First corn genome draft to be announced - consequences for bioenergy, food, climate change

The first draft of the corn genome sequence will be announced Thursday, Feb. 28, at the 50th Annual Maize Genetics Conference in Washington, D.C., and thus open a new era of corn research. The maize genome is notoriously complex, with twice as many genes as the human genome, lots of jumping genes, long pieces of repetitive code, and around 2.5 billion base pairs that make up the double helix of the plant's DNA. Cracking the code will open major avenues in research that could lead to the development of corn plants that sequester more carbon, yield more energy, are resilient to climate change and many other features. Insights into corn's genome might prove to be useful to the study of other grasses.

The implications
The draft of the corn genome provides plant scientists with a lot of data to work with. It is a lot like a collection of maps, diary entries, dried plants and animal specimens brought back by naturalists' expeditions: the raw material demands years of subsequent analysis and study and can yield surprising discoveries. One scientist said "this will enable so much exciting corn research. This will raise questions about the biology of corn and provide great tools to answer them."

Those answers could help scientists modify and improve corn plants. The genome, for example, could help scientists:

• develop crops that can withstand global climate change
• add nutritional value to grain
• sequester more atmospheric carbon in agricultural soils
• boost yields so crops can meet growing demands for food, feed, fiber and fuel

In addition, what scientists learn from the corn genome will allow them to better understand other grasses The genome of corn is very similar to the genomes of rice, wheat, sorghum, prairie grasses and turf grasses. Therefore, the draft of the corn genome can help researchers improve the other cereals and grasses.

Iowa State University researchers played an important role in this $32 million project. Patrick Schnable, a Baker Professor of Agronomy and director of the Center for Plant Genomics and the Center for Carbon Capturing Crops, and Srinivas Aluru, a Stanley Chair in Interdisciplinary Engineering and a Professor of Electrical and Computer Engineering, led the work at Iowa State and provided the project with expertise in corn genomics and supercomputing.

Understanding the corn genome will accelerate efforts to develop crops that can meet society's growing needs for food, feed, fiber and fuel. This project is also a wonderful example of how Iowa State researchers are able to work across disciplines to solve problems important to Iowa and the world. - Gregory Geoffroy, Iowa State University's president

Earlier, Iowa State researchers and their U.S. Department of Agriculture collaborators already developed the B73 inbred corn line that was sequenced by the genome project. Created decades ago, the B73 line is noted for the high grain yields it contributes to hybrids. Derivatives of B73 are still widely used to produce many commercial hybrids:
energy :: sustainability :: biomass :: bioenergy :: biofuels :: ethanol :: corn :: genomics :: genetics :: plant breeding :: biotechnology ::

The overall corn genome project is led by Richard Wilson, the director of the Genome Sequencing Center at the Washington University School of Medicine in St. Louis. He will make a brief announcement about the sequencing project and researchers will take questions during a news conference at 12:30 p.m. Thursday, Feb. 28, in the Hoover Room of the Marriott Wardman Park Hotel in downtown Washington. Wilson will also make remarks about the draft genome during a reception from 6:30-8 p.m. Thursday at the Smithsonian Institution's National Museum of Natural History on the National Mall. And Wilson will present a scientific talk about the draft genome at 8:35 p.m. Friday, Feb. 29, back at the Marriott Wardman Park Hotel. Wilson's talk will describe the draft corn genome, explain the work needed to produce it and look ahead to the research that needs to be done to improve it.

The genome project also includes researchers at the University of Arizona in Tucson and the Cold Spring Harbor Laboratory in New York. The $32 million, three-year research project is supported by the National Science Foundation, the U.S. Department of Agriculture and the U.S. Department of Energy.

Supercomputing
Schnable and Aluru led Iowa State's work to refine assemblies of the genomic sequences generated by researchers at Washington University. In addition, they identified almost 100 genes which have nearly identical copies in the genome. Schnable said these nearly identical paralogs may have played important roles during the evolution and domestication of corn and may have contributed to the ability of breeders to mold this important crop species to meet human needs. The Schnable and Aluru teams also discovered several hundred new corn genes that are not present in other plants. Some of these genes may be responsible for unique attributes of corn.

