Quantitative Genetics and Maize Breeding

Jianming Yu, Professor                    Google Scholar    ResearchGate    LinkedIn
Pioneer Distinguished Chair in Maize Breeding
Department of Agronomy, Iowa State University
Ames, IA 50011-1010
Phone: 515-294-2757
Fax: 515-294-3163
Email: jmyu@iastate.edu

The focus of this program is to address significant questions in plant breeding by combining cutting-edge genomic technologies and quantitative genetics theories. We conduct different research projects in Genomic Selection, Genome-Wide Association Studies, Heterosis, and Genotype by Environment Interaction. Some projects have a strategy and methodology focus, and others concetrate on a specific trait. 

General Information

Dr. Yu's research integrates knowledge in plant breeding, quantitative genetics, genomics, molecular genetics, and statistics with an ultimate goal of developing and applying new strategies and methods in trait dissection and crop improvement. 

His 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) to efficiently integrate high throughput genotyping into various breeding processes, gene cloning of traits with agronomic and domestication importance (e.g., grain quality, drought tolerance, tannin, and shattering), and DNA and genome evolution across taxonomic groups.

Research Highlights

Association Mapping and Genome-Wide Association Studies (GWAS)
Contribution of rare alleles to "missing heritability"
Genome-wide landscape of genetic polymorphisms underlying quantitative trait variation
Composite-resequencing based GWAS (CR-GWAS) to integrate rare allele testing, function prediction, and gene network.
R-square statistics for mixed model association mapping
Inaccuracy of variance-covariance matrix in mixed model association mapping
Unified mixed model association mapping framework
Nested association mapping (NAM) concept

Genomic Selection (GS)
Genomic prediction to revitalize the germplasm bank
Genomic selection in maize pedigree breeding programs

Genome and Chromosome Evolution (The Beauty of the Nature)
Average genome size and variation within taxonomic groups
Random repeat and non-repeat expansion of chromosomes
Distribution of the size of the chromosome within a species

DNA Base Composition (The Magic)
(To be announced soon)

QTL/Gene Cloning with an Integrated Approach (It Worked)
Parallele domestication of Shattering1 in cereals (sorghum, rice, and maize)
Independent domestication events of nonshattering sorghums in Africa
Multiple naturally occurred non-functional alleles of Tannin1 (Tan1)

Genotype by Environment Interaction
Changing landscape of gene-gene interaction underlying adaption

Genetics/Breeding for Bioenergy
A new wave of crop improvement

News Release

New strategy to accelerate plant breeding by turbocharging gene banks (2016)

Iowa State University agronomist explores the genetics that allow hybrid plants to perform better than parents (2015)

Researchers find patterns in evolving genomes of thousands of species (2015)

ISU Plant Science Institute's Faculty Scholars Program award announcement (2015)

2014 University of Minnesota Emerging Leader in Plant Sciences Award (2014)

Unlocking New Possibilities for Plants in Each New Generation (2013)

Tannins in sorghum and benefits focus of genetic research (2012)

Genes underlying the key domestication process in sorghum and other cereals (2012)

Harnessing the power of plants: University team studies sorghum genetics to fuel green energy research (2011)

Chromosomes' Big Picture: Similarities Found in Genomes Across Multiple Species; Platypus Still out of Place (2011)

ASA-CSSA-SSSA Early Career Professional Award Recipient (2010)

Cornell geneticists improve methods for identifying what controls complex traits, from disease to crop yields (2006)

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UPDATE (5/24/2017): The Challenge of Change, Harnessing University Discovery, Engagement, and Learning to Achieve Food and Nutrition Security is released by the APLU. 
Challenge 1. Increase yields, profitability, and environmental sustainability simultaneously
Challenge 2. Develop the varieties and breeds needed for sustainable food systems
Challenge 3. Decrease food loss and waste through more efficient distribution systems
Challenge 4. Create and share resources that serve all populations
Challenge 5. Ensure inclusive and equitable food systems
Challenge 6. Address the dual burdens of undernutrition and obesity to ensure full human potential
Challenge 7. Ensure a safe and secure food supply that protects and improves public health

UPDATE (10/3/2016): Congratulations to Xiaoqing Yu for publishing findings from a major research project, Genomic prediction contributing to a promising global strategy to turbocharge genebanks, in Nature Plants! "The success of this project illustrates that a global, cost-effective strategy may be designed to assess the vast amount of valuable germplasm archived in 1,750 gene banks."

