A pangenome and pantranscriptome of hexaploid oat
Abstract
Abstract Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health 1,2 . Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues 3 . Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales 4 . In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.
Article Details
Authors (75)
Raz Avni
Nadia Kamal
Lidija Bitz
Eric N. Jellen
Wubishet A. Bekele
Tefera T. Angessa
Petri Auvinen
Oliver Bitz
Brian Boyle
Francisco J. Canales
Craig H. Carlson
Brett Chapman
Harmeet Singh Chawla
Yutang Chen
Dario Copetti
Samara Correia de Lemos
Viet Dang
Steven R. Eichten
Kathy Esvelt Klos
Amit M. Fenn
Anne Fiebig
Yong-Bi Fu
Heidrun Gundlach
Rajeev Gupta
Georg Haberer
Tianhua He
Matthias H. Herrmann
Axel Himmelbach
Catherine J. Howarth
Haifei Hu
Julio Isidro y Sánchez
Asuka Itaya
Jean-Luc Jannink
Yong Jia
Rajvinder Kaur
Manuela Knauft
Tim Langdon
Thomas Lux
Sofia Marmon
Vanda Marosi
Klaus F. X. Mayer
Steve Michel
Raja Sekhar Nandety
Kirby T. Nilsen
Edyta Paczos-Grzęda
Asher Pasha
Elena Prats
Nicholas J. Provart
Adriana Ravagnani
Robert W. Reid
Jessica A. Schlueter
Alan H. Schulman
Taner Z. Sen
Jaswinder Singh
Mehtab Singh
Nick Sirijovski
Nils Stein
Bruno Studer
Sirja Viitala
Shauna Vronces
Sean Walkowiak
Penghao Wang
Amanda J. Waters
Charlene P. Wight
Weikai Yan
Eric Yao
Xiao-Qi Zhang
Gaofeng Zhou
Zhou Zhou
Nicholas A. Tinker
Jason D. Fiedler
Chengdao Li
Peter J. Maughan
Manuel Spannagl
Martin Mascher