De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium-Resistant Genes in East Asian Genotypes

Kentaro K. Shimizu, Dario Copetti, Moeko Okada, Thomas Wicker, Toshiaki Tameshige, Masaomi Hatakeyama, Rie Shimizu-Inatsugi, Catharine Aquino, Kazusa Nishimura, Fuminori Kobayashi, Kazuki Murata, Tony Kuo, Emily Delorean, Jesse Poland, Georg Haberer, Manuel Spannagl, Klaus F.X. Mayer, Juan Gutierrez-Gonzalez, Gary J. Muehlbauer, Cecile MonatAxel Himmelbach, Sudharsan Padmarasu, Martin Mascher, Sean Walkowiak, Tetsuya Nakazaki, Tomohiro Ban, Kanako Kawaura, Hiroyuki Tsuji, Curtis Pozniak, Nils Stein, Jun Sese, Shuhei Nasuda, Hirokazu Handa

Research output: Contribution to journalArticlepeer-review

Abstract

Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog and the association of its A homeologous alleles with the spring/winter growth habit. Furthermore, the Norin 61 genome carries typical East Asian functional variants different from CS, ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.

Original languageEnglish (US)
Pages (from-to)8-27
Number of pages20
JournalPlant and Cell Physiology
Volume62
Issue number1
DOIs
StatePublished - Jan 1 2021

Bibliographical note

Funding Information:
JST CREST (JPMJCR16O3) to K.K.S., S.N., J.S. and T.B.; Swiss National Science Foundation 31003A-182318, CRSII5-183578, NCCR Evolving Language # 51NF40-180888 and European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie (MSC) grant agreement No 847585 to K.K.S.; MEXT KAKENHI The Birth of New Plant Species (JP16H06469, JP16H06464, JP16H06466, JP16K21727) to J.S., K.K.S., and H.T.; National Agriculture and Food Research Organization (NARO) Vice President Fund to H.H.; NBRP Genome Information Upgrading Project 2017, AMED to S.N., J.S., K.K. and K.K.S.; University of Zurich Research Priority Program Evolution in Action to K.K.S. and T.W.; German Federal Ministry of Food and Agriculture grant 2819103915 'WHEATSEQ' to N.S.; and Canadian Triticum Applied Genomics research project (CTAG2) funded by Genome Canada, Genome Prairie, the Western Grains Research Foundation, Government of Saskatchewan, Saskatchewan Wheat Development Commission, Alberta Wheat Commission, Viterra and Manitoba Wheat and Barley Growers Association to C.P.

Publisher Copyright:
© 2021 The Author(s). Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

Keywords

  • Adaptation
  • Asian germplasm
  • Bread wheat
  • Genome assembly
  • Norin 61
  • Polyploidy

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