The corn genome is an especially difficult jigsaw puzzle to put together, Schnable said. There are some 2.5 billion base pairs that make up the double helix of corn DNA. The corn genome also has long lines of repetitive code. And corn has 50,000 to 60,000 genes to identify and characterize. That's about twice the number of genes in humans. Plus, 50 percent or more of the corn genome is made up of transposons or jumping genes. Those are pieces of DNA that can move around the genome and change the function of genes.

Solving all those assembly challenges took a lot of computing power and some new software technology.

Aluru and his research team developed software called "PaCE" and "LTR_par" that runs on parallel computers -- including CyBlue, Iowa State's IBM Blue Gene/L supercomputer capable of 5.7 trillion calculations per second. PaCE can generate draft genome assemblies in hours or days instead of months. LTR_par identifies retrotransposons, another mobile genetic element that can cause genome changes such as mutations, gene duplications and chromosome rearrangements.

In addition to advancing our understanding of corn, the genome project has helped Iowa State launch several academic careers. As graduate students, Scott Emrich, Ananth Kalyanaraman and Sang-Duck Seo worked on the corn genome project. Emrich is now an assistant professor of computer science and engineering at the University of Notre Dame in Notre Dame, Ind.; Kalyanaraman is an assistant professor of electrical engineering and computer science at Washington State University in Pullman; and Seo is an assistant professor of art at the University of Nevada, Las Vegas.

And so, Schnable said, the corn genome project has already been very useful. As researchers turn the first draft into new chapters describing their discoveries, he said it will be even more important to researchers and society.

Picture: Several corn varieties are on display outside Patrick Schnable's Iowa State office. Credit: Iowa State University.

References:
Iowa State University: Iowa State researchers help piece together the corn genome's first draft - February 25, 2008.

Article continues

Compost can turn agricultural soils into a carbon sink - but no match to biochar

Applying organic fertilizers, such as those resulting from composting, to agricultural land could increase the amount of carbon stored in these soils and contribute significantly to the reduction of greenhouse gas emissions, according to new research published in a special issue of Waste Management & Research. The findings are interesting, but the bioenergy community has meanwhile gone way beyond this idea, and is instead looking at a similar but much more promising concept, namely creating soil carbon sinks with biochar, coupled to biofuel and bioenergy production.

The addition of biochar - inert carbon obtained from the pyrolysis of biomass - to soils makes for a much more stable and permanent soil carbon sink than storing carbon via compost; it also reduces fertilizer needs because of increased cation exchange capacity and the prevention of leaching and runoff of nutrients; it reduces nitrous oxide emissions substantially, boosts soil fertility and organic matter build up, and holds a huge overall potential for soil carbon storage (in fact, the system can effectively halt and reverse climate change).

When added to soils, biochar (also known as agrichar) remains unaltered for hundreds, possibly thousands of years (see the ancient Terra Preta soils). Compost derived carbon biodegrades in a matter of years, to release greenhouse gas emissions. Moreover, biochar systems can be based on the production of carbon-negative bioenergy, because the soil amendment is obtained from pyrolysis - itself a promising bioconversion technology that yields both biofuels (bio-oil) and combustible gas.

The new data on organic fertilizers and how they can play a role in creating soil carbon sinks, is fascinating though, in that they precisely highlight biochar's far greater potential. Carbon sequestration in soil has been recognized by the Intergovernmental Panel on Climate Change (IPCC) and the European Commission as one of the possible measures through which greenhouse gas emissions can be mitigated.

One estimate of the potential value of the compost approach - which assumed that 20% of the surface of agricultural land in the EU could be used as a sink for carbon - suggested it could constitute about 8.6% of the total EU emission-reduction objective.

An increase of just 0.15% in organic carbon in arable soils in a country like Italy would effectively imply the sequestration of the same amount of carbon within soil that is currently released into the atmosphere in a period of one year through the use of fossil fuels. - Enzo Favoino and Dominic Hogg, authors

Like biochar, increasing organic matter in soils via compost may cause other greenhouse gas-saving effects, such as improved workability of soils, better water retention, less production and use of mineral fertilizers and pesticides, and reduced release of nitrous oxide.

