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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.


Spatial principal components analysis (sPCA) of M. sinensis in Japan using 5359 SNPs across 782 individuals from 205 collection sites. (A–C) Interpolation of scores of lag vectors of the first three eigenvectors produced by sPCA. Scores are represented the darkness of greyscale pixels. The percentage of genetic variation between sites explained by each of the three eigenvectors is indicated. (This figure is available in colour at JXB online.)
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Figure 3: Spatial principal components analysis (sPCA) of M. sinensis in Japan using 5359 SNPs across 782 individuals from 205 collection sites. (A–C) Interpolation of scores of lag vectors of the first three eigenvectors produced by sPCA. Scores are represented the darkness of greyscale pixels. The percentage of genetic variation between sites explained by each of the three eigenvectors is indicated. (This figure is available in colour at JXB online.)

Mentions: If M. sinensis individuals were sorted by Q value, the values changed abruptly in several regions of the bar plot, suggesting barriers to gene flow (Fig. 1A). Spatial principal components analysis of nuclear SNP data indicated the geographical locations and relative strengths of these barriers to gene flow for M. sinensis in Japan (Fig. 3). The first three eigenvectors with positive spatial autocorrelation were chosen for analysis, based on a screeplot of genetic variance vs spatial autocorrelation (Supplementary Fig. S3). The first eigenvector, which had by far the highest variance (Fig. 3A; 12.7% of genetic variation between sites), represented a genetic gradient north to south in Japan, as well as differentiation of the region to the southwest of the Noto Peninsula. The second eigenvector, representing 2.7% of the genetic variation between sites, revealed central Honshu as the most divergent region, and a steep genetic cline near the Japanese Alps (Fig. 3B). The third eigenvector, representing 1.4% of genetic variation between sites, showed a gradient from east to west (Fig. 3C). None of these three eigenvectors revealed genetic structure within Hokkaido despite the large sample size in that region.


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)

Spatial principal components analysis (sPCA) of M. sinensis in Japan using 5359 SNPs across 782 individuals from 205 collection sites. (A–C) Interpolation of scores of lag vectors of the first three eigenvectors produced by sPCA. Scores are represented the darkness of greyscale pixels. The percentage of genetic variation between sites explained by each of the three eigenvectors is indicated. (This figure is available in colour at JXB online.)
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4493777&req=5

Figure 3: Spatial principal components analysis (sPCA) of M. sinensis in Japan using 5359 SNPs across 782 individuals from 205 collection sites. (A–C) Interpolation of scores of lag vectors of the first three eigenvectors produced by sPCA. Scores are represented the darkness of greyscale pixels. The percentage of genetic variation between sites explained by each of the three eigenvectors is indicated. (This figure is available in colour at JXB online.)
Mentions: If M. sinensis individuals were sorted by Q value, the values changed abruptly in several regions of the bar plot, suggesting barriers to gene flow (Fig. 1A). Spatial principal components analysis of nuclear SNP data indicated the geographical locations and relative strengths of these barriers to gene flow for M. sinensis in Japan (Fig. 3). The first three eigenvectors with positive spatial autocorrelation were chosen for analysis, based on a screeplot of genetic variance vs spatial autocorrelation (Supplementary Fig. S3). The first eigenvector, which had by far the highest variance (Fig. 3A; 12.7% of genetic variation between sites), represented a genetic gradient north to south in Japan, as well as differentiation of the region to the southwest of the Noto Peninsula. The second eigenvector, representing 2.7% of the genetic variation between sites, revealed central Honshu as the most divergent region, and a steep genetic cline near the Japanese Alps (Fig. 3B). The third eigenvector, representing 1.4% of genetic variation between sites, showed a gradient from east to west (Fig. 3C). None of these three eigenvectors revealed genetic structure within Hokkaido despite the large sample size in that region.

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.