REGULATORY ADAPTATION OF TRANSPOSABLE ELEMENTS AND THEIR EFFECT ON GENE EXPRESSION IN MAIZE AND THE ANDROPOGONEAE

Due to the high proportion of transposable elements (TEs) within maize and related grass genomes, especially near genic regions, TEs have become an abundant source of regulatory information that impacts gene expression and phenotypic variation. By deciphering which transposable elements contribute to expression, we can utilize these events to predict important agronomic traits such as yield and disease resistance with genome-wide prediction models in new maize and sorghum populations.The major goals and objectives of Experiment 1 are as follows:Collect genomic data as inputs to models from previously published sources, including gene expression, chromatin accessibility, methylation status, and genomic sequence.Generate transposable element annotations for maize using a combination of imputed short-read and whole-genome sequences.Build linear mixed models to determine TE insertion effects in maize.Identify causal TE insertions that contribute to gene expression variation through cis and trans, allele-specific, and measured expression estimates.Prepare manuscript.Release code and accompanying novel data after publication.The major goals and objectives of Experiment 2 are as follows:Describe what features of these transposable elements make them causal for gene expression.Use causal TE insertions in genomic prediction models and assess prediction accuracy in important physiological and agronomic traits.Generate transposable element annotations for sorghum and other Andropogoneae species using a combination of imputed short-read and whole-genome sequences.Use causal TE insertions from the prior experiment as inputs to a convolutional neural network model and predict how TE insertions impact expression in new maize populations, sorghum, and the other Andropogoneae.Prepare manuscript.Release code and accompanying novel data after publication.