Monthly Archives: January 2013

Scientists at A*STARs Genome Institute of Singapore (GIS) headed a study that discovered four processes by which gastric cancer is formed. This is extremely important since gastric cancer is the second most common cause of cancer deaths worldwide, claiming almost 750,000 lives annually, 60% of which are Asians.

Using what is known as next-generation sequencing technologies, GIS scientists were able to provide a comprehensive view of the gastric cancer genome, characterizing micro- and macro-scale mutations. This led to the identification of four distinct processes that cause mutations in gastric cancer. One of these was found to have a targeted impact on genes and is potentially triggered by bacterial infection. The other processes were found to have impact throughout the genome, and included oxidative damage processes and the failure of DNA proof-reading mechanisms.

The discovery of the mutative actions of these processes provides essential clues to the formation of gastric cancers, paving the way for diagnostics and targeted therapy.

The findings were published online in the December 2012 issue of Genome Biology.

First author and GIS Principal Investigator Dr Niranjan Nagarajan said, Cancers are constantly evolving, and therefore understanding how they do so is important for finding new treatments. Mutational processes in cancer had not previously been shown to have a targeted impact on the genome and on genes. With this study, we show evidence of this for the very first time. This is truly exciting since it moves us a critical step towards understanding and finding a cure for gastric cancer.

Co-author and GIS Principal Investigator Dr Patrick Tan said, This is the first time gastric cancers have been analyzed at the whole genome level. This work further showcases the reputation of Singapore as a world-leader in gastric cancer research.

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:: 28, Jan 2013 :: SINGAPORE SCIENTISTS LED BY A*STAR’S GENOME INSTITUTE OF SINGAPORE IDENTIFY FOUR DISTINCT ...

New Delhi, Jan. 27: Indian crop scientists have sequenced the chickpea genome, a feat they say will help boost yields of the nation's best-selling legume used in myriad dishes, from chhole to those requiring besan such as pakoras and bondas.

The chickpea sequencing effort, led by scientists in Hyderabad with collaborators elsewhere in India and other countries, has identified an estimated 28,269 genes or about 90 per cent of the genes in this staple crop. Their paper on the chickpea sequence appeared today in the journal Nature Biotechnology.

Scientists say the newly identified genes will help accelerate efforts to improve India's chickpea yields, which, at only 850kg per hectare in contrast to Canada's 1,600kg per hectare, are still much lower than what agricultural scientists believe can be achieved.

"India is the world's largest producer, largest consumer and largest importer of chickpeas," said Rajeev Varshney, a plant biologist at the International Crops Research Institute for Semi-Arid Tropics, Hyderabad, who led the genome-sequencing consortium.

"We don't produce enough to meet the domestic demand; so increasing the yield is important for India," Varshney told The Telegraph.

Some of the newly identified genes appear to control functions such as seed nutrition, adaptation to stress from heat and drought, and disease resistance. When scientists identify genes for specific traits, they can focus breeding efforts on those particular genes.

"It narrows the playing field ' we can use this molecular information to make breeding efforts more precise," said Douglas Cook, professor of plant pathology at the University of California, Davis, who played a key role in planning the project, assembling the sequence and analysing data.

Scientists are, for example, close to identifying specific genes that control flowering time. "This may allow breeders to rapidly adapt new varieties to changes in climate," Cook told this newspaper. "Similarly, we hope to find genes involved in disease resistance to important pests."

The consortium sequenced a widely cultivated Canadian kabuli chickpea variety as a reference genome and then sequenced 90 other lines from 10 countries, including 19 varieties of chickpea from India.

While Indian researchers had in the past contributed to international efforts to sequence the genomes of rice and tomato plants, the chickpea is the second genome-sequencing effort to be led by Indian crop scientists, after they sequenced the pigeon pea genome two years ago.

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Genome feat hope for chhole, pakora aficionados

Public release date: 28-Jan-2013 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

Hyderabad, India, and Shenzhen, China (28 January 2013) In a scientific breakthrough that promises improved grain yields and quality, greater drought tolerance and disease resistance, and enhanced genetic diversity, a global research team has completed high-quality sequencing of not one but ninety genomes of chickpea.

Nature Biotechnology, the highest ranked journal in the area of biotechnology, featured the reference genome of the CDC Frontier chickpea variety and genome sequence of 90 cultivated and wild genotypes from 10 different countries, as an online publication on 27 January 2013. The paper provides a map of the structure and functions of the genes that define the chickpea plant. It also reveals clues on how the sequence can be useful to crop improvement for sustainable and resilient food production toward improved livelihoods of smallholder farmers particularly in marginal environments of Asia and sub-Saharan Africa.

The research milestone was the result of years of genome analysis by the International Chickpea Genome Sequencing Consortium (ICGSC) led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) headquartered in Hyderabad, Andhra Pradesh India, involving 49 scientists from 23 organizations in 10 countries. ICRISAT is a member of the CGIAR Consortium.

The global research partnership succeeded in identifying an estimated 28,269 genes of chickpea after sequencing CDC Frontier, a kabuli (large-seeded) chickpea variety. Re-sequencing of additional 90 genotypes provided millions of genetic markers and low diversity genome regions that may be used in the development of superior varieties with enhanced drought tolerance and disease resistance. This will help chickpea farmers become more resilient to emerging challenges brought about by the threat of climate change. The genome map can also be used to harness genetic diversity by broadening the genetic base of cultivated chickpea genepool.

