Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia

Lindsay V. Clark, Elena Dzyubenko, Nikolay Dzyubenko, Larisa Bagmet, Andrey Sabitov, Pavel Chebukin, Douglas A. Johnson, Jens Bonderup Kjeldsen, Karen Koefoed Petersen, Uffe Jørgensen, Ji Hye Yoo, Kweon Heo, Chang Yeon Yu, Hua Zhao, Xiaoli Jin, Junhua Peng, Toshihiko Yamada, Erik J Sacks

Research output: Contribution to journalArticle

Abstract

Background and aims Miscanthus is a genus of perennial C4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. ×giganteus, a hybrid between M. sinensis and M. sacchariflorus. Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C4 relatives maize, sorghum and sugarcane. Methods A plant exploration was conducted in eastern Russia, at the northern extreme of the native range for Miscanthus, with collections including 174 clonal germplasm accessions (160 M. sacchariflorus and 14 M. sinensis) from 47 sites. Accessions were genotyped by restriction site-associated DNA sequencing (RAD-seq) and plastid microsatellites. Key Results Miscanthus sinensis was found in maritime climates near Vladivostok (43·6°N) and on southern Sakhalin Island (46·6°N). Miscanthus sacchariflorus was found inland at latitudes as high as 49·3°N, where M. sinensis was absent. Most M. sacchariflorus accessions were diploid, but approx. 2 % were tetraploids. Molecular markers revealed little population structure (Jost's D < 0·007 among diploid groups) but high genetic diversity (expected heterozygosity = 0·14) within the collection of Russian M. sacchariflorus. Genome-wide association (GWA) analysis for traits measured at the collection sites revealed three M. sacchariflorus single nucleotide polymorphisms (SNPs) significantly associated with the number of stems per unit area, one with height and one with basal stem diameter; three were near or within previously described sorghum quantitative trait loci for related traits. Conclusions This new Miscanthus germplasm collection from eastern Russia will be useful for breeding Miscanthus and sugarcane cultivars with improved adaptation to cold. Moreover, a strategy is proposed to facilitate the rapid utilization of new germplasm collections: by implementing low-cost SNP genotyping to conduct GWA studies of phenotypic data obtained at collection sites, plant breeders can be provided with actionable information on which accessions have desirable traits and alleles.

Original languageEnglish (US)
Pages (from-to)941-955
Number of pages15
JournalAnnals of Botany
Volume118
Issue number5
DOIs
StatePublished - Oct 1 2016

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Miscanthus sacchariflorus
Miscanthus
yield components
Russia
Miscanthus sinensis
germplasm conservation
Sorghum (Poaceae)
single nucleotide polymorphism
sugarcane
diploidy
Miscanthus giganteus
maritime climate
stems
plant breeders
energy crops
East Asia
cold tolerance
genotyping
tetraploidy
plastids

Keywords

  • Chloroplast
  • Miscanthus sacchariflorus
  • Miscanthus sinensis
  • Russia
  • genome-wide association analysis (GWAS)
  • germplasm
  • population genetics
  • restriction site-associated DNA sequencing (RAD-seq)
  • single nucleotide polymorphism (SNP)

ASJC Scopus subject areas

  • Plant Science

Cite this

Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia. / Clark, Lindsay V.; Dzyubenko, Elena; Dzyubenko, Nikolay; Bagmet, Larisa; Sabitov, Andrey; Chebukin, Pavel; Johnson, Douglas A.; Kjeldsen, Jens Bonderup; Petersen, Karen Koefoed; Jørgensen, Uffe; Yoo, Ji Hye; Heo, Kweon; Yu, Chang Yeon; Zhao, Hua; Jin, Xiaoli; Peng, Junhua; Yamada, Toshihiko; Sacks, Erik J.

In: Annals of Botany, Vol. 118, No. 5, 01.10.2016, p. 941-955.

Research output: Contribution to journalArticle

Clark, LV, Dzyubenko, E, Dzyubenko, N, Bagmet, L, Sabitov, A, Chebukin, P, Johnson, DA, Kjeldsen, JB, Petersen, KK, Jørgensen, U, Yoo, JH, Heo, K, Yu, CY, Zhao, H, Jin, X, Peng, J, Yamada, T & Sacks, EJ 2016, 'Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia', Annals of Botany, vol. 118, no. 5, pp. 941-955. https://doi.org/10.1093/aob/mcw137
Clark, Lindsay V. ; Dzyubenko, Elena ; Dzyubenko, Nikolay ; Bagmet, Larisa ; Sabitov, Andrey ; Chebukin, Pavel ; Johnson, Douglas A. ; Kjeldsen, Jens Bonderup ; Petersen, Karen Koefoed ; Jørgensen, Uffe ; Yoo, Ji Hye ; Heo, Kweon ; Yu, Chang Yeon ; Zhao, Hua ; Jin, Xiaoli ; Peng, Junhua ; Yamada, Toshihiko ; Sacks, Erik J. / Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia. In: Annals of Botany. 2016 ; Vol. 118, No. 5. pp. 941-955.
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T1 - Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia

AU - Clark, Lindsay V.