Please also read this excellent News and Views article, Plant breeding: Effective use of genetic diversity, from Dr. Patrick Brown.

UPDATE (5/8/2016): Congratulations to Sivakumar Sukumaran for publishing his drought tolerance dissertation research, QTL mapping for grain yield, flowering time, and stay-green traits in sorghum using genotyping-by-sequencing markers, in Crop Science! It represents dedicated research with extensive field components.

UPDATE (12/3/2015): Congratulations to Jinliang Yang from Pat Schnable's group for his discovery, Extreme-phenotype genome-wide association study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel! Great to design and investigate different ways of identifying the signals.

UPDATE (11/23/2015): Congratulations to Samuel Leiboff from Mike Scanlon's group for his discovery, Genetic control of morphometric diversity in the maize shoot apical meristem! GWAS revealed unexpected  candidate genes implicated in hormone transport, cell division, and cell size for maize shoot apical meristem morphology.
UPDATE (09/08/2015): Congratulations to Xin Li for his discovery, Dissecting repulsion linkage in the dwarfing gene Dw3 region for sorghum plant height provides insights into heterosis. Theories on heterosis were proposed more than a century ago, but specific examples are still scarce. QTL mapping, trait component mapping, repulsion linkage, GWAS, multi-locus mixed model, designed crosses, and breeding implications.

UPDATE (06/05/2015): The 2015 APSIM Training Course at ISU went very well. I enjoyed learning many aspects of crop models. It would be great if more plant breeders and geneticists get involved so that future developments would be geared towards things we are interested.

UPDATE (03/11/2015): Congratulations to Xianran Li for his major discovery with broad impact, Evolutionary Patterns of DNA Base Composition and Correlation to Polymorphisms in DNA Repair Systems!  Genome integrity, DNA repair, replication, evolution, mutation, cancer research, etc.

UPDATE (02/21/2015): Please note the 2015 Advanced Topics in Plant Breeding Summer Institute, June 29-July 4, 2015, Ames IA.
June 29-30: Genomic Prediction in Plant Breeding
July 1-2: Transforming Plant Breeding into an Engineering Discipline
July 3-4: Doubled Haploids in Plant Breeding

UPDATE (10/23/2014): Congratulations to Zhiwu Zhang for leading the GWAS method research published in BMC Biology, Enrichment of statistical power for genome-wide association studies.

UPDATE (06/09/2014): Two great review/perspective papers that deserve atttention, if one wants to have a solid understanding on GxE and its implications in plant breeding: 1. Predicting the future of plant breeding: complementing empirical evaluation with genetic prediction (Cooper et al. 2014); 2. The statistical analysis of multi-environment data: modeling genotype-by-environment interaction and its genetic basis (Malosetti et al. 2013).

UPDATE (04/29/2014): Vision and Change in Undergraduate Biology Education is a very relevant document for faculty.
UPDATE (02/01/2014): Graduate students in ISU Plant Breeding and Genetics program will host the 2014 R. F. Baker Plant Breeding Symposium, Moore’s Law: Does phenotyping get a turn? High throughput phenotyping advances, on Thursday, March 6, 2014.
UPDATE (12/13/2013): This document from ASPB, Unleashing a Decade of Innovation in Plant Science, has been out for a while.
Chapter 1. Predicting Traits: Increase the ability to predict plant traits from plant genomes in diverse environments.
Chapter 2. Assembling Traits: Assemble plant traits in different ways to solve problems
Chapter 3. Harnessing Plant Chemistry: Discover, catalog, and utilize plant-derived chemicals
Chapter 4. From Data to Solutions: Enhance the ability to find answers in a torrent of data
Chapter 5. Reimagine Graduate Training: Create a T-training environment for plant science doctoral students

UPDATE (11/05/2013): The principle underlying GWAS it to identify the signal flanking the causal gene, not necessarily the functional polymophisms (QTNs), particularly when there are multiple alleles with different QTNs. Check out Geoff Morris's new paper, Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits, in G3.