However, capitalizing on this potential climate-change mitigation measure is not a simple task. The issue is complicated by the fact that industrial farming techniques mean agriculture is actually depleting carbon from soil, thus reducing its capacity to act as a carbon sink:
energy :: sustainability :: biomass :: bioenergy :: biofuels :: compost :: carbon sink :: soil organic carbon :: carbon cycle :: biochar :: agrichar ::

According to Hogg and Favoino, this loss of carbon sink capacity is not permanent. Composting can contribute in a positive way to the twin objectives of restoring soil quality and sequestering carbon in soils. Applications of organic matter (in the form of organic fertilizers) can lead either to a build-up of soil organic carbon over time, or a reduction in the rate at which organic matter is depleted from soils (graph, click to enlarge). In either case, the overall quantity of organic matter in soils will be higher than using no organic fertilizer:

What organic fertilizers can do is reverse the decline in soil organic matter that has occurred in relatively recent decades by contributing to the build-up in the stable organic fraction in soils, and having the effect, in any given year, of ensuring that more carbon is held within the soil. - Enzo Favoino and Dominic Hogg, authors

But calculating the value of this technique to climate change policies is complicated. To refine previous calculations and to take account of the positive and negative dynamics of carbon storage in soil, Favoino and Hogg modelled the dynamics of compost application and build-up balancing this with mineralization and loss through tillage.

Their results suggest that soils where manure was added have soil organic carbon levels 1.34% higher than un-amended soils, and 1.13% higher than soils amended with chemical fertilizers, over a 50-year period. This is clearly significant given the evaluations reported above regarding carbon being lost from soils, and the increasing amount of carbon dioxide in the atmosphere, they say.

The article about the potential role of compost in reducing greenhouse gases is published on today in a special issue of Waste Management & Research, entitled Green House Gases and Solid Waste Management. The article will be free online for two months.

References:
Enzo Favoino and Dominic Hogg. "The potential role of compost in reducing greenhouse gases", Waste Management & Research, Vol. 26, No. 1, 61-69 (2008), DOI: 10.1177/0734242X08088584

Amonette, J.; Lehmann, J.; Joseph, S., "Terrestrial Carbon Sequestration with Biochar: A Preliminary Assessment of its Global Potential", American Geophysical Union, Fall Meeting 2007, abstract, December 2007.

Article continues

Pakistani utility purchases 7MW of green cogenerated power based on sugarcane waste biogas

In a first for Pakistan, utility Faisalabad Electric Supply Company (FESCO) has signed a power purchase agreement for 7 MW of green power to be provided by Shakarganj Sugar Mills, located at Jhang Faisalabad. Shakarganj will generate biogas from molasses, a waste product from sugarcane processing, to co-generate electricity and heat. The agreement was signed at the Pakistan Electric Power Company (PEPCO) headquarters between Ahmed Saeed Akhter, CEO of FESCO and CEO Ahsan Saleem, CEO of Shakarganj Sugar Mills.

Shakarganj's is the first power plant in the subcontinent using renewable biomass to produce biogas for cogeneration purposes. The plant will not use any fossil fuel and as such offers the opportunity to be taken up as a project under the UN's Clean Development Mechanism (CDM).

PEPCO, as part of its strategy to bridge the gap between supply and demand of electricity and to promote alternative energies has offered a very attractive tariff for generation of power through biogas produced from molasses, which is directly derived from sugar mills. The benchmark set by PEPCO for such projects is Rs 5.14 (€0.055/US$ 0.082) per kWh.

The contract with Shakarganj Sugar Mills is part of continuous effort of PEPCO to search for local and cheaper fuel, as fossil fuel based electricity generation keeps getting more costly.

Even though small in terms of power capacity, the agreement finalized today is seen as a landmark achievement for Pakistan, as it is set to be replicated amongst the country's large number of sugar mills. PEPCO's managing director Munawar Baseer Ahmad has expressed the hope that all available surplus capacity within the sugar industry will be availed after this break-through and will help end Pakistan's worries over its energy security.

Sugarcane is a key agricultural sector in Pakistan, with the crop grown on around 1 million hectares, mainly in Punjab (62%), Sindh (26%) and the North West Frontier Province (16%). The sector employs more than 1 million people indirectly. Around 80 large sugar mills (map, click to enlarge)crush approximately 45 million tonnes of cane into finished products each year:
energy :: sustainability :: biomass :: bioenergy :: biofuels :: sugarcane :: molasses :: cogeneration :: biogas :: Pakistan ::

PEPCO stressed that green power generation through biogas carries a number of advantages like opportunities to achieve Clean Development Mechanism (CDM) project status and thus obtaining carbon credits; reductions in greenhouse gas emissions; and an opportunity, even for a developing country like Pakistan, to adhere to the spirit of the Kyoto Protocol. PEPCO will futher encourage other sugar mills interested in producing electricity from molasses because the technique is not only cost effective but also environment friendly.

