Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Deciphering the Genetic Basis of S/G Lignin Variation in Switchgrass through QTL Mapping and Transgenic Approaches


Jianxin Zhao1,4, Katrien M. Devos1,4* (, Winnie Gimode1,4, Anne E. Harman-Ware2,4, Fang Chen3,4, Tom H. Pendergast IV1,4, and Gerald A. Tuskan4


1University of Georgia; 2National Renewable Energy Laboratory; 3University of North Texas; and 4Center for Bioenergy Innovation



The Center for Bioenergy Innovation (CBI) vision is to accelerate domestication of bioenergy-relevant, nonmodel plants and microbes to enable high-impact innovations along the bioenergy and bioproduct supply chain while focusing on sustainable aviation fuels (SAF). CBI has four overarching innovation targets: (1) Develop sustainable, process-advantaged biomass feedstocks, (2) Refine consolidated bioprocessing with cotreatment to create fermentation intermediates, (3) Advance lignin valorization for biobased products and aviation fuel feedstocks, and (4) Improve catalytic upgrading for SAF blendstocks certification.


Switchgrass (Panicum virgatum) is being domesticated as a sustainable bioenergy crop due to its wide adaptability, high yield, and low agricultural inputs. Life cycle analysis (LCA) has shown that, overall, feedstock yield is the main driver of fuel cost. When only considering the highest yielding accessions, however, biomass quality becomes an important player in biofuel yield and, hence, cost. Because the lignin S/G ratio may affect ethanol production as well as lignin monomer yields, researchers determined lignin monomeric composition using both pyrolysis molecular-beam mass spectrometry (pyMBMS) and thioacidolysis in an F2 population derived from a cross between the lowland genotype AP13 and the upland genotype VS16 (Qi et al. 2021). Quantitative trait locus (QTL) mapping for the S/G lignin ratio obtained using both methods identified colocalizing QTL on chromosome 9N. The 9N QTL region harbors the genes PvBLH6, which encodes a BEL1-like homeodomain protein 6 transcription factor, and PvKNAT1, a member of the Arabidopsis TALE homeodomain transcription  factor  family.  In Arabidopsis, BLH6 has been shown to interact with KNAT7 to affect secondary cell wall biosynthesis, including lignin content (Liu et al. 2014). Because lignin content was affected in the knat7 and blh6 knat7 loss-of-function mutants but not in the blh6 mutant, researchers transformed the AP13 (PvKNAT1AP13) and VS16 (PvKNAT1VS16) alleles of PvKNAT1, which differed by several nonsynonymous single nucleotide polymorphisms (SNPs), into a knat1-null Arabidopsis mutant. PvKNAT1VS16 but not PvKNAT1AP13 rescued the phenotype of the knat1 null mutant. These data suggest that only PvKNAT1VS16 is functional. T3 transgenic Arabidopsis plants homozygous for the presence of PvKNAT1VS16 and PvKNAT1AP13 are being grown for assessment of the lignin S/G ratio. The study demonstrates how combining genetic mapping in switchgrass with transgenic analyses in Arabidopsis can help uncover critical variants in genes contributing to traits of importance to the bioeconomy.


QTL on chromosome 9N for lignin SG ration


Liu, Y., et al. 2014.BEL1-LIKE HOMEODOMAIN6 and KNOTTED ARABIDOPSIS THALIANA7 Interact and Regulate Secondary Cell Wall Formation via Repression of REVOLUTA,” Plant Cell 26, 4843–61. DOI:10.1105/tpc.114.128322.

Qi, P., et al. 2021. “Quantitative Trait Locus Mapping Combined with Variant and Transcriptome Analyses Identifies a Cluster of Gene Candidates Underlying the Variation in Leaf Wax Between Upland and Lowland Switchgrass Ecotypes,” Theor Appl Genet 134, 1957–75. DOI:10.1007/s00122-021-03798-y.

Funding Information

Funding was provided by the Center for Bioenergy Innovation (CBI) led by Oak Ridge National Laboratory. CBI is funded as a U.S. Department of Energy Bioenergy Research Centers supported by the Office of Biological and Environmental Research in the DOE Office of Science under FWP ERKP886. Oak Ridge National Laboratory is managed by UT- Battelle, LLC for the U.S. Department of Energy under contract no. DE-AC05-00OR22725.