Populus trichocarpa natural variants as feedstocks for biofuel production

Fuels developed from lignocellulosic biomass offer a potential renewable and clean alternative to conventional fossil-fuel-based energy sources. Populus is one of DOE’s “flagship” plant species that is of special interest as a biofuel feedstock. However, there are still significant biological and technological barriers that need to be overcome in order to achieve cost-effective, sustainable production and conversion systems for Populus biomass into biofuels. In particular, plant cell wall recalcitrance poses tremendous challenges for Populus feedstock to become economically competitive. We took a forward genetics approach by screening a population of 1,100 Populus trichocarpa natural variants for enhanced sugar release and ethanol production phenotypes using the Separate Hydrolysis and Fermentation system. Further screens for uncompromised biomass productivity phenotypes in these candidates resulted in several elite natural variants that have superior sugar release and ethanol production phenotypes with better biomass productivity than population average. Using fully-resequenced 1,100 Populus trichocarpa genomes, SnpEff was applied to predict high-impact single nucleotide polymorphisms (SNPs) resulting in gain/loss stop codon, frame-shift, splice site changes (donor or acceptor), or loss of start codon in these elite natural variants. It was found that a number of genes relevant to cell wall biosynthesis possess homozygous high-impact SNPs in these variants. This was further confirmed by RNA sequencing-based gene expression profiling. We propose that the observed phenotypes are caused by a combination of these high-impact SNPs. Thus, these variants represent a “natural stacking” of genes involved in cell wall biosynthesis and are excellent targets for biofuel production.