According to the country's leading electricity company, biogas from molasses will help Pakistan reduce its increasing dependence on imported fuel oil and fast depleting locally available gas resources.

Pakistan's Secretary of the Ministry of Water and Power Resources, Muhammad Ismail Qureshi, added that this agreement is likely to bring out the large dormant capacity for local, renewable power generation from biomass, along with new green field projects. A feasibility study of the future energy role for the sugar industry in Pakistan will include co-generation of biogas produced from molasses.

Pakistan's Ministry of Water and Power earlier launched a policy and support scheme to facilitate the sugar industry into becoming a player in the energy sector, drawing on the maximal utilization of biomass resources.

FESCO distributes and supplies electricity to about 2.44 million customers within its service territory with a population of over 15.5 million under a Distribution License granted by National Electric Power Regulatory Authority (NEPRA). The company's geographical service area comprises Faisalabad, Sargodha, Mianwali, Khushab, Jhang, Bhakker, T.T Singh districts.

Shakarganj Sugar Mills is one of Pakistan's larger sugar producers involved in creating a variety of products from sugar cane. In 2006 it produced around 130,000 tons of sugar, 80,000 tons of molasses and 35 million liters of ethanol. The company is diversifying into bioenergy production, focusing on both liquid biofuels and biomass based power.

Map: sugarcane mills in Pakistan. Credit: Pakistan Sugar Mills Association.

References:
FESCO: PEPCO Finalizes a Unique Power Contract - [s.d.] February 24, 2008.

Pakistan Sugar Mills Association.

Qureshi, S. "Significance of sugar industry in national economy", Economic Review, July 2004.

Article continues

Sugarcane ethanol exports double Jamaica Broilers Group revenues

An interesting case of the profitability of efficient biofuel production comes from the Jamaica Broilers Group, which we have been tracking over the past year. The group announced revenues were fuelled by ethanol, whose sales of $1.8 billion in the quarter ended January 5, 2008 and boosted the poultry company's turnover to $5.2 billion, or just about double the $2.8 billion earned in the comparative period a year ago. The group's subsidiary JB Ethanol built an exported oriented fuel-grade ethanol plant that became operational in July 2007. The group also invested in a $120 million cogeneration plant.

The ethanol facility, which has the U.S. as the principal market for its ethanol products:

• Possesses a production capacity of 60 million gallons per year of Fuel Grade Ethanol;
• Has a storage capacity of 14 million gallons, following the erection of storage tanks for raw material (hydrous ethanol) and finished product (anhydrous ethanol);
• Can process locally-produced hydrous ethanol from Jamaican sugar cane – thereby providing an outlet for this product and directly supporting the privatization strategy of Jamaican Sugar assets;
• Utilized the expertise of several major international firms to help make the plant a reality – including Dedini, a leading Brazilian company, which supplied the Dehydration Plant and Equipment, Chicago Bridge and Iron Works, a major tank construction company in the USA, which supplied and installed the tanks; Bauche Energy of Brazil, which provides an on-going supply of the critical raw materials needed to make the Jamaican plant profitable

Ethanol exports boosted sales by Jamaica's top poultry producer by $2.4 billion, or more than 88 per cent. The company produces a highly efficient biofuel from sugarcane. According to a statement by chairman R. Danny Williams and CEO Robert Levy "anhydrous ethanol market prices have rebounded since December 2007 and this is expected to impact positively our fourth quarter consolidated results."

United States traded ethanol, the market to which JB Ethanol sells its output, is now selling above US$2.20 gallon on front month contracts, up from US$1.75 at yearend. The substantial growth in group revenues led to boosted profit numbers:
energy :: sustainability :: biomass :: bioenergy :: biofuels :: ethanol :: efficiency :: biofuel trade :: Jamaica ::

But Broilers also faced heavier than normal expenses to eke out those results - raw material and production costs, or cost of sales, more than doubled from $2.1 billion to $4.4 billion year over year or close to 110 per cent - leading to a decline in profit margins in the current period.

