Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centred around the Yellow Sea

Lindsay V. Clark, Xiaoli Jin, Karen Koefoed Petersen, Kossanou G. Anzoua, Larissa Bagmet, Pavel Chebukin, Martin Deuter, Elena Dzyubenko, Nicolay Dzyubenko, Kweon Heo, Douglas A. Johnson, Uffe Jørgensen, Jens Bonderup Kjeldsen, Hironori Nagano, Junhua Peng, Andrey Sabitov, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Stephen P. LongErik J. Sacks

Research output: Contribution to journalArticle

Abstract

BACKGROUND AND AIMS: Miscanthus, a C4 perennial grass native to East Asia, is a promising biomass crop. Miscanthus sacchariflorus has a broad geographic range, is used to produce paper in China and is one of the parents (along with Miscanthus sinensis) of the important biomass species Miscanthus × giganteus. The largest study of M. sacchariflorus population genetics to date is reported here. METHODS: Collections included 764 individuals across East Asia. Samples were genotyped with 34 605 single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RAD-seq) and ten plastid microsatellites, and were subjected to ploidy analysis by flow cytometry. KEY RESULTS: Six major genetic groups within M. sacchariflorus were identified using SNP data: three diploid groups, comprising Yangtze (M. sacchariflorus ssp. lutarioriparius), N China and Korea/NE China/Russia; and three tetraploid groups, comprising N China/Korea/Russia, S Japan and N Japan. Miscanthus sacchariflorus ssp. lutarioriparius was derived from the N China group, with a substantial bottleneck. Japanese and mainland tetraploids originated from independent polyploidization events. Hybrids between diploid M. sacchariflorus and M. sinensis were identified in Korea, but without introgression into either parent species. In contrast, tetraploid M. sacchariflorus in southern Japan and Korea exhibited substantial hybridization and introgression with local diploid M. sinensis. CONCLUSIONS: Genetic data indicated that the land now under the Yellow Sea was a centre of diversity for M. sacchariflorus during the last glacial maximum, followed by a series of migrations as the climate became warmer and wetter. Overall, M. sacchariflorus has greater genetic diversity than M. sinensis, suggesting that breeding and selection within M. sacchariflorus will be important for the development of improved M. × giganteus. Ornamental M. sacchariflorus genotypes in Europe and North America represent a very narrow portion of the species' genetic diversity, and thus do not well represent the species as a whole.

Original languageEnglish (US)
Pages (from-to)731-748
Number of pages18
JournalAnnals of botany
Volume124
Issue number4
DOIs
StatePublished - Oct 29 2019

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Miscanthus sacchariflorus
Miscanthus sinensis
Yellow Sea
introgression
tetraploidy
population structure
diploidy
Korean Peninsula
China
Miscanthus giganteus
Japan
East Asia
single nucleotide polymorphism
Russia
Miscanthus
center of diversity
genetic variation
energy crops
ploidy
plastids

Keywords

  • Miscanthus sacchariflorus
  • Miscanthus sacchariflorus ssp
  • Miscanthus sinensis
  • Miscanthus × giganteus
  • bioenergy
  • hybridization
  • lutarioriparius
  • plastid haplotype
  • polyploidy
  • population genetics
  • restriction site-associated DNA sequencing (RAD-seq)

ASJC Scopus subject areas

  • Plant Science

Cite this

Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centred around the Yellow Sea. / Clark, Lindsay V.; Jin, Xiaoli; Petersen, Karen Koefoed; Anzoua, Kossanou G.; Bagmet, Larissa; Chebukin, Pavel; Deuter, Martin; Dzyubenko, Elena; Dzyubenko, Nicolay; Heo, Kweon; Johnson, Douglas A.; Jørgensen, Uffe; Kjeldsen, Jens Bonderup; Nagano, Hironori; Peng, Junhua; Sabitov, Andrey; Yamada, Toshihiko; Yoo, Ji Hye; Yu, Chang Yeon; Long, Stephen P.; Sacks, Erik J.

In: Annals of botany, Vol. 124, No. 4, 29.10.2019, p. 731-748.

