Category Archives: Genome

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

GREAT Leaders Genome: A Leadership Clinic for New and Potential Leaders

By: joe garcia

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GREAT Leaders Genome: A Leadership Clinic for New and Potential Leaders - Video

IranBiotech 2013 Genome data interpretation2
15-19 January 2013, Tehran. Marianna Ivanova, Oftalmic CEO speech. Part 2

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IranBiotech 2013 Genome data interpretation2 - Video

Genome Community Faces A Genetics And Health Forum Project

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Genome Community Faces A Genetics And Health Forum Project - Video

Genome How To Sequence A Genome 5 Preparing Dna For Sequencing

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Genome How To Sequence A Genome 5 Preparing Dna For Sequencing - Video

OmicsOffice SeqSolve Custom Genome Annotation Tutorial
Learn how to load in OmicsOffice-SeqSolve and use your Custom Genome Annotation in the NGS data analysis

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OmicsOffice SeqSolve Custom Genome Annotation Tutorial - Video

Genome structural variation (2013)
The Primer on Medical and Population Genetics is a series of informal weekly discussions of basic genetics topics that relate to human populations and disease. Experts from across the Broad Institute community give in-depth introductions to the basic principles of complex trait genetics, including human genetic variation, genotyping, DNA sequencing methods, statistics, data analysis, and more. Videos of these sessions are made freely available for viewing here and are geared toward a wide audience that includes research technicians, graduate students, postdoctoral fellows and established investigators just entering the field. For more information, please visit: -Program in Medical Population Genetics (www.broadinstitute.org -Primer videos (www.broadinstitute.org

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Genome structural variation (2013) - Video

Human Genome Analysis in Excel
DNA is the software of life and provides a 3 billion character puzzle that is still not completely understood. This year I will attempt to import my complete genome into MIcrosoft Excel and use PIvot Tables and Charts to learn more about the DNA sequence and how it provides a blueprint for cellular composition and sources biological processes.

By: abravermancan

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Human Genome Analysis in Excel - Video

Public genome data is a significant risk to individuals, according to research led out by Yaniv Elrich, a geneticist at the Whitehead Institute for Biomedical Research.

The team that Elrich led was able to de-anonymise genome data using only public information and careful Internet searches. A little chillingly, individuals could be associated with patrilineal genetic characteristics, even if they werent in the databases. A family members presence in the database can be enough, if theyre related in the male line and carry the same surname.

Working with data published in two public genomic databases, Ysearch and SMGF, Elrich demonstrated the privacy risk by matching chromosome data with 50 individuals, in a paper published in Science (abstract here, full paper available free with registration).

Among the genome data recorded in the databases is a genetic marker called short tandem repeats (for which genetic science hasnt yet identified a specific purpose), which are passed down the male line.

As the paper notes, it had been assumed that listing surnames in the databases didnt place individual identity at risk, since surnames could match thousands of individuals. However, the genome data has become a genealogy tool as well, in databases such as YBase.

DNA sequencing pioneer Dr Craig Venter volunteered as a test subject in the research. With only the relevant DNA sequence, Dr Venters age, and the US state where he lives, Erlich was able to retrieve just two possible records one of which was Dr Venter.

With a known surname, the searches become even more accurate: Combining the recovered surname with additional demographic data can narrow down the identity of the sample originator to just a few individuals, Erlich states in the paper.

Surname inference from personal genomes puts the privacy of current de-identified public data sets at risk, it continues.

In five surname recovery cases, we fully identified the CEU* individuals and their entire families with very high probabilities data release, even of a few markers, from one person can spread through deep genealogical ties and lead to the identification of another person who might have no acquaintance with the person who released his genetic data.

*CEU refers to a particular genetic dataset: multigenerational families of northern and western European ancestry in Utah who had originally had their samples collected by CEPH (Centre dEtude du Polymorphisme Humain).

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Public genome databases can leak identity

Using publicly available information, researchers found they could figure out the identities of 50 individuals who had loaned their genes to science. Karen Hopkin reports

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Since the first human genome sequence was published, thousands of people have submitted their DNA for scientific analysis. They made these donations anonymouslyor so they thought. Now, using publicly available information, researchers found they could figure out the identities of 50 individuals who had loaned their genes to science. Their results, although not the names of the people, are in the journal Science. [Melissa Gymrek et al., Identifying Personal Genomes by Surname Inference]

Biomedical research depends on the participation of human subjects, and issues of privacy have always been a concern. When scientists share genomic data, they first strip away identifying information, like the individuals name and date of birth. But is that really enough?

Researchers looked at a specific set of markers in genomes whose sequences were in a public database. And they found that by matching up these markers with sequences that people had submitted to genealogy web sites, they could identify some of the genome donors relatives and, with a bit more sleuthing, come up with their actual names.

Of course, many people now post online accounts of whats on their minds or even on their menus. But even those who are relatively relaxed about their privacy might think twice about their genomes going public.

Karen Hopkin

[The above text is a transcript of this podcast.]

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Genome Donators Can Be Sleuthed Out