My Thoughts on Technology and Jamaica: BBSRC Professor Kell’s Chinese Spring Wheat Genome started from the Bottom of the Wheat Field

Tuesday, July 29, 2014

BBSRC Professor Kell’s Chinese Spring Wheat Genome started from the Bottom of the Wheat Field

“In the face of this year's wheat crop losses, and worries over the impact on prices for consumers, this breakthrough in our understanding of the bread wheat genome could not have come at a better time. This modern strategy is a key component to supporting food security and gives breeders the tools to produce more robust varieties with higher yields”

BBSRC (Biotechnology and Biological Sciences Research Council) Chief Executive Professor Douglas Kell of the University of Liverpool on the decoding of the Chinese Spring Wheat (Triticum aestivum L.)Genome

After nearly four (4) years of Research a Team at BBSRC (Biotechnology and Biological Sciences Research Council) led by Professor Douglas Kell of the University of Liverpool and has finally cracked the Bread Wheat Genome as reported in “Genetic blueprint for wheat deciphered”, published Saturday, July 19, 2014, The Jamaica Observer.

The Bread Wheat, also known as the Chinese Spring Wheat (Triticum aestivum L.), has a Genome that consists of some 20 Chromosomes located inside of the nucleus of each cell. These Chromosomes which are composed of DNA (Deoxyribonucleic Acid) are in turn composed of sequences of three bases composed of combinations of Adenine (A), Guanine (G), Cytosine (C) or Thiamine (T) called Codons.

Each Codon represents an Amino Acid that makes up a protein molecule and specific sequences of Codons representing a Protein are called Genes. Amazingly, for such a simple organism, the Chinese Spring Wheat (Triticum aestivum L.) has a Genome that’s five (5) times the size of the Human Genome, due to the fact that it’s a grass that was bred by humans to be edible by cross-breeding with other edible grasses.

According to their publication in the Journal Nature, there is a total of 124,000 Genes, representing 124,000 proteins that were located by the BBSRC Team, but only 90,000 of those Genes were sequence:

1.      The positions of the Codons within the DNA worked out
2.      Proteins that these Genes produce
3.      Genotype (Genetic characteristics) and Phenotype (Physical characteristics) they represent

The Genome Sequencing Study was led by Professor Douglas Kell of the University of Liverpool and co-authored by Dr Anthony Hall, from the University Institute of Integrative Biology. It coincides rather neatly with a French Research Team announcing recently they'd mapped a complete Bread Wheat Chromosome, known as 3B. This leaves that Research Team with a long journey ahead of them, as they have some 20 more Chromosomes to decipher in order to completely decode the Genome of Bread Wheat.

Their four year quest was funded by the BBSRC (Biotechnology and Biological Sciences Research Council) of which Professor Douglas Kell of the University of Liverpool is Chief Executive. His team pooled their efforts and resources with the following Universities and Institutes:

1.      Institute of Bioinformatics and Systems Biology in Germany
2.      Cold Spring Harbor Laboratory in the USA
3.      University of California in the USA
4.      University of Bristol in the UK
5.      University Institute of Integrative Biology in the UK

Researchers focused on a cultivated wheat variety known as Chinese Spring Wheat (Triticum aestivum L.) and have decoded 90,000 of the 124,000 Genes that make up the Wheat Genome. This, published in the Journal Nature, is a landmark discovery and is of greatest significance to the Agriculture Sciences World as Wheat is the World's third biggest crop after maize and rice.

Professor Kell’s Wheat – Started from the Bottom of the Wheat Field Now we here

Four years?

Back in 2010, Professor Douglas Kell of the University of Liverpool, who was then head of the Britain's Biotechnology and Biological Sciences Research Council (BBSRC) announced they’re cracked the Wheat Genome as stated in “Scientists: We've Cracked Wheat's Genetic Code”, published  Aug. 27, 2010 | 11:08 a.m. EDT, Associated Press.

Back then, I was so impressed by the news that I’d done a pair of articles predicting how it would revolutionize the development of GM (Genetic Modified) Foods by making Wheat more Drought resistant as stated in my blog article entitled “Wheat Genome Cracked - Nature Valley vs the Island of Dr. Moreau” and “Wheat Genome Cracked - GM for US and Jamaica's Agriculture Revitalization”.

I suspect that this discovery differs because of the variety of Wheat whose Genome was sequenced, that being the Chinese Spring Wheat (Triticum aestivum L.). Additionally, it’s also the method used to sequence the Chinese Spring Wheat (Triticum aestivum L.) Genome.

