title: Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago.
abstract: The genus Miscanthus is a perennial C4 grass native to eastern Asia and is a promising candidate bioenergy crop for cool temperate areas. Flowering time is a crucial factor governing regional and seasonal adaptation; in addition, it is also a key target trait for extending the vegetative phase to improve biomass potential. Homologues of CONSTANS (CO)/Heading date 1(Hd1) were cloned from Miscanthus sinensis and named MsiHd1. Sequences of MsiHd1 homologues were compared among 24 wild M. sinensis accessions from Japan, 14 from China, and three from South Korea. Two to five MsiHd1 alleles in each accession were identified, suggesting that MsiHd1 consists of at least three loci in the Miscanthus genome. Verifying the open reading frame in MsiHd1, they were classified as putative functional alleles without mutations or non-functional alleles caused by indels. The Neighbor-Joining tree indicated that one of the multiple MsiHd1 loci is a pseudogene locus without any functional alleles. The pseudogene locus was named MsiHd1b, and the other loci were considered to be part of the MsiHd1a multi-locus family. Interestingly, in most Japanese accessions 50% or more of the MsiHd1a alleles were non-functional, whereas accessions from the East Asian mainland harboured only functional alleles. Five novel miniature inverted transposable elements (MITEs) (MsiMITE1-MsiMITE5) were observed in MsiHd1a/b. MsiMITE1, detected in exon 1 of MsiHd1a, was only observed in Japanese accessions and its revertant alleles derived from retransposition were predominantly in Chinese accessions. These differences in MsiHd1a show that the dependency on functional MsiHd1a alleles is different between accessions from the East Asian mainland and Japan.
authors.affiliation: Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.
authors.forename: Hironori
authors.initials: H
authors.lastname: Nagano
authors.affiliation: Department of Crop Sciences, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Lindsay V
authors.initials: LV
authors.lastname: Clark
authors.affiliation: College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Zhao
authors.affiliation: Science and Technology Center, China Seed Group Co. Ltd, Wuhan, Hubei 430206, China.
authors.forename: Junhua
authors.initials: J
authors.lastname: Peng
authors.affiliation: Kangwon National University, Chuncheon, Gangwon 200-701, South Korea.
authors.forename: Ji Hye
authors.initials: JH
authors.lastname: Yoo
authors.affiliation: Kangwon National University, Chuncheon, Gangwon 200-701, South Korea.
authors.forename: Kweon
authors.initials: K
authors.lastname: Heo
authors.affiliation: Kangwon National University, Chuncheon, Gangwon 200-701, South Korea.
authors.forename: Chang Yeon
authors.initials: CY
authors.lastname: Yu
authors.affiliation: Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.
authors.forename: Kossonou Guillaume
authors.initials: KG
authors.lastname: Anzoua
authors.affiliation: Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.
authors.forename: Tomoaki
authors.initials: T
authors.lastname: Matsuo
authors.affiliation: Department of Crop Sciences, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Erik J
authors.initials: EJ
authors.lastname: Sacks
authors.affiliation: Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan yamada@fsc.hokudai.ac.jp.
authors.forename: Toshihiko
authors.initials: T
authors.lastname: Yamada
mesh_terms: D000483:Alleles; D001208:Asia; D018533:Biomass; D004251:DNA Transposable Elements; D007564:Japan; D010802:Phylogeny; D006109:Poaceae / Q000145:classification / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements
keywords: Bioenergy; MITEs.; Miscanthus sinensis; flowering time gene; gene duplication; geographical allelic differentiation