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Dr. Yu obtained his Ph.D. from University of Minnesota in 2003. He joined the faculty in the Department of Agronomy at Kansas State University in August 2006. At K-State, he established a lab in Genetic and Genomics for Crop Improvement, where developing novel methods of utilizing cutting edge genetic and genomic tools for complex trait dissection and plant breeding is the focus. Research in this lab spans from association mapping  methods, plant breeding methodology, molecular mapping of complex traits (e.g., drought tolerance, salt tolerance, grain quality), to bioinformatics across multiple species.

Dr. Yu is part of a team at K-State Center for Sorghum Improvement and K-State Sorghum Translational Genomics Program.

UPDATE (11/22/2011): Some colleagues started using Google Scholar Citations. A neat tool to keep publications organized. Here is mine.

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.