Chickpea is the second largest cultivated grain food legume in the world, grown in about 11.5 million hectares mostly by resource poor farmers in the semi-arid tropics. The highly nutritious, drought-tolerant chickpea contributes to income generation and improved livelihoods of smallholder farmers in African countries like Ethiopia, Tanzania and Kenya, and is crucial to the food security in India (being the largest producer, consumer and importer of the crop). Chickpea is also an important component of the pulse industry in Australia, Canada and USA.

"ICRISAT and its partners have once again demonstrated the power of productive partnerships by achieving this breakthrough in legume genomics," says Dr William Dar, Director General, ICRISAT. "Under the CGIAR Research Program (CRP) on Grain Legumes led by ICRISAT along with other CGIAR Consortium members and program as well as national partners, genome sequencing will play a crucial role in speeding up the development of improved varieties for smallholder farmer crops such as chickpea."

"In the face of the growing global hunger and poverty amid the threat of climate change, the chickpea genome sequence will facilitate the development of superior varieties that will generate more income and help extricate vulnerable dryland communities out of poverty and hunger for good, particularly those in the drylands of Asia and sub-Africa for whom ICRISAT and our partners are working," Dr Dar adds.

"Genetic diversity, an important prerequisite for crop improvement, is very limited and has been a serious constraint for chickpea improvement. This study will provide not only access to 'good genes' to speed up breeding, but also to genomic regions that will bring genetic diversity back from landraces or wild species to breeding lines," explains Dr Rajeev Varshney, coordinator of ICGSC and Director Center of Excellence in Genomics, ICRISAT.

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Global research team decodes genome sequence of 90 chickpea lines

Jan. 28, 2013 In a scientific breakthrough that promises improved grain yields and quality, greater drought tolerance and disease resistance, and enhanced genetic diversity, a global research team has completed high-quality sequencing of not one but ninety genomes of chickpea.

Nature Biotechnology featured the reference genome of the CDC Frontier chickpea variety and genome sequence of 90 cultivated and wild genotypes from 10 different countries, as an online publication on 27 January 2013. The paper provides a map of the structure and functions of the genes that define the chickpea plant. It also reveals clues on how the sequence can be useful to crop improvement for sustainable and resilient food production toward improved livelihoods of smallholder farmers particularly in marginal environments of Asia and sub-Saharan Africa.

The research milestone was the result of years of genome analysis by the International Chickpea Genome Sequencing Consortium (ICGSC) led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) headquartered in Hyderabad, Andhra Pradesh India, involving 49 scientists from 23 organizations in 10 countries. ICRISAT is a member of the CGIAR Consortium.

The global research partnership succeeded in identifying an estimated 28,269 genes of chickpea after sequencing CDC Frontier, a kabuli (large-seeded) chickpea variety. Re-sequencing of additional 90 genotypes provided millions of genetic markers and low diversity genome regions that may be used in the development of superior varieties with enhanced drought tolerance and disease resistance. This will help chickpea farmers become more resilient to emerging challenges brought about by the threat of climate change. The genome map can also be used to harness genetic diversity by broadening the genetic base of cultivated chickpea genepool.

Chickpea is the second largest cultivated grain food legume in the world, grown in about 11.5 million hectares mostly by resource poor farmers in the semi-arid tropics. The highly nutritious, drought-tolerant chickpea contributes to income generation and improved livelihoods of smallholder farmers in African countries like Ethiopia, Tanzania and Kenya, and is crucial to the food security in India (being the largest producer, consumer and importer of the crop). Chickpea is also an important component of the pulse industry in Australia, Canada and USA.

"ICRISAT and its partners have once again demonstrated the power of productive partnerships by achieving this breakthrough in legume genomics," says Dr William Dar, Director General, ICRISAT. "Under the CGIAR Research Program (CRP) on Grain Legumes led by ICRISAT along with other CGIAR Consortium members and program as well as national partners, genome sequencing will play a crucial role in speeding up the development of improved varieties for smallholder farmer crops such as chickpea."

"In the face of the growing global hunger and poverty amid the threat of climate change, the chickpea genome sequence will facilitate the development of superior varieties that will generate more income and help extricate vulnerable dryland communities out of poverty and hunger for good, particularly those in the drylands of Asia and sub-Africa for whom ICRISAT and our partners are working," Dr Dar adds.

"Genetic diversity, an important prerequisite for crop improvement, is very limited and has been a serious constraint for chickpea improvement. This study will provide not only access to 'good genes' to speed up breeding, but also to genomic regions that will bring genetic diversity back from landraces or wild species to breeding lines," explains Dr Rajeev Varshney, coordinator of ICGSC and Director -- Center of Excellence in Genomics, ICRISAT.

"At the moment, it takes 4-8 years to breed a new chickpea variety. This genome sequence could reduce to half the time to breed for a new variety with market-preferred traits." he adds.

According to Professor Jun Wang, Director of BGI, "The collaboration between BGI and ICRISAT has yielded significant achievements in orphan crops research, like the pigeonpea genome before and now, the chickpea genome. I believe that our partnership will revolutionize research on orphan crops, which are key staple crops in many low-income countries and are extremely important to smallholder farmers worldwide. The chickpea genome sequencing project was undertaken by the ICGSC led by ICRISAT, the University of California-Davis (USA) and BGI-Shenzhen (China) with key involvement of national partners in India, USA, Canada, Spain, Australia, Germany and Czech Republic.

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Genome sequence of 90 chickpea lines decoded