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

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Individuals were selected for resistance against the imperfect fungus Seiridium cardinale Wag in six populations of Mediterranean cypress (Cupressus sempervirens L.). The collections of resistant clones and their base populations were surveyed at several isozyme gene loci. A total of 140 adult trees and of 109 clones were genotyped at six isozyme gene loci. The comparison yielded information on changes in genetic variation due to artificial selection. The genetic structure of most clone collections were similar to their base populations. Nevertheless, the number of rare alleles among the resistant clones had consistently decreased, although the numbers of investigated trees were similar to those of the clones. Possible implications for breeding strategies are discussed.



Presentation during the international conference: "Dynamics and conservation of genetic diversity in forest ecosystems", Strasbourg, 2-5 December 2002

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

  1. 1. Loss of alleles due to resistance breeding The case of cypress Strasbourg 2002
  2. 2. Aristotelis C. Papageorgiou Department of Forestry, Environment and Natural Resources, Democritus University of Thrace, Greece Sotirios Xenopoulos Institute of Mediterranean Forest Ecosystems and Forest Products, National Agricultural Research Foundation, Greece Reiner Finkeldey, Hans H. Hattemer Institute of Forest Genetics and Forest Tree Breeding, Georg August University Göttingen, Germany17 February 2013 Loss of alleles due to resistance breeding: the cas 2
  3. 3. 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 cardinale17 February 2013 Loss of alleles due to resistance breeding: the cas 3
  4. 4. 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).17 February 2013 Loss of alleles due to resistance breeding: the cas 4
  5. 5. Outcome of the research • Mechanism of resistance described • Genetic variation for resistance discovered • Cypress clones resistant against the disease were produced and tested17 February 2013 Loss of alleles due to resistance breeding: the cas 5
  6. 6. 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).17 February 2013 Loss of alleles due to resistance breeding: the cas 6
  7. 7. 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?17 February 2013 Loss of alleles due to resistance breeding: the cas 7
  8. 8. 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 populations17 February 2013 Loss of alleles due to resistance breeding: the cas 8
  9. 9. Material used for genetic analysis Base Number of trees in Number of Populations base population clones AL 28 12 MY 29 17 SA 21 20 KO 21 16 RO 21 21 SY 20 2317 February 2013 Loss of alleles due to resistance breeding: the cas 9
  10. 10. Material & Methods • Megagametophytes (2n) and needles from clone ramets analyzed • Clones were genotyped • Plantations: Tatoi,• Horizontal starch gel Megalopolis, Lappa electrophoresis• Six polymorphic enzyme loci• PGI-B, PGM-A, PGM-B, NDH-A, GDH-A, LAP-A 17 February 2013 Loss of alleles due to resistance breeding: the cas 10
  11. 11. Allele frequency change: PGI-B17 February 2013 Loss of alleles due to resistance breeding: the cas 11
  12. 12. Allele frequency change: NDH-A17 February 2013 Loss of alleles due to resistance breeding: the cas 12
  13. 13. Allele frequency change: PGM-B17 February 2013 Loss of alleles due to resistance breeding: the cas 13
  14. 14. Allele frequency change: LAP-A17 February 2013 Loss of alleles due to resistance breeding: the cas 14
  15. 15. 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-A17 February 2013 Loss of alleles due to resistance breeding: the cas 15
  16. 16. Expected heterozygosity17 February 2013 Loss of alleles due to resistance breeding: the cas 16
  17. 17. Observed heterozygosity17 February 2013 Loss of alleles due to resistance breeding: the cas 17
  18. 18. Changes in allelic multiplicity17 February 2013 Loss of alleles due to resistance breeding: the cas 18
  19. 19. 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) 17 February 2013 Loss of alleles due to resistance breeding: the cas 19
  20. 20. 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 unchanged17 February 2013 Loss of alleles due to resistance breeding: the cas 20
  21. 21. “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 bottleneck17 February 2013 Loss of alleles due to resistance breeding: the cas 21
  22. 22. Gene pool of populations vs. clones Number of Observed Expected alleles heterozygosity Heterozygosity Populations 19 0,36 0,43 Clones 18 0,36 0,4017 February 2013 Loss of alleles due to resistance breeding: the cas 22
  23. 23. Genetic distances between the total clone set and the base populations (d0 ) AL MY SA KO RO SYPGI-B 0.135 0.080 0.093 0.044 0.121 0.068PGM-A 0.242 0.332 0.049 0.076 0.056 0.060PGM-B 0.219 0.215 0.186 0.136 0.323 0.219NDH-A 0.281 0.247 0.172 0.219 0.169 0.065GDH-A 0.108 0.080 0.234 0.155 0.163 0.069LAP-A 0.343 0.298 0.130 0.152 0.130 0.114Mean 0.221 0.208 0.144 0.131 0.160 0.09917 February 2013 Loss of alleles due to resistance breeding: the cas 23
  24. 24. 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 population17 February 2013 Loss of alleles due to resistance breeding: the cas 24
  25. 25. 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 (?)17 February 2013 Loss of alleles due to resistance breeding: the cas 25
  26. 26. 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 17 February 2013 Loss of alleles due to resistance breeding: the cas 26
  27. 27. 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 comments17 February 2013 Loss of alleles due to resistance breeding: the cas 27

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