[all at arabidopsis.uk] Thlaspi arvense natural populations germplasm update

Sedbrook, John jcsedbr at ilstu.edu
Thu Jan 14 21:06:12 GMT 2021 

Hello All,

I hope the New Year is starting off well, all things considered!

Following are some important details regarding the status of the pennycress (Thlaspi arvense) seed collection efforts:

1. Markéta Machová (iNaturalist donor/collector) in the Czech Republic successfully sent to NASC 63 seed packets collected throughout Europe (seed list attached).

2. Dan Wrench (iNaturalist donor/collector) in the United Kingdom recently sent at least 7 collected samples to NASC (seed list attached).

3. Unfortunately, the 29 samples assembled by Alexander Wirth (iNaturalist donor/collector) from throughout Germany are stuck in a DHL warehouse in Germany because of COVID lockdown. DHL has provided no guidance as to when (or even if!) they will be delivered to NASC (seed list attached none the less).

4. Maliheh Esfahanian (PhD student in my lab) has aliquoted seeds collected from over 260 sites in the United States and Canada (Julia Proulx is the iNaturalist Canadian samples donor/collector) (see attached Sedbrook list).
Emma, would it be okay for us to put in the mail to you on Monday these seed packets, with you keeping one set for the ABRC collection and you sending the other set to NASC?
Marcos, are packages being delivered to you now, or is there delivery uncertainty because of COVID and Brexit? If there is risk of the seeds getting stuck in limbo, perhaps ABRC should wait to send you the seeds.
Here is the ABRC address to where I will be sending the Sedbrook-list seeds upon confirmation from Emma:
Arabidopsis Biological Resource Center
Attn: Mariola Castrejon
055 Rightmire Hall
1060 Carmack Road
Columbus OH 43210
USA
Phone: 614 292-9371
Email: abrc at osu.edu<mailto:abrc at osu.edu>

Marcos, am I correct in thinking that you will soon be sending the Thlaspi arvense seeds that you have to the ABRC, with the ABRC forwarding small aliquots (30 to 50 seeds) to me? If so, do you know when you will be mailing those out? We are eager to get them in the pipeline for whole genome sequencing.

5. There are still about 100 collected populations from Canada to be sent to me, which we will then aliquot and distribute. There are also seeds stuck in limbo in Russia (not sure when we will get those).

6. Dario Galanti successfully sent ~200 seed samples (collected at about 30 sites throughout Europe) to NASC. These samples have been whole genome sequenced by Oliver, Claude, and Dario.

6. Ratan, how many seed populations do you have from Minnesota, and when will you be sending aliquots to the ABRC for the ABRC and NASC?

7. Win, am I correct you sent the seeds you collected to the ABRC? If so, how many populations?

Best wishes,
John


--
John C. Sedbrook, PhD
Professor of Genetics
School of Biological Sciences
Campus Box 4120
Normal, IL 61790  USA

Phone: 1 (309) 438-3374


From: Marcos Castellanos Uribe <Marcos.Castellanos at nottingham.ac.uk>
Date: Monday, November 16, 2020 at 10:51 AM
To: John Sedbrook <jcsedbr at ilstu.edu>
Cc: "Somers, David" <somers.24 at osu.edu>, Sean May <Sean.May at nottingham.ac.uk>, "Knee, Emma" <knee.2 at osu.edu>, "marco.castellanos at nottingham.ac.uk" <marco.castellanos at nottingham.ac.uk>, "all at arabidopsis.uk" <all at arabidopsis.uk>, Moisés Expósito Alonso <mexpositoalonso at carnegiescience.edu>, Jeremy Schmutz <jschmutz at hudsonalpha.org>, "Becker,Claude" <claude.becker at gmi.oeaw.ac.at>, Oliver Bossdorf <oliver.bossdorf at uni-tuebingen.de>, "M. David Marks" <marks004 at umn.edu>, Ratan Chopra <rchopra at umn.edu>, "Jacobson, Daniel A." <jacobsonda at ornl.gov>, Winthrop Phippen <wb-phippen at wiu.edu>, Katherine Frels <kfrels at umn.edu>, Dario Galanti <dario.galanti at uni-tuebingen.de>
Subject: Re: [all at arabidopsis.uk] Recap of Thursday's Thlaspi arvense germplasm meeting

[This message came from an external source. If suspicious, report to abuse at ilstu.edu<mailto:abuse at ilstu.edu>]
Hi John,

Thank you for doing this. Hopefully, everything will go smoothly.

