Historic emal exchange etc.
Am I suitable for this task?
First I thought it was "long term breeding" and I searched for that on Googles. To my big surprise the nine first hits concerned with forestry was associated to me (collaborators more visible)! The tenth ranking hit was TREEBREEDEX Orleans meeting. However, I do not understand the search engine fully, e.g. it now give a preference for hits close to Uppsala (probably as my IP number is close to Uppsala. Other search efforts gave more modest results but still many hits associated to me.
I looked also on management of breeding populations. It was noteworthy how few hits were to forestry.
From:
Dag Lindgren
Sent: den 16 november 2010 22:19
To: 'Lee, Steve'
Cc: Darius LZUU
Subject: RE: TreeBreedEx Deliverable - Activity 4 - D4.2
I started with this yesterday, I indicate how I will continue. In your last email you indicated that you would come back before the end of summer. Darius says it takes months till his report is ready (he has comments from me and Gunnar Jansson to work with, but did not mention comments from you).
State: there are two important documents which ought to get ready but are not which I intended to look at. It is the Swedish breeding review, which I have in an almost ready draft, and it is the Darius D document, the version from June has not been modified yet according to comments from mainly me and Gunnar and it does not seem to be done soon. In connection with the Swedish breeding review there should be POPSIM runs, but those are not presentable yet. At least I have had a look at the latest versions of these documents Nov 10. I said I would start with this early November but I had to assist my son with house reconstruction first week in November and second week I spend some time on the Swedish plan and others, so I started first Nov 15, but now I intend to be at home till early January and the outside weather and darkness has limited appeal. Maybe I take out a month salary for myself from our TREEBREEDEX money, OK? I would like to transfer it to Anders Fries but the prefect does not allow payments to him and the paper excersize is too bad.
From:
Dag Lindgren
Sent: den 14 juni 2010 14:56
To: 'Lee, Steve'
Cc: 'Darius'
Subject: RE: TreeBreedEx Deliverable - Activity 4 - D4.2
So I start think on November about 1st and spread a first very rough draft which probably contains mistakes I will regret to among others you around Xmas. My next time target survived your first response and also a direct response from Luc, so it remains to be seen what happens later.
It is not just that I do not want to work in summer but there are things I promised and I am so slow so now I have to write something to Poland and think about it and I should really write a comment to Darius also but it remains to be seen if it will come. It is interesting things in his report, e.g. 50% or less programs uses controlled crosses including high input long-term and with important species. How to interpret that?
From:
Lee, Steve
[mailto:steve.lee@forestry.gsi.gov.uk]
Sent: den 14 juni 2010 11:32
To: Dag Lindgren
Cc: Buiteveld J; Darius LFRI;
Luc.Paques@orleans.inra.fr;
Gerry.Douglas@Teagasc.ie
Subject: RE: TreeBreedEx Deliverable - Activity 4 - D4.2
Dag,
Thanks for the reply.
I understand you reluctance to work in summer - I would do the same. Starting work in November is fine but March 15 is too late for our requirements. The extended contract finishes end of March 2011 and everything needs to be together by then. I would need to take your 'Chapter' and link it with Patrick Martens over-view chapter in some way.
But we have some time on our side just now. I shall read through the report of Darius, see what is missing, and suggest refinements to what we ask from you. I should do that before the end of summer. Darius has suggested he may eb able to help also.
Thanks you for suggesting to help, it is much appreciated.
Now, get back to that canoe !
Best wishes,
Steve
From:
Dag Lindgren
[mailto:Dag.Lindgren@genfys.slu.se]
Sent: 10 June 2010 11:38
To: Lee, Steve
Cc: Buiteveld J; Darius LFRI;
Luc.Paques@orleans.inra.fr;
Gerry.Douglas@Teagasc.ie
Subject: RE: TreeBreedEx Deliverable - Activity 4 - D4.2
OK a straight answer. As you did not comment I assume you agreed what was in my response below. I start work Nov 1. First a draft with my own thoughts and some look into TBX documents to present and discuss with some others willing (Darius is a strong candidate) around Xmas and when making further digging in documents and delivering the final chapter Mars 15. The title of the chapter as you suggest, and I give it a try to make the considerations suggested below as well as a few others.
Some comments
You are right that I often am not so enthusiastic. I am a bit pessimistic that Man will survive if not improving. But now this is more your problem than mine. The chapter I will write in the winter will probably increase survival probability, that is a major reason for me to agree writing it.
Of course Darius document is more analytical than Martens but the task was to make an enquiry and describe what was done, not suggesting best strategies.
I looked at presentations from Orleans.