Research output: Contribution to journalArticle

Clark, LV, Jin, X, Petersen, KK, Anzoua, KG, Bagmet, L, Chebukin, P, Deuter, M, Dzyubenko, E, Dzyubenko, N, Heo, K, Johnson, DA, Jørgensen, U, Kjeldsen, JB, Nagano, H, Peng, J, Sabitov, A, Yamada, T, Yoo, JH, Yu, CY, Long, SP & Sacks, EJ 2019, 'Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centred around the Yellow Sea', Annals of botany, vol. 124, no. 4, pp. 731-748. https://doi.org/10.1093/aob/mcy161
Clark, Lindsay V. ; Jin, Xiaoli ; Petersen, Karen Koefoed ; Anzoua, Kossanou G. ; Bagmet, Larissa ; Chebukin, Pavel ; Deuter, Martin ; Dzyubenko, Elena ; Dzyubenko, Nicolay ; Heo, Kweon ; Johnson, Douglas A. ; Jørgensen, Uffe ; Kjeldsen, Jens Bonderup ; Nagano, Hironori ; Peng, Junhua ; Sabitov, Andrey ; Yamada, Toshihiko ; Yoo, Ji Hye ; Yu, Chang Yeon ; Long, Stephen P. ; Sacks, Erik J. / Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centred around the Yellow Sea. In: Annals of botany. 2019 ; Vol. 124, No. 4. pp. 731-748.
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abstract = "BACKGROUND AND AIMS: Miscanthus, a C4 perennial grass native to East Asia, is a promising biomass crop. Miscanthus sacchariflorus has a broad geographic range, is used to produce paper in China and is one of the parents (along with Miscanthus sinensis) of the important biomass species Miscanthus × giganteus. The largest study of M. sacchariflorus population genetics to date is reported here. METHODS: Collections included 764 individuals across East Asia. Samples were genotyped with 34 605 single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RAD-seq) and ten plastid microsatellites, and were subjected to ploidy analysis by flow cytometry. KEY RESULTS: Six major genetic groups within M. sacchariflorus were identified using SNP data: three diploid groups, comprising Yangtze (M. sacchariflorus ssp. lutarioriparius), N China and Korea/NE China/Russia; and three tetraploid groups, comprising N China/Korea/Russia, S Japan and N Japan. Miscanthus sacchariflorus ssp. lutarioriparius was derived from the N China group, with a substantial bottleneck. Japanese and mainland tetraploids originated from independent polyploidization events. Hybrids between diploid M. sacchariflorus and M. sinensis were identified in Korea, but without introgression into either parent species. In contrast, tetraploid M. sacchariflorus in southern Japan and Korea exhibited substantial hybridization and introgression with local diploid M. sinensis. CONCLUSIONS: Genetic data indicated that the land now under the Yellow Sea was a centre of diversity for M. sacchariflorus during the last glacial maximum, followed by a series of migrations as the climate became warmer and wetter. Overall, M. sacchariflorus has greater genetic diversity than M. sinensis, suggesting that breeding and selection within M. sacchariflorus will be important for the development of improved M. × giganteus. Ornamental M. sacchariflorus genotypes in Europe and North America represent a very narrow portion of the species' genetic diversity, and thus do not well represent the species as a whole.",
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author = "Clark, {Lindsay V.} and Xiaoli Jin and Petersen, {Karen Koefoed} and Anzoua, {Kossanou G.} and Larissa Bagmet and Pavel Chebukin and Martin Deuter and Elena Dzyubenko and Nicolay Dzyubenko and Kweon Heo and Johnson, {Douglas A.} and Uffe J{\o}rgensen and Kjeldsen, {Jens Bonderup} and Hironori Nagano and Junhua Peng and Andrey Sabitov and Toshihiko Yamada and Yoo, {Ji Hye} and Yu, {Chang Yeon} and Long, {Stephen P.} and Sacks, {Erik J.}",
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TY - JOUR

T1 - Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centred around the Yellow Sea

AU - Clark, Lindsay V.

AU - Jin, Xiaoli

AU - Petersen, Karen Koefoed

AU - Anzoua, Kossanou G.

AU - Bagmet, Larissa

AU - Chebukin, Pavel

AU - Deuter, Martin

AU - Dzyubenko, Elena

AU - Dzyubenko, Nicolay

AU - Heo, Kweon

AU - Johnson, Douglas A.

AU - Jørgensen, Uffe

AU - Kjeldsen, Jens Bonderup

AU - Nagano, Hironori

AU - Peng, Junhua

AU - Sabitov, Andrey

AU - Yamada, Toshihiko

AU - Yoo, Ji Hye

AU - Yu, Chang Yeon

AU - Long, Stephen P.

