SNP Markers in Four Candidate Genes Associated with Recurrent Selection for Dry Matter Digestibility in Divergent Switchgrass Populations

Saccharification efficiency of switchgrass biomass is highly correlated with lignin concentration and lignin structure. Divergent selection for in vitro dry matter digestibility (IVDMD) in switchgrass, initiated in 1974 in Lincoln, NE, resulted 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 the association of polymorphisms in lignin biosynthesis pathway genes with recurrent selection for IVDMD in the divergent populations and to facilitate marker-assisted selection for improved switchgrass biomass quality. Four candidate genes encoding caffeic acid O-methyltransferase (COMT1 & COMT2), cinnamyl alcohol dehydrogenase (CAD2) and 4-coumarate:coenzyme A ligase 1 (4CL1) 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. About 200 SNP markers and insertions were identified within the 11-kb exon and intron regions, 26 of which were significantly associated with selection, over-and-above the effects of drift. To validate these results, 1400 individuals from the divergent populations were measured for cell wall traits in 2012 and 2013 and will be genotyped using the SNP markers from the four candidate genes. An association analysis between lignin concentration and candidate lignin genes in these individuals will be conducted.