1, The Darius and Dag new strategy suggest 50 % (or 40 with some extra considerations mentioned below) more gain at the same diversity, cost and time compared to the Andersson strategy as presented for Scots pine. This is a spectacular improvement with a simple trick and I would like to think that a breeding strategy meeting or subsequent activities discussed that. Did you?
2. Raffin maritime pine claims a rather large loss of diversity in selected characters. I and Skogforsk do not think this conclusion can be safely drawn from the data and have decided to neglect that as an indication of a strong decline of variation due to breeding.
Now I must break for the day because I have a canoeing appointment, but you salaried workers can continue thinking.
From:
Lee, Steve
[mailto:steve.lee@forestry.gsi.gov.uk]
Sent: den 10 juni 2010 11:32
To: Dag Lindgren
Cc: Buiteveld J; Darius LFRI;
Luc.Paques@orleans.inra.fr;
Gerry.Douglas@Teagasc.ie
Subject: RE: TreeBreedEx Deliverable - Activity 4 - D4.2
Dag: Thank you for your reply. You do not conclude whether you can, or can not write this chapter - and I do not want to make you your mind for you - but I have to say you do not sound too positive.
Darius: Thank you for your document - were you hoping to complete by the Poland meeting? - sadly I shall not be attending but I will be keen to receive the most up to date draft. You should have been in Edinburgh ! - we could have discussed Sitka seed and you would have tasted the malt whiskey.
Let me read Darius's document please and try to get a feel for what migth still be missing - it migth be that Darius is covering much of what we need - a quick scan shows it is long and comprehensive. Let me get back to each of you once I have considered this point. Maybe I could persude Darius to do any extra bit extra work that might be needed .......... ?
I'll get back to you later in June.
Many thanks for both your efforts.
Regards,
Steve
From:
Dag Lindgren
[mailto:Dag.Lindgren@genfys.slu.se]
Sent: 09 June 2010 20:05
To: Lee, Steve
Cc: Buiteveld J; Darius LFRI;
Luc.Paques@orleans.inra.fr;
Gerry.Douglas@Teagasc.ie
Subject: RE: TreeBreedEx Deliverable - Activity 4 - D4.2
Dear Steve,
Thank you for the long letter. I appreciate it very much. You suggest me writing a chapter: “So what are we asking you to do? We would like you to write a chapter please (10-pages tops) on 'Long-term breeding: Should I do it? How should I do it? Why should I do it' We would like you to cover as many aspect from above in the decision process as possible - both theoretical, but also consider actual existing long-term programmes.”
At first sight it seems perfectly suited for my competence and what I like to do.
Cost is no problem, if I do it I can probably do it for free (in spite of getting no salary) or at least within my own TBX budget.
Even considering Darius reaction one may say that the activities are mainly descriptive and not very analytic.
But other problems.
I thought this problems was mainly taken care of by the Orleans breeding strategy meeting, but I was not even there (I just retired and wanted to trap down).
I am suggested to write a chapter but what does that mean? – how will the end product be presented?
I seem even not be among those responding to the enquiry. So is it up to me to complement it as a last minute thought? As we do not do actual breeding, I just think on how it can be done.
I retired October 1, and now I do not earn a penny. I should not work much and continuously less and give priority to private projects and feel few obligation for professional activities. I actually have already promised to do several things which I have not done. The main thing is that I will deliver two speeches at the IUFRO world congress and one in the upcoming TREEBREEDEX activity in Poland. This must be done now and does not give room for more commitments before September. I feel it was stupid to engage, but for IUFRO they gave my student the Outstanding Doctoral Research Award and it is the third time in a row the IUFRO word congress awards my students, no forest scientist in the history has got “hat trick” in this way before, and if IUFRO awards my students in that they I cannot neglect IUFRO completely! For Poland I was asked something about networks of field trials and In also felt I cannot neglect TREEBREEDEX completely and the Polish appeared at my seed orchard meeting and invited my two years ago when I actually made that presentation I was invited to give in Orleans, but I felt I need not do it twice besides to work less when retiring and it was in the end better documented in Poland http://daglindgren.upsc.se/Meetings/Poland07/Poland07.htm. Now I regret very much to accept the Polish suggestion because I believe networks are needed but based on experience I do not believe long term networks will work well and I have no time or spirit to really analyze the examples. So no good lecture. There are also other commitments. The most important is not a lot of additional things during the comparable pleasant time in this northern location, in winter it is less important to avoid work. Thus I do not want to start something new until November 1, start discussing with others around Xmas and maybe Finnish till Mars 15, but I guess that is difficult. If you just want me to write what spontaneously come up in my head and it is just meant for a smaller circle I can spend little time on it and make it faster.
