Newsletter Summary 98-99

 This is the beginning of a newsletter service managed by Dag Lindgren. I will share documents, information and thoughts connected to forest tree breeding (such things there information is not easily available through other sources and which I have easy access to). I feel that there is too little discussion and communication about what is essential in forest tree breeding in this world, and want to do a contribution in a way which is rather easy for me and others. If someone wants to spread a comment or raise a matter for discussion or something else through this mailing list it is warmly welcome (currently I believe it just to press the answer all button). Relevant, interesting and informative discussions have appeared in this way in many other fields, unfortunately more seldom in forest genetics. Hopefully this service will stimulate breeders in their thinking and operations and scientists (like me) to design relevant studies. These letters will be sent at irregular intervals. It is sent to some of those I have identified as potentially interested. Those who ask for being added to the mailing list will get the future letters. Probably I will expend the circle who gets it when sending next letter (the first letter is sent just to some breeders and some people around me at Umeå). For those who feel that they have been unwillingly put up on the mailing-list, just return this mail to me with a "Quit sending me E-mails of this kind", and you will be removed from the list.

Rotation time in the breeding population
People like me (Studia Forstalia Suecica 166 p16) and many others have earlier argued that the key problem is to maximise gain per year. However, when we did not consider diversity.

We loose diversity in generations shifts by genetic drift. There is no way around that (even if there are counteracting forces like mutations acting in a long term perspective). Were we not interested in diversity we would keep breeding programs and production populations much more narrow than we do, so we care for diversity. How should we consider diversity when discussing rotation time in the breeding population?

Some possible options are listed:
*Increase the size of the breeding population so the diversity loss at generation shifts becomes insignificant;
*Start with a larger breeding population;
*Maximise a goal, which weights gain and diversity, a fixed time ahead;
*Get as much gain combined with as much diversity as fast as possible;
*Get as much gain as possible for a given diversity loss.
*Get as much gain as possible per unit diversity lost and unit time.
*Run a short generation program including hefty inbreeding to adapt the population to high inbreeding and low diversity in the same time as we get gain.
*Make the production population rotation short also so we become aware of possible side effects faster and thus probably forget about diversity faster.

Site of interest

The main website of interest for forest geneticists and forest tree breeders is

"Forest Genetics and Tree Breeding"

http://www.metla.fi/info/vlib/forestgen/breeding.htm

From this site you can reach almost all other interesting places. It is very well managed and updated (by Matti Haapanen). Strongly recommended!!!!! The site is very useful as a starting point for forest genetic net-surfing and for following up the latest news.

The news and discussion club of forest geneticists and tree breeders is FORESTGEN, information about that is found at the site mentioned above. From a discussion point of view it is mediocer, but a subscription results in announcements on meetings, positions, books etc; so I suggest forest geneticists/tree breeders to subscribe.

 

I have frequently commented on the lack of creative visible discussions among forest geneticists in Sweden and the World. Some efforts by me failed or have only met limited success, this is actually one of the reasons I have decided to start this newsletter service, which at least is certain to function as a monologue even if it fails as an opening for a dialogue.

 

Contributions to the discussion

 

Effective size

 

I discourage using the concept "inbreeding effective population size" in tree breeding.

 

If need for the concept is felt, one of the following concepts may be more informative:

·        Variance effective population size

·        Status number

·        Inbreeding (F)

·        Selfing rate

·        Expected increment in inbreeding.

 

I am thinking at the following expressions at the moment

·          effective clone number (only to be used when the offspring (the seed crop) is not of much interest)

·          effective parent number to a population

 

Are those concepts suitable, is their another existing terminology which is preferable?

 

 

Population semantics revisited

 

Some time ago we discussed population semantics on FORESTGEN; what should we call the probability that two genes taken at random from the gene pool of a population are equal by descent? The conclusion following the discussion was that "group coancestry" was a preferable term, because of the link to Cockerham. This link was pointed out by two different discussion contributors. Cockerham's intention was not to coin a concept, and his concept can actually be used "between populations" as well.

