Saccharification efficiency of switchgrass biomass is highly correlated with lignin concentration and lignin structure. Divergent selection for in vitro dry matter digestibility in switchgrass was initiated in 1974 by Kenneth P. Vogel, USDA-ARS, Lincoln, NE, resulting in seven divergent populations with very distinct IVDMD, sugar release efficiency, lignin concentration and other cell wall traits. The objectives of this project are to identify single-nucleotide polymorphic (SNP) markers associated with low lignin concentration in the divergent populations and to facilitate marker-assisted selection for improved switchgrass biomass quality. Candidate genes encoding the important enzymes in the lignin biosynthesis pathway were sequenced in the divergent populations to identify SNP markers. The effects of selection and genetic drift on allele frequency changes were mathematically separated to identify SNP markers under selection pressure. A total of 60 SNP markers were identified within the exon and intron regions of caffeic acid O-methyltransferase (COMT), 3 of which were significantly associated with selection, over-and-above the effects of drift. To validate these results, a total of 1400 individuals from the divergent populations will be genotyped using SNP markers and cell wall traits will be measured in summer 2012. A theoretical analysis of marker-assisted selection for reduced lignin or altered lignin structure in these individuals will be conducted. The allele-specific expression levels of the candidate genes will also be analyzed to further understand the genetics of differences in lignin characteristics of switchgrass.