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Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression.

Clark LV, Stewart JR, Nishiwaki A, Toma Y, Kjeldsen JB, Jørgensen U, Zhao H, Peng J, Yoo JH, Heo K, Yu CY, Yamada T, Sacks EJ - J. Exp. Bot. (2015)

Bottom Line: Unexpectedly, rare (~1%) diploid M. sinensis individuals from northern Japan were found with 6-27% M. sacchariflorus ancestry.In contrast to limited introgression between diploid M. sacchariflorus and M. sinensis in northern China, selection for adaptation to a moderate maritime climate probably favoured cross-ploidy introgressants in southern Japan.These results will help guide the selection of Miscanthus accessions for the breeding of biomass cultivars.

View Article: PubMed Central - PubMed

Affiliation: Department of Crop Sciences, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA.

No MeSH data available.


Structure and DAPC results using 20 704 nuclear SNPs. Msi=Miscanthus sinensis, Msa=M. sacchariflorus, Mxg=M.×giganteus. (A) Bar plot of Q values (proportion ancestry estimated in Structure) for 745 individuals from the Japan dense-sampling set and 645 individuals from the previously published region-wide set (Clark et al., 2014). Each of five runs included 253 individuals from the Japan-dense set (one per accession) plus all 645 individuals from the region-wide set; mean Q values are shown for individuals that were present in more than one run. Each of the eight groups is represented by a different colour. The narrower bottom bar indicates DAPC group assignments. (B) Mean Q values for 81 ornamental individuals and 42 naturalized individuals from the USA, when the parameters USEPOPINFO and PFROMPOPFLAGONLY were used in Structure to assign ancestry from native populations. (C) Map of Q values for Msi individuals in Japan, including 667 from the Japan-dense set and 128 from the region-wide set. Five individuals with Msa ancestry 6–27%, including four diploids and one of undetermined ploidy, are indicated with arrows. (D) Map of Q values for 78 Msa–Mxg complex individuals from Japan, all from the Japan dense-sampling set. Four individuals with Msi ancestry 39–42% are indicated with arrows, and the ploidy determined by flow cytometry is indicated; all other individuals shown were tetraploid except for six of undetermined ploidy. The red ellipse indicates the sampling area for all four Msa–Mxg individuals with an Msi plastid haplotype (other individuals within the ellipse have an Msa plastid haplotype). (E) Latitude vs Q values for 89 native-collected Msa–Mxg complex individuals, Mxg ‘Illinois’ (assuming origin in Yokohama, Japan; indicated with an arrow), 28 random Msi individuals that were subjected to flow cytometry, and five Msi individuals with Msa ancestry >5%. Colour and shape of symbols in (E) are used redundantly to indicate plastid haplotype and collection location, and fill is used to indicate ploidy, with filled points outlined in black to make them more easily visible.
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Figure 1: Structure and DAPC results using 20 704 nuclear SNPs. Msi=Miscanthus sinensis, Msa=M. sacchariflorus, Mxg=M.×giganteus. (A) Bar plot of Q values (proportion ancestry estimated in Structure) for 745 individuals from the Japan dense-sampling set and 645 individuals from the previously published region-wide set (Clark et al., 2014). Each of five runs included 253 individuals from the Japan-dense set (one per accession) plus all 645 individuals from the region-wide set; mean Q values are shown for individuals that were present in more than one run. Each of the eight groups is represented by a different colour. The narrower bottom bar indicates DAPC group assignments. (B) Mean Q values for 81 ornamental individuals and 42 naturalized individuals from the USA, when the parameters USEPOPINFO and PFROMPOPFLAGONLY were used in Structure to assign ancestry from native populations. (C) Map of Q values for Msi individuals in Japan, including 667 from the Japan-dense set and 128 from the region-wide set. Five individuals with Msa ancestry 6–27%, including four diploids and one of undetermined ploidy, are indicated with arrows. (D) Map of Q values for 78 Msa–Mxg complex individuals from Japan, all from the Japan dense-sampling set. Four individuals with Msi ancestry 39–42% are indicated with arrows, and the ploidy determined by flow cytometry is indicated; all other individuals shown were tetraploid except for six of undetermined ploidy. The red ellipse indicates the sampling area for all four Msa–Mxg individuals with an Msi plastid haplotype (other individuals within the ellipse have an Msa plastid haplotype). (E) Latitude vs Q values for 89 native-collected Msa–Mxg complex individuals, Mxg ‘Illinois’ (assuming origin in Yokohama, Japan; indicated with an arrow), 28 random Msi individuals that were subjected to flow cytometry, and five Msi individuals with Msa ancestry >5%. Colour and shape of symbols in (E) are used redundantly to indicate plastid haplotype and collection location, and fill is used to indicate ploidy, with filled points outlined in black to make them more easily visible.

