The reference durum wheat genome (Svevo Rel.1) was previously sequenced and assembled using a short-read sequencing approach and recently an international consortium was established to achieve a Platinum-quality reference genome (Svevo Rel.2), fulfilling the ultimate requirements for contiguity, completeness and correctness. PACBIO HiFi long read 35X sequencing was coupled with Bionano Optical Mapping, producing 259 Hybrid scaffolds (N50 = 112.3 Mb) that were ordered by Hi-C data into 14 contiguous pseudomolecules spanning 10.4 Gb.

The new assembly was aligned with Svevo Rel.1, and discrepancies were manually checked. The Svevo Rel.2 is available in the GrainGenes database. A complete and accurate gene annotation was then obtained by coupling Illumina RNA-Seq and Nanopore Isoseq sequencing of 58 samples representing a range of tissues and developmental stages from Svevo plants grown under optimal conditions as well as exposed to different biotic, abiotic, and nutrient stress. Immunity receptor genes containing LRR and storage protein gene families have been manually curated.

The expression of 68,154 high-confidence genes has been integrated into a transcriptome atlas (https://bar.utoronto.ca/), together with more than 100,000 low-confidence, TE-related or long non-coding genes. The entire QTLome of durum wheat consisting of around 7,000 loci identified by linkage or association mapping for a range of traits (phenology, biotic stress resistance, abiotic stress tolerance, grain yield and components, grain quality) has been anchored on the new genome.

The analysis of the QTL data allowed us to identify QTL clusters containing loci confirmed across multiple tetraploid panels and populations, and phenotyping experiments, and some clusters co-locate with known master gene regulators. The Svevo Rel.2 allowed us to resolve a specific region previously part of the unanchored chromosome sequence known to be involved in durum wheat domestication. One of the two loci controlling the free-threshing (tenacious glumes) trait, the TG1 locus, was physically assigned to a region of chromosome 2B unassembled in Svevo Rel.1. Notably, a large inversion encompassing TG1 distinguishes the free threshing from the tenacious glume phenotypes.

Research supported by: PRIN-2020 project PanWheatGrain, AGRITECH - National Research Centre for Agricultural Technologies, EU project PRO-GRACE, CEREALMED-Enhancing diversity in Mediterranean cereal farming systems.

Emails

Luigi Cattivelli luigi.cattivelli@crea.gov.it; Elisabetta Mazzucotelli elisabetta.mazzucotelli@crea.gov.it; Victor Llaca victor.llaca@corteva.com; Kevin Fengler kevin.fengler@corteva.com; Gina Zastrow-Hayes gina.zastrow-hayes@corteva.com; Cristian Forestan cristian.forestan@unibo.it; Yael Lev-Mirom yael@evo.haifa.ac.il; David Swarbreck David.Swarbreck@earlham.ac.uk; Heidrun Gundlach h.gundlach@helmholtz-muenchen.de; Pavla Navratilova navratilova@ueb.cas.cz; Hana Šimková simkovah@ueb.cas.cz; Primetta Faccioli primetta.faccioli@crea.gov.it; Paolo Bagnaresi paolo.bagnaresi@crea.gov.it; Mario Giorgioni mario.giorgioni@crea.gov.it; Francesca Desiderio francesca.desiderio@crea.gov.it; AnaPaola Valladares anapaodares@gmail.com; Matteo Bozzoli matteo.bozzoli@unibo.it; Thomas Lux thomas.lux@helmholtz-muenchen.de; Harmeet Chawla harmeet.chawla@umanitoba.ca; Raul Pirona raul.pirona@cnr.it; Massimiliano Lauria massimiliano.lauria@ibba.cnr.it; Aldo Ceriotti aldo.ceriotti@ibba.cnr.it; Giovanni Giuliano Giovanni.Giuliano@enea.it; Agata Gadaleta agata.gadaleta@uniba.it; Matteo Dell’Acqua Matteo.DellAcqua@santannapisa.it; Nicola Pecchioni nicola.pecchioni@crea.gov.it; Anna Maria Mastrangelo annamaria.mastrangelo@crea.gov.it; Daniela Marone daniela.marone@crea.gov.it; Marco Silvestri marco.silvestri@barilla.com; Justin Faris justin.faris@usda.gov; Steven Xu steven.xu@usda.gov; Julio Isidro Sanchez j.isidro@upm.es; Alessandra Stella alessandra.stella@ibba.cnr.it; Barbara Lazzari lazzari@ibba.cnr.it; Paolo Cozzi cozzi@ibba.cnr.it; Filippo M Bassi F.Bassi@cgiar.org; Michael Baum M.BAUM@CGIAR.ORG; Assaf Distelfeld adistelfe@univ.haifa.ac.il; Nathalie Chantret nathalie.chantret@inrae.fr; Vincent Ranwez vincent.ranwez@inrae.fr; Nicholas Provart nicholas.provart@utoronto.ca; Taner Sen taner.sen@usda.gov; Stefania Masci masci@unitus.it; Francesco Sestili francescosestili@unitus.it; Luca Curci pasqualeluca.curci@ibbr.cnr.it; Gabriella Sonnante gabriella.sonnante@ibbr.cnr.it; Michele Morgante michele.morgante@uniud.it; Manuel Spannagl manuel.spannagl@helmholtz-muenchen.de; Anthony Hall anthony.Hall@earlham.ac.uk; Curtis Pozniak curtis.pozniak@usask.ca; Marco Maccaferri marco.maccaferri@unibo.it; Roberto Tuberosa roberto.tuberosa@unibo.it