BETHESDA, MARY. — The International Wheat Genome Sequencing Consortium (I.W.G.S.C.) said it has completed the quality control testing for the production of a whole genome assembly for bread wheat. The production of the genome was announced in January 2016. The resource is now available for researchers via the I.W.G.S.C. wheat sequence repository at URGI-INRA-Versailles, France.
The availability of the resource will allow wheat breeders and scientists to accelerate bread wheat crop improvement programs and genomics research. The newly available dataset will provide information regarding the identification of which genes are associated with crop increase, stress response and disease resistance. Ultimately, the resource is expected to lead to the production of improved wheat varieties for farmers, the I.W.G.S.C. said.
Since the January announcement, the I.W.G.S.C. said it has fine-tuned the data to ensure the highest possible quality genome assembly is available to researchers. The data collected was based on Illumina sequencing data assembled by NRGene, a genomic big-data company, software program DeNovoMAGIC. The research accurately represents more than 90% of the wheat genome, contains over 97% of known genes, and assigns the data to 21 chromosomes. The research allows researchers and breeders to utilize breakthrough information regarding the highly complex bread wheat genome toward improving wheat varieties.
“It is very important because never before this genome was sequenced,” said Gil Ronen, chief executive officer of NRGene. “Wheat is a very important crop and before NRGene started there was not a single genome sequence of wheat… The genome of wheat is five times greater than the genome of a human being; it’s very, very hard to reveal, to construct, to write the book of the genome of wheat, which possesses 16 billion letters.”
The wheat genome is highly complex, with three sets of seven chromosomes, and very large, five times that of the human genome. For years, scientists have been working to map the bread wheat genome to no avail, until the breakthrough in January by NRGene.
“They were trying for 10 years, spending hundreds of millions of dollars, and they could not write the book, and then they approached us,” Mr. Ronen said. “We did it completely different; we did the full map all together. We used different algorithms we used different software … and so, we took this challenge and they produced data according to our recipe and this data can be produced anywhere in the world. It’s not unique data, D.N.A. data, and … we constructed the full genome of wheat in two weeks.”
Following the completion of the research in January, the data underwent a long, strict and difficult evaluation, Mr. Ronen said.
“They have many, many different laboratory protocols and different tools that they collected during the 10 years for evaluating the accuracy of our book,” Mr. Ronen said. “So after six months … they are going to list this to the public … because they found it to be very, very accurate, and almost complete. And this is without, after checking six months, they didn’t change even a single letter, they didn’t find a single mistake.”
The release represents the next step the I.W.G.S.C. has taken toward establishing a “gold standard reference sequence,” or a complete map of the wheat genome that precisely positions all genes and other genomic structures along the 21 wheat chromosomes.
|Kellye Eversole, executive director of the I.W.G.S.C.|
“The I.W.G.S.C. policy has always been to make all data publicly available as soon as they have passed the quality checks,” said Kellye Eversole, executive director of the I.W.G.S.C. “By doing so, the scientific community can start exploiting the data now while the Consortium progresses toward a gold standard reference sequence, anticipated to be released in 2017.”
The dataset is available to researchers and breeders under the “Toronto Statement,” customary bylaws in the scientific community to prepublication of data sharing. The I.W.G.S.C. reserves the right under these laws to publish the first analyses of the data, which includes descriptions of whole chromosome or genome-level analyses of genes, gene families, repetitive elements, and comparisons with other organisms. The data may be accessed via the I.W.G.S.C. web site.
The I.W.G.S.C. said it will continue to improve and increase the newly released research, and will look to complete a high quality, ordered sequence of the wheat genome that includes annotating and identifying the precise locations of genes, regulatory elements, and markers along the chromosomes. The final result of the research will come in the form of a full integration of all genomic resources produced under the I.W.G.S.C. umbrella over the last decade, including individual physical and genetic maps.
An almost complete map of the bread wheat genome would greatly improve the practices and outputs of farmers because researchers can identify and target the precise location of the necessary genes in order to increase the crop’s productivity, tolerance, etc.
“Where are the genes that are critical to increase yield, to increase grain size, number of grains, etc. etc.?” Mr. Ronen added. “Where are the genes that are critical for getting drought tolerance or heat tolerance … any type of tolerance of the plant to direct environmental changes?”
Scientists say that access to the almost complete map may speed up the process of identifying a specific gene and then developing a new variety, he said.
“Instead of … a process that would take, before, 10 to 15 years per gene now could take a few months to find out the same genes because the map is there,” he said. “Now the time to develop dramatically better varieties is shortened. Before, to get a very good, new variety it would take seven years. Now it can take four years.”
The implications of breeders and researchers utilizing the research are far-reaching, the I.W.G.S.C. said. Wheat accounts for 20% of all calories consumed in the world, and to meet the projected 2050 world population of 9.6 billion, wheat productivity must increase at 1.6% each year, according to the I.W.G.S.C. The research released may allow breeders to improve wheat crop traits such as yield, drought sustainability, and more that may increase productivity on land already cultivated, rather than committing additional land to cultivation. The providing of detailed maps of genes and gene-networks that may be improved by breeding will lead to the improvement and preservation of biodiversity, water and nutrient resources.
Mr. Ronen compared the release of this data to the public and its potential impact on the agriculture industry as similar to that of Google on the internet.
“There were not good search engines,” he said. “Now Google came and changed it altogether. Google introduced a new algorithm. A very sophisticated algorithm. So we did exactly the same to a much smaller world, which is D.N.A. data analysis.”