NSF Postdoctoral Fellowship in Biology FY 2015

Campbell Michael S, Salt Lake City UT

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 Michael S. Campbell is "Of Rice and Men: Graph-Based Tools and Resources for Advancing Genome Assisted Crop Improvement " The host institutions for the fellowship are Cold Spring Harbor Laboratories and EMBL-EBI and the sponsoring scientists are Dr. Doreen Ware and Dr. Paul Kersey. Humans have been domesticating crop plants to increase yield and productivity ever since agriculture began over 10,000 years ago. Genome sequencing in the last decade now provides unprecedented resources for mining crops for new traits and for advancing breeding methods. These DNA sequences can now be used to guide the future of plant breeding through a process called genome assisted crop improvement. Central to genome assisted crop improvement is the use of a single consensus, or 'reference' DNA sequence to represent the genome of an entire species. Unfortunately, these reference sequences do not capture sequence variation characteristic of every population. Breeding is therefore hampered without full access to the diversity of gene variants. Recently, the human genomics community has begun to experiment with a promising solution to this problem called a 'Variant Graph', wherein a graph structure is used to represent sequence variation that is lost with the reference-genome approach. In this project, Variant Graphs will be developed for rice as a model crop plant, will help to identify new trait variants and will ultimately be applicable to any crop species. The outcomes will provide essential information to plant breeders and therefore significantly impact the speed and performance of crop improvement efforts, helping to ensure a secure and constant food supply. This project will develop methods for, and explore the utility of, a Variant Graph approach to create a pan-genome reference and structural annotation resource for rice, starting with the genomes of three diverse rice strains and then expanding to 3,000. The bioinformatics and statistically based approach to genome representation and annotation will give a population level view of the variant material available to plant breeders and will provide a clear picture of the genome of each individual accession. The research efforts are directed towards rice genomes, but the tools and techniques developed are relevant to all agricultural plants and animals. The infrastructure to replicate this resource for other agricultural plants will be established and made available through the iPlant Collaborative (iplantcollaborative.org). The rice resources will be publicly available through the Gramene website (gramene.org).