TY - JOUR
T1 - 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
AU - Shimizu, Kentaro K.
AU - Copetti, Dario
AU - Okada, Moeko
AU - Wicker, Thomas
AU - Tameshige, Toshiaki
AU - Hatakeyama, Masaomi
AU - Shimizu-Inatsugi, Rie
AU - Aquino, Catharine
AU - Nishimura, Kazusa
AU - Kobayashi, Fuminori
AU - Murata, Kazuki
AU - Kuo, Tony
AU - Delorean, Emily
AU - Poland, Jesse
AU - Haberer, Georg
AU - Spannagl, Manuel
AU - Mayer, Klaus F.X.
AU - Gutierrez-Gonzalez, Juan
AU - Muehlbauer, Gary J.
AU - Monat, Cecile
AU - Himmelbach, Axel
AU - Padmarasu, Sudharsan
AU - Mascher, Martin
AU - Walkowiak, Sean
AU - Nakazaki, Tetsuya
AU - Ban, Tomohiro
AU - Kawaura, Kanako
AU - Tsuji, Hiroyuki
AU - Pozniak, Curtis
AU - Stein, Nils
AU - Sese, Jun
AU - Nasuda, Shuhei
AU - Handa, Hirokazu
N1 - Generated from Scopus record by KAUST IRTS on 2022-09-13
PY - 2021/1/1
Y1 - 2021/1/1
N2 - 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.
AB - 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.
UR - https://academic.oup.com/pcp/article/62/1/8/6006781
UR - http://www.scopus.com/inward/record.url?scp=85103606101&partnerID=8YFLogxK
U2 - 10.1093/pcp/pcaa152
DO - 10.1093/pcp/pcaa152
M3 - Article
C2 - 33244607
SN - 1471-9053
VL - 62
SP - 8
EP - 27
JO - Plant and Cell Physiology
JF - Plant and Cell Physiology
IS - 1
ER -