NSF Postdoctoral Fellowship in Biology FY 2019: Deconvolution of cis-regulatory variation underlying kernel development in maize

Marand Alexandre P, Madison WI

Investigators

Abstract

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2019. 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. Alexandre Marand is "Deconvolution of cis-regulatory variation underlying kernel development in maize" The host institution for the fellowship is the University of Georgia and the sponsoring scientist is Dr. Robert Schmitz. Determining the DNA sequences that coordinate gene expression is a critical objective for solving fundamental questions in biology, such as the origins of human disease and the genetic basis of crop yields. Emerging evidence has suggested that these sequences, termed cis-regulatory elements, are major players controlling phenotype (trait) variability in a wide array of species. Advances in genome-wide profiling techniques have enabled identification of these sequences, as well as the genes they regulate. It remains unclear if the positions and interactions of cis-regulatory elements relative to their target genes accounts for major phenotypic differences within a species. This project aims to address these fundamental questions by characterizing how cis-regulatory elements control kernel development in maize. The project was specifically tailored to foster the fellows training in genomics and scientific communication. The broader impacts will allow the fellow to expand on past efforts to encourage underrepresented groups to consider careers in science. The goal of this research is to identify cis-regulatory elements orchestrating dynamic patterns of transcriptional regulation contributing to kernel development in maize (Zea mays L.). For Objective 1 of this study, the fellow will leverage Assay for Transposase Accessible Chromatin (ATAC) and Chromatin Conformation Capture coupled Chromatin Immunoprecipitation (HiChIP) sequencing approaches to identify regulatory elements and their target genes, respectively, in developing and mature kernels from two distinct maize genotypes. In Objective 2, the fellow will generate ATAC-seq and HiChIP profiles from reciprocal hybrids apart of Objective 1 to determine the extent of novel regulatory interactions in hybrids, how parent-of-origin (including imprinting) impacts gene expression, the influence of genetic variation towards transcriptional regulation, and the integrated network of genetic, transcriptional and regulatory variation paramount for determining kernel phenotypes in maize. All data generated by this project will be disseminated via public repositories, including NCBI and the host laboratory website. Analytical software and source code will be open source and available on github. 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.