Postdoctoral Fellowship: PRFB: Determinants of Evolutionary Success for Active Transposable Element Populations in the Maize Genomic Ecosystem

Martin, Galen, Lafayette IN

Investigators

Abstract

This action funds an NSF Plant Genome Postdoctoral Research Fellowship in Biology for FY 2025. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to Dr. Galen Martin is "Determinants of evolutionary success for active transposable element populations in the maize genomic ecosystem." The host institution for the fellowship is Purdue University, and the sponsoring scientist is Dr. Damon Lisch. Transposable elements are diverse DNA sequences that can copy themselves and are a major part of plant DNA. Their proliferation often comes at the expense of the plants, which have defense responses to prevent transposable element activity. The ebb and flow of this conflict over time results in vast differences in the overall content of DNA among plants, some of which has been essential for crop domestication and improvement. Competition among transposable elements and with their host for energy and DNA space lends itself to the idea of transposable elements as populations within the ‘ecosystem’ of the plant DNA. This study aims to test hypotheses relevant to this idea using corn as a model. The project will examine transposable element proliferation in corn plants with active transposable elements to characterize how transposable element numbers, types, and location affect success of both transposable element and the host plant. This project will shed light on the evolution of transposable elements in an agriculturally important plant, and it will provide training in new techniques for the postdoctoral fellow and facilitate mentorship for multiple undergraduate trainees. The Fellow will use the Mutator (Mu) system, which includes an active autonomous terminal inverted repeat DNA transposable element, MuDR, and several classes of related non-autonomous elements, each of which contains unique internal sequences. Mu elements preferentially insert near transcription start sites of actively expressed genes, suggesting that niche targeting provides fitness benefits to Mu elements. The Fellow will generate diverse populations of Mu insertions and track their transposition, including copy numbers and insertion sites, to test whether deviations from this insertional niche reduce their fitness. Relative Mu fitness will be evaluated by counting changes in copy number and distribution of each class of Mu elements from generation to generation in several lineages, each with its own distinct population of elements. Each lineage will then be “frozen” in place using Mu killer, a locus that can reliably and heritably silence all Mu activity in a single generation. The Fellow will evaluate the effects of Mu amplification on host (maize) phenotype and fitness by quantifying insertion allele-specific expression and traits such as leaf damage, seed set, and pollen sterility before and after Mu insertion and before and after silencing. All sequencing and phenotyping data generated will be publicly available on the NCBI Sequence Read Archive and genetic material will be made available through The Maize Genetics Cooperation Stock Center. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.