 

The background of that discussion was that I disliked the term "average coancestry" because it is ambiguous and interpreted in different ways (is self-coancestry included or not? does self-coancestry get equal or half weight compared to cross-coancestry? is it average for individuals or groups? etc.). The distinction is important and confusion connected to the term has led to the suggestion of algorithms, which do not do what they are assumed to do. Still we first used the term "average coancestry" and the selection method (GMS) was initially called "coancestry-adjusted selection", which is reflected in Zheng et al (1997). "Adjusted" I also saw disadvantages with in the associations it gives. 

 

The selection method which considers both gain and group coancestry can be called Population-merit selection (PMS) or Group-merit selection (GMS). Population-merit was used by Lindgren and Mullin (1997), which can be considered a strong argument. Actually, Population-merit was initially suggested by a referee of the Lindgren and Mullin (1997) article. Apart from the history, I now feel Group-merit selection may be slightly superior as it leads associations to Group-coancestry and associates to something different and looser than population, group selection is a concept in evolution and this use is not too different. I may also use that term in the future if others do. A selected group from a population of candidates seems possible to talk about. Group-merit can be seen as the result of a semantic evolution during some years and will be used in future paper by Andersson, Rosvall and others.

 

We see here how a disparate terminology is born and evolve and some of us are actively involved in this process and this arises in spite of an active, frequent, friendly and intimate discussion. A way to see it is as an evolutionary process, when we successively search and find better semantics. As far as I see we all still mean the same thing.

 

Some additional comments:

1)   The concept Population-merit selection is not connected to the algorithm used for finding the optimum (e.g. the optimum can alternatively be found by integer linear programming).

2)   To search the optimum by Lagrangian multipiers or linear deployment (as I have done in many previous studies) has the disadvantage that it does not constrain the optimum to integers, this may be severe for long-term breeding applications.

3)   Dr Mullin recommends ___-selection, thus to connect the words with a binding sign.

4)   Population-merit has a much wider application as a goal of breeding than selection.

5)   There are many others who develop similar ideas, so semantic influence from elsewhere may be important, and efforts from us to standardise are anyway predicted to have limited influence.

6) I guess the word "status number" will stay, the word has spread beyond our group, and the similar concept "founder genome equivalents" is ambiguous (Lindgren and Kang 1997). Maybe "effective" could be added, "status effective number" (Lindgren et al 1996).

7) In Swedish I have used status-nummer (following discussion with the editor of SkogsFakta).

 

"Effective parents" or "status number"?

Lindgren and Mullin (1998) coined status number in seed orchard crops.

I think that was a good idea. It is also a good idea to use the concept as is done

in Andersson, El-Kassaby and Lindgren (in review).

For these studies it is important that parents may be related or inbred.

 

I know that I have encouraged "status number" in orchard or stand related papers by Kjaer, Bila, Kang etc etc. But now I still ask myself if it is useful to always use status number for describing differences in flowering or ramet number between genotypes. The strength but also problem with status number is that it refers to a reference population, and sometimes this is not informative and even misleading.

 

It seems that "effective number of clones in a seed orchard" could be more relevant when fertility variations are only based on ramet number (it is actually the gene pool of the orchard, not its crop, we are discussing). cf (Kang, Harju, Lindgren, Nikkanen, Almqvist.....1999?). But in general it is misleading to talk about effective number of clones, as often what is thought of is the crop of the seed orchard or the relationship of the orchard clones to the crop.

 

In studies where predictions of status number of the crop are based only on flowering (or seed production), thus the fertility of the parents is the only important variation, would it not give better associations to use "effective number of parents to predicted crop"? It leads associations and focus towards the parents and their characteristics as parents, thus fertility. It is rather clear it is a state, not a rate.

 

By using other terminology than status number we need not make the assumption that parents are unrelated and not inbred. We could instead point out that if parents (or clones) are non inbred and unrelated, the concept is identical to status number. But the concept itself would be unrelated to that assumption.

 

The real problem comes when we go multigenerational. If fertility variations are the same, still the status number of a constant population declines over time as trees grow more related. For this situation it is not good at all to link status number to fertility variations.

 

"Effective parents" or "status number"?

