has been extensively implemented in major breeding companies.
- Uncovered the first case of domestication triangle, in which human genetics interact with sorghum genetics and the environment to influence the proportion of tannin sorghums grown by farmers in different parts of Africa (Nature Plants 5:1229-1236). Crop domestication is a complex process of dynamically balancing two competing forces: artificial selection and natural selection. This discovery could help uncover future cases.
- Uncovered patterns of genome-wide nucleotide patterns in maize and soybean (Genome Biology 20:74). By examining how the process of domestication have affected the genomes of corn and soybean, the team found out that the [AT]-increase is more pronounced in genomic regions that are non-genic, pericentromeric, transposable elements; methylated; and with low recombination. These findings established the critical links among UV radiation, mutation, DNA repair, methylation, and genome evolution.
- Identified the Shattering1 gene and its homologs underlying the parallel domestication of multiple cereal species: sorghum, maize, rice, and foxtail millet (Nature Genetics 44:720-724). Several follow-up studies further validated the findings in foxtail millet and an additional subspecies of rice. In addition, this paper highlighted the challenge and solution to allelic heterogeneity in genetic mapping.
- Cloned the pair of genes in sorghum underlying a trait (tannin in the sorghum grain) with incomplete domestication: Tannin1 (PNAS 109:10281-10286) and Tannin2 (Nature Plants 5:1229-1236).
Genomes and Chromosomes
- Revealed the patterns in DNA base composition divergence in multiple species (Nucleic Acids Research 43:3614-3625). Base composition was found to follow the individual-strand base equality rule at the genome, chromosome, and polymorphic-site levels. Intriguingly, clear separation of base-composition values calculated across polymorphic sites was consistently observed between basal and derived groups across 8 population comparison sets.
- Revealed the patterns in chromosome size variation across diploid eukaryotic species with linear chromosomes (Molecular Biology and Evolution 28:1901-1911). Strikingly, variation in chromosome size for 886 chromosomes in 68 eukaryotic genomes can be viably captured by a single model.
Yu received the Iowa State University Mid-Career Achievement in Research Award in 2017, the Emerging Leaders in Applied Plant Sciences Award from University of Minnesota in 2014, and the Young Crop Scientist Award from Crop Science Society of America (CSSA) in 2010. Yu was elected to Fellow of CSSA in 2018, and Fellow of American Association for the Advancement of Science (AAAS) in 2018.