Next-Generation Platforms for the Genetic Analysis of Complex Traits.

Phenotypic variation of most agronomically important crop traits is under polygenic control, and understanding the genetic basis of phenotypic variation within and between populations is important for connecting genotypes to phenotypes. To that end, the largest public mapping resource of any species for evaluating the genetic architecture of complex traits was constructed in maize. The Nested Association Mapping (NAM) population of 5,000 recombinant inbred lines captures a wide range of allelic diversity and exploits the benefits of linkage analysis and association mapping to facilitate fine mapping of quantitative trait loci (QTL). To conduct whole-genome association studies on the NAM population, millions of single-nucleotide polymorphisms (SNPs) were scored with genotyping-by-sequencing across parents of the NAM population. Not only advancing association studies, these SNPs allowed a comprehensive evaluation of whole-genome patterns of DNA variation in maize, which revealed extensive variation in recombination rates and genomic regions that are potentially key to domestication and adaptation. In a large-scale effort with an overall goal of nutrient dense maize, we have conducted over 8,500 high-pressure liquid chromatography runs to quantify 14 carotenoid and 7 tocochromanol compounds in grain from the nested association mapping (NAM) population. The genetic architecture of these traits will be discussed, as well as the development of proximal remote sensing approaches for field-based, high-throughput phenotyping of plants.