Ola Rosvall has made a comment:

Det är inte bra att förorena statusnr.begreppet genom att flytta referensen till plantageträden med ett antagande att de är obesläktade och särskilt inte på sikt. Jag tycker att det är viktigt att behålla founderanknytningen i statusnr. Vad man skall kalla nedgången i diversitet pga obalansen i plantageträdens genbidrag vet jag ej. Ditt förslag är förklarande, vilket är bra. Kanske kan det byggas upp på nåt annat sätt: Efficient crop parent number fast ditt är nog bättre. Kan man använda use efficiency: Parent use efficency 75 %.

 

Is environmentalism short-term commercial, while production is long-term idealism?

 

A switch in commercial versus idealistic motives has occurred. "Environmental concern" is now one of the strongest commercial market forces. An investment in "environment concern" has the potential of a fast (often immediate) return on investment. "Production concern" on the other hand is a concern for idealists, who worry about the future of mankind (or some smaller part of it, like people living in remote forested areas), but production is not so interesting for forest managers any more. An investment in "forest production concern" is doubtful from an economic-commercial point of view and often not likely to give a "reasonable" return on the investment (at least not on typical forest land in Sweden). It is not only that the waiting time for the return is extremely long and thus has a low value if discounted today, but a "production" profile may be directly harmful for marketing products. It reduces the trustworthiness of the "environment concern" behind the timber products, and this has an immediate negative value. The trend is to sacrifice the grand-children's need of products so the current generation get a more pleasant environment for itself. The trend is to let the production occur in countries, where rotation - and thus return of investment - is fast. The wood products will be of benefit to the people living today. Environment is more focused on where growth is slow, then production is of no significance for the current generation. Surprisingly, and contradictory to my conclusions, still Swedish forestry invests rather much in tree breeding, so perhaps I stray away from reality in my reflection here.

 

 

Status-nummer etc på svenska?

I vardagligt tal kanske vi helt enkelt kan säga "effektivt antal"?

Men då skall det av sammanhanget vara klart att det är status-nummer vi menar.

Kan vi kalla "group coancestry" för "genomsnittligt släktskap"?

Vad skall vi kalla "group merit selection"?

may use the list for shorter announcements also in between, e.g. I announced a seminar November 20.

 

Seminar

 

Prof. Steve McKeand, Deployment philosophy, scale, gains, experiences and risks connected to half-sib plantations with P taeda.

ure and time for discussion)  May 20, 1999.

 

Background

There is a spectacularly striking difference between EU and much of the new world concerning the view on need of diversity in the forest regeneration material. The EU (Swedish) policy is (somewhat oversimplified): At least 30 clones in a seed orchard and selective harvesting is banned.

 

Virtually all plantations with P. taeda in the southern United States use seed orchard material. Seeds are typically harvested by clone, treated by clone, sown by clone (the magnitude 0.5 million plants from the same mother are propagated together in the nursery). The half-sib families are lifted and packed by clone (the plant boxes are identified by clone, like Swedes write provenance on their boxes) and finally planted to form a stand consisting of a single half-sib family. There are a number of mother clones in use in parallel, so on the landscape level there is a mix of different half sib families. There are big advantages with this in the seed and nursery stage. Everyone seems to be satisfied with the system, and it does not seem to draw much criticism or be a controversial issue. Essentially all industrial forest plantations are established with open-pollinated seeds harvested from single clones.  Small landowners use both single families and mixtures of families (mixes vary from fewer than 10 to a few dozen families). The scale of regeneration with P. taeda is about one billion seedlings planted per year.

 

How is it possible that systems arrive at so radically different conclusions? Are there scientific reasons for the difference? If so, why do scientists not have a more coherent view on what is favourable and what is dangerous? The reasons for these large differences in deployment strategies needs to be debated considering that the matter is of central importance to tree improvement, and its possible dangers or blessings.

 

 

 

NAM or Random Mating or what?