AU - Dzyubenko, Elena

AU - Dzyubenko, Nikolay

AU - Bagmet, Larisa

AU - Sabitov, Andrey

AU - Chebukin, Pavel

AU - Johnson, Douglas A.

AU - Kjeldsen, Jens Bonderup

AU - Petersen, Karen Koefoed

AU - Jørgensen, Uffe

AU - Yoo, Ji Hye

AU - Heo, Kweon

AU - Yu, Chang Yeon

AU - Zhao, Hua

AU - Jin, Xiaoli

AU - Peng, Junhua

AU - Yamada, Toshihiko

AU - Sacks, Erik J

PY - 2016/10/1

Y1 - 2016/10/1

N2 - Background and aims Miscanthus is a genus of perennial C4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. ×giganteus, a hybrid between M. sinensis and M. sacchariflorus. Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C4 relatives maize, sorghum and sugarcane. Methods A plant exploration was conducted in eastern Russia, at the northern extreme of the native range for Miscanthus, with collections including 174 clonal germplasm accessions (160 M. sacchariflorus and 14 M. sinensis) from 47 sites. Accessions were genotyped by restriction site-associated DNA sequencing (RAD-seq) and plastid microsatellites. Key Results Miscanthus sinensis was found in maritime climates near Vladivostok (43·6°N) and on southern Sakhalin Island (46·6°N). Miscanthus sacchariflorus was found inland at latitudes as high as 49·3°N, where M. sinensis was absent. Most M. sacchariflorus accessions were diploid, but approx. 2 % were tetraploids. Molecular markers revealed little population structure (Jost's D < 0·007 among diploid groups) but high genetic diversity (expected heterozygosity = 0·14) within the collection of Russian M. sacchariflorus. Genome-wide association (GWA) analysis for traits measured at the collection sites revealed three M. sacchariflorus single nucleotide polymorphisms (SNPs) significantly associated with the number of stems per unit area, one with height and one with basal stem diameter; three were near or within previously described sorghum quantitative trait loci for related traits. Conclusions This new Miscanthus germplasm collection from eastern Russia will be useful for breeding Miscanthus and sugarcane cultivars with improved adaptation to cold. Moreover, a strategy is proposed to facilitate the rapid utilization of new germplasm collections: by implementing low-cost SNP genotyping to conduct GWA studies of phenotypic data obtained at collection sites, plant breeders can be provided with actionable information on which accessions have desirable traits and alleles.

AB - Background and aims Miscanthus is a genus of perennial C4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. ×giganteus, a hybrid between M. sinensis and M. sacchariflorus. Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C4 relatives maize, sorghum and sugarcane. Methods A plant exploration was conducted in eastern Russia, at the northern extreme of the native range for Miscanthus, with collections including 174 clonal germplasm accessions (160 M. sacchariflorus and 14 M. sinensis) from 47 sites. Accessions were genotyped by restriction site-associated DNA sequencing (RAD-seq) and plastid microsatellites. Key Results Miscanthus sinensis was found in maritime climates near Vladivostok (43·6°N) and on southern Sakhalin Island (46·6°N). Miscanthus sacchariflorus was found inland at latitudes as high as 49·3°N, where M. sinensis was absent. Most M. sacchariflorus accessions were diploid, but approx. 2 % were tetraploids. Molecular markers revealed little population structure (Jost's D < 0·007 among diploid groups) but high genetic diversity (expected heterozygosity = 0·14) within the collection of Russian M. sacchariflorus. Genome-wide association (GWA) analysis for traits measured at the collection sites revealed three M. sacchariflorus single nucleotide polymorphisms (SNPs) significantly associated with the number of stems per unit area, one with height and one with basal stem diameter; three were near or within previously described sorghum quantitative trait loci for related traits. Conclusions This new Miscanthus germplasm collection from eastern Russia will be useful for breeding Miscanthus and sugarcane cultivars with improved adaptation to cold. Moreover, a strategy is proposed to facilitate the rapid utilization of new germplasm collections: by implementing low-cost SNP genotyping to conduct GWA studies of phenotypic data obtained at collection sites, plant breeders can be provided with actionable information on which accessions have desirable traits and alleles.

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KW - Miscanthus sacchariflorus

KW - Miscanthus sinensis

KW - Russia

KW - genome-wide association analysis (GWAS)

KW - germplasm

KW - population genetics

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

KW - single nucleotide polymorphism (SNP)

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