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 miniaturemore »
- Authors:
-
- Hokkaido Univ., Hokkaido (Japan)
- Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Crop Sciences
- Huazhong Agricultural Univ., Hubei (China)
- China Seed Group Co. Ltd., Hubei (China)
- Kangwon National Univ., Gangwon (South Korea)
- Univ. of Illinois, Urbana-Champaign, Urbana, IL (United States)
- Publication Date:
- Research Org.:
- Univ. of Illinois at Urbana-Champaign, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1344522
- Grant/Contract Number:
- SC0012379
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Experimental Botany
- Additional Journal Information:
- Journal Volume: 66; Journal Issue: 14; Journal ID: ISSN 0022-0957
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; bioenergy; MITEs.; Miscanthus sinensis; flowering time gene; gene duplication; geographical allelic differentiation
Citation Formats
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., and Yamada, Toshihiko. Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago. United States: N. p., 2015.
Web. doi: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. United States. 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., and Yamada, Toshihiko. Thu .
"Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago". United States. https://doi.org/10.1093/jxb/erv292. https://www.osti.gov/servlets/purl/1344522.
@article{osti_1344522,
title = {Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago},
author = {Nagano, Hironori and Clark, Lindsay V. and Zhao, Hua and Peng, Junhua and Yoo, Ji Hye and Heo, Kweon and Yu, Chang Yeon and Anzoua, Kossonou Guillaume and Matsuo, Tomoaki and Sacks, Erik J. and Yamada, Toshihiko},
abstractNote = {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. In conclusion, these differences in MsiHd1a show that the dependency on functional MsiHd1a alleles is different between accessions from the East Asian mainland and Japan.},
doi = {10.1093/jxb/erv292},
journal = {Journal of Experimental Botany},
number = 14,
volume = 66,
place = {United States},
year = {Thu Jun 18 00:00:00 EDT 2015},
month = {Thu Jun 18 00:00:00 EDT 2015}
}
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Works referenced in this record:
Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants.
journal, June 1994
- Bureau, T. E.; Wessler, S. R.
- The Plant Cell, Vol. 6, Issue 6
CONSTANS and the evolutionary origin of photoperiodic timing of flowering
journal, January 2011
- Valverde, F.
- Journal of Experimental Botany, Vol. 62, Issue 8
Stowaway: A New Family of Inverted Repeat Elements Associated with the Genes of Both Monocotyledonous and Dicotyledonous Plants
journal, June 1994
- Bureau, Thomas E.; Wessler, Susan R.
- The Plant Cell, Vol. 6, Issue 6
Genetic variability and phytogeography of <i>Miscanthus sinensis</i> var. <i>condensatus</i>, an apomictic grass, based on RAPD fingerprints
journal, January 2000
- Chou, Chang-Hung; Chiang, Yu-Chung; Chiang, Tzen-Yuh
- Canadian Journal of Botany, Vol. 78, Issue 10
The CCAAT binding factor can mediate interactions between CONSTANS‐like proteins and DNA
journal, April 2006
- Ben‐Naim, Orna; Eshed, Ravit; Parnis, Anna
- The Plant Journal, Vol. 46, Issue 3
Hd1 , a Major Photoperiod Sensitivity Quantitative Trait Locus in Rice, Is Closely Related to the Arabidopsis Flowering Time Gene CONSTANS
journal, December 2000
- Yano, Masahiro; Katayose, Yuichi; Ashikari, Motoyuki
- The Plant Cell, Vol. 12, Issue 12
Characterization of a Genetic Resource Collection for Miscanthus (Saccharinae, Andropogoneae, Poaceae) using AFLP and ISSR PCR
journal, May 2002
- Hodkinson, T. R.
- Annals of Botany, Vol. 89, Issue 5
CONSTANS and the evolutionary origin of photoperiodic timing of flowering
journal, January 2011
- Valverde, F.
