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

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Date
2021-01Type
- Journal Article
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Cited 11 times in
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Cited 12 times in
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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 key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 23 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. Further, the Norin 61 genome carries typical East Asian functional variants 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. Show more
Permanent link
https://doi.org/10.3929/ethz-b-000454044Publication status
publishedExternal links
Journal / series
Plant & Cell PhysiologyVolume
Pages / Article No.
Publisher
Oxford University PressSubject
Adaptation; Asian germplasm; Bread wheat; Genome assembly; Polyploidy; Norin 61Organisational unit
02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science03969 - Studer, Bruno / Studer, Bruno
02207 - Functional Genomics Center Zurich / Functional Genomics Center Zurich
Funding
847585 - RESPONSE - to society and policy needs through plant, food and energy sciences (EC)
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Citations
Cited 11 times in
Web of Science
Cited 12 times in
Scopus
ETH Bibliography
yes
Altmetrics