Our mailing address is:


Marcos Castellanos
Nottingham Arabidopsis Stock Centre (NASC)
University of Nottingham,
Sutton Bonington Campus,
Plant Science Building,
Loughborough,
LE12 5RD
UK

Email: all at arabidopsis.uk<mailto:all at arabidopsis.uk>
T: +44 115 9513306


Our last working day is December 18th.

If there are any issues with sending the lines (time-wise), please tell the citizen scientists to contact us so we can discuss alternative delivery arrangements.

Many thanks again for including both stock centres in this project.


Kind regards,
---
Dr Marcos Castellanos
Operations Manager,
Nottingham Arabidopsis Stock Centre (NASC)
University of Nottingham,
Sutton Bonington Campus,
Plant Science Building,
School of Biosciences,
Loughborough,
LE12 5RD,  UK

On 16 Nov 2020, at 00:42, Sedbrook, John <jcsedbr at ilstu.edu<mailto:jcsedbr at ilstu.edu>> wrote:

Thank you to everyone who was able to join in on last Thursday’s Zoom meeting to discuss what Thlaspi arvense (pennycress) germplasm has been collected (natural populations), what pennycress EMS populations have been generated, and the logistics of getting aliquots of these seeds to the ABRC and NASC for curation and public distribution while keeping compliant with the Nagoya Protocol.

Here is a summary of the natural seed-population collections (not an exhaustive list) along with work flow and questions for Dave/Emma and Sean/Marcos:
In North America,
~120 United States populations collected by Winthrop Phippen at Western Illinois University
100 to 200 United States populations collected by Katherine Frels and colleagues at the University of Minnesota
~200 United States populations collected by John Sedbrook and colleagues either personally or with the help of iNaturalist citizen scientists
100 to 200 Canadian populations collected by iNaturalist citizen scientists (assuming no problems with USDA APHIS or UPS, these will be sent to me before year’s end)
Win, Katherine, and I will aliquot two sets of these seeds and send to the ABRC (seed information will include state from which collected (perhaps nearby city as well), GPS coordinates where collected, date collected, and name of collector). The ABRC will keep and curate one set and will mail the other set to NASC.
Dave or Emma, could you please provide us with your mailing address including who to address the seeds to?
Ratan and I will grow up individual plants from these populations and isolate genomic DNA for sequencing by DOE JGI. We will provide seeds from these genome-sequenced plants to the ABRC and NASC for curation/distribution.

In Europe,
~200 Western European populations collected by Dario Galanti/Oliver Bossdorf (the genomes of these populations have been sequenced and analyzed by Galanti/Bossdorf/Claude Becker).
100 to 150 populations collected in 2020 by iNaturalist citizen scientists in United Kingdom, Germany, Czech Republic, Poland, France, Austria, Sweden, Finland, Ukraine, Lithuania, Hungary, Russia, and South Korea. The Western European seeds are currently in the hands of three citizen scientists (in Czech Republic, Germany, and the U.K.). The Russian seeds are in the hands of a professor at Moscow State University who recently stopped replying to emails (hope he is okay!).
I will ask the three citizen scientists to send the seeds before the end of the year to NASC (including information in which country each seed population was collected, GPS coordinates of where collected, date collected, and collector’s name). NASC will keep aliquots for their curation and mail aliquots to the ABRC for their curation. The ABRC will forward to me aliquots of 100 seeds each population (or whatever can be spared in cases where seed numbers are limiting). I will grow up one plant from each aliquot and prep genomic DNA for JGI sequencing. Seeds from these plants will be sent to ABRC who will in turn send aliquots to NASC.
Sean or Marcos, could you please provide me with your mailing address including who to address the seeds to; I will pass this mailing info on to the three European citizen scientists. Regarding Russia, it is our hope we will eventually get ahold of our professor contact there who will in turn connect us with his botanical garden contact who can help get official permission to send the seeds to NASC, ABRC, or me.

