1: Characterize on a genome wide basis transformation-associated changes in genome sequence/structure to assess the potential for unintended effects during genetic engineering. 1A: Model of early stage product development: transformation 1B: Model of middle stage product development: introgression 1C: Model of late stage product development: evaluation 2: Identify genetic loci that govern selected grain composition traits for maize under target environments. 2A: Estimate the maize grain metabolome. 2B: Estimate the relative impact of genetic versus environmental factors in determining the maize grain metabolome.
We will examine genome-wide responses to plant transformation using next generation DNA sequencing. These changes will be compared with the degree of genetic variation within varieties that occurs due to genetic drift and also with genomic responses to tissue culture. This will help establish how plant genomes change in unexpected ways to transformation, which may contribute to unintended effects to crop composition and quality. We will also test how these genomic responses are mitigated through introgression into elite varieties, through both DNA sequence analysis, compositional analysis via mass spectrometry and agronomic evaluation. In parallel, we will continue our characterization of the genetic and environmental factors that control the maize grain metabolome that was initiated at the end of the previous project cycle. We will use ultra performance liquid chromatography with a range of chemistries to interrogate the grain metabolome more thoroughly. We will also expand the number of varieties, the number of environments, and compare public sector germplasm to that used in the private sector. In addition to the survey-style questions, we will test specific gene/trait associations to potentially identify new traits for maize grain improvement.