Operating profit, for example, rose $86 million to $307 million, but measured against revenues the margin fell from eight per cent in the 2007 period to six per cent. Net profit was also $32 million improved in the quarter, but again the margin was lower at four per cent, down from six per cent in the January 2007 period.

The company's nine month results also ran a similar track, but with one difference: bottom line income fell over the period. Revenues gained almost $4 billion to end the period at $12.3 billion, but cost of sales also doubled to $10.4 billion.

The St Catherine company's poultry operation remained its cash cow, accounting for $5.3 billion of sales, and will likely be boosted higher in the fourth quarter ending April following a price hike on chicken meat announced by the group this week.

Ethanol's turnover was $3.1 billion.

But rising production costs allowed Broilers only a slight gain in gross profit of $1.9 billion for the group (9-month 2007: $1.86 billion). Operating profit for the group also rose from $496 million to $670 million, though the newly added ethanol segment joined the problematic fish business as a drag on earnings. Fish losses were $19.9 million this period, while startup ethanol lost $7.16 million.

Still, feed and farm supplies as well as the flagship poultry segment were sufficient to spike operating income above year ago levels.

The reversal in fortunes began to manifest at the pretax profit line - which was weighed down by a more than seven-fold increase in debt serving costs - which dropped from $457 million a year ago to $377 million in the review period. At the bottom line, nine-month net profit slid from $354.5 million to $277.4 million, or from 29 cents per share to 23 cents per share.

The company said its financing charges of $292.6 million were linked to the servicing of increased foreign and local currency loans that were acquired "to meet increasing working capital needs." JB's balance sheet shows a quadrupling of its debt from $231 million at financial year end April 2007 to $933 million in January, reflecting the higher leverage. Compared to a year ago, Broilers' long-term liabilities have grown six-fold.

References:
Jamaica Broilers Group: Annual Report for the Financial Year 2007 [*.pdf] - February 2008.

Article continues

African small farmers association seeks biofuels investors

A small young farmers association called Key Farmers Cameroon is looking for technical assistance and investors to research biofuel production opportunities. The farmer funded non-profit carries out capacity building through training with poor farmer groups in marginalised rural communities in the Manyu amd Meme Divisions of Cameroon's Southwest province.

Created in 2003 as a community self-help Common Initiative Group of volunteers to combat hardship, hunger, diseases and poverty, Key Farmers Cameroon's work consists of "providing training support to farmers so they could improve on agricultural production and productivity as a means to fight poverty and misery in their households and communities."

Over the years as Key Farmers expanded its activities, it became an umbrella organisation with 20 autonomous farmers groups working with more than 500 small farmers in 25 villages in the Upper Banyang sub-division, particularly in the Awanchi and Betieku clans.

The association is interested in co-operating with biofuel producers and consultants in research activities concerning green fuels. The market could offer new opportunities for marginalised farmers in the region. Members of Key Farmers Cameroon "have enough farmlands and are looking for partners who are interested to promote the production of oil palm in the area." Any other investors interested in growing jatropha, sugar cane and other energy crops are invited for partnership:
energy :: sustainability :: biomass :: bioenergy :: biofuels :: palm oil :: jatropha :: sugarcane :: poverty alleviation :: rural development :: Cameroon ::

The specific capacities of Key Farmers Cameroon are focused on the different project areas envisaged to increase the standard of living of the rural people and includes the following objectives:

• To assist and train young farmers to acquire new skills and knowledge that would improve crop production and productivity to make them self-reliant and increase their incomes
• To empower and train youths on the Agro-forestry and tree crops of high value as a means to increase family incomes, protect the environment and improve their health
• To create an agricultural multipurpose centre in the Kendem area for capacity-building and to accommodate young farmers in income-generating, promoting crop production and marketing particularly palm oil, plantains, non–timber forest product, tree farming and the empowerment of women and youths in their fight to alleviate poverty and misery
• Other related objectives are in the campaign against HIV/AIDS, support to poor and disadvantaged pupils to help develop skills on income-generating activities to sustain their education and way of life. Also the sensitisation of farmers on methods of saving money for agricultural exploitation and community development

The organisation is looking for "long term cooperation" and prefers collaboration with "social entrepreneurs" in the biofuels sector. Please contact Biopact for more information.

Article continues