Fwd: FW: Application to Illumina Agricultural Greater Good Initiative - African pigs and related species

-------- Original Message --------

From: ARCHIBALD Alan <alan.archibald@roslin.ed.ac.uk>

Sent: 31 October 2019 14:22
To: DJIKENG Appolinaire <appolinaire.djikeng@ctlgh.org>; Djikeng,
Appolinaire (ILRI) <A.Djikeng@cgiar.org>; Dzama, K <kdzama@sun.ac.za>
<kdzama@sun.ac.za>; Mapholi, Ntanganedzeni <maphon@unisa.ac.za>; Okoth,
Edward (ILRI) <E.OKOTH@CGIAR.ORG>; Richard Osei-Amponsah
<rich12668@yahoo.co.uk>; Sargent, Carole <cas1001@cam.ac.uk>
Cc: EORY Lel <Lel.Eory@roslin.ed.ac.uk>; MATIKA Oswald
<oswald.matika@roslin.ed.ac.uk>
Subject: Application to Illumina Agricultural Greater Good Initiative -
African pigs and related species

Dear all,

In previous bilateral correspondence we have discussed the possibilities
of characterising the genomes of African indigenous pigs and related
Suidae species by sequence analyses.

The Illumina Agricultural Greater Good Initiative may offer an
opportunity to turn this ambition into reality. Illumina will provide
the reagents to generate 20 Terrabases of sequence data on their NovaSeq
platform to the winner of the 2019-20 competition.

As far as I can see, there has not been a pig project amongst previous
Illumina Agricultural Greater Good Initiative winners. Previous winning
projects have included one to sequence African goats and one to use
Illumina SNP chips to characterise African sheep and goats.

I think that we could use the current global African Swine Fever crisis
to justify a project to characterise African indigenous pigs and Suidae
species known to be tolerant to ASFV.

20 Terrabases of sequence data would provide 30x genome coverage of 220
individuals assuming a genome size of 3 Gbp. At 15x genome coverage 20
Tbp would allow 400+ individuals to be sequenced.

The application could be based around the argument that 1) until
recently ASF was essentially confined to Africa where it is a constraint
on pig production; 2) knowledge of genetic diversity in tolerant African
Suidae species such as the common warthog is very limited; 3) knowledge
of the genetic diversity of African indigenous pigs is also limited.
Sequence data on African indigenous pigs and related Suidae species,
e.g. warthog, would support analyses to identify signatures of selection
that may have been shaped by African environmental challenges, including
diseases such as ASF. The signatures of selection identified in other
pig populations to date do not appear to include ones shaped by disease
challenges.

The limitations of the Illumina awards include lack of support for
sample collection and processing, including the isolation of DNA. There
is also no provision for data analyses or compute.

The challenges to deliver such a project include the logistics of sample
collection, DNA isolation, and regulatory issues in terms of
transferring DNA samples to a sequencing centre with a NovaSeq platform.
Edinburgh Genomics has the NovaSeq platform, but if there are centres in
Africa with necessary NovaSeq hardware, then they may simplify the
sample transfer issues. The regulatory challenges include compliance
with the Nagoya Protocol and with veterinary hygiene. The latter may be
particularly acute given the ASF context.

In the past Illumina have provided reagents to the winners to support
data generation in the winners' labs. However, some of the wording in
the 2019-20 announcement suggests that Illumina will generate the data
on samples provided to them - transferring DNA from African pigs and
warthogs to Illumina in San Diego may be a challenge from a legal and
regulatory viewpoint. I will seek clarification.

The final challenge is completing an application in time for the 6
December deadline. Fortunately the application form is relatively simple
and the case for support required is brief.

All data generated in any such project would be the shared property of
the applicants and collaborators. Authorship of publications would be
shared by all participants. There would be opportunities for training,
although separate funding would be required to support travel and
exchanges between laboratories.

So the questions are:

- Are you interested in joining such an application

- What samples (indigenous African pigs and warthogs) could you
share?

Regards

Alan Archibald

Professor Alan L. Archibald FRSE

Chair of Mammalian Molecular Genetics

The Roslin Institute and Royal (Dick) School of Veterinary Studies
University of Edinburgh Easter Bush Midlothian EH25 9RG Scotland, U.K.

tel: +44 (0) 131 651 9100

fax: +44 (0) 131 651 9105

email: alan.archibald@roslin.ed.ac.uk

web: https://www.ed.ac.uk/roslin [1]

Note: With effect from 1 April 2018 I am working part-time (3 days a
week).

From: Illumina <community@illumina.com>
Sent: 18 October 2019 09:51
To: ARCHIBALD Alan <alan.archibald@roslin.ed.ac.uk>
Subject: Don't miss the opportunity to win 20 Tb of NovaSeq sequencing
data: learn about the Illumina Agricultural Greater Good Initiative

View on Webpage [2]

Learn More and Apply [3]

www.illumina.com [4]

At Illumina, we believe in a sustainable future and we are committed to
supporting innovative solutions to feed the planet responsibly.

Our Greater Good Initiative grant program recognizes researchers making
tangible contributions focused on reducing global hunger, malnutrition,
and poverty. We are committed to enabling ground-breaking studies that
change the world for the better with your help.

Launched for the first time in 2011, The Greater Good Initiative grant
program is designed to help identify measures that can increase crop
yields and improve livestock welfare to alleviate poverty in the
developing world.

The Grand Prize winner will receive 20 terabases of Illumina NovaSeq
sequencing data on samples of your choice (check Terms & Conditions
[3]). The winner will be announced during the Illumina Workshop at PAG
XXVIII in San Diego on January 11-15, 2020.

Who can apply?
The grant program is open to basic researchers in agrigenomics at
academic, government, or nonprofit institutions.

To get inspired, watch this video [5] and learn how the grant has helped
our past winners to advance their research.

How to apply?
Applications for the 2020 Agricultural Greater Good Initiative grants
are currently being accepted. The deadline for all 2020 applications is
December 6, 2019.

[3]

LEARN MORE AND APPLY [3]

[3]

At any time, you may update your marketing email preferences, or
unsubscribe from marketing emails by clicking here [6].

Illumina Cambridge | The Illumina Centre
19 Granta Park | Great Abington, Cambridge, CB21 6DF

www.illumina.com [7] | Unsubscribe [8] | Update Profile [9]

[10] [11] [12] [13]

Update Profile [14]



Links:
------
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[2]
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[4]
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[5]
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[6]
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