Sean, it is our understanding that you will handle compliancy with the Nagoya Protocol.

Phew! I’d say that’s a pretty good start for pennycress wild population germplasm collections and curation for the common good! Info on the EMS populations to be sent to the ABRC and NASC will have to wait for another email.

Any questions/comments/suggestions are welcome.

Best regards,
John

--
John C. Sedbrook, PhD
Professor of Genetics
School of Biological Sciences
Campus Box 4120
Normal, IL 61790  USA

Phone: 1 (309) 438-3374


From: John Sedbrook <jcsedbr at ilstu.edu<mailto:jcsedbr at ilstu.edu>>
Date: Friday, November 6, 2020 at 5:46 PM
To: "Somers, David" <somers.24 at osu.edu<mailto:somers.24 at osu.edu>>, Sean May <Sean.May at nottingham.ac.uk<mailto:Sean.May at nottingham.ac.uk>>
Cc: "all at arabidopsis.uk<mailto:all at arabidopsis.uk>" <all at arabidopsis.uk<mailto:all at arabidopsis.uk>>, Moisés Expósito Alonso <mexpositoalonso at carnegiescience.edu<mailto:mexpositoalonso at carnegiescience.edu>>, Jeremy Schmutz <jschmutz at hudsonalpha.org<mailto:jschmutz at hudsonalpha.org>>, "Becker,Claude" <claude.becker at gmi.oeaw.ac.at<mailto:claude.becker at gmi.oeaw.ac.at>>, Oliver Bossdorf <oliver.bossdorf at uni-tuebingen.de<mailto:oliver.bossdorf at uni-tuebingen.de>>, "M. David Marks" <marks004 at umn.edu<mailto:marks004 at umn.edu>>, Ratan Chopra <rchopra at umn.edu<mailto:rchopra at umn.edu>>, "Jacobson, Daniel A." <jacobsonda at ornl.gov<mailto:jacobsonda at ornl.gov>>, Winthrop Phippen <wb-phippen at wiu.edu<mailto:wb-phippen at wiu.edu>>, Katherine Frels <kfrels at umn.edu<mailto:kfrels at umn.edu>>, "Knee, Emma" <knee.2 at osu.edu<mailto:knee.2 at osu.edu>>
Subject: Re: Available to meet to discuss Thlaspi arvense germplasm? Meet next Thursday, November 12th

Hi Dave,

Thanks very much. Speaking on behalf of the growing pennycress research community, we feel very fortunate to have both ABRC and NASC interest and support.

I will send out a Zoom invite for Thursday’s meeting, for which anyone is welcome to attend.

Best regards,
John

--
John C. Sedbrook, PhD
Professor of Genetics
School of Biological Sciences
Campus Box 4120
Normal, IL 61790  USA

Phone: 1 (309) 438-3374


From: "Somers, David" <somers.24 at osu.edu<mailto:somers.24 at osu.edu>>
Date: Friday, November 6, 2020 at 5:07 PM
To: John Sedbrook <jcsedbr at ilstu.edu<mailto:jcsedbr at ilstu.edu>>, Sean May <Sean.May at nottingham.ac.uk<mailto:Sean.May at nottingham.ac.uk>>
Cc: "all at arabidopsis.uk<mailto:all at arabidopsis.uk>" <all at arabidopsis.uk<mailto:all at arabidopsis.uk>>, Moisés Expósito Alonso <mexpositoalonso at carnegiescience.edu<mailto:mexpositoalonso at carnegiescience.edu>>, Jeremy Schmutz <jschmutz at hudsonalpha.org<mailto:jschmutz at hudsonalpha.org>>, "Becker,Claude" <claude.becker at gmi.oeaw.ac.at<mailto:claude.becker at gmi.oeaw.ac.at>>, Oliver Bossdorf <oliver.bossdorf at uni-tuebingen.de<mailto:oliver.bossdorf at uni-tuebingen.de>>, "M. David Marks" <marks004 at umn.edu<mailto:marks004 at umn.edu>>, Ratan Chopra <rchopra at umn.edu<mailto:rchopra at umn.edu>>, "Jacobson, Daniel A." <jacobsonda at ornl.gov<mailto:jacobsonda at ornl.gov>>, Winthrop Phippen <wb-phippen at wiu.edu<mailto:wb-phippen at wiu.edu>>, Katherine Frels <kfrels at umn.edu<mailto:kfrels at umn.edu>>, "Knee, Emma" <knee.2 at osu.edu<mailto:knee.2 at osu.edu>>
Subject: Re: Available to meet to discuss Thlaspi arvense germplasm? Meet next Thursday, November 12th

