Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.).
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.
Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK.
Mike Robert
MR
Allwright
Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK.
Adrienne
A
Payne
CNR-IVALSA, Sesto Fiorentino, via Madonna del Piano, 10, 50019 Sesto Fiorentino, FI Italy.
Giovanni
G
Emiliani
Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK.
Suzanne
S
Milner
Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK.
Maud
M
Viger
Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK.
Franchesca
F
Rouse
Laboratory of Genetics, Wageningen University and Research, 6708PB Wageningen, The Netherlands.
Joost J B
JJ
Keurentjes
US1279 EPGV, CEA-IG/CNG, INRA, 91057 Evry, France.
Aurélie
A
Bérard
Georg-August-Universität Göttingen, 37077 Göttingen, Germany.
Henning
H
Wildhagen
US1279 EPGV, CEA-IG/CNG, INRA, 91057 Evry, France.
Patricia
P
Faivre-Rampant
Georg-August-Universität Göttingen, 37077 Göttingen, Germany.
Andrea
A
Polle
Dipartimento di Scienze agroalimentari, ambientali e animali, Università di Udine, Via delle Scienze 206, 33100 Udine, Italy ; Istituto di Genomica Applicata (IGA), via J. Linussio 51, 33100 Udine, Italy.
Michele
M
Morgante
Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK.
Gail
G
Taylor
Genetics; Leaf area; Lignocellulosic; Salicaceae; Short rotation coppice (SRC); Yield