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Research Program Genetic Gains (RPGG) Review Meeting 2021: Update on Sequencing & Informatics Services Unit By Ms Anu Chitikineni

  1. Wednesday 06-January, 2021 Anu Chitikineni Senior Manager – CEGSB a.chitikineni@cgiar.org Sequencing & Informatics Services Unit (SISU) Research Program – Genetic Gains
  2. SSR genotyping High-throughput sequencing Medium throughput sequencing High Performance Computational Genome Analysis facilitySNP genotyping  600 cores  830 TB storage  7.5 TB RAM Genotypingandsequencingplatforms
  3. Sequencing & genotyping  Whole genome re-sequencing  Transcriptome sequencing  Genotyping by sequencing  Small RNA sequencing  Chip sequencing  Targeted sequencing  SNP and SSR genotyping  DArT genotyping  16s rRNA sequencing  Metagenome sequencing Informatics  High throughput computational facility (600 cores, ~830 TB storage and 7.5 TB RAM)  QC analysis of sequence data  Sequence alignment to genome  Structural variant analysis  GBS analysis  ChIP-Seq and methylation analysis  RNA-Seq and transcriptome profiling  Whole proteome analysis  NGS data management and sharing
  4. SSR 6.5M data points 1.7M samples DArT 75K data points 2K samples KASPar 1.5M data points 4K samples VeraCode SNP assays 75K data points 1K Samples GBS 5TB data 18K samples RNA-seq 2TB data 280 Samples Small RNA 130 GB data 132 Samples WGRS 45TB data 4.5K samples 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017  Sequencing Costs may vary according to the genome size & coverage Sequencing & Genotyping Technologies…
  5. High throughput DNA extraction methods @CEGSB NaOH DNA extraction • Where no refrigerator, no centrifuge • 5 min/plate + = Zou et al., (2017) PLoS Biology • 30 seconds/sample, Modifying to scale to full-plate extractions Conventional Phenol-Chloroform Macherey Nagel DNA Extraction
  6. Capacity Building Activities: • Hosting students/scientists from developing countries • 15 CEGSB training courses organized and > 485 scientists (120 women) trained • >150 PhD students/researchers trained • Around 10 international and national conferences/ workshops organized • InterDrought-V conference-2017 >900 delegates- 315 organizations of 56 countries. Also 6 NGGIBCI conferences. • Encouraging adoption of molecular breeding in developing countries by providing services & training.
  7. CEGSB Trainings (2008-2020) Trainings conducted Total participants trained From 36 countries 117 368 193 NARS/Public/CGIAR Institutes 422 63 20 PVT. companies Participants from India: 365; ESA : 49; WCA: 40 and others 31
  8. 10+ conferences organized 3000+ participants
  9. Collaborations with Asia • Training of 365 scientists from India, 16 from other Asian countries including Bangladesh, Myanmar, Nepal, Pakistan, Srilanka, Philippines, Malaysia, Thailand, and Uzbekistan, 3 from S Arabia, Turkey and Syria • Research collaborations: RP Asia scientists - Pooran Gaur, Srinivasan Samineni, P Janila, SK Gupta, Ashok Kumar, Govindaraj M, Mamta Sharma, Gopalakrishnan, Hari Sudini, Rajan Sharma, and several others • Sequencing & genotyping support: ICAR institutes- IIPR, IIMR, DGR, IARI, IIVR, IIRR, etc., several SAUs and many Private sector organizations India Andhra Pradesh 45 Assam 16 Chandigarh 1 Chhattisgarh 4 Gujarat 12 Haryana 7 Himachal Pradesh 10 Jammu & Kashmir 1 Jharkhand 1 Karnataka 45 Kerala 7 Madhya Pradesh 7 Maharashtra 22 Manipur 1 Nagaland 1 New Delhi 13 Orissa 2 Punjab 5 Rajasthan 12 Tamil Nadu 22 Telangana 96 Uttar Pradesh 25 Uttarakhand 5 West Bengal 5 Total 365
  10. Research scholars/ Visiting Scientists from Asia hosted Country Master’s Ph.D. Scientists Others Total 1 India 19 40 7 2 68 2 China 12 12 3 South Korea 1 1 4 Thailand 1 1 Total 20 41 19 2 82 & in addition to Asia, ESA, WCA, also hosted from several developed countries – Australia, Germany, Austria, Spain, UK and USA as well as Middle East and Arab world like Syria, Turkey, Saudi Arabia
  11. Collaborations with WCA: CEG Training 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Total 1 Burkina Faso 1 1 4 6 12 2 Ghana 1 1 2 2 6 3 Mali 1 2 1 4 8 4 Niger 1 1 5 Nigeria 1 1 1 1 2 2 5 13 Hosted 40 students/scientists from WCA (Issa Faye, Adama Zongo, Sanusi Gaya, Dramane Sako etc.)
  12. Collaborations with ESA • More than 50 scientists have been trained (Ethiopia-13, Malawi-10, Mozambique-1, Tanzania-13, Uganda-10 • ICRISAT Nairobi- Damaris Odeny, Gangarao NVPR, Eric Manyasa Henry Ojulong, Akpo Essegbemon, Chris Ojiewo • ICRISAT Malawi- Patrick Okori, Wanjiku Gichohi • ICRISAT Bulawayo- look forward to collaborate • Supporting NARS: Tanzania (Happy Daudi), Uganda (David Okello)- Groundnut, Ethiopia(Nigussie Girma), Kenya (Paul Kimurto)-Chickpea
  13. List of scholars from ESA hosted at CEGSB 1 Mussa Jarso Hedo Male Ethiopia (from EIAR) 2 Kebede Teshome Kibret Male Ethiopia Haramaya University 3 Serah C Songok Female Kenya Egerton University 4 Seleman Kaoneka Male Tanzania University of Nottingham 5 Obala Jimmy Male Uganda Makerere University 6 Alice Kosegi Female Kenya Egerton University 7 Tsegaye Getahun Bogale Male Ethiopia Addis Ababa University
  14. CEGSB’s JOURNEY 2007- 2020 15 papers in Nature Journals 500+ Journal articles 11 crop genomes sequenced 180+ partners from 35 countries 115 R&D Projects US$ 99 M brought 15 trainings, 485 scientists & 200+ students/post- docs/ visiting scientists 15 conferences/ workshops/Symposia with 3000+ participants 50+ Awards & fellowships More than a decade of excellence in science and partnership…. 6 Mol. Breeding varieties released
  15. Opportunities.. A range of marker genotyping platforms have been made available to breeders/ researchers from ICRISAT and NARS from all regions. It will be great if CESGB/SISU can be upgraded with new machines. GTD/FB colleagues developing new marker genotyping platforms- mid- density SNP arrays. Therefore, researchers and breeders are encouraged to avail sequencing and genotyping facilities from SISU to accelerate their research and modernize breeding programs.  Based on the track record in genomics and capacity building, CEGSB/ICRISAT may be projected as “genomics hub” in Asia under ONE CGIAR. We had some discussions on this aspect from some sequencing labs/centres in CGIAR including BeCA.
  16. • Playing a significant role in capacity building of NARS partners around the world that are key to ICRISAT and CRP. However, SISU staff doesn’t receive any support from institutional activities – CRP, CtEH, AVISA, etc. Some provisions should be made so that staff providing services can be taken care. • Not all researchers/breeders from ICRISAT are availing sequencing/ genotyping services from SISU/CEGSB. It is requested that like IRRI and other centres, all genotyping/sequencing work (including outsourcing) should be done through SISU/CEGSB for better pricing/ coordinated data analysis/ data storage, etc. Challenges..
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