- Journal of Experimental Botany, Vol. 62, Issue 8
Genetic Diversity and Population Structure of Miscanthus sinensis Germplasm in China
journal, October 2013
- Zhao, Hua; Wang, Bo; He, Junrong
- PLoS ONE, Vol. 8, Issue 10
Hd1, a Major Photoperiod Sensitivity Quantitative Trait Locus in Rice, Is Closely Related to the Arabidopsis Flowering Time Gene CONSTANS
journal, December 2000
- Yano, Masahiro; Katayose, Yuichi; Ashikari, Motoyuki
- The Plant Cell, Vol. 12, Issue 12
Characterization of Epistatic Interaction of QTLs LH8 and EH3 Controlling Heading Date in Rice
journal, March 2014
- Chen, Jingbin; Li, Xiaoyan; Cheng, Cheng
- Scientific Reports, Vol. 4, Issue 1
Cytogenetic Analysis of Miscanthus‘Giganteus’, an Interspecific Hybrid
journal, December 1993
- Linde-Laursen, Ib
- Hereditas, Vol. 119, Issue 3
A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy
journal, January 2012
- Swaminathan, Kankshita; Chae, Won; Mitros, Therese
- BMC Genomics, Vol. 13, Issue 1
Miniature Inverted-Repeat Transposable Elements and Their Relationship to Established DNA Transposons
book, January 2002
- Feschotte, Cédric; Zhang, Xiaoyu; Wessler, Susan R.
- Mobile DNA II
Contrasting geographic patterns of genetic variation for molecular markers vs. phenotypic traits in the energy grass Miscanthus sinensis
journal, November 2012
- Slavov, Gancho; Robson, Paul; Jensen, Elaine
- GCB Bioenergy, Vol. 5, Issue 5
Characterization of the repetitive sequences in a 200-kb region around the rice waxy locus: diversity of transposable elements and presence of veiled repetitive sequences
journal, January 2002
- Nagano, Hironori; Kunii, Motoyuki; Azuma, Takayuki
- Genes & Genetic Systems, Vol. 77, Issue 2
Characterization of a Genetic Resource Collection for Miscanthus (Saccharinae, Andropogoneae, Poaceae) using AFLP and ISSR PCR
journal, May 2002
- Hodkinson, T. R.
- Annals of Botany, Vol. 89, Issue 5
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
journal, June 1980
- Kimura, Motoo
- Journal of Molecular Evolution, Vol. 16, Issue 2
CONSTANS is a photoperiod regulated activator of flowering in sorghum
journal, January 2014
- Yang, Shanshan; Weers, Brock D.; Morishige, Daryl T.
- BMC Plant Biology, Vol. 14, Issue 1
CONSTANS and the CCAAT Box Binding Complex Share a Functionally Important Domain and Interact to Regulate Flowering of Arabidopsis
journal, November 2006
- Wenkel, Stephan; Turck, Franziska; Singer, Kamy
- The Plant Cell, Vol. 18, Issue 11
The Role of Casein Kinase II in Flowering Time Regulation Has Diversified during Evolution
journal, December 2009
- Ogiso, Eri; Takahashi, Yuji; Sasaki, Takuji
- Plant Physiology, Vol. 152, Issue 2
Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum
journal, September 2011
- Murphy, R. L.; Klein, R. R.; Morishige, D. T.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 39, p. 16469-16474
Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes
journal, January 2013
- Han, Yujun; Qin, Shanshan; Wessler, Susan R.
- BMC Genomics, Vol. 14, Issue 1
Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait
journal, October 2004
- Caicedo, A. L.; Stinchcombe, J. R.; Olsen, K. M.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 44
Evaluation of morphological traits, winter survival and biomass potential in wild Japanese Miscanthus sinensis Anderss. populations in northern Japan
journal, March 2015
- Anzoua, Kossonou G.; Suzuki, Kenji; Fujita, Shinichi
- Grassland Science, Vol. 61, Issue 2
The Role of Casein Kinase II in Flowering Time Regulation Has Diversified during Evolution
journal, December 2009
- Ogiso, Eri; Takahashi, Yuji; Sasaki, Takuji
- Plant Physiology, Vol. 152, Issue 2
Characterization of Epistatic Interaction of QTLs LH8 and EH3 Controlling Heading Date in Rice
journal, March 2014
- Chen, Jingbin; Li, Xiaoyan; Cheng, Cheng
- Scientific Reports, Vol. 4, Issue 1
Genetic structure of Miscanthus sinensis ssp. condensatus (Poaceae) on Miyake Island: implications for revegetation of volcanically devastated sites
journal, December 2004
- Iwata, Hiroyoshi; Kamijo, Takashi; Tsumura, Yoshihiko
- Ecological Research, Vol. 20, Issue 2
The ecology and agronomy of Miscanthus sinensis , a species important to bioenergy crop development, in its native range in Japan: a review
journal, April 2009
- Stewart, J. Ryan; Toma, Yo; FernÁNdez, FabiÁN G.