AU - Sacks, Erik J.

PY - 2019/10/29

Y1 - 2019/10/29

N2 - BACKGROUND AND AIMS: Miscanthus, a C4 perennial grass native to East Asia, is a promising biomass crop. Miscanthus sacchariflorus has a broad geographic range, is used to produce paper in China and is one of the parents (along with Miscanthus sinensis) of the important biomass species Miscanthus × giganteus. The largest study of M. sacchariflorus population genetics to date is reported here. METHODS: Collections included 764 individuals across East Asia. Samples were genotyped with 34 605 single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RAD-seq) and ten plastid microsatellites, and were subjected to ploidy analysis by flow cytometry. KEY RESULTS: Six major genetic groups within M. sacchariflorus were identified using SNP data: three diploid groups, comprising Yangtze (M. sacchariflorus ssp. lutarioriparius), N China and Korea/NE China/Russia; and three tetraploid groups, comprising N China/Korea/Russia, S Japan and N Japan. Miscanthus sacchariflorus ssp. lutarioriparius was derived from the N China group, with a substantial bottleneck. Japanese and mainland tetraploids originated from independent polyploidization events. Hybrids between diploid M. sacchariflorus and M. sinensis were identified in Korea, but without introgression into either parent species. In contrast, tetraploid M. sacchariflorus in southern Japan and Korea exhibited substantial hybridization and introgression with local diploid M. sinensis. CONCLUSIONS: Genetic data indicated that the land now under the Yellow Sea was a centre of diversity for M. sacchariflorus during the last glacial maximum, followed by a series of migrations as the climate became warmer and wetter. Overall, M. sacchariflorus has greater genetic diversity than M. sinensis, suggesting that breeding and selection within M. sacchariflorus will be important for the development of improved M. × giganteus. Ornamental M. sacchariflorus genotypes in Europe and North America represent a very narrow portion of the species' genetic diversity, and thus do not well represent the species as a whole.

AB - BACKGROUND AND AIMS: Miscanthus, a C4 perennial grass native to East Asia, is a promising biomass crop. Miscanthus sacchariflorus has a broad geographic range, is used to produce paper in China and is one of the parents (along with Miscanthus sinensis) of the important biomass species Miscanthus × giganteus. The largest study of M. sacchariflorus population genetics to date is reported here. METHODS: Collections included 764 individuals across East Asia. Samples were genotyped with 34 605 single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RAD-seq) and ten plastid microsatellites, and were subjected to ploidy analysis by flow cytometry. KEY RESULTS: Six major genetic groups within M. sacchariflorus were identified using SNP data: three diploid groups, comprising Yangtze (M. sacchariflorus ssp. lutarioriparius), N China and Korea/NE China/Russia; and three tetraploid groups, comprising N China/Korea/Russia, S Japan and N Japan. Miscanthus sacchariflorus ssp. lutarioriparius was derived from the N China group, with a substantial bottleneck. Japanese and mainland tetraploids originated from independent polyploidization events. Hybrids between diploid M. sacchariflorus and M. sinensis were identified in Korea, but without introgression into either parent species. In contrast, tetraploid M. sacchariflorus in southern Japan and Korea exhibited substantial hybridization and introgression with local diploid M. sinensis. CONCLUSIONS: Genetic data indicated that the land now under the Yellow Sea was a centre of diversity for M. sacchariflorus during the last glacial maximum, followed by a series of migrations as the climate became warmer and wetter. Overall, M. sacchariflorus has greater genetic diversity than M. sinensis, suggesting that breeding and selection within M. sacchariflorus will be important for the development of improved M. × giganteus. Ornamental M. sacchariflorus genotypes in Europe and North America represent a very narrow portion of the species' genetic diversity, and thus do not well represent the species as a whole.

KW - Miscanthus sacchariflorus

KW - Miscanthus sacchariflorus ssp

KW - Miscanthus sinensis

KW - Miscanthus × giganteus

KW - bioenergy

KW - hybridization

KW - lutarioriparius

KW - plastid haplotype

KW - polyploidy

KW - population genetics

KW - restriction site-associated DNA sequencing (RAD-seq)

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DO - 10.1093/aob/mcy161

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JO - Annals of Botany

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