[This message came from an external source. If suspicious, report to abuse at ilstu.edu<mailto:abuse at ilstu.edu>]
Hi John,
We at the ABRC are definitely interested in participating in the discussion.  I think we have spoken already about our interest in expanding our collections beyond Arabidopsis. We already have some Thlaspi in our collection and are keen to expand. Next Thursday would work for me.

Best,
Dave

David E. Somers
Professor
Department of Molecular Genetics
Center for Applied Plant Sciences (CAPS)
Center for RNA Biology

Director Arabidopsis Biological Resource Center

The Ohio State University
(614) 292-2551

________________________________
From: Sedbrook, John <jcsedbr at ilstu.edu<mailto:jcsedbr at ilstu.edu>>
Sent: Thursday, November 5, 2020 12:36 PM
To: Sean May <Sean.May at nottingham.ac.uk<mailto:Sean.May at nottingham.ac.uk>>
Cc: all at arabidopsis.uk<mailto:all at arabidopsis.uk> <all at arabidopsis.uk<mailto:all at arabidopsis.uk>>; Moisés Expósito Alonso <mexpositoalonso at carnegiescience.edu<mailto:mexpositoalonso at carnegiescience.edu>>; Somers, David <somers.24 at osu.edu<mailto:somers.24 at osu.edu>>; Jeremy Schmutz <jschmutz at hudsonalpha.org<mailto:jschmutz at hudsonalpha.org>>; Becker,Claude <claude.becker at gmi.oeaw.ac.at<mailto:claude.becker at gmi.oeaw.ac.at>>; Oliver Bossdorf <oliver.bossdorf at uni-tuebingen.de<mailto:oliver.bossdorf at uni-tuebingen.de>>; M. David Marks <marks004 at umn.edu<mailto:marks004 at umn.edu>>; Ratan Chopra <rchopra at umn.edu<mailto:rchopra at umn.edu>>; Jacobson, Daniel A. <jacobsonda at ornl.gov<mailto:jacobsonda at ornl.gov>>; Winthrop Phippen <wb-phippen at wiu.edu<mailto:wb-phippen at wiu.edu>>; Katherine Frels <kfrels at umn.edu<mailto:kfrels at umn.edu>>
Subject: Re: Available to meet to discuss Thlaspi arvense germplasm? Meet next Thursday, November 12th

Sean (Cc others including David Somers of the ABRC and Jeremy Schmutz of the DOE JGI),

Thank you very much for your rapid and detailed response. I am thrilled to hear you are well-versed with the Nagoya protocol, and that NASC is open to discussing curation of additional Thlaspi arvense natural populations and lines.

Regarding Nagoya, a complication with Thlaspi arvense is that, while it is catching on as a model system for a variety of molecular and ecological studies, it is also being domesticated into an oilseed cash crop to be grown throughout temperate regions of the world. Thlaspi arvense germplasm could have considerable basic science importance. Hopefully that, along with the fact that it is considered a common weed, would make Thlaspi arvense exempt from Nagoya protocol restrictions.

Most of the germplasm we are looking to have curated were either collected by us or by “citizen scientists” who we contacted through iNaturalist. In total, there are over 500 natural populations collected from the following countries: United States, Canada, United Kingdom, Germany, Czech Republic, Poland, France, Austria, Sweden, Finland, Ukraine, Lithuania, Hungary, Russia, and South Korea. Seeds collected this year by citizen scientists throughout Europe are being held by a few people in the U.K., Germany, Czech Republic, and Russia until we figure out what if any Nagoya protocol paper work should be filled out. I have obtained the proper USDA APHIS permit to import the seeds from the above-listed countries. In a perfect world, aliquots of seeds would be split between NASC, ABRC, and here at Illinois State University.