- GCB Bioenergy, Vol. 1, Issue 2
() Represses Sorghum Flowering in Long Days: Alleles Enhance Biomass Accumulation and Grain Production
journal, January 2014
- Murphy, Rebecca L.; Morishige, Daryl T.; Brady, Jeff A.
- The Plant Genome, Vol. 7, Issue 2
The Coincidence of Critical Day Length Recognition for Florigen Gene Expression and Floral Transition under Long-Day Conditions in Rice
journal, May 2013
- Itoh, Hironori; Izawa, Takeshi
- Molecular Plant, Vol. 6, Issue 3
A latitudinal cline in flowering time in Arabidopsis thaliana modulated by the flowering time gene FRIGIDA
journal, March 2004
- Stinchcombe, J. R.; Weinig, C.; Ungerer, M.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 13
Molecular control of seasonal flowering in rice, arabidopsis and temperate cereals
journal, March 2014
- Shrestha, Roshi; Gómez-Ariza, Jorge; Brambilla, Vittoria
- Annals of Botany, Vol. 114, Issue 7
The Coincidence of Critical Day Length Recognition for Florigen Gene Expression and Floral Transition under Long-Day Conditions in Rice
journal, May 2013
- Itoh, Hironori; Izawa, Takeshi
- Molecular Plant, Vol. 6, Issue 3
Preservation of Duplicate Genes by Complementary, Degenerative Mutations
journal, April 1999
- Force, Allan; Lynch, Michael; Pickett, F. Bryan
- Genetics, Vol. 151, Issue 4
Diversification of the rice Waxy gene by insertion of mobile DNA elements into introns.
journal, January 1991
- Umeda, Masaaki; Ohtsubo, Hisako; Ohtsubo, Eiichi
- The Japanese Journal of Genetics, Vol. 66, Issue 5
Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the subunit of protein kinase CK2
journal, June 2001
- Takahashi, Y.; Shomura, A.; Sasaki, T.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 14
Epistasis among the three major flowering time genes in rice: coordinate changes of photoperiod sensitivity, basic vegetative growth and optimum photoperiod
journal, October 2007
- Uwatoko, Naohiro; Onishi, Atsushi; Ikeda, Yuji
- Euphytica, Vol. 163, Issue 2
Higher genetic diversity and gene flow in wild populations of Miscanthus sinensis in southwest China
journal, June 2013
- Xu, Wen-Zhi; Zhang, Xin-Quan; Huang, Lin-Kai
- Biochemical Systematics and Ecology, Vol. 48
The Arabidopsis B-Box Zinc Finger Family
journal, November 2009
- Khanna, Rajnish; Kronmiller, Brent; Maszle, Don R.
- The Plant Cell, Vol. 21, Issue 11
Genotypic and environmentally derived variation in the cell wall composition of Miscanthus in relation to its use as a biomass feedstock
journal, May 2010
- Hodgson, Edward M.; Lister, Susan J.; Bridgwater, Anthony V.
- Biomass and Bioenergy, Vol. 34, Issue 5
Miniature Inverted-Repeat Transposable Elements (MITEs) Have Been Accumulated through Amplification Bursts and Play Important Roles in Gene Expression and Species Diversity in Oryza sativa
journal, November 2011
- Lu, C.; Chen, J.; Zhang, Y.
- Molecular Biology and Evolution, Vol. 29, Issue 3
A latitudinal cline in flowering time in Arabidopsis thaliana modulated by the flowering time gene FRIGIDA
journal, March 2004
- Stinchcombe, J. R.; Weinig, C.; Ungerer, M.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 13
Tourist: a large family of small inverted repeat elements frequently associated with maize genes.
journal, October 1992
- Bureau, T. E.; Wessler, S. R.
- The Plant Cell, Vol. 4, Issue 10
Assessment of genetic diversity of native species in Izu Islands for a discriminate choice of source populations: Implications for revegetation of volcanically devastated sites
journal, December 2005
- Iwata, Hiroyoshi; Kamijo, Takashi; Tsumura, Yoshihiko
- Conservation Genetics, Vol. 7, Issue 3
CONSTANS is a photoperiod regulated activator of flowering in sorghum
journal, January 2014
- Yang, Shanshan; Weers, Brock D.; Morishige, Daryl T.