So how did they do it?

They realized that the different families of Wheat were related to each other and to similar Food Grasses with simpler Genomes such as Rice and Barley and some of its ancestors, which had long ago been decoded using conventional Genome Sequencing Methods as explained in “Scientists decipher Genetic code of wheat” published 28 November 2012, ScienceDaily.

The Team hypothesized that the more advanced Grasses such as Wheat not only were complex and thus had more Genomes, but shared the same Chromosomes and even Genes with these predecessors to who them they were related but just happened to still be around. Evolution mean that they're all related, just slightly differentiated from their common Grass Ancestor.

Knowing the complete Genome of those Grasses, they simply just used a special algorithm developed by the John Innes Centre to do a count of the total number of Chromosomes in each Genome and the location of the Genes within each Chromosome. Then they’d look for Genetic markers that were similar for each Gene making up the Chromosome within the Chinese Spring Wheat (Triticum aestivum L.) Genome to those in Rice and Barley and earlier grasses.

They did the comparison against Genome Databases provided by the Institute of Bioinformatics and Systems Biology in Germany and Cold Spring Harbor Laboratory and the University of California in the US. The unidentified Chromosomes within the Wheat (Triticum aestivum L.) Genome was then sequenced using the conventional Genome Sequencing methods, thus greatly speeding up the process.

Chinese Spring Wheat Genome – Jacob’s Ladder Sequencing of Complex Plants

Think of it like designing a smartphone or an Aeroplane, both fields with which I'm all too familiar being as I'd made design improvements to the Twin-Engine Airbus E-Fan All-Electric Airplane as detailed in my blog article entitled “Airbus Group and the E-Fan – EU's Flightpath 2050 heralds All-Electric Aircraft as Fischer–Tropsch Process makes Kerosene Renewable”.

Because many persons have done it before, you don't need to start from ground zero and design the smartphone or airplane; you just use the blueprints for a simpler model and add to the design, as Airbus had done. Simple as that!

By identifying the differences in the Genomes of Chinese Spring Wheat (Triticum aestivum L.) to that Rice and Barley and some of its ancestors, they were able to not only quickly sequence the complex Wheat Genome, but separate the known Genes within the Chromosomes and determine the Genes and their known genotype and phenotype. Thus, their map wasn’t just a listing of Genomes for the purpose of bragging of the academic triumph of sequencing a plant that was heretofore difficult.  It had straight-out-the-Lab practical applications to Crop Breeders as well.

They could use the information to identify features of other hardier Grasses and thus cross-breed them with the Chinese Spring Wheat (Triticum aestivum L.), either in the field over several Generations or via companies using Laboratory techniques to create the desired traits required to make Chinese Spring Wheat (Triticum aestivum L.) more suited to surviving various environments.

This technique can lead to the sequencing of even more complex Grasses, such as Sugar Cane, as suggested by the rather upbeat Professor Neil Hall from the University's Institute of Integrative Biology, who apparently is trying to get a photo-op here, quote: “Wheat is a large and complex genome; arguably the most complex genome to be sequenced to date. Although the genome has not been fully decoded, we now have instrumentation that can read DNA hundreds of times faster than the systems that were used to sequence the human genome. This technology can now be applied to other Genomes previously considered to be too difficult for detailed Genetic study, such as sugar cane, an important biofuel crop”.

That means in the near future, companies that specialize in making GMO (Generically Modified Organisms) from this information such as Monsanto, can make varieties of Chinese Spring Wheat (Triticum aestivum L.) that can grow in virtual any climate Region of the World under various conditions i.e. high Temperature, extreme dryness, extreme sunlight, etc.

Possessing this knowledge also means that we can a means of staving off Global Hunger by being able to produce varieties of a plant that's a staple of 30% of the World's population. It's also used to make the most common of foods, that being Flour, which is used to make Bread and thus is literally our #BreadandButter. Its significance wasn’t lost upon co-chair of the IWGSC (International Wheat Genome Sequencing Consortium) Catherine Feuillet, quote: “We have reached a great milestone in our roadmap”.

With our World population projected to reach some 9 billion by 2050. Wheat Production has been falling globally by some 5.5% from 2000 to 2008 due to Climate Change, according to a study in the journal Science by researchers at the IWGSC.  Having the ability to modify wheat to grow anywhere, even in the Desert, will be a priority going forward!
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