ARPA-E announces $30M funding opportunity for energy crop development

October 1, 2014 | Jim Lane

In Washington, the Advanced Research Projects Agency (Energy) announced a $30 million funding opportunity entitled Transportation Energy Resources from Renewable Agriculture, or TERRA.

ARPA-E is making up to $30 million available for the TERRA program to develop automated, predictive and systems-level approaches to enable the quick and easy identification of traits that can be leveraged to increase biomass yield through accelerated breeding cycles.

ARPA-E’s TERRA program seeks to develop technologies that can increase the precision, accuracy and throughput of energy crop breeding to enable predictive algorithms for plant growth, more detailed measurements of plant physiology and more sophisticated bioinformatics for gene discovery and trait association.

The project sponsors write:

There is an urgent need to accelerate energy crop development for the production of renewable transportation fuels from biomass.

Increasing the nation’s capacity to produce better bioenergy crops will help to alleviate many of the challenges presently faced by current biofuel feedstock. Biofuels may serve as a promising alternative to fossil fuels — especially for the transportation sector. They are a sustainable energy source, can be grown in the U.S. and have the potential to mitigate greenhouse gas emissions.

The technical challenge

Recent technological advancements have made it possible to extract large volumes of data from a variety of crops; however, even with these resources the data cannot yet be processed into the knowledge needed to predict performance in the field. Increased information and analytics could improve crop yields to help lower the cost of biofuel production.

Building upon precision agriculture innovations and data-intensive computational approaches, ARPA-E believes that it is now possible to accelerate plant breeding, using robust high-throughput precision phenotyping.

What is a phenotype, anyway?

[Note for newer readers: A phenotype is an observable or measurable physical trait, such as color, height, size, shape, behavior or chemical composition. Phenotype is determined by the individual’s genotype, the information encoded in the DNA polymers present in its genome, as well as how that genome interacts with the environment. Phenotyping is the measurement of phenotypes, a process that can require substantial effort and may be highly dependent on data interpretation by a plant breeder. The development of advanced plant phenotyping technologies is substantially behind that of genotyping, and thus poses a key bottleneck on the path toward increased bioenergy crop yields. While agriculture has the capability to increase biomass yields and mitigate the effects of anthropogenic greenhouse gas emissions, the slow pace of conventional breeding limits this capability.]

Why is phenotype critical?

As Donald Danforth Plant Science Center president Dr. James C. Carrington told the Digest in 2011:

“The big arching question? In this age of genomic science, when we can sequence, in days, thousands of variants: how does genomic structure relate to phenotype. Genotype to phenotype, that’s the biggest, broadest question out there in plant biology. What are the genetic traits than confer yield, drought resistance, flood tolerance, more efficient in using nitrogen, phosphorus and potassium. We don’t understand that nearly enough.

“Take a phenotype into two different environmental conditions. There’s a different time to flower, different time to granulate. The interactions of genotypes are causing different phenotypes.”

The mission

TERRA will enable breeders to evaluate more individual plants, to select appropriate plants for breeding earlier in the growing season, to capture better information about them during their development, and to associate this information with the best genes to propagate. Success will be measured by the prospective ability to predict yield gains early, specifically, to identify which genes can improve carbon capture efficiency in newly cultivated bioenergy crops. Although other crops will be considered, this program intends to focus on energy sorghum as a model system because of its potential for improvement through breeding, its resources for genetic analysis, its geographic adaptability, and its commercial utility.

ARPA-E seeks to establish multidisciplinary teams to leverage advancements in sensor technologies, computational analytics and low-cost nucleotide sequencing. It is the objective of the program to establish the key intermediate phenotypes related to yield, that can be collected with enough accuracy to predict the growth of an individual plant or population of plants of a particular genetic makeup, and to do so across a high volume (multiple thousands of breeder plots) at the field level.

“The realization of commercially viable agriculture for energy purposes requires unprecedented increases in productivity and resource use efficiency.”

ARPA-E relates:

In 2013, 36% of U.S. energy consumption was from petroleum, producing 42% of its energy-related carbon dioxide emissions.1 Thus, the more rapid development of transportation fuels with decreased, neutral, or negative carbon emissions is required to reduce the amount of foreign oil imports and limit the rate of increase of CO2 in the atmosphere, addressing two of ARPA-E’s core missions.

Economical production of the large amounts of biomass needed to displace petroleum will require significant productivity and efficiency improvements from the agricultural sector, which is also responsible for human and animal nutrition. In 2014, the United Nations warned that world agriculture must increase its output 60% by 2050 (1.6% per year, on average) to support global population growth and economic development.

A conventional breeding approach takes many years to improve crop varieties. The rate of crop improvement through breeding is strongly correlated to technology, increasing with better and more complete field data, i.e. the precision and accuracy of trait measurements and the throughput of screening. The ability to rapidly identify plants in a breeding population with desirable traits will increase the rate of genetic gain of the crop and improve the yield of bioenergy from agriculture.

Hall and Richards report that the annual genetic gain for the main cereal crops best varieties and hybrids falls well below 1.16–1.31% per year and are not able to satisfy projected growing demand. Consequently, the realization of commercially viable agriculture for energy purposes requires unprecedented increases in productivity and resource use efficiency.