Loss of alleles due to resistant breeding: the case of cypress

Loss of alleles due to resistance breeding

The case of cypress

Strasbourg 2002

3 May 2023 Loss of alleles due to resistance breeding: the case of cypress

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Aristotelis C. PapageorgiouAristotelis C. PapageorgiouDepartment of Forestry, Environment and Natural

Resources,Democritus University of Thrace, Greece

Sotirios XenopoulosSotirios XenopoulosInstitute of Mediterranean Forest Ecosystems and

ForestProducts, National Agricultural Research Foundation,

Greece

Reiner Finkeldey, Hans H. HattemerReiner Finkeldey, Hans H. HattemerInstitute of Forest Genetics and Forest Tree Breeding,Georg August University Göttingen, Germany


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The Mediterranean cypress

• Occurs naturally from Afghanistan to Greece

• Cultivated all over the world – amenity tree and plantations

• Typical element of the Mediterranean landscape

• Stress tolerant• Endangered by the

fungus Seiridium cardinale


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Breeding for resistance• AGRIMED (1980-1988)• CAMAR (1991-1994)• AIR II (1993-1997)• FAIR (1997-2000)Research Group: INRA, University

of Montpellier (France); CNR, University of Florence (Italy); MAICH, NAGREF, University of Thessaloniki (Greece); University of Lisbon and Vila Real (Portugal); IVIA (Spain); University Göttingen (Germany).


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Outcome of the research• Mechanism of

resistance described• Genetic variation for

resistance discovered

• Cypress clones resistant against the disease were produced and tested


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Resistant clones in Greece• 1981: Seeds harvested from 6

base populations (15 trees in each stand)

• 1982: Nursery; 15 families per stand, 40 trees per family

• 1984: Inoculation• 1987: Trees were evaluated and

classified as resistant (5%) and susceptible (95%)

• 1988: Material from resistant trees was propagated in several clone plantations in Greece (grafting).


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Questions• What is the genetic diversity of the new

populations that will be founded with the resistant material?

• What are the changes in genetic variation due to artificial selection?

• Are there any correlations between genetic markers and resistance?

• What is the best way to treat the resistant material, in order to maintain high levels of adaptability?


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Base populations• Samos, Rodos, Symi and

Kos – Aegean islands• Alepohori, Mystras –

Peloponnese• Aegean populations are

considered natural, while those from the Pelopon-nese are domesticated

• Genetic studies revealed a founder effect in the Peloponnese populations


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Material used for genetic analysis

Base Populations

Number of trees in base population

Number of clones

AALL 28 12 MMYY 29 17 SSAA 21 20 KKOO 21 16 RROO 21 21 SSYY 20 23


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Material & Methods

• Horizontal starch gel electrophoresis

• Six polymorphic enzyme loci

• PGI-B, PGM-A, PGM-B, NDH-A, GDH-A, LAP-A

• Megagametophytes (2n) and needles from clone ramets analyzed

• Clones were genotyped

• Plantations: Tatoi, Megalopolis, Lappa


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Allele frequency change: PGI-B


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Allele frequency change: NDH-A


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Allele frequency change: PGM-B


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Allele frequency change: LAP-A


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Allelic structures• Clone collections showed – in general -

no major differences in comparison with the base populations

• Most “typical” structures of populations remained unchanged in the clones

• A few changes were observed, without any specific trend in favor of a specific variant

• Exceptional changes in PGM-B and LAP-A


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Expected heterozygosity


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Observed heterozygosity


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Changes in allelic multiplicity


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Which alleles are lost?• AL: PGM-B3 (0,220), GDH-A3

(0,018), LAP-A3 (0,036)• MY: GDH-A1 (0,017), LAP-A2

(0,069)• SA: PGM-B1 (0,025), GDH-A3

(0,071), LAP-A2 (0,024)• KO: GDH-A3 (0,111), LAP-A2 (0,075)• RO: GDH-A3 (0,095)• SY: PGM-B1 (0,026)


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Diversity and heterozygosity

• Loss of alleles was observed in 3 loci and 5 clone collections; The alleles lost have low frequencies in the base populations

• Diversity was less in almost all clone collections; differences were not significant

• Observed heterozygosity remained more or less unchanged


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“Man made” bottleneck• Alleles are lost during

the breeding procedure• Despite the large

breeding population (15 families, 40 trees / family) in each population, strong selection intensity after the first inoculation caused a bottleneck


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Gene pool of populations vs. clones

Number of

alleles

Observed heterozygo

sity

Expected Heterozygo

sityPopulation

s19 0,36 0,43

Clones 18 0,36 0,40


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Genetic distances between the total clone set and the base populations

(d0 )AL MY SA KO RO SY

PGI-B 0.135

0.080

0.093

0.044

0.121

0.068

PGM-A 0.24

20.33

20.04

90.07

60.05

60.06

0PGM-B 0.21

90.21

50.18

60.13

60.32

30.21

9NDH-A 0.28

10.24

70.17

20.21

90.16

90.06

5GDH-A 0.10

80.08

00.23

40.15

50.16

30.06

9LAP-A 0.34

30.29

80.13

00.15

20.13

00.11

4Mean 0.22

10.20

80.14

40.13

10.16

00.09

9


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Total clone collection• When all resistant clones are considered as a

set, only one allele is lost (PGM-B1), which is very rare in two base populations (SA and SY)

• Large differentiation among populations and clone arrays; a rare allele in a given set may be frequent in another

• Similar structures of pooled data for populations and clones

• The totality of the clones is not representative any base population


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Literature review• Almost all comparisons consider pooled data• No differences in genetic structures between pooled

data from populations and clones – variation “captured”• Private and locally rare alleles are lost in the population

level: Picea sitchensis (Chaisurisri & El Kassaby 1994), Pseudotsuga menziesii (El Kassaby & Ritland 1996)

• No alleles are lost – even increased – in pooled data: Thuja plicata (El Kassaby et al. 1993), Picea sitchensis (Chaisurisri & El Kassaby 1994), Pseudotsuga menziesii (El Kassaby & Ritland 1996)

• Alleles are lost in pooled data: Picea glauca (Cheliak et al. 1988), Picea abies (Bergmann & Ruetz 1991), Picea glauca X engelmanni (Stoehr & El Kassaby 1997) – low differentiation (?)


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Breeding strategies• To avoid allele loss, selection

pressure should be lower• The mixture of clones from

different origins can reduce allele loss and increase adaptability

• However, adaptedness is probably reduced if a mixture of clones is planted

• In species with little differentiation, mixed sets of clones may still have less alleles

• More research is needed for the detection of possible associations between markers and resistance


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Acknowledgements• Eric Teissier du Cros for his advice, support

and coordination of the cypress projects• C. Andreoli, F.A. Aravanopoulos, G. Brofas,

A. Doulis, B. Fady, E. Gillet, L. Leinemann, G. Lyrintzis, G. Mantakas, K.P. Panetsos, C. Pichot, P. Raddi, S. Raddi, P. Ramos, A. Santini, P. Tsopelas, M. Ziehe (and many more) for their assistance and advice

• A. Drouzas and L. Iliadis for useful comments

Education

Loss of alleles due to resistant breeding: the case of cypress