Location: Cereal Crops Research
Project Number: 3060-21000-038-036-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jul 1, 2020
End Date: Jun 30, 2022
To produce whole-genome transcriptome annotations for a global pangenome project which consists of approximately 20 diverse hexaploid oat accessions. This resource will be useful for characterizing core gene sets, identifying novel gene sequences, and accumulating comparative sequence information which will be of particular use for agronomic and quality traits mapping and evolutionary genomic analyses.
Whole-genome sequencing technology and analysis has progressed to the point that the first complete, chromosome-level oat genome assemblies have been developed for two diploid oat species (Avena atlantica, AsAs genome; and A. eriantha, CpCp genome) and for the European A. sativa (AACCDD genome) cultivar ‘Belinda’. Consequently, at the Plant & Animal Genome XXVIII Conference January 11-15, 2020, the oat genomics community coalesced around an Oat Pangenome Project (OPP) that would involve multiple labs worldwide and result in the production of whole-genome sequence assemblies for approximately 20 diverse hexaploid oat accessions. These include three disease resistant accessions in the National Small Grains Collection (NSGC) Avena fatua PI 388828, Amagalon (CIav9364), and Victoria (AFRI # RP-84), and other accessions from around the globe. These whole genome sequences will be annotated to identify genes with an approach combining de novo prediction, comparative analysis, and cDNA sequencing. To sample as much of the transcriptome as possible, RNA will be extracted from 2 -6 botanical and developmental tissues types and pooled for PacBio IsoSeq sequencing library construction. We will also develop a gene expression atlas of a subset of tissue types to immediately utilize the novel annotations and provide a rich genomic resource for oat researchers. For this purpose, we will collect RNA from 56 tissue types in 3 biological replicates of each line. These samples will be individually converted into RNA-Seq and 3’ RNA Illumina libraries and sequenced to approximately 30M read depth coverage. Sequences will be processed with standard bioinformatic workflows including alignment to the newly developed annotation, and conversion to relative count values. This mRNA count information will be provided along with the gene models and sequence data. The ARS PIs will share sequence data of the accessions and provide supplies and resources to accommodate RNA work, facilitate sequencing, analyze the IsoSeq and RNA-Seq data, and organize annotation for release with the genomes. The Cooperator will grow and dissect plants, extract RNA from specifically dissected hexaploidy oat tissue types, create sequencing libraries, sequence libraries with Illumina platform (at list one replicate of whole transcriptome sequencing) and share isoSeq libraries for sequencing. The ARS PIs and Cooperator will collaborate with each other and with oat researchers worldwide to annotate these genomes and provide an expression atlas for all members of the oat community.