NSF Postdoctoral Fellowship in Biology FY 2015

Josephs Emily B, Davis CA

Investigators

Abstract

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2015. 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 Emily Josephs is "Polygenic adaptation in regulatory networks" The host institution for the fellowship is the University of California, Davis and the sponsoring scientists are Drs. Graham Coop, Jeffrey Ross-Ibarra, and Julin Maloof. Domestication of wild plants has produced the diversity of crop plants available today. During crop breeding, ancestral wild genomes gradually changed as domestication specific traits were selected. The process is a type of genome adaptation similar to natural selection. This project investigates genome adaptation in two crop species, maize and tomato, by comparing gene regulatory changes between the crops and their wild relatives. Expression of genes will be compared and bioinformatics methods will be developed to assess and compare genome change. The information will uncover key regulatory networks that are at the foundation of breeding programs and in the long run could provide new tools for genome-assisted breeding strategies. Workshops at high schools, public presentations and research experiences for undergraduates will expose diverse audiences to basic knowledge about agriculture from a genomic perspective. Understanding the genetic basis of adaptation has been a longstanding goal of researchers studying evolution through natural and domestication selection. Polygenic adaptation, which is thought to be particularly important for domestication, is difficult to detect with current population genetic methods. This research will develop methods to detect coordinated changes in gene expression systematically across regulatory networks due to polygenic adaptation. These methods will be applied to two systems: domestication in maize, using publicly available data, and environmental adaptation in wild tomatoes, using gene expression data that will be generated as part of the research. The raw tomato gene expression data generated will be available on NCBI's Sequence Read Archive and processed data will be archived on the Dryad Digital Repository. The scripts used to conduct analyses will be made available for use by other researchers on GitHub.