I am not that happy with the situation at our department in Umeå and how I fitted in the last years. I hoped TREEBREEDEX would lead to some type of EU support or some contact which could be developed for me or my collaborators Anders Fries and Jan-Erik Nilsson or some task I would feel satisfying and suitable. Apart from the seed orchard conference this has not happened. I wanted to be a scientist how could support breeding and seed orchards with theory, but I feel that most of the surrounding world including EU, Skogforsk, TREEBREEDEX and others has not fully appreciated that. With TREEBREEDEX breeding strategy was postponed till the very late and it seems late for me to go in now. Is it not better with novel tree which will carry on and are on the track.
I have also health problems and am unsatisfied myself with what I do, my time is out and I feel often burned out and insufficient. My memory is bad, it takes long to do things, I have difficulties to focus and care less of missing deadlines, it is lots of errors and mistakes in first drafts, by continuous thinking it becomes better. Sometimes I am dull and misunderstand and it takes long time to get an idea. I felt for retiring already with the conference 2007. But looking back on my last time I really feel proud of some things. E.g. the grandfather balance idea with Darius boosts Swedish pine breeding 50% higher gain at the same diversity and cost just by another way at viewing at the problem! But it may be only 40% because we assumed pollen could be collected on chosen trees in the trials, but it seems the pollen production is late and it is hardly practical possible to come at the narrow time interval to many places, so probably the male selections will be harvested as the females, scions for topgrafting and pollination with low pollen quantities. Just emphasizes that the needed knowledge is much what is feasible rather than better knowledge of the genetics of the system. I have been the driving force behind four marker works, one conventional seed orchard study and three different variants of BwB (the idea of one presented in the Polish paper).I got the WP seed orchards launched. I thought about how to deploy vegetative propagation and my 35 year old point that it is better to use it for mulitiplying the progeny of good parents than using tested good clones is now accepted as the standard model in Sweden. And see wolf, so even if I feel very insufficient some of the end products seem very good even this last years. But my point is that it takes time if I shall do something which I feel not ashamed of.
Wolf: early this year I decided to entertain myself with something different than forest genetics where still my genetic background would be useful . Swedish wolf is very controversial. There are political decisions and intensive debate on different webs. There is much information in Swedish. Very different to tree breeding where it is no functioning forum for real discussion (including the TREEBREEDEX efforts) and not easy to get access to the ideas well expressed in Swedish. It took longer time to read and understand and to develop a relevant formula for connectedness among groups, but now I think I am ready to document my conclusions. I learned that purging has often been found to be surprisingly ineffective, and have some difficulty to understand why, the theory of what the cause of inbreeding depression is does not seem to be as well understood as I thought four months ago. I learned that greenies do not worry much that things happen naturally, but it is allowed to move wolves. Actually almost the same people who criticize Swedes for using eastern spruce provenances want import of eastern wolf provenances to strengthen the genetics by reducing inbreeding. But the claim that it is needed with thousands of wolves in Sweden to keep the genetic variation but you need to move only one wolf each generation from the east to keep sustainable genetic connectness with the Russian wolves (over Finland) and they are many thousands. So from a genetic point of view it does not matter how many wolves we have in Sweden as long as we continuously import a very low number. That’s what I found. Now we see if I manage with keeping Swedish wolves down to about 200 for the next 10 years by claiming that it is no genetic reason to get it higher in spite of that all other genetic expertice claims the opposite, wants a bet? But for number I have said that we tree breeders need not worry if we loose say 5 or 10 % of the diversity in a century due to drift because the variation in variation is anyway larger than that, and tree breeders in hundred or two hundred years will have stronger tools and more knowledge and we will not leave them without options, but for trees with a short generation time (say 5 years as for wolves) it will be needed larger breadth of the breeding populations than I think is maintained. That was a new thought I got for diversity related to TREEBREEDEX which covers a wide span of generation intervals.
Darius: yes I got the 12 Mb file, thank you. See you in Poland.
Gerry: Thanks for the recent information about the progress on seed orchard sites in cooperation with UK and it seems a very politically correct idea if northern Ireland could be used for spreading the blessing to both countries! In a conference I attended at Iceland the president participated in tree planting with the participants to communicate the support for building a new forest, a tip for raising the support of the thought of supporting new forests at Ireland. I hope I do not offend anyone by including this thanks in this letter.
Best regards Dag
Hello Steve and Dag,
Luckily our survey on breeding strategies can answer to most of the questions listed below.
I am attaching the very draft version so that you could see what is.
