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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

Shimizu, Kentaro K; Copetti, Dario; Okada, Moeko; Wicker, Thomas; Tameshige, Toshiaki; Hatakeyama, Masaomi; Shimizu-Inatsugi, Rie; Aquino, Catharine; et al (2021). 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. Plant & Cell Physiology, 62(1):8-27.

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.

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Plant and Microbial Biology
07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
Special Collections > NCCR Evolving Language
08 Research Priority Programs > Evolution in Action: From Genomes to Ecosystems
Dewey Decimal Classification:580 Plants (Botany)
Scopus Subject Areas:Life Sciences > Physiology
Life Sciences > Plant Science
Life Sciences > Cell Biology
Uncontrolled Keywords:Plant Science, Cell Biology, Physiology, General Medicine
Language:English
Date:25 March 2021
Deposited On:27 Nov 2020 14:03
Last Modified:24 Oct 2024 01:37
Publisher:Oxford University Press
ISSN:0032-0781
OA Status:Hybrid
Free access at:PubMed ID. An embargo period may apply.
Publisher DOI:https://doi.org/10.1093/pcp/pcaa152
PubMed ID:33244607
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