We have PAM, positive assortative mating, but what to call the opposite? Random mating? Ola claims that it is common that authors use that as a contrast to PAM. NAM  ("Non Assortative Mating") is an idea. I have earlier used it for "Negative Assortative Mating", but that may not be a strong argument. What about "Random mate assignment"? RM could then be used, but stand for "random mate" instead of "random mating". I suggested "random mateing" but Tim does not accept it linguistically. PAM should perhaps be read "positive assortative mate assignment"

 

 

Number of representation of initial plus trees in the forming of a closed breeding population

I have since long argued that it would be more beneficial for tree breeding to transmit genes from more of the tested plus trees but in the same time let the plus trees be differently represented in an optimal fashion allowing more offspring from the best (in contrast to the base alternative in Swedish breeding, which is to let a fixed number of tested plus trees (50) be equally represented in the next generation of the breeding population). I have felt it important that the reasons for this opinion are well understood. Now I feel pleased to express that what is possible to do to meet this desire from me has been done. Förädlingsrådet has discussed the issue in December 1998. I made a presentation and my presentation is in the enclosed document. After the meeting I wrote down my comments on a number of questions and comments about unequal representation, which were raised at the meeting, this is also enclosed. A grant was given to study the phenomenon from Föreningen Skogsträdsförädling, and Ola Rosvall was subsequently asked to write about the results from this project in the recent yearbook of Föreningen. I enclose this article. I see it as important that it is well documented why decisions and actions are made and relevant arguments commented in connection with that, so now my opinion is well documented and properly discussed. This matter concerns the transition from an open to a closed breeding population, and is not dealt with in Ola Rosvall's thesis. This matter is of more immediate interest for breeders' actions than what happens in later generations.

The issue of unequal representation (unbalance) in a long term closed breeding population with particular attention to the Swedish program has been thoroughly discussed in Ola Rosvall's thesis. It appears that the possible advantage with unbalance, at least considering the specific plans for Norway spruce, is smaller and more doubtful than I would have guessed.

 

Sigfrid Blomqvist avled 6 mars 1999. En av den moderna svenska skogsträdsförädlingens pionjärer.

 

 

A fine Award

At IUFRO's next World-Congress in Malyasia next summer, IUFRO will at its opening cermony give its "Outstanding Doctoral Research Award" to Run-Peng Wei. That is in competition with all PhDs in the World for the past five years within Forest Genetics and Plant Physiology. This is a large honour to Run-Peng. But it is also a clear indication that Sweden, Swedish University of Agricultural Sciences, its Faculty of Forestry and the Swedish Forest Genetics keep internationally high standards.

 

Literature by Dag Lindgren et al with summaries of highlights!

 

Lit list 1997

Below I list and comment some of the papers I have been involved in which were published 1997, it is only papers which I consider of interest for forest tree breeding. The points which I find most relevant to breeding are emphasised in the summary (thus the summaries are not the authors summaries).

 

Lindgren D, Gea LD, & Jefferson PA 1997. Status number for measuring genetic diversity. Forest Genetics 4(2) 69-76

Summary: Argues for use of status number to monitor breeding, compares with inbreeding effective population size (which is shown to give rather senseless information), offers an algorithm for calculation of status number from a coancestry (relationship) matrix, demonstrates how status number develops over time in a real breeding program.

 

Lindgren D & Kang KS. 1997. Status number - a useful tool for tree breeding Research Report of the Forest Genetic Research Institute of Korea 33:154-165.

Summary: Reveiw of lit on status number till end of 1997. Points out the similarity with variance effective population size. Demonstrates its use for describing seed orchard crops. Makes a discussion of the concept "founder genome equivalents" used in animal gene conservation. This concept can have two meanings, the one recommended by the inventor is equivalent to status number, but the variant most used by others is not. Remark: I believe our article is the last article in the closing volume of this series.

 

Lindgren D & Lindgren K. 1997. Long distance pollen transfer may make gene conservation difficult. In: Kurm M and Tamm Y (editors), Conservation of Forest Genetic resources. Nordic Group for Forest Genetics and Tree Breeding Meeting in Estonia June 3-7, 1996. Estonian Agricultural University, Tartu. SBN 9985-830-11-3. Forestry studies 28:51-62.

Summary: Genes are able to migrate over several hundred  kilometres with fertile pollen, where are indications on a gene flow over some hundred kilometres from south to north.

 

Lindgren D & Mullin TJ 1997. Genetic variance within a full sib family. Swedish University of Agricultural Sciences. Department of Forest Genetics and Plant Physiology. Arbetsrapport 55:1-4.

Summary: Derives the additive variance within a full sib family. This is a function of the initial variance and the inbreeding of the parents, but the relatedness of the parents does not matter, neither does the size of the family. This is a known relationship, it is just the way of proving the relationship which is fresh.

