Developing Sorghum as A Dedicated Energy Crop

Posted on January 1st in articles

Developing Sorghum
as A Dedicated Energy Crop

Advances in DNA marker assisted breeding has created a perfect storm for the development of new, efficient and cost-effective feedstocks

As biofuel conversion technologies continue to advance, ever more emphasis is being placed on the feedstocks these processes will use. Ultimately, feedstock is the single largest cost driver for biofuels and, in many cases, the main barrier to cost competitiveness and scalability.
Enabling a substantial reduction in petroleum use for liquid fuels will require a variety of different types of biomass. Sorghum is emerging as an ideal candidate to meet a great portion of the biofuel industry’s growing needs. In addition to sorghum’s tremendous yield potential, it is also naturally tolerant to drought and heat and requires less fertiliser than corn, allowing it to be grown in areas with marginal rainfall, higher temperatures and with lower inputs.

Classical vs. Marker Assisted Breeding for recurrent backcrossing scheme. Classical Breeding Approach (left panels); Two parents are crossed to produce an F1 hybrid. The F1 is ‘back crossed’ to the desired parent background (P1) to select plants that most closely resemble the P1 parent but also contain a desired trait from P2. Marker Assisted Breeding Approach (right panels); The same backcrossing strategy is used but DNA markers are used to select for the chromosome region of interest from P2 (red line) while at the same time selecting for Parent 1 genome in all regions outside of the desired trait. DNA Marker analysis allows the selection of one individual with desired gene and little P2 genome for next cycle of backcrossing. White and black bars represent chromosomes and recombined chromosomes of Parent 1 and Parent 2

Sorghum’s relatively short growing season also makes it suitable for areas in colder climates with fewer growing days or for use in crop rotation systems. Sweet sorghum is a variety of sorghum with high sugar content in its stalk. It can be used as a complement to sugarcane in existing Brazilian sugar to ethanol mills, and as a feedstock for advanced biofuels and other bio-based products produced from sugars. High biomass sorghum is a highyielding crop that can be used as a feedstock for biopower and cellulosic biofuels.

One of sorghum’s most attractive characteristics is its potential for genetic improvement tailored to energy related uses. Compared to corn or soya, little effort has gone into the breeding and improvement of sorghum and, due to a variety of historically quirks, this is especially true for sweet and high biomass varieties. At the same time, as a seed propagated annually that has already been successfully hybridised, sorghum is on a much steeper curve in terms of rate of improvement due to the number of breeding cycles that can take place in a shorter time period compared to perennial and vegetatively propagated crops. The confluence of this potential with the application of modern biotechnology tools creates a phenomenal opportunity to develop a low cost, high yielding dedicated energy feedstock for both conventional fermentationbased approaches, as well as advanced cellulosic approaches to producing biofuels.

Feedstock developer NexSteppe is dedicated to developing and commercialising the crops and associated supply chain solutions necessary to enable the biofuels, biopower and bio-based product industries with optimal feedstocks. The company has a focus on sorghum and has built a library of germplasm sourced from public and private collections spanning the globe.

While NexSteppe is using conventional breeding techniques and cutting edge analytics to achieve this vision, a major catalyst to its business is the application of biotechnology in the form of marker assisted breeding. Through a partnership with DuPont Pioneer, NexSteppe has access to resources in marker assisted breeding technology which will accelerate the development of sorghum as a dedicated energy crop.

The introduction of DNA marker assisted breeding in plants over the past 20 years has led to a revolution in the way plant scientists and breeders approach the commercial development of improved breeding lines and crops. Classical breeding begins with the identification of varieties that contain desirable traits that a breeder wants to combine into a single, true breeding variety with improved characteristics.

Simple traits such as flower colour can be inherited in a simple fashion by single genes and more complex traits can be inherited through the action of many genes, such as grain yield and stress tolerance. Plant breeding seeks to make novel combinations of genes through genetic crossing (cross pollination) of different varieties followed by selection for the desired traits and counter-selection for unwanted traits. Selection has traditionally been done on visible or measurable traits called phenotypes.