We were recently awarded a DOE Joint Genome Institute Community Science Project (JGI CSP) grant to whole-genome sequence 500 of these natural populations, the data of which will be made publicly available.

Thank you for pointing out the Hammond et al. paper. I was aware of it, but didn’t realize you were a co-author! 😊

Meeting by Zoom next Thursday, November 12th, to discuss things further would be great. Sean, would 5PM your time (United Kingdom) work okay? That would be 6PM Germany/Austria time, 12PM U.S. Eastern time, 11AM Central time, and 9AM Pacific time in case anyone else would like to join in. If another time would work better for anyone, please say so in order to try and accommodate.

Best wishes,
John

--
John C. Sedbrook, PhD
Professor of Genetics
School of Biological Sciences
Campus Box 4120
Normal, IL 61790  USA

Phone: 1 (309) 438-3374


From: Sean May <Sean.May at nottingham.ac.uk<mailto:Sean.May at nottingham.ac.uk>>
Date: Thursday, November 5, 2020 at 9:51 AM
To: John Sedbrook <jcsedbr at ilstu.edu<mailto:jcsedbr at ilstu.edu>>
Cc: "all at arabidopsis.uk<mailto:all at arabidopsis.uk>" <all at arabidopsis.uk<mailto:all at arabidopsis.uk>>, Moisés Expósito Alonso <mexpositoalonso at carnegiescience.edu<mailto:mexpositoalonso at carnegiescience.edu>>
Subject: Re: Available to meet to discuss Thlaspi arvense germplasm?

[This message came from an external source. If suspicious, report to abuse at ilstu.edu<mailto:abuse at ilstu.edu>]
John,

Hello, yes, very happy indeed to discuss this. Thursday 12th would be best for me - I currently have that afternoon/evening free of scheduled meetings.

As you probably know, we already hold 23 lines of Thlaspi (and 20 of Noccaea caerulescens, which used to be Thlaspi) that are integrated into our catalogue and offered with the same cost recovery and conditions as arabidopsis.

All of these were collected in the UK, France or US, so Nagoya is not a concern on them (in the first two cases, no exercised sovereign rights, and no Nagoya ratification in US).
We do have to consider phytosanitary regulations but these have not been a problem (e.g. they will increase for us after Jan 1st to Europe - but we are already discussing this with DEFRA and have it in hand).

For arabidopsis we have a fairly standard response to Nagoya (copied below between the === and indented).

In the case of new Thlaspi lines, Nagoya application would depend on where they came from, when they were collected and how.

I am a standing member of the UKPGRG ( http://ukpgrg.org<https://urldefense.com/v3/__http:/ukpgrg.org__;!!KGKeukY!k7LLmSMwFnYgm7x81zExd9xQmAmOQx1e1nBoffqb5rtdBMPlUgmonbTLsVb6st8vKA$> ) which is an advisory group to the UK government on Plant Genetic Resources - and we are regularly briefed on changes / negotiations on the CBD/ITPGRFA and Nagoya, such that we will see any changes coming. I have also given talks on Nagoya to PG students on the off-chance that you would like my slide deck.

It is very good to hear that interest in Thlaspi is increasing - even I’ve worked on it :) - though not for a while….

John P. Hammond, Helen C. Bowen, Philip J. White, Victoria Mills, Kevin A. Pyke, Alan J. M. Baker, Steven N. Whiting, Sean T. May and Martin R. Broadley New Phytol 2006 170(2):239-60  A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes. https://www.doi.org/10.1111/j.1469-8137.2006.01662.x<https://urldefense.com/v3/__https:/www.doi.org/10.1111/j.1469-8137.2006.01662.x__;!!KGKeukY!k7LLmSMwFnYgm7x81zExd9xQmAmOQx1e1nBoffqb5rtdBMPlUgmonbTLsVaoIunZug$>

Cheers,

Sean


Professor Sean Tobias May. D.Phil.
Director, http://arabidopsis.info<https://urldefense.com/v3/__http:/arabidopsis.info__;!!KGKeukY!k7LLmSMwFnYgm7x81zExd9xQmAmOQx1e1nBoffqb5rtdBMPlUgmonbTLsVYedxs0ew$> [NASC].


