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.

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

9. 10+ conferences organized
3000+ participants

10. 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

11. 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

12. 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.)

13. 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

14. 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

15. 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

16. 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.

17. • 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..