 

Lindgren D & MullinTJ 1997. Balancing gain and relatedness in selection. Silvae Genetica. 46:124-129.

Summary: Population merit (thus a suitable scaled genetic gain minus group coancestry) is the entity to maximise in breeding and selection. Technically this is done by an iterative such algorithm. Population-merit selection is shown to be considerable superior to restricted selection and the superiority remains over generations. Remark: The use of population-merit can be seen as the optimal way of balancing gain and diversity. Restricted selection (thus maximising the influence of individual parents) is a less optimal way, which still is used in many of our studies, either because the population-merit concept was not yet invented, or too difficult to apply.

 

Lindgren D & Persson A. 1997. Vitalization of results from provenance tests. In: Mátyás C (ed). Perspectives of Forest Genetics and Tree Breeding in a Changing World. IUFRO World Series; Vol 6: 73-85.  ISBN 3-901347-07-0.

Summary: A list of possible uses of mature provenance tests, several are interesting for breeding.

 

Lindgren  D, Wei R-P & Lee S. 1997. How to calculate optimum family number when starting a breeding program. For. Sci. 43(2): 206-212.

Summary: Argues to start with offspring with many more plus trees than needed later. (Thus if a breeding population size 50 is headed for in later generations, many more plus trees should be included in the initial crosses). Argues that cost components are more important for optimisation than variance components, thus the optimum is not much dependent on heritability but very depending on the cost of additional plus trees and crosses. Argues to invest a large share of available funds in creating offspring from many plustrees in the early phase of the breeding programme.

 

Spanos K, Andersson EW & Lindgren D,  1997. Multigenerational comparison between restricted phenotypic and restricted combined index selection for gain and diversity. In: Kurm M and Tamm Y (editors), Conservation of Forest Genetic Resources. Nordic Group for Forest Genetics and Tree Breeding Meeting in Estonia June 3-7, 1996. Estonian Agricultural University, Tartu. SBN 9985-830-11-3. Forestry studies 28:86-100.

Summary: To consider the performance of sibs (combined index selection) when selecting leads to very low diversity. However, combined index selection is still rather efficient when heritability is low. Setting a limit on the highest contribution a parent can give to the offspring preserves diversity. Remark: Other studies reported here shows that it is possible to get considerable better combinations of diversity and gain than obtained by restricting.

 

Wei R-P, Lindgren D & Yeh FC. 1997. Expected gain and status number following restricted individual and combined- index selection.  Genome, 40:1-8.

Summary: Proper restriction can reduce diversity loss to acceptable levels, they are often urgently needed if selection is based on predicted breeding values. To restrict phenotypic selection to the good families can improve gain considerable. A sufficient family number is essential for high gain combined with sufficient diversity.

 

Zheng YQ, Lindgren D, Rosvall O & Westin J. 1997. Combining genetic gain and diversity by considering average coancestry in clonal selection of Norway spruce. Theor Appl Genet 95:1312-1319.

Summary: Applies population merit selection to a real breeding material. Extends the concept to finding optimal number of clones in a clone mixture.

 

Lit list 1998

Below I list and comment some of the publications I have been involved in which were published 1998. Only studies which I consider of interest for forest tree breeding are listed. The points which I find most relevant to breeding are emphasised in the summary (thus it is not the authors summaries).

 

 

Andersson EW, Lindgren D,  Spanos KA, & MullinTJ 1998. Genetic diversity after one round of selection. Forest Tree Improvement 26:47-55.

 

Andersson EW, Spanos KA, MullinTJ & Lindgren D 1998, Phenotypic selection can be better than selection for breeding value. Scand. J. For. Res. 13:7-11.

Summary: Results show that for moderate to high heritabilities unrestricted phenotypic selection is at least as efficient as is combined index selection when compared at the same level of diversity consumed. Combined index selection however has an advantage in terms of selection efficiency in cases where the heritability is low especially for large family sizes with the reliability of family means that follow.

 

Andersson EW, Spanos KA, MullinTJ & Lindgren D 1998. Phenotypic selection compared to restricted combined index selection for many generations. Silva Fennica, 32:111-120.

