Saturday, December 3, 2011

Brave new world of genomics

REPOST
Written by Paul Icamina
Malaya Business Insight , 02 December 2011

LESS bones in bangus and smaller heads in tilapia to make room for more meat. Fast-growing crops resistant to disseases and adverse environments.

All these and more from an ambitious research venture and the quest to encourage new discoveries and innovations in gene science – from the Philippine Genome Center (PGC) launched by the University of the Philippines (UP) last Monday. The center will be based at the UP-Ayala Land TechnoHub in Quezon City.
"PGC will combine basic and applied research for the development of health diagnostics, therapeutics, DNA forensics and preventive products and improved crop varieties," said Dr. Carmencita David Padilla, PGC Executive Director.

"The PGC will use the knowledge of genomics in revolutionizing agriculture, health, and researches," she said "Research will play a key role in advancing science."

Genomics involve studies on the entire hereditary information of an organism embedded in the genome, encoded either in the DNA or, for many types of virus, in RNA.



In DNA, the genome make up the instructions stored in a manual on how to create, for example, a human being. It may be compared to a book (genome) that contains 23 chapters (chromosomes); each chapter contains 48 million to 250 million letters (A,C,G,T) without spaces. The book contains over 3.2 billion letters and fits into a cell nucleus about the size of the period in this sentence. At least one copy of the book (all 23 chapters) is contained in most cells of the human body.

Genomics hope to learn from this book, for example what variations in genetic information reflect particular traits in individuals or, say, diseases.

At the PGC, researchers will be trained on advanced knowledge and emerging technologies and have access to state-of-the-art tools for genomic research on identified priorities.

Conceived at UP in mid-2009, the PGC has since formed research groups of scientists and established research collaborations with academe here and abroad.

Priority crops must be endemic to the country and have big commercial potentials. So far, the PGC has identified the abaca, pili and the saba banana – all endemic in the Philippines.

Abaca exports earn about $80 million a year. At least 85 percent of current exports come only from the Philippines, the rest from Ecuador. But abaca’s potential is limited by the bunchy top virus. The PGC hopes to develop a variety resistant to the disease.

Another local crop is pili, which is found only in the Philippines, with harvests worth P75 million a year. The problem is that farmers cannot identify the male from the female plant in the seedling stage. Meaning, farmers stand to lose if they sow male plants that don’t bear nuts.

The PGC hopes to develop gene markers to determine sex at the early stage so that farmers can plant one male (as a source of pollen) for every every eight females that bear fruit.

The saba variety Musa balbisiana is grown only in the Philippines; most of it is exported to Japan as banana chips worth $40 million annually. Exports could be more if it is not beset by the same problem found in abaca – the bunchy top virus. PGC aims to identify the gene that causes the virus in banana; it also hopes to develop a variety that has a delayed ripening trait to make it more attractive for fresh saba to be shipped abroad.

Not GMOs

"All these are doable in genomics," said Dr. Antonio C. Laurena who is in charge of the PGC program on agriculture, livestock and fisheries while the program director, Dr. Rita P. Laude of UP Los Banos (UPLB), is on a study leave.

"We want to find out ways to fast-track the development of better crops and livestock, fisheries and forestry," he said.

"These are not gene modified organisms or GMOs where you transfer an individual gene from one organism to another, like the Bacillus turengensis from bacteria transferred to Bt corn," explained Laurena, a research professor at the UPLB Institute of Plant Breeding, who studies plant variety improvements.

"In genomics, you don’t do genetic engineering, you just have to know the genes responsible for certain traits, then select that gene, monitoring it through molecular markers, then fast track molecular marker-assisted breeding for desirable traits," he said. "Then you produce the plants through conventional breeding."
Molecular markers identify the gene responsbible for certain traits after which desirable offsprings are selected. While undesirable offsprings are ignored, research attention is devoted to these lines with desirable traits that are then bred conventionally.

In livestock, Laurena said, the focus is on microorganisms in the stomachs of ruminants because fed with rice straw, water buffaloes or carabaos gain much greater weight than cattle.

Scientists want to know why. "The feeling is that there are microorganisms in the carabao stomach that degrades rice straw more efficiently and turns it into useful nutrients. Research at the PGC will look into these microorganisms," Laurena said.

In forestry, a genomics roadmap is under development. One candidate tree is the fast-growing gmelina. Researchers would like to know what gene causes it to grow fast so that this gene could be transfered to other hardwoods like narra and red lauan so these can be grown and harvested faster.
They will also look at the gene responsible in making kamagong resistant to termite infestation so this trait can be transferred as well to other important forest trees.

In fisheries, the priority is to use genomics to produce milkfish or bangus that has less bone and tilapia with a smaller head – all to make way for more meat. Genomic research will also try to make them grow faster.
"It will be the first time that genomics will be used in Philippine agriculture," said Laurena, adding research and development will start hopefully in January.

It will not be cheap, but worth it, he said.

" The PGC does not have one budget but we submit our proposals to the Department of Science and Technology (DOST) and compete with the rest," Padilla said. "I am optimistic that in the coming years, the budget will be bigger."

In abaca genomics research, for example, the PGC is asking P14 million from the DOST to develop a virus resistant variety in three years of research.

This funding is only about $320,000, well worth it considering that abaca exports are valued at $80 million a year. With disease resistance, abaca production can double or even triple exports to $160 million or $240 million in just three years, Laurena pointed out.

Add to this the value added traits of enhanced fiber quality with more tensile strength and higher fiber yield to increase production.

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