09 May 2014
No. 1622


High throughput sequencing and high performance computational facility at ICRISAT to boost genomics for breeding

The inauguration of the new facility at CEG led by Prof C Madramootoo (4th from right) with
(L-R) Drs W Dar, O Muoyo, P Sereme, R Chikwamba, R Varshney and D Delmer. Seen behind is Dr G Agarwal. Photo: PS Rao, ICRISAT

New high-end facility key in advancing “The 3000 Chickpea Genome Sequencing Initiative”

The Illumina HiSeq 2500 – the world’s most powerful sequencer – promises full utilization of modern genomics tools in breeding and research programs at ICRISAT and in other partner institutes in developing countries of Asia and sub-Saharan Africa.

To analyze, store and share huge sequence data, a high performance computational genome analysis (HPCGA) facility with two servers, each having 80 cores (total 160 cores), running on 1,000 Gb and 500 Gb RAM, respectively, with a total storage capacity of 100 Tb has been established.

The first of its kind among CGIAR Centers, this facility is envisioned to make ICRISAT’s Center of Excellence in Genomics (CEG) a leader in crop genome sequencing and analysis to elevate crop improvement programs.

The CEG makes available highly sophisticated protocols and equipment required for genomics research to NARS partner scientists to boost their breeding works, and offers genotyping and sequencing service at a cost, coupled with support in data analysis and interpretation. It also empowers NARS partners in Asia and Africa in modern breeding by providing training courses on data analysis and use of molecular markers in breeding programs.

“Now we will be able to sequence and analyze several hundred genomes and several thousand transcriptomes of chickpea, pigeonpea, and sorghum per day with this new facility, and share the benefits with our NARS partners,” said Dr Rajeev Varshney, Research Program Director - Grain Legumes, and Director, CEG. The Illumina HiSeq 2500 delivers the highest daily throughput and can generate 160 Gb per day or 1Tb per run sequence data.

The new facility at CEG was inaugurated by ICRISAT Board Chair, Prof Chandra Madramootoo, along with former Board Chair, Dr Nigel Poole; Dr Deborah J Delmer, Chair of the Board’s Program Committee; other members of the Board; and Director General Dr William D Dar, as a side event of the 70th Governing Board meeting held recently.

“Genomics is an integral part of ICRISAT’s three-pillar approach to speed up breeding, along with phenotying and breeding informatics. This facility will ensure leading edge science in the development of improved varieties for smallholder farmer crops such as chickpea, pigeonpea and sorghum,” Dr Dar emphasized.

“It feels good to see such modern facilities that can deliver excellent outputs in genomics,” Dr N Poole said. Prof C Madramootoo and Dr Molapo Qhobela, outgoing Board member, appreciated ICRISAT’s efforts not only in establishing the advanced facility but also in demonstrating its use in generating high-quality outputs for applications in crop improvement as well as in publishing high impact factor publications.

Ms Anu Chitikineni, Manager, CEG, explained that the HiSeq 2500 machine could sequence a large number of samples in parallel at greater depth. For instance, the machine can process 146 (rapid run mode) and 74 (high output mode) genomes (1X coverage) or more than 1,400 transcriptomes (10% of the genome) of chickpea, pigeonpea, or sorghum in just one day. The HiSeq 2500 system is perfect for large-scale sequencing projects or studies involving large number of samples. Dr Krishnamohan Katta and Dr Gaurav Agrawal, Special Project Scientists – Computational Genomics, briefed the Board members on the storage and analysis power of the facility.

During the inauguration of the facility, “The 3000 Chickpea Genome Sequencing Initiative” was launched by Prof C Madramootoo. He pressed the “start” button to sequence the first set of 96 lines from the 3000 chickpea germplasm set. “Sequencing efforts will not only provide useful alleles for chickpea improvement but also enhance the visibility of ICRISAT at the international level,” said Prof Madramootoo.

Highlighting the importance of inviting partners in this initiative, Dr Dar said, “By working with partners around the world, we should be able to better understand genome architecture and mine good genes to enhance chickpea productivity.”

The project aims to undertake the sequencing of the global chickpea collection to identify superior alleles and use them in the breeding program for chickpea improvement. The initiative is being coordinated by Dr R Varshney, along with a team of ICRISAT scientists namely, Manish Roorkiwal, Anu Chitikineni, Mahendar Thudi, Hari Upadhyaya, Pooran Gaur, Vinay Kumar, N Lalitha, Abhishek Rathore, Trushar Shah, Krishna Mohan Katta and Gaurav Agarwal. The project will be undertaken as part of the CGIAR Research Program on Grain Legumes.

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Agri-Biz Idol Camps encourage and engage India’s youth in agribusiness

Left) First prize winner Mr V Dev making a presentation on ‘Hyacinth removal device’. (Right) Ms N Kittur receiving the award from Mr Karuppanchetty. Photo: ICRISAT

Highlighting opportunities in agribusiness for the youth, the National Agriculture Innovation Project (NAIP) of the Indian Council of Agricultural Research (ICAR) has embarked on a unique initiative called Agri-Biz Idol Camps. Aimed at reaching out to the youth and start-up entrepreneurs and to showcase the tremendous potential of agribusiness, the camps were successfully organized in five Indian cities, namely Hyderabad, New Delhi, Pune, Coimbatore and Anand from 5 to 9 May.

