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.

Source: ICRISAT Happenings