- BMC Plant Biology, Vol. 14, Issue 1
The Gene Pool of Miscanthus Species and Its Improvement
book, July 2012
- Sacks, Erik J.; Juvik, John A.; Lin, Qi
- Genomics of the Saccharinae
SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum
journal, January 2012
- Kim, Changsoo; Zhang, Dong; Auckland, Susan A.
- Theoretical and Applied Genetics, Vol. 124, Issue 7
Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait
journal, October 2004
- Caicedo, A. L.; Stinchcombe, J. R.; Olsen, K. M.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 44
Genetic diversity of natural Miscanthus sinensis populations in China revealed by ISSR markers
journal, June 2013
- Zhang, Qi Xiang; Shen, Yi Ke; Shao, Ruo Xuan
- Biochemical Systematics and Ecology, Vol. 48
Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants: Analysis of CONSTANS
journal, December 2001
- Robson, Frances; Costa, M. Manuela R.; Hepworth, Shelley R.
- The Plant Journal, Vol. 28, Issue 6
Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum
journal, September 2011
- Murphy, R. L.; Klein, R. R.; Morishige, D. T.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 39, p. 16469-16474
High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis
journal, March 2012
- Ma, Xue-Feng; Jensen, Elaine; Alexandrov, Nickolai
- PLoS ONE, Vol. 7, Issue 3
Characterization and detection of epistatic interactions of 3 QTLs, Hd1, Hd2, and Hd3, controlling heading date in rice using nearly isogenic lines
journal, November 2000
- Lin, H. X.; Yamamoto, T.; Sasaki, T.
- Theoretical and Applied Genetics, Vol. 101, Issue 7
SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum
journal, January 2012
- Kim, Changsoo; Zhang, Dong; Auckland, Susan A.
- Theoretical and Applied Genetics, Vol. 124, Issue 7
The Arabidopsis B-Box Zinc Finger Family
journal, November 2009
- Khanna, Rajnish; Kronmiller, Brent; Maszle, Don R.
- The Plant Cell, Vol. 21, Issue 11
Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice
journal, February 2009
- Takahashi, Y.; Teshima, K. M.; Yokoi, S.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 11
The effect of the environment on the grain colour and quality of commercially grown Canada hard white spring wheat, Triticum aestivum L. ‘Snowbird’
journal, January 2013
- Lukow, Odean M.; Adams, Kathy; Suchy, Jerry
- Canadian Journal of Plant Science, Vol. 93, Issue 1
Genetic Diversity and Population Structure of Miscanthus sinensis Germplasm in China
journal, October 2013
- Zhao, Hua; Wang, Bo; He, Junrong
- PLoS ONE, Vol. 8, Issue 10
Cytogenetic Studies of Different Miscanthus Species with Potential for Agricultural Use
journal, November 1994
- Lafferty, J.; Lelley, T.
- Plant Breeding, Vol. 113, Issue 3
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
journal, July 1987
- Saitou, N.; Nei, M.
- Molecular Biology and Evolution, Vol. 4, Issue 4, p. 406-425
Molecular control of seasonal flowering in rice, arabidopsis and temperate cereals
journal, March 2014
- Shrestha, Roshi; Gómez-Ariza, Jorge; Brambilla, Vittoria
- Annals of Botany, Vol. 114, Issue 7
Caloramator viterbensis sp. nov., a novel thermophilic, glycerol-fermenting bacterium isolated from a hot spring in Italy
journal, July 2002
- Seyfried, M.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 52, Issue 4
CONSTANS and the CCAAT Box Binding Complex Share a Functionally Important Domain and Interact to Regulate Flowering of Arabidopsis
journal, November 2006
- Wenkel, Stephan; Turck, Franziska; Singer, Kamy
- The Plant Cell, Vol. 18, Issue 11
Phylogeography based on intraspecific sequence variation in chloroplast DNA of Miscanthus sinensis (Poaceae), a native pioneer grass in Japan
journal, July 2013
- Shimono, Yoshiko; Kurokawa, Shunji; Nishida, Tomoko
- Botany, Vol. 91, Issue 7
Preservation of Duplicate Genes by Complementary, Degenerative Mutations
journal, April 1999
- Force, Allan; Lynch, Michael; Pickett, F. Bryan
- Genetics, Vol. 151, Issue 4
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