Genomics-Enabled Improvement of Andropogoneae Grasses as Feedstocks for Enhanced Biofuel Production

Lead Project PIs: Stephen Moose (PI), Matt Hudson and Ray Ming
Lead Campus: UC-Berkeley and Joint Genome Institute

An economically viable and sustainable renewable fuels industry will require significant increases in global production of cellulosic biomass.  The majority of this biomass is projected to be obtained from agricultural sources.  A wide variety of plant species have been proposed as potential feedstock crops.  Among these, crop species within the Andropogoneae tribe emerge as leading candidates because they perform C4 photosynthesis, which exhibits the highest efficiencies of carbon fixation, water use, and nitrogen economy.  Maize (Zea mays L.), sugarcane (Saccharum spp.), and Sorghum are established and highly productive biomass crops that collectively are cultivated across the global spectrum of agricultural production environments.  Increased yields from these crops have already helped meet rising world demand for edible carbohydrates and created surpluses that now support starch and sugar conversion to ethanol.  Miscanthus also shows promise as a leading feedstock crop, based on its exceptional biomass yields with minimal production inputs in recent European and U.S. field trials.  Each of these closely related Andropogoneae grasses also offer complementary advantages in their forms of harvestable carbon, adaptation to diverse climates, genetics resources, genomic information, and functional genomics tools. 

The above four crops (and others) will be preferred fuelstocks in specific climates and production systems.  However, Saccharum and Miscanthus species possess additional advantages that suggest they will become a leading source of cellulosic biomass in global biofuel production.  Unlike maize and sorghum which are annual crops, Saccharum and Miscanthus are perennials that require much lower production inputs.  In addition to sugarcane cultivars that have been selected for maximum sugar yields, “energy canes” derived from interspecific crosses of Saccharum officianarum  with S. spontaneum have already produced biomass yields in excess of 50 Mg/ha in some trials.  The sterile and non-invasive Miscanthus x giganteus (Mxg) hybrid cultivar performs cold-tolerant photosynthesis that extends the season for biomass accumulation, and extensive nutrient remobilization by rhizomes results in a very high proportion of insoluble carbohydrates in harvested biomass that are more stable in storage compared to sugars.  Furthermore, although maize grain will continue to be the major fuelstock for the U.S. ethanol industry and maize stover will initially be a significant source of cellulosic biomass; concerns have been raised about the diversion of major food and feed crops (e.g. maize and sorghum) to fuel production and a decline in soil quality after extensive stover removal.  

Though the Andropogoneae crop species are already contributing to the production of renewable energy, none possess the full complement of traits desired for cellulosic fuelstocks. Opportunities exist to increase harvestable carbon yields, improve the efficiency of conversion to biofuels, and enhance tolerance to abiotic stress or pathogen attack.  During the 20^th century, innovations such as plant breeding, quantitative genetics, molecular markers, and biotechnology contributed to the improvement of maize, sorghum and sugarcane.  Recent advances in genomics and functional genomics enable rapid and cost-effective approaches to obtain information about genes and their expression, leading to greater efficiency and precision of genetic improvements.  In contrast to well-developed genomics resources for maize and sorghum, available genomics tools for Saccharum are limited and essentially no information exists for Miscanthus, which presents a unique opportunity to initiate a crop improvement effort with the benefit of genomics knowledge. 

The primary goal of this program proposal is to build the information and resources necessary to enable genomics-driven improvement of Andropogoneae fuelstock crops. Our efforts will focus on Saccharum and Miscanthus, where current information is most limiting and the potential for research impact is greatest.

This program proposes six integrated activities that will employ the latest tools of genomic science to rapidly advance Saccharum and Miscanthus biology and identify genes with utility in improving cellulosic biomass yields and quality:

1. We will conduct deep sequencing of the Miscanthus transcriptome, including noncoding RNAs and directed re-sequencing of low-abundance transcripts, to characterize its complement of expressed genes;

2. We will obtain draft genome sequences for Miscanthus and Saccharum, using newly developed high-throughput sequencing technologies and assembly methods guided by comparisons to available genome sequences from sorghum and maize;

3. We will develop genome-scale expression profiling platforms for Miscanthus and Saccharum and use these platforms to identify candidate genes associated with biomass yield, quality, and sustainability.

4. We will assess genetic diversity within Miscanthus and Saccharum to assist development of appropriate populations for genetic improvement;

5. We will identify molecular markers for high-density genetic mapping in Miscanthus and Saccharum, and associate marker genotypes with phenotypes that contribute to biomass yield and composition in structured genetic populations. 

6. We will assemble information from the above and related efforts into an integrated bioinformatics system to facilitate investigations of gene structure and function.

We expect that the first phase of this Program will deliver sequences for most of the expressed genes of Saccharum and Miscanthus, thousands of functional genetic markers, a perspective on genetic diversity, robust tools for functional genomics, and characterization of gene expression changes associated with processes important for biomass accumulation, composition, and sustainability.  These datasets will provide the toolbox for both basic and applied studies of Saccharum and Miscanthus biology, as well as their close relatives Sorghum and maize.  Through our collaborations with Saccharum and Miscanthus breeders, we will also initiate the application of this information in a predictive genome-scale approach to improving biomass yields and conversion efficiency for these fuelstock crops. Furthermore, we will educate and train a cadre of young scientists that will be well-positioned to further expand the Andropogoneae grasses not only as a premier model for plant comparative genomics, but also as leading fuelstock species for a wide range of production environments.