The lignin content of biomass can impact the ease and cost of biomass processing. Lignin reduction through breeding and genetic modification therefore has potential to reduce costs in biomass-processing industries (e.g. pulp and paper, forage, and lignocellulosic ethanol). We investigated compositional changes in two low-lignin alfalfa (Medicago sativa) lines with antisense down-regulation of p-coumarate 3-hydroxylase (C3H) or hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyltransferase (HCT). We investigated whether the difference in reactivity during lignification of 4-coumaryl alcohol (H) monomers versus the naturally dominant sinapyl alcohol and coniferyl alcohol lignin monomers alters the lignin structure. Sequential base extraction readily reduced the H monomer content of the transgenic lines, leaving a residual lignin greatly enriched in H subunits; the extraction profile highlighted the difference between the control and transgenic lines. Gel permeation chromatography of isolated ball-milled lignin indicated significant changes in the weight average molecular weight distribution of the control versus transgenic lines (CTR1a, 6000; C3H4a, 5500; C3H9a, 4000; and HCT30a, 4000).The advent of large-scale liquid fuel production from biomass has served to highlight how difficult it is to commercially process biomass effectively and efficiently. Much of the difficulty is due to the recalcitrant nature of lignocelluloses (1), a complex interlinking structure composed of cellulose, hemicelluloses, and lignin that makes up the bulk of terrestrial biomass. Accessibility to the cell wall is influenced by lignin, which provides structural integrity to the cell wall. Both total lignin content and lignin monomer composition may impact the ease with which biomass is processed. This study examines whether lignin molecular weight is altered by changing the lignin monomer composition and if these changes affect the ease with which lignin can be removed by chemical processing.Three monomers (Fig. 1), 4-coumaryl alcohol (H), 2 coniferyl alcohol (G), and sinapyl alcohol (S), polymerize in what is thought to be a combinatorial fashion to form the bulk of the lignin polymer (2, 3). The amount of each unit depends on the species, age, cell type, and tissue type (4, 5). The presence of each additional methoxy group on a lignin unit results in one less reactive site (S Ͻ G Ͻ H) and therefore fewer possible combinations during the polymerization reaction. For example, the S unit has no vacant 5-position; therefore 5,5Ј-cross-linking is unavailable for lignin S subunits. As a result, lignin rich in S subunits is more easily depolymerized than lignin rich in G subunits.The relative level of S and G lignin subunits is expressed as the S/G ratio, an important measurement used in the assessment of biomass. H lignin subunits are present in low levels in natural materials (4.9% of lignin in wild-type alfalfa (1) and 0.8% in Norway Spruce (6)); consequently, less is known about lignin high in H subunits and its impact on biomass processing. I...