UPDATE (07/05/2013): Pre-harvest sprouting (PHS) is a major issue in wheat production. I still remember how bad the bread tasted in some years when I was growing up. I was told that it is because of "Ya Mai Mian (Sprouted Wheat Flour, i.e., flour made from wheat kernels that are sprouted before harvest). Well, after years of research, we now have a better understanding of the genetics behind the different levels of PHS resistance in wheat. Check out the QTL cloning paper from Dr. Guihua Bai's group in Genetics. Congratulations!.
UPDATE (07/01/2013): The impact factor of The Plant Genome from CSSA is 2.463. 
UPDATE (02/06/2013): Take a look at this candidate gene association mapping paper in drought tolerance of perennial ryegrass from Dr. Yiwei Jiang's group at Purdue. Congratulations to the first-author, Xiaoqing Yu!
UPDATE (01/21/2013): The workshop GS + GWAS at the 2013 PAG meeting was a great success! The meeting room was too small and folks had to sit on the floor, stand in the back of the room,, or even watched from outside of the glass doors. Zhiwu took some very nice pictures and they were passed to the meeting organizer.

Thanks to all speakers, my co-organizer, Dr. Dorian Garrick, and who attended!

UPDATE (01/20/2013): Another significant publication from our NSF SAM group, Mendelian and non-Mendelian regulation of gene expression in the maize shoot apex, at PLoS Genetics. Congratulations to Lin Li!

UPDATE (12/13/2012): My graduate student published his first-author paper, Association Mapping for Grain Quality in a Diverse Sorghum Collection, at The Plant Genome.

, News came that The Plant Genome will get its Impact Factor in 2013.

UPDATE (08/25/2012): This is a new paper from the SAM (Shoot Apical Meristem) group, Ontogeny of the Maize Shoot Apical Meristem, at Plant Cell. It is classified as a Large-Scale Biology article, and open access.

UPDATE (06/18/2012): Check out this paper, Genic and non-genic contributions to natural variation of quantitative traits in maize, at Genome Research. In this research, we addressed several critical questions in genetic architecture of complex quantitative traits: genic versus nongenic contribution, allele frequency and genetic effect, appropriate genome scans with NAM, and sequencing/genotyping priority of future routine GWAS in species with complex genomes. A comprehensive, exploratory research.

UPDATE (06/13/2012): Here is another paper from our group, Presence of tannins in sorghum grains is conditioned by different natural alleles of Tannin1, at PNAS. It involves QTL mapping, meta-QTL fine mapping, association mapping, transformation validation with an Arabidopsis mutant, and nucleotide diversity analysis across wild, landraces, and cultivars. More broadly, it involves domestication, natural selection, and health benefit. Technically, you will see the effect of allele frequency in association mapping, and the general direction of the research => “haplotype”.

[NOTE: A quick comparison of three recent gene-cloning results in sorghum => multiple, natural alleles in Ma1 (flowering time)Sh1 (shattering), and Tan1 (tannin).]

UPDATE (05/29/2012): This is a News and Views article by Kenneth Olsen at Nature Genetics about the Sh1 paper: One gene’s shattering effects.

UPDATE (05/22/2012): Take a look at our new paper, Parallel domestication of the Shattering1 genes in cereals, at Nature Genetics.  It contains the map-based cloning of Sh1, haplotype analysis and association mapping, diverse origins of sorghum, comparative genomics across cereals, rice mutant analysis, and maize high-resolution  QTL analysis with GBS markers. You will have to praise either the mother nature or the wisdom of ancient farmers who made this transition from the hunter-gatherer stage to agriculture.

UPDATE (04/14/2012): Computer Simulation in Plant Breeding is a comprehensive review chapter in Advances in Agronomy that highlights the critical role of computer simulation in breeding method comparison, genetic mapping, gene network and genotype-by-environment interaction, and crop modeling research. The indispensable role of computer simulation in many classic and contemporary research topics were reviewed, including breeding method, mapping power and resolution, marker-assisted selection, genomic selection, association mapping, meta-QTL analysis, plant breeding  process, crop modeling, virtual plan and E-cell, and climate change.

UPDATE (10/24/2011): Here is a good example of the broad application of association mapping. Once you have assembled a diverse population, there are many traits that you can work on, such as soilborne wheat mosaic virus in U.S. winter wheat. Take a look at this new paper from Dr. Guihua Bai’s group in Phytopathology 101:1322-1329. It is essentially a combination of germplasm screening + association mapping + allelic dynamics analysis + robust markers for selection all at once. You may argue that the trait itself is not that complex though. But a very nice work.

UPDATE (08/10/2011):  Validating the gene-trait relationship identified through mutational study in natural populations can be challenging, so is identifying new genes through association mapping. Ever wonder why? “Frequency” is one of the key factors that make us struggle and the ultimate reason is “Genetics”, not the lack of “Super-Statistics” for you. It sure helps to take an integrated approach to tackle various issues in GWAS. Checkout Chengsong’s paper on Rare-Variant Testing, Function Prediction, and Gene Network in G3 (open access).