Director of Equality, Diversity and Inclusivity.
School of Biosciences
Sutton Bonington Campus
University of Nottingham
Loughborough. LE12 5RD. UK.
+44 115 9513306

https://what3words.com/worm.desiring.crops<https://urldefense.com/v3/__https:/what3words.com/worm.desiring.crops__;!!KGKeukY!k7LLmSMwFnYgm7x81zExd9xQmAmOQx1e1nBoffqb5rtdBMPlUgmonbTLsVYQnjPONA$>

Preferred pronouns: they, them, their, who.

http://twitter.com/#!/NASCArabidopsis<https://urldefense.com/v3/__http:/twitter.com/*!/NASCArabidopsis__;Iw!!KGKeukY!k7LLmSMwFnYgm7x81zExd9xQmAmOQx1e1nBoffqb5rtdBMPlUgmonbTLsVYoYKxJwQ$>
http://orcid.org/0000-0001-5282-3250<https://urldefense.com/v3/__http:/orcid.org/0000-0001-5282-3250__;!!KGKeukY!k7LLmSMwFnYgm7x81zExd9xQmAmOQx1e1nBoffqb5rtdBMPlUgmonbTLsVY_MGqq2Q$>

<image001.png>

===

A lot of plant research work (particularly in arabidopsis) is out of scope of Nagoya at the moment for several reasons:

Firstly, the essence of Nagoya relates to ‘utilisation’ - arabidopsis itself is not directly commercially utilised so ABS is not applicable and genetic resources as testing/reference tools are out of scope of Nagoya.
Directly, speaking to our position: Handling, storing and cataloguing biological material including curation of phenotypes (including molecular phenotypes) are also out of scope of 'utilisation'.

Additionally - almost all arabidopsis lines are laboratory generated from accessions that were collected (accessed) before 12 October 2014 (the Nagoya date trigger).

There is also no originating country that exercises sovereign rights over arabidopsis nor asserted access benefit (ABS) agreements (actually a very large proportion of the transgenics in arabidopsis were generated in the USA which has [unfortunately] not ratified the Nagoya Protocol).

Almost all of our lines are transgenics which are currently subject to other separate legal regulations and agreements (e.g. ACGM) which supersede/override Nagoya.

There *is* some discussion about the expansion of Nagoya into sequence information and thereby synthetic biology, but that is extremely contentious. So at the moment it does not appear that putting sequences from other species into arabidopsis would be subject to Nagoya based on the sequences.

From this information, we do not think there is anything you need to do in terms of registration with the stocks that you order/receive from us and we have performed due diligence in exploring responsibilities with regard to Nagoya.

In addition, we can supply the origin and date of donation into our collection for any line you need (this is also on our catalogue for you to help yourself).

===

------


On 5 Nov 2020, at 14:29, Sedbrook, John <jcsedbr at ilstu.edu<mailto:jcsedbr at ilstu.edu>> wrote:

Dear Professor May and/or to whom it may concern,

I am writing on behalf of a growing international community of researchers who are using Thlaspi arvenseas a model system. Would you be available to discuss a few related issues, namely the possibility of the Nottingham Arabidopsis Stock Centre curating Thlaspi arvense germplasm from throughout Europe and the world, as well as your insights and advice on how to best handle Nagoya protocol regulations.

If interested and available to talk next week, the following dates and times would work for me:

Monday, November 9th, before 5PM (All suggested times are your local time)
Tuesday, November 10th, before 7:30PM
Wednesday, November 11th, before 5PM
Thursday, November 12th, any time
Friday, November 13th, before 5PM

Thank you and best wishes,
John Sedbrook

--
John C. Sedbrook, PhD
Professor of Genetics
School of Biological Sciences
Campus Box 4120
Normal, IL 61790  USA

Phone: 1 (309) 438-3374




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