Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago

Hironori Nagano, Lindsay V. Clark, Hua Zhao, Junhua Peng, Ji Hye Yoo, Kweon Heo, Chang Yeon Yu, Kossonou Guillaume Anzoua, Tomoaki Matsuo, Erik J. Sacks, Toshihiko Yamada

Research output: Contribution to journalReview article

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.

Original languageEnglish (US)
Pages (from-to)4227-4237
Number of pages11
JournalJournal of experimental botany
Volume66
Issue number14
DOIs
StatePublished - Jan 1 2015

Fingerprint

Miscanthus sinensis
heading
Alleles
alleles
loci
Miscanthus
Pseudogenes
pseudogenes
Japan
Republic of Korea
DNA Transposable Elements
Far East
energy crops
South Korea
Sequence Homology
Poaceae
East Asia
transposons
Biomass
Open Reading Frames

Keywords

  • Bioenergy
  • Flowering time gene
  • Gene duplication
  • Geographical allelic differentiation
  • MITEs
  • Miscanthus sinensis

ASJC Scopus subject areas

  • Physiology
  • Plant Science

Cite this

Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago. / Nagano, Hironori; Clark, Lindsay V.; Zhao, Hua; Peng, Junhua; Yoo, Ji Hye; Heo, Kweon; Yu, Chang Yeon; Anzoua, Kossonou Guillaume; Matsuo, Tomoaki; Sacks, Erik J.; Yamada, Toshihiko.

In: Journal of experimental botany, Vol. 66, No. 14, 01.01.2015, p. 4227-4237.

Research output: Contribution to journalReview article

Nagano, H, Clark, LV, Zhao, H, Peng, J, Yoo, JH, Heo, K, Yu, CY, Anzoua, KG, Matsuo, T, Sacks, EJ & Yamada, T 2015, 'Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago', Journal of experimental botany, vol. 66, no. 14, pp. 4227-4237. https://doi.org/10.1093/jxb/erv292
Nagano, Hironori ; Clark, Lindsay V. ; Zhao, Hua ; Peng, Junhua ; Yoo, Ji Hye ; Heo, Kweon ; Yu, Chang Yeon ; Anzoua, Kossonou Guillaume ; Matsuo, Tomoaki ; Sacks, Erik J. ; Yamada, Toshihiko. / Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago. In: Journal of experimental botany. 2015 ; Vol. 66, No. 14. pp. 4227-4237.
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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.",
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