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ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Research Project #438003

Research Project: Comparative Evaluation of Avena Genome Structure

Location: Small Grains and Potato Germplasm Research

Project Number: 2050-21000-038-007-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2020
End Date: Jul 31, 2024

Use whole genome sequence and transcriptome information on four hexaploid Avena lines derived from accessions held by the National Small Grains Collection to evaluate the complex genomic organization of cultivated milling oat in relation to that of its wild relatives, and to discover genomic variation that can be developed into molecular genetic tools for crop improvement.

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. Four Avena accessions in the National Small Grains Collection (NSGC) have been identified for their potential to yield insights into oat disease resistance gene variation, and the complicated genomic relationships between cultivated oat and the wild relatives that have been used in breeding for rust resistance. This project will seek to identify key candidate genes Pc91 and Pc92 for crown rust resistance in the A. magna portion of the Amagalon genome and Pg-a for stem rust (P. graminis f. sp. avenae) resistance in the A. longiglumis portion of its genome. It will also seek to identify the Pc2 crown rust resistance/Victoria blight susceptibility gene region in Victoria; and breakpoints and nearby genes for the normal 7C and 17A configuration in Victoria versus the 7C-17A rearrangement found in A. fatua PI 388828 and most spring-habit oats, comparisons that would also confirm whether this is truly a translocation or instead a homoeologous recombination event. Finally, it will seek to identify the genomic components of hulless-ness by comparing the center-of-origin landrace PI 182478 with hulless oat types from other regions. For this project, the ARS PIs will provide seed of four Avena accessions (Amagalon, Victoria , PI 182478 and PI 388828) and expertise on the probable genomic location and identity of candidate rust resistance genes. The University Cooperator will provide genomic sequence data with assembly; expertise on Avena cytogenetics and evolution; and will identify and assign a graduate student to perform the sequence comparison work. The ARS PI and University Cooperator will collaborate with each other and with oat researchers worldwide to annotate these genomes in the context of other oat genomes currently under analysis. In this extension to our original project, a domesticated oat relative (Avena abyssinica) will be sequenced and the information used to enhance our ability to interpret the genome sequences of domesticated oat (Avena sativa) and a wild oat relative (Avena barbata). Through comparison between domesticated and un-domesticated oat relatives for genome structure and patterns of gene expression, we can improve our understanding of the genetic architecture of how oat adapts to production agriculture; we will obtain a better understanding of the major chromosomal breakpoints that influence successful use of unadapted germplasm in oat improvement programs; and we will gain insight into the evolution of domesticated oat and other cereal crops.