Mentions: Structure analysis of the Japan dense-sampling set identified K=4 (three M. sinensis and one M. sacchariflorus) as the most reproducible estimate (Supplementary Fig. S1). Thus, the high density sampling in this study enabled identification of three M. sinensis groups in Japan (northern, central, and southern, hereafter called N, Central, and S Japan when referring to genetic clusters as opposed to geographic regions; Fig. 1A, C), where previous low density sampling had identified only two groups (northern and southern). A combined analysis of the Japan dense-sampling set with the region-wide set at K=8 identified the seven genetic groups from the previous study (six M. sinensis and one M. sacchariflorus; Clark et al., 2014) plus the one additional M. sinensis group identified in the analysis of the Japan dense-sampling set (Fig. 1A, C). The first principal component of the SNP data was strongly correlated with M. sacchariflorus ancestry identified by Structure (r2=0.99; Supplementary Fig. S2A), and Structure runs on simulated hybrids indicated that even highly backcrossed (BC5) individuals could be distinguished from the parent species (Supplementary Fig. S2B, Table S1).


Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression.

Clark LV, Stewart JR, Nishiwaki A, Toma Y, Kjeldsen JB, Jørgensen U, Zhao H, Peng J, Yoo JH, Heo K, Yu CY, Yamada T, Sacks EJ - J. Exp. Bot. (2015)

