Category Archives: Genome

Global research team decodes chickpea genome
Global research team decodes chickpea genome 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. Link to full paper on Nature Biotechnology Journal: http://www.nature.com

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Global research team decodes chickpea genome - Video

New Technology and ENCODE Reveals Incredible Genome
New Technology Reveals More Genome Complexity http://www.icr.org ENCODE Reveals Incredible Genome Complexity and Function http://www.icr.org

By: Dave Flang

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New Technology and ENCODE Reveals Incredible Genome - Video

It Takes a Genome How a Clash Between Our Genes and Book Review
http://www.qbba.com Human beings have astonishing genetic vulnerabilities. More than half of us will die from complex diseases that trace directly to those vulnerabilities, and the modern world weve created places us at unprecedented risk from them....

By: Teva West

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It Takes a Genome How a Clash Between Our Genes and Book Review - Video

Chickpea genome decoded
In a breakthrough that promises improved grain yields and quality, greater drought and disease resistance and enhanced genetic diversity, a global research team has completed high-quality sequencing of not one but 90 genomes of chickpea. For more log on to http://www.newsx.com Follow NewsX on Facebook at https

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Chickpea genome decoded - Video

New delhi, Jan 28:

In a major breakthrough, a team of global scientists led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) have decoded the genome sequence of chickpea or chana.

The genome sequencing would help plant breeders develop newer varieties that can yield more and are drought and disease tolerant. The development assumes significance as India is the largest producer, consumer and importer of chickpea.

It will be a boon to small farmers as genome sequencing will play a crucial role in accelerating the development of new and improved varieties, said William Dar, Director-General, ICRISAT. Genome sequencing could help raise the yield potential to about 2 tonnes per hectare from the current 1 t per ha, he said.

About 49 scientists from 23 organisations in 10 countries, including the Indian Council of Agriculture Research, collaborated in the genome analysis. The Hyderabad-based ICRISAT led the International Chickpea Genome Sequencing Consortium that sequenced 90 chikpea genomes. The University of California-Davis, BGI-Shenzen and research partners in countries such as Canada, Australia and Germany collaborated in the genome analysis.

An estimated 28,269 genes of chickpea were identified during the project that last for more than two years, said Rajeev Varshney, leader of the chickpea genome sequencing consortium.

Varshney said the sequencing would help reduce the time to breed new chick pea varieties as plant breeders would now have access to genes with the required traits. Currently, it takes four to eight years to breed a new chickpea variety.

Chick pea is mainly grown by small and marginal farmers. Any breakthrough in research through new varieties would help farmers realise better incomes, said Ashish Bahuguna, Agriculture Secretary.

Chickpea is the second largest pulse crop in the world, grown in about 11.5 million hectares. The highly nutritious crop is grown mostly by poor farmers and in dry areas. Besides India, chana is also is grown in a number of African countries including Ethiopia, Tanzania and Kenya. It is also an important component of the pulse industry in Australia, Canada and the US.

Vishwanath.kulkarni@thehindu.co.in

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Icrisat-led global team decodes genome sequence of chickpea

New delhi, Jan 28:

In a major breakthrough, a team of global scientists led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) have decoded the genome sequence of chickpea or chana.

The genome sequencing would help plant breeders develop newer varieties that can yield more and are drought and disease tolerant. The development assumes significance as India is the largest producer, consumer and importer of chickpea.

It will be a boon to small farmers as genome sequencing will play a crucial role in accelerating the development of new and improved varieties, said William Dar, Director-General, ICRISAT. Genome sequencing could help raise the yield potential to about 2 tonnes per hectare from the current 1 t per ha, he said.

About 49 scientists from 23 organisations in 10 countries, including the Indian Council of Agriculture Research, collaborated in the genome analysis. The Hyderabad-based ICRISAT led the International Chickpea Genome Sequencing Consortium that sequenced 90 chikpea genomes. The University of California-Davis, BGI-Shenzen and research partners in countries such as Canada, Australia and Germany collaborated in the genome analysis.

An estimated 28,269 genes of chickpea were identified during the project that last for more than two years, said Rajeev Varshney, leader of the chickpea genome sequencing consortium.

Varshney said the sequencing would help reduce the time to breed new chick pea varieties as plant breeders would now have access to genes with the required traits. Currently, it takes four to eight years to breed a new chickpea variety.

Chick pea is mainly grown by small and marginal farmers. Any breakthrough in research through new varieties would help farmers realise better incomes, said Ashish Bahuguna, Agriculture Secretary.

Chickpea is the second largest pulse crop in the world, grown in about 11.5 million hectares. The highly nutritious crop is grown mostly by poor farmers and in dry areas. Besides India, chana is also is grown in a number of African countries including Ethiopia, Tanzania and Kenya. It is also an important component of the pulse industry in Australia, Canada and the US.

Vishwanath.kulkarni@thehindu.co.in

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Global team led by ICRISAT scientists decode genome sequence of chana

The fruit fly Drosophila has long been one of the workhorses of genetics and developmental biology. But for many genomic studies, fruit flies have had one big disadvantage: their small size.

As sequencing has become more sophisticated, experiments that were not possible in the fly just a few years ago, such as analyzing gene expression changes in a few cells, are now quite possible, says Don Fox, an Assistant Professor in the Department of Pharmacology and Cancer Biology.

Fox is taking advantage of that new potential to investigate two separate but partially overlapping areas of study. First of all, he wants to know which genes spring into action when tissues get injured and how that changes as flies advance into old age. Second, his lab is preoccupied with cells in the fly gut that are particularly prone to duplicating their genomes, forming genomically unstable polyploid cells similar to those that turn up in many human cancers. Fox wants to know exactly what it is that makes those cells unstable.

He is using sequencing approaches both to characterizethosepolyploidgenomesandto explore gene expression changes over time, with data generated in the IGSPs Genome Sequencing & Analysis Core Resource. Fortunately for Fox who arrived at Duke a year ago well-versed in genetics and cell biology and just beginning to tackle questions on a genomic scale his new lab is positioned right across the hallway from his colleague and long-time IGSP member Dave MacAlpine.

MacAlpine and his team are experts in genome biology,havingplayed animportantrolein modENCODE, an effort to classify all of the regulatory elements in the fly genome. The MacAlpine and Fox labs meet weekly in what is a mutually beneficial collaborative arrangement; Fox gains support in genomics and bioinformatics while MacAlpine gainssupportinmovingfromapproachesin Drosophila cell lines to those in whole fruit flies.

Its allowed my lab to be kind of fearless, Fox says. We can take on these bioinformatics-heavy experiments, which can easily be overwhelming. When I was contemplating where to start a lab, that opportunity for collaboration at Duke was a huge selling point.

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Sophisticated Genome Biology in the Tiny Fruit Fly

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