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

Abstract

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

Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus

“…4c). Despite the relatively larger population size ( n = 732) when compared to populations used in previous GWAS in forest trees (typically between ~300 and ~700 individuals), our results are consistent with the fact that very few associations were also found for growth in all those reported GWAS to date [52–59]. Population sizes used have been small, such that experiments have suffered from low power to detect the likely large number of small effect loci controlling growth.…”

“…Population sizes used have been small, such that experiments have suffered from low power to detect the likely large number of small effect loci controlling growth. Integrating linkage mapping data from bi-parental pedigrees with association populations has been attempted but results have not improved and only a handful of associations have been found, again explaining very little of the genetic variation [56, 57, 59]. Our direct comparison between GS and GWAS is novel and more explicitly corroborates the fact that while genome-wide regression is able to account for large proportions of the pedigree-heritability (e.g.…”

Independent and Joint‐GWASfor growth traits inEucalyptusby assembling genome‐wide data for 3373 individuals across four breeding populations

“…Various studies attempted GWAS for growth traits in forest trees, namely in Populus (Porth et al ., ; Allwright et al ., ; Du et al ., ; Fahrenkrog et al ., ), Pinus (Bartholomé et al ., ; Lu et al ., ) and Eucalyptus (Cappa et al ., ; Müller et al ., ; Resende et al ., ). Despite the considerably large number of individuals used in our study for each population and for the combined dataset, our results suggested that much larger numbers will be necessary to identify discrete regions capturing larger fractions of the genetic variance of complex traits as indicated by simulations (Spencer et al ., ; Visscher et al ., ).…”

Impact of RAV1-engineering on poplar biomass production: a short-rotation coppice field trial

“…Recent advances have been made in the identification of putative loci underlying phenotypic variation of growth- and development -related traits. These works explored natural genetic variation by means of QTLs [11] genome-wide association studies (GWAS), from populations of Populus species growing in common gardens [12–14], and as SRC [15]. …”