Summary: The consistency of the results were verified for five generations. The methods compared were unrestricted phenotypic selection and restricted combined index selection. A variety of crossing schemes were compared as were family numbers and also the introduction of a strong dominance component. Results were surprisingly stabile and showed that apart from rather unlikely events, that combined index selection has no or insignificant advantages over selection on the phenotype.

 

Comment: The technically easy mass-selection (phenotypic selection) seems to have a place in many breeding operations. If selection is guided by a known family structure (selecting good individuals from good families) the advantage of high gain is approximately balanced by the disadvantage of high relatedness. This is an observation I think Run-Peng Wei deserves a very big heap of credit for, it was first noted by Wei and Lindgren (1991). A closer examination of why it is so could be a scientifically interesting study. The value of knowing the exact pedigree has probably been over-stated by forest geneticists. I remember from my early days in forest genetics, when we discussed a simple breeding program where forests were planted from seed orchards and selections to new seed orchards were made in these forests. We said that this was a stupid and unsophisticated idea, we are much more clever now and keep track of pedigrees. I wonder how unsophisticated it really was, this deserves to be studied more in detail.

 

Bila AD & Lindgren D 1998  Fertility variation in Milletia sthulimannii, Brachystegia speciformis, Brachystegia bohemi and Leucaena leucocephala  and its effects on relatedness in seeds. Forest Genetics, 5:119-129.

Summary: Accumulated fertility in a tree population can be reasonable well described by a power function (y=x^a), where a is a parameter describing the variation in fertility. Fertility variation can also be described as relative status number, which varied between 0.38 and 0.67 in the objects studied. Thus the "effective" number of trees can be considered to be between 38 and 67% of the census number of trees (but genetic drift is when not considered). This can also be viewed as a measure of the relatedness of the seed crop. The effect of keeping the female contribution constant (thus collecting equal amount of seeds from each tree) could be quantified. This action has a large effect (in spite of that paternal contributions are still unknown) and is recommended for gene conservation purposes. The required number of trees for getting estimates of fertility variation was derived.

 

Lindgren D. 1998. Balansen mellan produktion och genetisk mångfald. (In Swedish) Skogsfakta, 7

Summary: Popularised summary in Swedish about group coancestry and status number, and how these entities may be balanced to combine gain and diversity in an optimal way. The optimum for seed orchard establishment and thinning is "linear deployment". It is recommended that Swedish breeders or breeding related scientists make certain that they get a copy of this.

Comment: till now I thought Skogsfakta was a useable channel for reaching concerned Swedes, now I have serious doubts!

 

Lindgren D & MullinTJ 1998. Relatedness and status number in seed orchard crops. Canadian Journal of Forest Research, 28:276-283.

Summary: Formulae are derived for group coancestry and status number in seed orchard crops considering inbreeding and coancestry of seed orchard genotypes, male and female reproductive success and pollen contamination (including its relatedness to the seed orchard and to itself). This method of characterising seed orchards (or rather their crops) seems to be very general and useful.

Comment: I now lead a project which will estimate the diversity connected to all Swedish seed orchards using this method as a basis. Of course I use standardised estimates of most influences, so for most seed orchards the only really important seed orchard specific input will be clonal number.

 

Ruotsalainen S & Lindgren D 1998. Predicting genetic gain of backward and forward selection in forest tree breeding. Silvae Genetica. 47: 42-50.

Summary: Backward selection of the parent and forward selection of the best of its kids were compared. The better the parent, the less likely it is that the best kid is better. Some type of combination of backward and forward selection can be beneficial. High selection intensity when plus trees were selected, low heritability and small progenies are factors which favour selection backwards following wind-pollination.

Comments: In the situation wind-pollinated progeny and grafts of mother is the basis of the breeding program, crossing between the best mothers seems the best way to advance breeding, but the not top ranking mothers could sometimes be replaced by selection forwards (especially if a high fraction of the families are expected to contribute to long term breeding), and for some percentiles of mothers it may be a good idea to advance the breeding population with both types of selections.

