“Breeding without breeding” with only forests and combined seed orchards/breeding populations

 

Dag Lindgren and Xiao-Ru WangSwedish University of Agricultural Sciences 

andUmeå University

Seed orchard MeetingIUFRO WP 02-09-06

Korea 090909

http://www-genfys.slu.se/staff/dagl/korea09/

Acknowledgements

• Yousry El-Kassaby• Anders Fries• Takeshi Torimaru• Matti Haapanen

A system with only clonal seed orchards and forests

Seed orchard

Forests

Selection

Actually this system is used for half of Swedish plantations today

Seed orchard

Forests

Selection

• Clonal seed orchards (grafts) and forests are managed and paid for anyway by forestry (sunk cost, not a cost for breeding).

• Recombination is done anyway in seed orchards and the plustree hybrids are planted anyway in forests.

• Phenotypic selection can be done fast and efficiently without any measurements in young forests by subjectively choosing good trees and without any knowledge of the ancestry of the trees.

• Phenotypic selection in plantations has the potential to work well even in advanced generations.

• No permanent organisation for managing clonal archives, controlled crosses, field tests and measurments is needed (BwB = ”Breeding without Breeders”). The investment in genetic evaluations to make a new seed orchard need to be done only a few years before the establishment of the new seed orchard instead of supporting long term breeding 35 years before material for new seed orchards are obtained as done in Sweden today. 

But what about relatedness?

Mass selection (phenotypic selection) offer a good and near optimal trade off between gain and gene diversity

Modified From Lindgren and Wei (1993) and developed by Lindgren and Wei 2006

0 1

Combined index (maximizes gain)

Mass selection (easy)

Between family(exhausts diversity)

Within family(conserves diversity)

Gai

n

0.5Diversity MaxMi

n

Phenotypic selection in a progeny plantation gives a near optimal gain at the relatedness level 

obtained (diversity)

Phenotypic selection (mass-selection) in improved forests has problems, e.g.

• Contamination with unimproved trees and pollen reduces gain.

• Relatedness will not be controlled or known and perhaps large.

These problems can be overcome if trees are phenotypically pre-selected in the forest and the ancestry of the pre-selected trees clarified by markers. A variant of ”Breeding without Breeding” as coined by Yousry El-Kassaby.

Simple ”Breeding without Breeding” Cycle

Seed orchard

Forest

Select considering

Pre-selection

Do markers work?

• We made a study where the trees in the forest was seeds in a seed orchard harvest (the same as presented by A Fries at this meeting). 

• The mothers (seed orchard clones) were known, but pretended unknown.

• The study: Wang X-R, Torimaru T, Lindgren D and Fries A 2009. Marker-based parentage analysis facilitates low input ‘breeding without breeding’ strategies for forest trees. TGG in press.  

Material & methods

• Seed orchard with 28 clones (Västerhus)• 8-12 seeds/clone, 305 seeds in total• Nine selected SSR (microsatellite) markers• Parent-pair analysis with both parents unknown• Simple exclusion analysis assuming null allele

Västerhus spring 2006.  Photo: Yoshinari Morogushi

The simple system with only seed orchard and forest. This is Västerhus seed orchard the pollination year of 

seeds studied.

Commercial plantation with seeds from the orchard

Photo: Dag Lindgren

Selections are done in the forest from the seed orchard. Needles are 

collected for ancestry of pre-selected trees

Photo Takeshi Torimaru 0806

Results

• For the offspring from the seed orchard, clones both parents can be determined for  93-97% offspring.

• Thus, in principle BwB is technically possibile. • The cost for the marker analyses is reasonable (given the competence exists).

Old trial with crosses from some of the Västerhus clone and others

• A pilotstudy with 35 trees was done in a progeny test where some progenies of Västerhus clones were planted.

• Few needles <9 m! That made collection problematic. It is practical to select trees at an age when fresh needles <5m!

• All trees analysed, which did not origin from Västerhus clones, could correctly be excluded.

• Ancestry for a few trees did not agree with documentation. It would be compatible with 10% erroneus pedigree in progeny-trials. We found it not reliable enough to go on with.

• But it illuminates that pedigreed tests may not be quite certain, thus the advantage over BwB is less than calculated. 

Experiences and development• The required competence for marker analyses and statistical 

analyses is high. We do not recommend it without involvement of an experienced molecular lab and some skill in the mathematical/statistical analyses.

• Theoretically there exits a large number of marker loci (SSR), but in practice brand new suitable loci (little trouble with null-alleles and high polymorphy) are not easily identified.

