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

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°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.


Map illustrating the nations and major river locations from which the P. nigra association population is drawn and the colours employed to illustrate these nations in subsequent figures
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Fig1: Map illustrating the nations and major river locations from which the P. nigra association population is drawn and the colours employed to illustrate these nations in subsequent figures

Mentions: The P. nigra population [54, 63, 64] is a wide, natural population of more than 1000 diverse genotypes drawn from riparian ecosystems across Western Europe; namely France, Italy, Spain, Germany, Netherlands and Hungary [39, 65]. Cuttings taken from mature trees in situ were established and propagated in a stool bed at INRA, UAGPF, Orléans and ramets from this stool bed, established for more than 5 years, were cut and established for this work in a field trial (common garden) in Northington, south-east UK; (51°12′N, 1°21′E) in 2009. It is possible that sites of propagation can significantly influence structural and functional aspects of the genome in clonally propagated Populus, including response to drought stress [66]. In this study, however, sourcing all plant material for this trial from a stable, well established stool bed should act to minimise this variation, although it cannot be entirely ruled out. Such effects may otherwise bias estimates of heritability, inter-trait correlations and genetic potential in common garden experiments [67]. 931 genotypes (714 genotyped on the Illumina array representing 20 sampled sites) were planted at 0.80 × 0.80 m spacing in double rows, spaced by 3 m. The site was laid out in six fully replicated, randomised blocks with 4 rows per block and a double row of guards surrounding the site as a whole. Trees were coppiced to 5 cm in February 2010 and 2013 and received mechanical weed control as required. No fertiliser was applied at any time or irrigation post establishment, although trees were irrigated in 2009. The latitude and longitude of the sampled subpopulations and their sample sizes (n) are provided in Table 1; a map of the region from which the population is drawn is shown in Fig. 1.Table 1


Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)
Map illustrating the nations and major river locations from which the P. nigra association population is drawn and the colours employed to illustrate these nations in subsequent figures
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5017058&req=5

Fig1: Map illustrating the nations and major river locations from which the P. nigra association population is drawn and the colours employed to illustrate these nations in subsequent figures
Mentions: The P. nigra population [54, 63, 64] is a wide, natural population of more than 1000 diverse genotypes drawn from riparian ecosystems across Western Europe; namely France, Italy, Spain, Germany, Netherlands and Hungary [39, 65]. Cuttings taken from mature trees in situ were established and propagated in a stool bed at INRA, UAGPF, Orléans and ramets from this stool bed, established for more than 5 years, were cut and established for this work in a field trial (common garden) in Northington, south-east UK; (51°12′N, 1°21′E) in 2009. It is possible that sites of propagation can significantly influence structural and functional aspects of the genome in clonally propagated Populus, including response to drought stress [66]. In this study, however, sourcing all plant material for this trial from a stable, well established stool bed should act to minimise this variation, although it cannot be entirely ruled out. Such effects may otherwise bias estimates of heritability, inter-trait correlations and genetic potential in common garden experiments [67]. 931 genotypes (714 genotyped on the Illumina array representing 20 sampled sites) were planted at 0.80 × 0.80 m spacing in double rows, spaced by 3 m. The site was laid out in six fully replicated, randomised blocks with 4 rows per block and a double row of guards surrounding the site as a whole. Trees were coppiced to 5 cm in February 2010 and 2013 and received mechanical weed control as required. No fertiliser was applied at any time or irrigation post establishment, although trees were irrigated in 2009. The latitude and longitude of the sampled subpopulations and their sample sizes (n) are provided in Table 1; a map of the region from which the population is drawn is shown in Fig. 1.Table 1

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°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.