GLBRC's Publications


Our researchers consistently turn out new and innovative research that can lead to publications and new technology. On this page we'll highlight new research publications and/or activities in the GLBRC that underscore the great work that our researchers are doing.

To explore the genetic architecture of flowering time, we developed a recombinant inbred line population from a cross between two diverse accessions of the grass Brachypodium distachyon that have different flowering behavior. We then used a genotyping-by-sequencing approach to identify six quantitative trait locis that control differences in flowering time.

We performed genome-wide association studies to characterize the genetic architecture and genes underlying flowering time regulation in switchgrass. We then identified association with flowering time at multiple loci, including in a homolog of the gene FLOWERING LOCUS T and in a locus containing the gene TIMELESS, a homolog of a key circadian regulator in animals.

We collected sorghum stem RNA-seq transcriptome profiles and composition data for approximately 100 days of development beginning at floral initiation. Our analysis identified more than 200 differentially expressed genes involved in stem growth, cell wall biology, and sucrose accumulation.

The production of fuels from lignocellulosic biomass can play an important role in reducing our dependence on fossil fuels while meeting an increasing energy demand. In an effort to meet these goals, regional biomass processing depots have been introduced as a way to improve the biomass supply network.

Excess sugars made during periods of drought are converted to inhibitors during biomass pretreatment.

The electrochemical oxidation of alcohols is a major focus of energy and chemical conversion efforts, with potential applications ranging from fuel cells to biomass utilization and chemical synthesis. 

Formaldehyde addition during biomass pretreatment leads to near-theoretical yields of lignin monomers.  

With a sensitive analytical method for diagnostically detecting incorporation of chemically labile ester bonds introduced into lignin polymers by augmenting the prototypical monomers with monolignol ferulate conjugates (“zip monomers”), we reexamined the lignin of three plants known to produce such conjugates in their extractives and found that these plants also used monolignol ferulate conjugates in their lignification. This discovery prompted a survey of a set of plants representing spermatophytes or “seed plants,” including 13 gymnosperms and 54 angiosperms.  

A stress-tolerant yeast strain was evolved for enhanced xylose utilization under aerobic or anaerobic growth conditions, the causative mutations identified by whole-genome sequencing, and systems-level effects of the mutations on cellular metabolism were analyzed. Rapid xylose utilization was found to be dependent upon genetic interactions among four genes, uncovering a surprising connection between Fe-S cluster assembly and cell signaling that facilitates aerobic respiration and anaerobic fermentation of xylose. 

We measured soil N2O emissions, CH4 uptake, NO3- leaching, and soil organic carbon accumulation for switchgrass under various N fertilizer rates over a three-year period after establishment. We found for annual N2O emissions by fertilizer rate an exponential increase that was stronger every year, and also that switchgrass yields became less responsive each year to N fertilizer. Nitrate leaching also increased exponentially in response to added N, but methane uptake and soil organic carbon didn’t change detectably. Overall, N fertilizer inputs at rates greater than crop need curtailed the climate benefit of ethanol production almost two-fold, from a maximum mitigation capacity of −5.71 ± 0.22 Mg CO2e ha−1 yr−1 in switchgrass fertilized at 56 kg N ha−1 to only −2.97 ± 0.18 Mg CO2e ha−1 yr−1 in switchgrass fertilized at 196 kg N ha−1. Minimizing N fertilizer use will be an important strategy for fully realizing the climate benefits of cellulosic biofuel production.

The flowering of many plant species is coordinated with seasonal environmental cues such as temperature and photoperiod. In winter wheat and barley, three genes – VRN1, VRN2, and FT – form a regulatory loop that regulates the initiation of flowering. Here, we test whether the circuitry of this regulatory loop is conserved across Pooid grasses. Our studies reveal that some aspects of the regulatory loop, such as the cold repression of VRN2, are unique to wheat and barley. However, this study, as well some of our previous work, demonstrates that VRN2 is a repressor of flowering that functions broadly in grasses from rice to Brachypodium, and thus VRN2 is a target for fine tuning of flowering in grass biofuel crops. 