• There is a technical development and the methods can be improved, but we do not recommend to take for granted that this BwB application functions well for seed orchards with more than 50 clones even in a decade.

• The pollen contamination in Swedish Scots pine is near 50%, this BwB application would function better when pollen contamination is lower. 

Comments about this simple BwB

• If breeders start using BwB, the step to other uses of the same samples of DNA is short. BwB may open the door to other applications of molecular breeding.

• Simple BwB produces trees with uncertain breeding values (phenotypic selection). There is a desire to have tested clones in advanced seed orchards, but that is probably not optimal, so do not be afraid of using untested clones in sufficient numbers.

• BwB means a wait for good pollen production, artificial crosses can be made earlier.

”Progeny test”

• It is possible to link good trees in the forest to parents in a seed orchard. Thus it is also possible to determine breeding value of the orchard clones for ”ability to give good offspring”. Such a ”progeny-test” seems to cost only a fraction of conventional progeny-testing allthough less accurate.

Swedish long term breeding

• Sweden has since six decades invested much in field trials, breeders and breeding organisation. Thanks to that, the new seed orchards have three time more genetic gain than the first batch.

• Swedish long term breeding is mainly based on within family selection with all parents equally represented, thus parental breeding values does not matter. This simple BwB system with phenotypic pre-selection, followed by equalising parental contributions is similar to the Swedish system.

Comparison

• We compared this simple low-input system with current Swedish long term breeding. Under our assumptions the low input system produced somewhat less than half the annual gain, but annual costs can be cut almost 90%!

• Sweden is (hopefully) willing to pay the higher cost for the more powerful and better controlled high intensity breeding for valuable crops (Scots pine and Norway spruce).

BWB in minor species?

• Low need for seeds justifies low-input solutions.• The pollen contamination is usually low or absent, which

makes BWB much more effective.• But I guess that grafted seed orchards are complicated

for minor species, it is preferable with seedling seed orchards (”gene resource populations” combining different objectives).

• BWB in its present form can only handle clonal seed orchards. But in the future we may identify grandparents with markers, and when BWB can be used for seedling seed orchards.

BwB with grandparents

• It seems considerable more effective to keep grandparents under control than parents. Thus it seems desirable to develop BwB systems where pedigree is tracked to grandparents.

• Lindgren D, Danusevičius D & Rosvall O 2008. Balanced forest tree improvement can be enhanced by selecting among many parents but keeping balance among grandparents. Canadian Journal of Forest Research  38(11): 2797–2803.

 

• It can be argued that Scots pine in southern Sweden is a candidate for converting the current high input breeding to low input BwB. The recent planting is low mainly because of damage by animals (moose) and the plant number supported hardly justifies the current breeding effort.

• But forestry wants seed orchards in reserve because demand may increase.

• Could these seed orchards be simple BwB?

Some consideration starting BwB with F1-hybrids with plustree parents in an advanced system like Scots pine in southern Sweden:

• To make BwB powerful in a system whith F1-clones, many untested phenotypic F1-clones should be in the seed orchard. The final selections from the forest should not include offspring from many F1-clones to get gain from among family selection.

• The F1-clones will be related, but it is not desirable with related clones in a seed orchard

• Simple BwB can only handle 50 clones.• Advanced seed orchards should have rather few clones for high

gain.• If the aims - 1) preserving diversity for breeding and 2) high gain

immediatly for forestry - are served by the same seed orchard, both will loose.

• How can those problems be handled?

An simple orchard-forest BwB design for advanced generations  

• Have orchards with the major contributions from the 20 best clones. But in addition have say 100 clones with very few (two) copies. The production loss will be very low and partly balanced by more diversity and flexibility.

• The extra 100 clones can be spatially close.• Selective harvests are done from these extra clones in

batches of 40 and special forests (not large) established and documented.

• For next seed orchard BwB selection (phenotypic pre-selection followed by marker analyses and final selection) is done in the special gene resource forests besides the ordinary forests. In the gene resource forest the rare clones will get good representation.

A system with only clonal seed orchards and forests,but more clones

Seed orchard

Forests

Selection

Small special forests

Selective harvests

Flexibility• The suggested seed orchards can also be a

starting point for OP-progeny tests with subsequent ”BwB” selections.

• The seed orchards can be established today, and a decision can be made in 15 years, when they are adult, if it will be OP-progeny-tests or simple BwB (commercial forests planned for selection).

• Thanks for attention