The camps helped participants understand the various business incubation services offered by NAIP’s Business Planning and Development (BPD) Units. The BPDs primarily act as an agriculture incubation center helping start-ups or entrepreneurs foraying into the agri-business to flourish by providing comprehensive business solutions.

At the camp in Hyderabad on 5 May, start-ups and agri-students were provided with an ideal platform to pitch their business ideas and develop new agri-ventures. Thirty-four students from the National Academy of Agricultural Research Management (NAARM) took part in the event along with representatives from five industries.

A total of 12 ideas were pitched at the event, of which two best presentations have been shortlisted for the Agri-Innovation Conclave to be held in New Delhi on 18-19 May. The top two ideas shortlisted are ‘Innovative hyacinth removal device’ by Mr Godasu Narsimhu and Mr Vasu Dev; and ‘Hydroponics based vertical farming’ by Ms Nazhat Kittur and Mr Shelke Sagar.

Present on the occasion were Dr SL Goswami, Director, NAARM; Dr Kalpana Sastry, Joint Director, NAARM; Mr SM Karuppanchetty, Chief Operating Officer, Agri-Business Incubation Program (ABI), ICRISAT; Brigadier Ganeshan from Palle Srujana (an NGO); and Mr Rakesh Reddy, Director, Vishvawani Management Institute.

The BPDs cover the entire spectrum of agribusiness including agriculture, horticulture, veterinary and livestock, fisheries and marine products, animal husbandry, crop production, food processing and agri-inputs, agri-engineering, textile and industrial processing, and postharvest management. ICRISAT’s ABI is currently extending its handholding and mentoring services to the 22 BPDs set up under the World Bank-funded NAIP.

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Inanglupa movement advocates a new Philippine agriculture

Unveiling of the Inanglupa movement logo by Dr WD Dar, with members of the movement’s advisory council and other supporters. Photo: J Soriano, ICRISAT

ICRISAT Director General Dr William D. Dar is spearheading a social movement, called Inanglupa (Mother Earth) that advocates an inclusive, science-based, climate-resilient and market-oriented Philippine agriculture by the year 2020 and beyond.

“Our movement will complement and enhance efforts of the government – particularly the Departments of Agriculture (DA), Environment and Natural Resources (DENR), and Science and Technology (DOST) – local government units, the private sector, academe and farmers’ groups to attain food and nutrition security, economic prosperity, and environmental sustainability,” said Dr Dar, founder and president of Inanglupa, during its recent launch in the Philippines.

“Through Inanglupa, we will help empower small farmers in marginal, rainfed and upland areas, enabling them to adopt natural resource management technologies such as soil and water management, and rainfall harvesting to nurture their crops and ensure they have the needed macro and micro elements for productive and sustainable growth,” added Dr Dar. He also stressed that the movement will complement the Yamang Lupa program, which adopts the Bhoochetana principles, a partnership between ICRISAT and the DA.

The group has crafted an Inanglupa roadmap to attain its vision of a new Philippine agriculture by the year 2020 and beyond, with five development outcomes: food sufficiency, ensuring nutritional security, increasing per capita income, climate-resilient agriculture, and social development.

“These goals could be achieved by partnering with concerned agencies like the DA, DENR and DOST and other stakeholders to pursue an innovative agenda,” said Dr Dar.

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Understanding social media for development

The social media team at the Forests Asia Summit 2014. Photo: ICRISAT

To better utilize social media in communicating developmental messages effectively, the Center for International Forestry Research (CIFOR) organized a training program for social media professionals, journalists, communication officers of non-profit organizations, and students as part of the Forests Asia Summit 2014 held in Jakarta, Indonesia on 5-6 May.

Over sixty participants were trained in the best social media channels involving live tweeting, blogging, and podcasting, as well as their uses within a professional environment, and how to pull all these tools into a strategy for social reporting.

The participants were also given an opportunity to join the main summit, in which 2000 participants including the President of Indonesia, Dr Susilo Bambang Yudhoyono, ministers from various Southeast Asian countries, CEOs, civil society leaders, development experts and the world’s top scientists, were in attendance.

Participating in the social media training, Mr Showkat Nabi Rather, Media Liaison Officer, Strategic Marketing and Communication, published two blog posts and contributed live tweets during the main summit. His post titled, ‘Believe it or not! Indonesia planted 4 billion trees in last 4 years’ http:/www.cifor.org/forestsasia/believe-indonesia-planted-4-billion-trees-4-last-years was among the three best blogs at the summit.

The social media training led by Mr Peter Casier, Social Media Consultant from the CGIAR Consortium was one of the best social media campaigns by the CGIAR. The total reach was 2,435,281 users on Twitter with over 8000 tweets and 30 blog posts.

The Forests Asia Summit organized by CIFOR and co-hosted by the Indonesian Ministry of Forestry – was the largest in Asia in recent years and attracted more than 1,000 leading stakeholders from Southeast Asia and across the world. Thousands more participated online or through nationwide broadcasts.

There were special learning events with leading global experts on the green economy, the Southeast Asian haze crisis, climate change negotiations, and Sustainable Development Goals.

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