This study assessed the possibility of producing reliable predictions for genomic selection using a small sample size of two different switchgrass populations genotyped by exome sequencing and tested in two different locations for three important agronomic traits: biomass yield, plant height, and heading date (flowering time). We assessed various prediction procedures, differing by prediction model and also by type of marker-data transformation. 

This study aimed to elucidate the incorporation pathways of tricin into maize lignin by applying liquid chromatography-mass spectrometry-based tools developed for oligolignol profiling. Twelve tricin-containing products (each with up to eight isomers) were observed and authenticated by comparisons with a set of synthetic tricin-oligolignol dimeric and trimeric compounds. 

As a feedstock for biomass-to-biofuel processes, woody biomass exhibits several advantages that facilitate logistics relative to herbaceous feedstocks, including year-round availability and high bulk density. As we envision biomass-to-biofuel processes that include diverse biomass feedstocks, the physical and chemical properties of said biomass will have an important impact on the conversion process.   

Lignocellulosic crop residues are a promising alternative feedstock for producing liquid fuels and chemicals for modern biobased economies, and biochemical conversion of lignocellulosic biomass to liquid fuels requires pretreatment and enzymatic hydrolysis of the biomass to yield fermentable sugars. To compete with traditional refineries, biorefineries must achieve high carbohydrate-to-fuel yields with low enzymatic input and facilitate lignin valorization to co-products extending beyond simply using lignin to generate heat and power. Most pretreatment processes require high enzymatic loadings to achieve higher sugar yields under industrially-relevant conditions.

In order to determine the structural basis for stereospecificity of bacterial enzymes involved in lignin bond cleavage, crystal structures of the enzymes involved were solved and the corresponding biochemical analyses for these proteins were performed. The detailed structural and biochemical characterization of LigE and LigF in this study, and the corresponding detailed structural and biochemical characterization of other members of this lignin degradation pathway (LigD, LigO, LigL, and LigG) in a second study, reveal important new aspects of the enzyme mechanisms and the determinants of substrate specificity.

To gain insight into how Bayberry fruits produce the highest amount of surface lipid known in nature, the authors examined the chemical and morphological development of the Bayberry wax layer, monitored its biosynthesis through radiolabeling studies, and identified transcripts for enzymes and proteins expressed during Bayberry surface wax production. The biochemical and expression data together indicate that Bayberry surface glycerolipids are synthesized by a pathway for triacylglycerol synthesis that is related to cutin biosynthesis, rather than conventional triacylglycerol assembly.

The method to deconstruct lignocellulosic biomass using ionic liquids (ILs) is a promising technology that can bypass expensive enzymatic pretreatments that are commonly used. A potential limitation to adoption of ILs for bioconversion is that residual IL solvent is toxic to microbes and can impede fermentation of biomass to biofuels. A technique called chemical genomics was used to identify yeast genes that confer sensitivity or resistance to IL, allowing researchers to identify a cellular substructure called the mitochondrion as the apparent target of IL toxicity. Targeted deletion of a gene identified from the chemical genomics screen in a xylose-fermenting strain of yeast greatly increased its IL tolerance, biomass-derived sugar conversion, and yields of ethanol.

The enzymatic hydrolysis of plant cell wall material is a formidable task due to its complexity. Enzyme cocktails containing multiple classes of polysaccharide-degrading enzymes are used in several existing cellulosic ethanol plants to hydrolyze plant biomass into fermentable sugars. These enzymes are classified into families in the carbohydrate active enzyme (CAZy) database, and they include glycoside hydrolases (GHs), pectic lyases (PLs), carbohydrate esterases (CEs), and others. Due to several experimental limitations, only a small fraction of the enzymes included in CAZy have a function assigned by biochemical analysis.

Lignin, a complex polyphenolic constituent of plant secondary cell walls, is one of the most abundant biopolymers on the planet and is an immensely important global carbon sink. The chemical recalcitrance of lignin, however, poses a major challenge for industrial biomass processing, most notably in pulp and paper production and in the emerging cellulosic biofuels industry.