G3: Genes, Genomes, Genetics  is a new open-access journal by the Genetics Society of America.

UPDATE (08/09/2011):  One of the common issues in association mapping is that some of the important genes may have different allelic frequencies in subpopulatoins. Controlling for population structure may, unfortunately, reduce the signal strength even we know it should be a true positive. Check out MingLi’s new paper online first at Theoretical and Applied Genetics to see what happened to the FAD2A gene and the association mapping of oleic acid, linoleic acid, and O/L content in peanut.

UPDATE (07/31/2011):  Check out Clare Nelson’s paper in SNP discovery in sorghum through restriction-site associated DNA (RAD) approach in BMC Genomics (open access). Several groups are working on genotyping-by-sequencing (GBS). Once the pipelines of multiplexing, alignment, SNP calling, and imputation are optimized, it would be great to see that students in Plant Breeding and Genetics will have more time to work on phenotyping, analysis, and interpretation, rather than scoring SSRs (of course, a bit experience in this can only help).

UPDATE (05/20/2011):  Finally, our paper in chromosome size, genome size, and repeat proportion is published in MBE. It is open access (Ouch! It cost a lot!). I agreed that we packed way too much work in a single paper. But please take a look at Fig. 3a and Supplementary Fig. 3. before you are bored with those derivation and simulation. I hope someone figures out how birds (and some other species) maintain genome integrity during mitosis and meiosis with those macrochromosomes and microchromosomes.

I guess we HAVE TO be serious to make such a general statement (Solute to my true statistician coauthors!).

UPDATE (05/05/2011):  You’ve got to love “Quantitative Genetics”! See Randy Wisser’s great research in multi-trait association mapping of maize multiple disease resistance in PNAS.

UPDATE (01/10/2011):  It is interesting to read individual papers about sequenced genomes. Will it be interesting to read a paper in which 68 eukaryotic genomes were analyzed all together? How about analysis of 128 species with sequenced genomes? Check out our stunning discovery of a fundamental and widely relevant principle: chromosome size variation in diploid eukaryotic species has a conserved boundary. Online first in Molecular Biology and Evolution.

UPDATE (09/17/2010):  Diversity and population structure analysis of 205 US elite winter wheat germplasm by Guihua Bai’s group is available at The Plant Genome. These analyses laid the groundwork for further trait mapping with this panel of elite wheat germplasm.

UPDATE (02/22/2010): Most of us do not have to worry about the computational burden for the large scale genome-wide association analysis (GWAS). But if you do, either you are a big boss or you are working for a big boss :-). Check out some new algorithms Zhiwu Zhang worked out in his new Nat Genetics publication (online first soon): sire model to reduce the dimension of the matrix; and noiteration for each marker and simply obtaining the solution with the variance component estimates from the model without the marker.

Another GREAT example to study “Quantitative Genetics”! (Others: QK mixed model, NAM, and genome-wide selection)

UPDATE (01/30/2010): Wondering how to properly use R2 for mixed models and our new publication “Variation explained in mixed-model association mapping” will be online first in Heredity.

UPDATE (12/15/2009): Check out the results of a comprehensive analysis of rice eating and cooking qualities with candidate gene association mapping plus transformation validation. This is collaboration led by Dr. Jiayang Li at Institute of Genetics and Developmental Biology, Chinese Academy of Sciences. Published in PNAS.

UPDATE (09/16/2009): Our initial molecular analysis of US historic sweet sorghum collection is Online First at Theoretical and Applied Genetics.

UPDATE (08/19/2009): We are funded by DOE/USDA Biomass Genomics Research to study nitrogen use efficiency in sweet sorghum with University of Nebraska.

UPDATE (08/07/2009): The first phase of MaizeNAM analysis (Yu et al. 2008) results are out in Science 325:714-718 (multi-family linkage analysis for flowering time) and Science 325:737-740 (linkage map and residual heterozygosity in pericentralmeric regions implicated for heterosis).

UPDATE (07/30/2009): Graduate Research Assistantship available. See Employment for details.

UPDATE (07/29/2009): Zhu and Yu 2009 in Genetics July issue. A systematic examination of genetic relationships in association mapping and corresponding methods, dimension determination, non-metric multidimentional scaling, … Sorry for a long story. See Publications.