Uniting The World's Maize Diversity For Dissection Of Complex Traits and Accelerating Breeding

Maize is one of the most diverse crops and species in the world.  This diversity is a tremendous resource for understanding the genetic basis of complex traits and for plant breeding in general.  However, it poses both a serious problem and substantial opportunity in relating these 10s of millions of variable sites to the complex traits they control.  We have recently combined whole genome next generation sequencing with QTL mapping on the maize Nested Association Mapping (NAM) population of 5,000 recombinant inbred lines and thousands of other breeding lines.  Through whole genome sequencing of maize and teosinte lines, we have identified more than 50 million variable regions in the genome.  We have also combined this deeper sequencing with reduced representation genotyping (or Genotyping-By-Sequencing) that has brought genotyping costs down to $10-20/sample.  By combining these two approaches to understand genome diversity, we were able to conduct GWAS that unites the world’s germplasm diversity and is providing insights into heterosis, central metabolism, development, and many other complex traits.  We can now show that copy number and intergenic variation is very important for a series of traits. While in many cases the association and genes are very interpretable, there still remain numerous associations that remain complex.  Despite this complexity, the ability to make predictions using diverse germplasm is high for many traits, which suggests great opportunities for merging, mining, and breeding with the world’s germplasm resources.  Already mining diverse germplasm is advancing to make more nutritional maize for the developing world.