The investigation of genetic variation in candidate genes from the lignin biosynthesis pathway. Alfalfa (Medicago sativa) is a commonly used forage crop. M. truncatula provides genomic sequence data to design primers that can be used in M. sativa to amplify its genes to determine the amount of sequence variation. This project consisted of investigating candidate genes for SNPs (single nucleotide polymorphism) that may associate with phenotypes of interest: 1.) Lignin, hemicellulose, cellulose content and 2.) Total above-ground biomass and regrowth.

Lignin content can influence biofuel performance and forage quality. By manipulating the lignin composition of alfalfa cell walls, can improve digestibility of alfalfa for animals. Is there any genetic variation in candidate genes and will SNPs found in lignin biosynthesis genes associate with phenotypic differences in yield and chemical composition of stems? I design primers based on M. truncatula genomic sequence or M. sativa coding sequences for the genes CCR, CAD, C4H, C3H in the lignin biosynthesis pathway. Amplified genes from several templates and 13 sets of sequences were produced. Screened accessions of medicago with C3H23 forage quality primer. After aligning my sequences, 2 SNPs (single nucleotide polymorphisms) were found. This finding raised more questions for this project and what is next for this project, if any of the SNPs found associate with the phenotypic data that is provided to the lab from our collaborators at University of Georgia. Determining this association can determine the phase of heterozygous individuals and the extent of linkage disequilibrium in candidate genes. This discovery can lead to the use of alfalfa as a biofuel crop.