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Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)

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ABSTRACT

Background: Second generation (2G) bioenergy from lignocellulosic feedstocks has the potential to develop as a sustainable source of renewable energy; however, significant hurdles still remain for large-scale commercialisation. Populus is considered as a promising 2G feedstock and understanding the genetic basis of biomass yield and feedstock quality are a research priority in this model tree species.

Results: We report the first coppiced biomass study for 714 members of a wide population of European black poplar (Populus nigra L.), a native European tree, selected from 20 river populations ranging in latitude and longitude between 40.5 and 52.1°N and 1.0 and 16.4°E, respectively. When grown at a single site in southern UK, significant Site of Origin (SO) effects were seen for 14 of the 15 directly measured or derived traits including biomass yield, leaf area and stomatal index. There was significant correlation (p < 0.001) between biomass yield traits over 3 years of harvest which identified leaf size and cell production as strong predictors of biomass yield. A 12 K Illumina genotyping array (constructed from 10,331 SNPs in 14 QTL regions and 4648 genes) highlighted significant population genetic structure with pairwise FST showing strong differentiation (p < 0.001) between the Spanish and Italian subpopulations. Robust associations reaching genome-wide significance are reported for main stem height and cell number per leaf; two traits tightly linked to biomass yield. These genotyping and phenotypic data were also used to show the presence of significant isolation by distance (IBD) and isolation by adaption (IBA) within this population.

Conclusions: The three associations identified reaching genome-wide significance at p < 0.05 include a transcription factor; a putative stress response gene and a gene of unknown function. None of them have been previously linked to bioenergy yield; were shown to be differentially expressed in a panel of three selected genotypes from the collection and represent exciting, novel candidates for further study in a bioenergy tree native to Europe and Euro-Asia. A further 26 markers (22 genes) were found to reach putative significance and are also of interest for biomass yield, leaf area, epidermal cell expansion and stomatal patterning. This research on European P. nigra provides an important foundation for the development of commercial native trees for bioenergy and for advanced, molecular breeding in these species.

Electronic supplementary material: The online version of this article (doi:10.1186/s13068-016-0603-1) contains supplementary material, which is available to authorized users.

No MeSH data available.


QQ and Manhattan plots for the Q + K (optimal) models for the 3 traits with SNPs reaching genome-wide significance. Red and blue lines on Manhattan plots illustrate genome wide (α < 8.79 × 10−6) and putative (α < 1.76 × 10−4) significance levels, respectively. a QQ plot for Height-11 associated SNP on chromosome 7; b Manhattan plot for Height-11 association; c QQ plot for Height-13 associated SNP on chromosome 4; d Manhattan plot for Height-13 associated SNP; e QQ plot for CNPL-13 associated SNP on chromosome 13; f Manhattan plot for CNPL-13 associated SNP
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Fig8: QQ and Manhattan plots for the Q + K (optimal) models for the 3 traits with SNPs reaching genome-wide significance. Red and blue lines on Manhattan plots illustrate genome wide (α < 8.79 × 10−6) and putative (α < 1.76 × 10−4) significance levels, respectively. a QQ plot for Height-11 associated SNP on chromosome 7; b Manhattan plot for Height-11 association; c QQ plot for Height-13 associated SNP on chromosome 4; d Manhattan plot for Height-13 associated SNP; e QQ plot for CNPL-13 associated SNP on chromosome 13; f Manhattan plot for CNPL-13 associated SNP

Mentions: In no case was the simple model selected and in many cases this model saw a large number of false positives arising from the lack of population structure correction (see QQ plots in Additional file 1: Figure S10). Under the simple model the number of ‘significant’ associations ranged from 1 (SP-12) to 2908 (CNPL-13) with a mean of 1112. The number of such associations showed strong positive regression with trait heritability; F1, 13 = 31.14, p < 0.001, r2 = 0.706 (Additional file 1: Figure S11). The P-model was selected for 3 traits; the Q-model for 1 trait; the K-model for 3 traits and the Q + K model for the remaining 8. The P + K model was not selected for any traits and appeared to represent overfitting. Under these optimal models only 3 trait-marker associations reach genome-wide significance; 1 for Height-11, 1 for Height-13 and 1 for CNPL-13 (all Q + K model). Figure 8 displays Manhattan and QQ plots for these genome-wide significant associations. Table 4 shows the numbers of trait-marker associations for the optimal models at a range of significance thresholds.Fig. 8


Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)
QQ and Manhattan plots for the Q + K (optimal) models for the 3 traits with SNPs reaching genome-wide significance. Red and blue lines on Manhattan plots illustrate genome wide (α < 8.79 × 10−6) and putative (α < 1.76 × 10−4) significance levels, respectively. a QQ plot for Height-11 associated SNP on chromosome 7; b Manhattan plot for Height-11 association; c QQ plot for Height-13 associated SNP on chromosome 4; d Manhattan plot for Height-13 associated SNP; e QQ plot for CNPL-13 associated SNP on chromosome 13; f Manhattan plot for CNPL-13 associated SNP
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5017058&req=5

Fig8: QQ and Manhattan plots for the Q + K (optimal) models for the 3 traits with SNPs reaching genome-wide significance. Red and blue lines on Manhattan plots illustrate genome wide (α < 8.79 × 10−6) and putative (α < 1.76 × 10−4) significance levels, respectively. a QQ plot for Height-11 associated SNP on chromosome 7; b Manhattan plot for Height-11 association; c QQ plot for Height-13 associated SNP on chromosome 4; d Manhattan plot for Height-13 associated SNP; e QQ plot for CNPL-13 associated SNP on chromosome 13; f Manhattan plot for CNPL-13 associated SNP
Mentions: In no case was the simple model selected and in many cases this model saw a large number of false positives arising from the lack of population structure correction (see QQ plots in Additional file 1: Figure S10). Under the simple model the number of ‘significant’ associations ranged from 1 (SP-12) to 2908 (CNPL-13) with a mean of 1112. The number of such associations showed strong positive regression with trait heritability; F1, 13 = 31.14, p < 0.001, r2 = 0.706 (Additional file 1: Figure S11). The P-model was selected for 3 traits; the Q-model for 1 trait; the K-model for 3 traits and the Q + K model for the remaining 8. The P + K model was not selected for any traits and appeared to represent overfitting. Under these optimal models only 3 trait-marker associations reach genome-wide significance; 1 for Height-11, 1 for Height-13 and 1 for CNPL-13 (all Q + K model). Figure 8 displays Manhattan and QQ plots for these genome-wide significant associations. Table 4 shows the numbers of trait-marker associations for the optimal models at a range of significance thresholds.Fig. 8

View Article: PubMed Central - PubMed

ABSTRACT

Background: Second generation (2G) bioenergy from lignocellulosic feedstocks has the potential to develop as a sustainable source of renewable energy; however, significant hurdles still remain for large-scale commercialisation. Populus is considered as a promising 2G feedstock and understanding the genetic basis of biomass yield and feedstock quality are a research priority in this model tree species.

Results: We report the first coppiced biomass study for 714 members of a wide population of European black poplar (Populus nigra L.), a native European tree, selected from 20 river populations ranging in latitude and longitude between 40.5 and 52.1&deg;N and 1.0 and 16.4&deg;E, respectively. When grown at a single site in southern UK, significant Site of Origin (SO) effects were seen for 14 of the 15 directly measured or derived traits including biomass yield, leaf area and stomatal index. There was significant correlation (p&nbsp;&lt;&nbsp;0.001) between biomass yield traits over 3&nbsp;years of harvest which identified leaf size and cell production as strong predictors of biomass yield. A 12&nbsp;K Illumina genotyping array (constructed from 10,331 SNPs in 14 QTL regions and 4648 genes) highlighted significant population genetic structure with pairwise FST showing strong differentiation (p&nbsp;&lt;&nbsp;0.001) between the Spanish and Italian subpopulations. Robust associations reaching genome-wide significance are reported for main stem height and cell number per leaf; two traits tightly linked to biomass yield. These genotyping and phenotypic data were also used to show the presence of significant isolation by distance (IBD) and isolation by adaption (IBA) within this population.

Conclusions: The three associations identified reaching genome-wide significance at p&nbsp;&lt;&nbsp;0.05 include a transcription factor; a putative stress response gene and a gene of unknown function. None of them have been previously linked to bioenergy yield; were shown to be differentially expressed in a panel of three selected genotypes from the collection and represent exciting, novel candidates for further study in a bioenergy tree native to Europe and Euro-Asia. A further 26 markers (22 genes) were found to reach putative significance and are also of interest for biomass yield, leaf area, epidermal cell expansion and stomatal patterning. This research on European P. nigra provides an important foundation for the development of commercial native trees for bioenergy and for advanced, molecular breeding in these species.

Electronic supplementary material: The online version of this article (doi:10.1186/s13068-016-0603-1) contains supplementary material, which is available to authorized users.

No MeSH data available.