Darius
From:
Lee, Steve
[mailto:steve.lee@forestry.gsi.gov.uk]
Sent: den 8 juni 2010 18:18
To: Dag Lindgren
Cc: Buiteveld J; Darius LFRI;
Luc.Paques@orleans.inra.fr
Subject: TreeBreedEx Deliverable - Activity 4 - D4.2
Dear Dag (and Darius)
Activity 4: Structure, Organisation and Long-Term Management of Forest Breeding Material
D 4.2: Optimisation of structure of breeding populations for long-term genetic improvement: Survey of methodological tools
I seek your help regarding meeting the above deliverable 4.2 under TreeBreedEx. I wonder if you might be able to assist?
At the moment, Patrick Martens has sent out a questionnaire - he did this way back in Year 1 - and received replies which he has collated (report attached). We fear this questionnaire really missed the mark i.e. did not meet the objective of this deliverable. Patrick's questionnaire asked about number of breeding programmes, how advanced is the programme, type of testing done (clonal, progeny etc). This is good back-ground stuff, but perhaps does not reach to the heart of the question. Joukje Buiteveld and myself (co-leaders of Activity 4) and Luc Paques (co-ordinator of TreeBreedEx) feel the key questions are left unanswered. We have just 10-months left of the contract (assuming we get the extension) - too little time for another questionnaire + analysis - and we are all weary of those anyway.
At the Edinburgh meeting we discussed ( in plenary session) how to proceed and agreed we should call upon you to see if you could help.
The aim of the survey should have been to investigate:
· What criteria have to be met before one can consider long-term breeding?
· Which methods and tools (software, simulation models) are available to organise and manage long-term breeding populations?
· What are the arguments to choose a particular method for long-term breeding e.g nucleus breeding; sub-lines; other?
· If people are using a certain method or tool, what kind of information do they get out of it
· How good are simulation tools?
· How do (or should) people balance gain with genetic diversity?
· Can we give examples from certain long-term programmes, as to which techniques are being used (e.g the programmes presented at the Orleans meeting last October) ?
Other questions which migth be asked include:
1. Do people manage breeding populations?
a. If yes, for which species? What size? How is it structured?
2. Do they have plans to conduct long-term breeding? (at least more than one generation breeding)
a. If yes, for which species, which populations? What objectives? What scale?
b. If not, what are the main reasons e.g. funding? training/knowledge gaps? lack of demand etc?
c. What are the criteria to decide to move on to the 2nd generation breeding population? Consider: Use of simulation and knowledge to do it, money, biology of the species, number of traits, which traits? variance components, molecular techniques, opportunity to buy improved breeding material from someone else within your ecological zone and skip 20 years of testing, forest policy in your country, need for new skills in organizations, and access to these tools, cost:benefit analysis
3. How do they manage their breeding populations ? (core population, sub-lining or other types)? Characteristics?
4. Which priorities do they have (genetic diversity vs. gain)?
a. How do they manage this?
b. How do they manage adverse correlations?
5. Do they use any tool to simulate breeding schemes?
a. Which ones are used? (like POPSIM, Breeding Cycler, XSIM, allelic models, etc)
b. What tools/ methods exist? (See also literature)
c. What can it do? (See also presentations of training session on simulation tools Orleans October 2009).
d. What about generation turnover - build into the model.
6. What kind of recombination techniques and selection techniques are they using to optimize their goals?
7. Which types of varieties are they developing?
A synthesis report which addresses these new questions and includes more detailed information (real figures on size of breeding populations etc.), a list of existing simulation tools with a short description still need to be produced. To obtain the necessary information a combination with the survey on optimization of testing strategies (Act. 5, task e, Darius Danusevisius) and additional information from literature should be made. what are we asking you to do? We would like you to write a chapter please (10-pages tops) on 'Long-term breeding: Should I do it? How should I do it? Why should I do it' We would like you to cover as many aspect from above in the decision process as possible - both theoretical, but also consider actual existing long-term programmes.
Do you think this is something you might be able to in your capacity as a TreeBreedEx member and charge time to Activity 4? I include Darius in this e-mail since his name was also getting mentioned at the meeting, I know this is an area he is familiar with, and he has produced a related questionnaire under Activity 5 ( I have not seen the report from that - please forward if their is one, Darius) - so Darius, perhaps this task is suited to you also.
I would be happy to develop this idea further. I hope you can help.
Regards,
Steve
*********************************************
Dr Steve J Lee
Programme Group Manager for Genetic Improvement
Forest Research
Northern Research Station
Roslin
Midlothian, EH25 9SY
SCOTLAND
Tel: (+44) 0131 445 2176 (Switchboard)
(+44) 0131 445 6926 (Direct line)
Mobile: 07872 697 252
Fax: (+44) 0131 445 5124
http://www.forestry.gov.uk/forestresearch