 

Zheng YQ,  Andersson EW  & Lindgren D 1998. A model for infusion of unrelated material into a breeding population. Silvae Genetica: 47:94-101

Summary: A model for introducing fresh material in breeding programs based on group merit was developed. It may not be uncommon that it occurs situations when it seems beneficial  to inject unrelated material (e.g. fresh plus trees or the best of the progeny tested plus trees which were truncated at an earlier stage) to maximise group merit (thus gain at a given diversity).

Comment: I guess, based on this study and many others, one can foresee a situation in the current Swedish program that it would soon turn beneficial to incorporate earlier unused unrelated breeding material if the number of founders was truncated to 50 immediately to sustain long term breeding populations of size 50. This problem can probably be avoided by using more than 50 founders from the beginning.

 

Gain and Diversity in Multi-Generation                                           Breeding Programs

                        Erik W. Andersson

 

 

Akademisk avhandling som för vinnande av skoglig doktorsexamen kommer att offentligen försvaras i Björken, SLU, Umeå, Fredagen den 21 maj 1999, kl 10.00.

 

Abstract

Progress in tree improvement comes from utilizing the genetic diversity found in unimproved forests. The balance between genetic gain and diversity is one of the most important considerations for all breeders. The sustainability in gain extraction over generations of the breeding program should be considered from its start. This thesis examines various strategies for selection in breeding. Using coancestry and its derivatives as a diversity measure, different methods are contrasted and compared for their efficiency in giving response to selection, considering the subsequent change in genetic diversity. It is concluded that restricted and unrestricted phenotypic selection and restricted (individual and family) index-selection, using data taking the performance of relatives into account, are fairly equal in terms of selection efficiency. However, a genuine and substantial improvement in selection response can be achieved by incorporating information on the population structure into the selection criterion. A possible way to enhance the efficiency in realized gain per unit decrease in diversity is to balance selection with relatedness. This can be seen as maximizing the allele containing capacity of the breeding population with regards to constraints on relatedness. Two ways to accomplish this, group merit selection and a linear programming method optimizing gain with a restriction on group coancestry are exemplified in this thesis. Benefits from coancestry-controlled selection are far from negligible, and can have a role to play in tree improvement. The breeding population should be seen as a dynamic entity regarding size and family contributions over time. A decision-model for infusion of fresh unrelated material is presented. The conclusion is that there often could be a place for refreshing the breeding population with new selections in the first cycles of breeding. The diversity of regeneration material affects forests over the long term. It is concluded that diversity of species undergoing domestication must be monitored, with comparable measures throughout the whole breeding program, including seed producing stages.

 

Key words:     breeding, coancestry, genetic diversity, selection, status number, tree improvement.

 

 

I see it as a part of a series of four dissertations, which develops the art of a joint consideration of gain and gene diversity in breeding and which comes in a logic and uninterrupted line, where one thesis builds on the previous.

 

The first part was

 

Wei, Run-Peng 1995, Predicting Genetic Diverstity and Optimizing Selection,

which mainly discusses gain and diversity changes at the inititation of breeding.

 

The second part was:

Gea, Luigi D 1997. Genetic diversity and gain. The concept of status number. PhD thesis, school of forestry. University of Canterbury, Christchurch, New Zealand.

This thesis develops the methods making it possible to analyse gain and diversity jointly over generations (this dissertation is not much known, most other countries do not expose their thesis to the surrounding world as Sweden does).

 

Erik Andersson is the third part:

Gain and Diversity in Multi-Generation Breeding Programs.

 

The last part in this "series" is planned to be defended Sept 3 by Ola Rosvall.

 

 

 

Eriks thesis is built on four papers, the abstract and comments are mine, not Erik's

 

Andersson EW, Spanos KA, MullinTJ & Lindgren D 1998. Phenotypic selection compared to restricted combined index selection for many generations. Silva Fennica, 32:111-120.

Summary: The methods compared were unrestricted phenotypic selection and restricted combined index selection for five generations. A variety of crossing schemes were compared as were family numbers and also the introduction of a strong dominance component. Results were surprisingly stabile and showed that apart from rather unlikely events, that combined index selection has no or minor advantages over selection on the phenotype.