While this process has been used to great success by breeders for many decades, it is very time and resource consuming. For example, traditional breeding schemes such as recurrent selection work by repeatedly crossing plants with desirable traits to one recurrent parent which has many desirable properties. In this way a valuable trait, such as disease resistance, from an otherwise inferior variety can by introduced (introgressed) into a high performing variety. This type of programme can take many years to accomplish by phenotypic selection. This is in large part because the phenotypes of interest may not be readily visible in the first generation, thus requiring the advancement of all of the progeny from a particular genetic cross to second and third generations before selections can begin.

In large-scale breeding programmes, with many traits under selection in multiple environments, this will result in large numbers of plants being grown and phenotyped, only a few of which will be advanced. Another obvious limitation is that the genes responsible for the traits of interest remain unknown. Therefore, further introgression of a desired trait from one inbred to another can again only be accomplished by extensive grow outs and visual selection.

Marker assisted breeding directly addresses these issues and allows breeders to observe gene segregation in their material and select for desirable genes while at the same time counter selecting for undesirable genes. The ability to make selections early in the growth cycle dramatically reduces costs and increases the number of traits that can be simultaneously bred. In addition, unlike phenotypic markers, molecular markers are not influenced by the environment, and can be reliably scored in every plant under observation.

Modern marker assisted breeding relies on the identification and development of a large number of molecular markers in the plant genome of interest. Molecular markers are differences in a DNA sequence between two individual plants and provide a ‘road map’ to the plant genome that allows breeders to follow the segregation of genes in a genetic cross (for example, parents and progeny in a genetic breeding programme).

These differences can take several forms including DNA nucleotide insertions, deletions, single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) among others. DNA polymorphisms serve as landmarks in the genome and behave as simple Mendelian genetic factors. As a result, their position on a genetic map, relative to one another and to a trait of interest, can be measured using standard genetic segregation analysis.

A critical aspect to effectively employ marker technology relates to the density of markers across a genome and the ease and cost of measuring (assaying) the genetic value at each marker location. Since the advent of whole genome sequencing in the late 90s, the cost of developing markers has decreased exponentially. Likewise the development of new high throughput genotyping systems has dramatically increased the speed and accuracy of assaying DNA markers. These advancements allow molecular biologists to develop marker systems that provide high genetic resolution and rapid assay readouts so that breeders can make selections early in the growth cycle and therefore only focus on the plants of interest.

The application of genomic methods to plant systems has also allowed whole genome sequencing of multiple cereals including sorghum, maize and rice. Bioinformatic analysis of the genomes of cereal species reveals a high degree of chromosomal synteny or genetic colinerairty between distant species. This means that genetic information from one crop can often be leveraged in another crop, further increasing the power of genetic analysis available to molecular biologists and breeders.

The revolution continues with the development of sophisticated statistical analysis to analyse population structure to identify closely related breeding populations and the application of methods such as Genome Wide Association Mapping to identify genes underlying complex quantitative traits. As marker density and statistical analysis continue to advance, the prospect of using genomic selection to predict phenotypes based on genomic marker information will further increase the speed and accuracy of molecular breeding.

Beyond the technical advantages of marker assisted breeding over transgenic approaches, there are also a number of practical and commercial advantages. Among them are cost and regulatory certainty. Sorghums are naturally outcrossing grasses with many close cousins that could be considered, at best, nuisances and at worst invasive species. To date, while transgenic approaches have the potential to confer significant advantages to crops like sorghum, as they have for corn and soya, the first step to any successful deregulation of said traits will be a robust gene-flow control strategy.

Efforts are underway at the research level to develop such a technology, but if history is any guide this process can take many years, perhaps a decade or more. Further, even after an effective genetic containment strategy is in place, deregulation of even core traits is a process that costs tens, if not hundreds, of million dollars and can take many years. This time and expense is exclusive of the investment required to actually develop the relevant traits, which is not only expensive but risky.

While there are differing views on the future of regulation of transgenes in non-food crops, it is fair to say there is tremendous uncertainty and significant risk in assuming a smooth path forward on this dimension. In comparison, marker assisted breeding is cheaper, faster, and more reliable and comes with none of the regulatory headaches associated with transgenic approaches.

It is clear that many challenges lie ahead for the development of robust bioenergy feedstocks that will help the US and other countries reduce their dependence on fossil fuels. While there are many biofuel feedstocks and processes under development, sorghum represents an attractive nearterm dedicated feedstock that will benefit greatly from recent advances in marker assisted breeding and genomic science.

Bioenergy Insight
Jan-Mar 2013