Structure and DAPC results using 20 704 nuclear SNPs. Msi=Miscanthus sinensis, Msa=M. sacchariflorus, Mxg=M.×giganteus. (A) Bar plot of Q values (proportion ancestry estimated in Structure) for 745 individuals from the Japan dense-sampling set and 645 individuals from the previously published region-wide set (Clark et al., 2014). Each of five runs included 253 individuals from the Japan-dense set (one per accession) plus all 645 individuals from the region-wide set; mean Q values are shown for individuals that were present in more than one run. Each of the eight groups is represented by a different colour. The narrower bottom bar indicates DAPC group assignments. (B) Mean Q values for 81 ornamental individuals and 42 naturalized individuals from the USA, when the parameters USEPOPINFO and PFROMPOPFLAGONLY were used in Structure to assign ancestry from native populations. (C) Map of Q values for Msi individuals in Japan, including 667 from the Japan-dense set and 128 from the region-wide set. Five individuals with Msa ancestry 6–27%, including four diploids and one of undetermined ploidy, are indicated with arrows. (D) Map of Q values for 78 Msa–Mxg complex individuals from Japan, all from the Japan dense-sampling set. Four individuals with Msi ancestry 39–42% are indicated with arrows, and the ploidy determined by flow cytometry is indicated; all other individuals shown were tetraploid except for six of undetermined ploidy. The red ellipse indicates the sampling area for all four Msa–Mxg individuals with an Msi plastid haplotype (other individuals within the ellipse have an Msa plastid haplotype). (E) Latitude vs Q values for 89 native-collected Msa–Mxg complex individuals, Mxg ‘Illinois’ (assuming origin in Yokohama, Japan; indicated with an arrow), 28 random Msi individuals that were subjected to flow cytometry, and five Msi individuals with Msa ancestry >5%. Colour and shape of symbols in (E) are used redundantly to indicate plastid haplotype and collection location, and fill is used to indicate ploidy, with filled points outlined in black to make them more easily visible.
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Figure 1: Structure and DAPC results using 20 704 nuclear SNPs. Msi=Miscanthus sinensis, Msa=M. sacchariflorus, Mxg=M.×giganteus. (A) Bar plot of Q values (proportion ancestry estimated in Structure) for 745 individuals from the Japan dense-sampling set and 645 individuals from the previously published region-wide set (Clark et al., 2014). Each of five runs included 253 individuals from the Japan-dense set (one per accession) plus all 645 individuals from the region-wide set; mean Q values are shown for individuals that were present in more than one run. Each of the eight groups is represented by a different colour. The narrower bottom bar indicates DAPC group assignments. (B) Mean Q values for 81 ornamental individuals and 42 naturalized individuals from the USA, when the parameters USEPOPINFO and PFROMPOPFLAGONLY were used in Structure to assign ancestry from native populations. (C) Map of Q values for Msi individuals in Japan, including 667 from the Japan-dense set and 128 from the region-wide set. Five individuals with Msa ancestry 6–27%, including four diploids and one of undetermined ploidy, are indicated with arrows. (D) Map of Q values for 78 Msa–Mxg complex individuals from Japan, all from the Japan dense-sampling set. Four individuals with Msi ancestry 39–42% are indicated with arrows, and the ploidy determined by flow cytometry is indicated; all other individuals shown were tetraploid except for six of undetermined ploidy. The red ellipse indicates the sampling area for all four Msa–Mxg individuals with an Msi plastid haplotype (other individuals within the ellipse have an Msa plastid haplotype). (E) Latitude vs Q values for 89 native-collected Msa–Mxg complex individuals, Mxg ‘Illinois’ (assuming origin in Yokohama, Japan; indicated with an arrow), 28 random Msi individuals that were subjected to flow cytometry, and five Msi individuals with Msa ancestry >5%. Colour and shape of symbols in (E) are used redundantly to indicate plastid haplotype and collection location, and fill is used to indicate ploidy, with filled points outlined in black to make them more easily visible.
Mentions: Structure analysis of the Japan dense-sampling set identified K=4 (three M. sinensis and one M. sacchariflorus) as the most reproducible estimate (Supplementary Fig. S1). Thus, the high density sampling in this study enabled identification of three M. sinensis groups in Japan (northern, central, and southern, hereafter called N, Central, and S Japan when referring to genetic clusters as opposed to geographic regions; Fig. 1A, C), where previous low density sampling had identified only two groups (northern and southern). A combined analysis of the Japan dense-sampling set with the region-wide set at K=8 identified the seven genetic groups from the previous study (six M. sinensis and one M. sacchariflorus; Clark et al., 2014) plus the one additional M. sinensis group identified in the analysis of the Japan dense-sampling set (Fig. 1A, C). The first principal component of the SNP data was strongly correlated with M. sacchariflorus ancestry identified by Structure (r2=0.99; Supplementary Fig. S2A), and Structure runs on simulated hybrids indicated that even highly backcrossed (BC5) individuals could be distinguished from the parent species (Supplementary Fig. S2B, Table S1).

Bottom Line: Unexpectedly, rare (~1%) diploid M. sinensis individuals from northern Japan were found with 6-27% M. sacchariflorus ancestry.In contrast to limited introgression between diploid M. sacchariflorus and M. sinensis in northern China, selection for adaptation to a moderate maritime climate probably favoured cross-ploidy introgressants in southern Japan.These results will help guide the selection of Miscanthus accessions for the breeding of biomass cultivars.

View Article: PubMed Central - PubMed

Affiliation: Department of Crop Sciences, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA.

No MeSH data available.