 

Comment: The technically easy mass-selection (phenotypic selection) seems to have a place in many breeding operations. If selection is guided by a known family structure (selecting good individuals from good families) the advantage of high gain is approximately balanced by the disadvantage of high relatedness. The value of knowing the exact pedigree has probably been over-stated by forest geneticists. I remember from my early days in forest genetics, when we discussed a simple breeding program where forests were planted from seed orchards and selections to new seed orchards were made in these forests. We said that this was a stupid and unsophisticated idea, we are much more clever now and keep track of pedigrees. I wonder how unsophisticated it really was. It should be remembered that "phenotypic" in the sense of this paper means that information about parents or sibs is not used, it is not discussing when breeding values are based on offspring. This situation corresponds to a selection with a higher heritability.

 

Rosvall O & Andersson EW 1999. Group-merit selection compared to conventional restricted selection for trade-offs between genetic gain and diversity. Forest Genetics 6:1-14.

Abstract: The Group-merit selection was devised by Lindgren and Mullin (1997), although they called the method population merit selection. The superiority over a range of circumstances has been investigated for a simulated long term breeding program based on single pair mating. The largest superiority was obtained for low heritability. This means that the superiority is not very high if the breeding program is based on breeding values obtained from progeny-testing. Selection intensity was not important for the superiority. The superiority was sustainable over generations.

Comment: I have later found that for more complicated designs the Lindgren & Mullin algorithm can miss the optimum. I think this has little practical importance and it is most important in situations of almost balanced selection. For the mating design used in this paper the algorithm does not miss the optimum.

Andersson EW, Sanchez-Rodrigues L & Andersson B. 1999. Group coancestry controlled selection in a Pinus sylvestris L. breeding program. TAG in press.

Abstract: Integer Linear Programming was used to maximize gain when group coancestry was seen as a restriction. Real OP-progeny test data were used to choose parents while the second generation offspring from crosses between the selected was simulated. Selection which allows the best-performing families to contribute a greater number was superior.

Comment: The method is expected to give identical results to that of Lindgren and Mullin (1997). It has the advantage of relaying on ready programs instead of home made, and it can find the optimum directly for a given group coancestry, while the Lindgren and Mullin (1997) algorithm has to find such a solution by iteration. On the other hand ILP is useless in more complicated cases than this. I remind that "linear deployment" is a good approximation (see Wei's thesis).

 

Zheng YQ,  Andersson EW  & Lindgren D 1998. A model for infusion of unrelated material into a breeding population. Silvae Genetica: 47:94-101

Summary: A model for introducing fresh material in breeding programs based on group merit was developed. It may not be uncommon that it occurs situations when it seems beneficial to inject unrelated material (e.g. fresh plus trees or the best of the progeny tested plus trees which were truncated at an earlier stage) to maximise group merit (thus gain at a given diversity).

Comment: I guess, based on this study and many others, one can foresee a situation in the current Swedish program that it would in the future turn beneficial to incorporate earlier unused unrelated breeding material if the number of founders was truncated to 50 immediately to sustain long term breeding populations of size 50. This problem can probably be avoided by using more than 50 founders from the beginning. A possible, but considerable less favourable option, is to make certain that the highest ranking not selected plus trees are kept in archives some decades ahead. 

 

Ola Rosvall's thesis

Ola Rosvall's thesis is now in print. The public defence is planned for Sept 3rd at Umeå with Bailian Li as opponent. If you have not got it by Aug 20, you may ask me or Ola Rosvall.

Its title is:

Enhancing Gain from Long-Term Forest Tree Breeding while Conserving Genetic Diversity

List of publications included

Rosvall, O., Lindgren, D. and Mullin, T.J. 1999. Sustainability robustness and efficiency of a multi-generation breeding strategy based on within-family clonal selection. Silvae Genetica: 47(5- 6), 307- 321.

Rosvall, O., and Andersson, E.W. 1999. Group-merit selection compared to conventional restricted selection for trade-offs between genetic gain and diversity. Forest Genetics 6(1):11- 24.

Rosvall, O., and Mullin, T.J. 1999. Positive assortative mating with selection restrictions on group coancestry enhances gain while conserving genetic diversity in long-term forest tree breeding. Manuscript.

Rosvall, O., Mullin, T.J., and Lindgren, D. 1999. Controlling parent contributions during positive assortative mating and selection increases gain in long-term forest tree breeding. Manuscript.