PI: Jessica Schlueter (University of North Carolina-Charlotte)
CoPIs: Cory Brouwer (University of North Carolina-Charlotte), Eric Jellen and Jeff Maughan (Brigham Young University)
Senior Personnel: Jeremy Jay (University of North Carolina-Charlotte)
Key Collaborators: Tim Langdon (Aberystwyth University, United Kingdom), Nicholas Tinker (Agriculture and Agri-Food Canada) and Eric Jackson (General Mills, Manhattan, KS)
Oat is a grain crop that is high in fiber and used in a number of foods that carry an FDA label listing oats as being capable of "reducing the risk of heart disease". Although oat has this important health benefit, the understanding of how oat fiber develops is lacking. Genomic resources for oats have significantly lagged behind that for other grains. The fact that oat has a very large and complex polyploid genome compared to other crop plants has contributed to the challenges in identifying the gene networks that control fiber development and other economically important processes and pathways in oats. The goal of this project is to generate a draft genome sequence of cultivated oats by sequencing related wild oat genomes that are smaller in size to that of cultivated oats to assist in sequence assembly and annotation.
This project will utilize high throughput sequencing strategies, optical mapping and diploid genetic resources to facilitate the assembly and annotation of a functional hexaploid oat (Avena sativa) genome sequence. The specific objectives include: 1) finishing the sequencing of the A. ventricosa diploid CC-genome as well as creating an A. eriantha diploid CC-genome assembly; 2) generating physical optical maps for six hexaploid Avena genomes, two CC-diploid genomes, two AA-diploid genomes and a putative diploid DD-genome by using cutting edge BioNano optical mapping technology; 3) increasing GBS marker density across parental lines of a selected linkage mapping population to provide additional anchor points for assembled contigs that will be combined with short-read (HiSeq) and long-read (PacBio) sequencing to assemble and anchor the hexaploid oat genome (AADDCC); and, 4) annotating the sequenced genomes by generating RNA-seq data for each species in conjunction with ab initio prediction methods. Importantly, annotations will be evaluated and manually curated through user-contributed annotation as part of the Plant Pathway Elucidation Project (P2EP; http://p2ep.org) which is a collaborative effort between academia and industry established at the North Carolina Research Campus. The goal of this program is to tie together educational opportunity, scientific discovery and the development of a knowledge base to "advance scientific research, create opportunities for industry and consumers, and enhance human health". Students and postdoctoral fellows associated with this project will participate in the P2EP summer sessions. All data generated in this project will be disseminated widely through the P2EP website, OatGlobal (http://oatglobal.org) and Gramene (http://gramene.org). All sequence information will be accessible through the GenBank Short Read Archive (SRA) and the Gene Expression Omnibus (GEO). Batch download datasets will also be available at the project website.
