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With Population Parameters Previously Determined (P3D) and compression, Zhiwu Zhang et al. have reduced computing time while maintaining or increasing statistical power for mixed linear models (MLM) in genome wide association studies (GWAS). The SAS code and demonstration data described in Nature Genetics can be found here.
In collaboration with several U.S. groups, we have produced A First Generation Haplotype Map of Maize for the 27 founder lines of NAM. This survey of genetic diversity provides a foundation for uniting breeding efforts across the world and for dissecting complex traits through genome-wide association studies. The SNP data set generated for the HapMap project is available at Panzea.
Two new publications report on the genetic structure of the maize NAM population, implications for heterosis, and the genetic architecture of flowering time. This work was done with our collaborators in the Holland (USDA-ARS, NCSU), McMullen (USDA-ARS, Missouri), and Kresovich (Cornell) labs plus many others! Data on about the experiments is available through Panzea and the germplasm through the USDA-ARS stock center.
Feng Tian discovered a massive selective sweep on chromosome 10--the largest to date in maize. Studying the genes under this sweep will help us to better understand maize domestication and local adaptation.
Peter Bradbury used microarrays to identify and map genome specific markers in wheat, a challenging feat for the hexaploid species with three distinct genomes.
The Maize Diversity Group has released the ultimate germplasm resource to date for localizing QTLs! The NAM population (5000 RILs from 25 families) that captures a substantial portion of maize diversity is available at the USDA Maize Stock Center. Markers scores are available at Panzea.
With colleagues from around the US, we have dissected the genetic basis of proVitamin A content in maize. We found that the lycopene epsilon cyclase has natural variation to increase proVitamin A content 3-5 fold. This result could in developing more nutritious maize.
Using 454 sequencing with colleagues at CSHL, we have identified SNPs between B73 and Mo17. SNPs are available at Panzea.
Happy 200th birthday Darwin! He even had insights on maize!
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