Genetic Diversity of Stone Fruit Cultivars Preserved On-Farm in Southern Spain

Authors
P. Rallo
M. R. Rocio Jiménez
L. Casanova
A. Morales-Sillero
M. Paz Suárez
Department of Agroforestry Sciences, ETSIA, University of Seville, Carretera de Utrera, km 1, 41013 Seville, Spain.
Abstract
Old traditional cultivars are valuable genetic resources for crop improvement, but a great number of them have disappeared in the past century. This study aimed to characterize traditional cultivars of different Prunus species collected in small family orchards in southwestern Spain and to evaluate their genetic diversity and relationships. One hundred and twelve accessions belonging to 36 traditional cultivar denominations were analyzed using eight SSR loci transferable across the genus Prunus. The most useful loci to analyze different Prunus species were UDP96-005, BPPCT-002, UDP98-410 and ps02a12. A total of 152 alleles were observed, and 112 were unique to certain species. Sixty-eight different genotypes were found, revealing the possible existence of homonyms among traditional cultivar names. The clustering analysis was consistent with the taxonomic classification of the different species studied and with the geographical origins of the accessions within each species. The results showed wide genetic variability of traditional cultivars of stone fruits grown in small family orchards, which highlights the need to preserve them using both in-situ and ex-situ strategies. Twenty-eight of these accessions are currently conserved ex-situ at the University of Sevilla, Spain. The use of highly transferable SSRs has been proven as efficient in multi-species surveys performed on-farm.

Keywords

Subjects

1. Bortiri, E., Heuvel, B. V. and Potter, D. 2006. Phylogenetic Analysis of Morphology in Prunus Reveals Extensive Homoplasy. Plant Syst. Evol., 259: 53-71.
2. Bouhadida, M., Casas, A. M., Gonzalo, M. J., Arús, P., Moreno, M. A. and Gogorcena, Y. 2009. Molecular Characterization and Genetic Diversity of Prunus Rootstocks. Sci. Hortic., 120:237–245.
3. Bouhadida, M., Martín, J. P., Eremin, G., Pinochet, J., Moreno, M. A. and Gogorcena, Y. 2007. Chloroplast DNA Diversity in Prunus and Its Implication on Genetic Relationships. J. Am. Soc. Hortic. Sci., 132: 670-679.
4. Bouhadida, M., Moreno, M. A., Gonzalo, M. J., Alonso, J. M. and Gogorcena, Y. 2011. Genetic Variability of Introduced and Local Spanish Peach Cultivars Determined by SSR Markers. Tree Genet. Genom., 7: 257-270.
5. Bourguiba, H., Krichen, L., Audergon, J. M., Khadari, B. and Trifi-Farah, N. 2010. Impact of Mapped SSR Markers on the Genetic Diversity of Apricot (Prunus armeniaca L.) in Tunisia. Plant Mol. Biol. Rep., 28: 578-587.
6. Buhner-Zaharieva, T., Moussaoui, S., Lorente, M., Andreu, J., Núñez, R., Ortiz, J. M. and Gogorcena, Y. 2010. Preservation and Molecular Characterization of Ancient Varieties in Spanish Grapevine Germplasm Collections. Am. J. Enol. Vitic., 61: 557-562
7. Cipriani, G., Lot, G., Huang, W. G., Marrazzo, M. T., Peterlunger, E. and Testolin, R. 1999. AC/GT and AG/CT Microsatellite Repeats in Peach Prunus persica (L) Batsch: Isolation, Characterization and Cross-Species Amplification in Prunus. Theor. Appl. Genet., 99: 65-72.
8. De La Rosa, R., James, C. M. and Tobutt, K. R. 2002. Isolation and Characterization of Polymorphic Microsatellites in Olive (Olea europaea L.) and Their Transferability to Other Genera in the Oleaceae. Mol. Ecol. Notes, 2: 265-267.
9. Dirlewanger, E., Cosson, P., Tavaud, M., Aranzana, M. J., Poizat, C., Zanetto, A., Arus, P. and Laigret, F. 2002. Development of Microsatellite Markers in Peach Prunus persica (L.) Batsch and Their Use in Genetic Diversity Analysis in Peach and Sweet Cherry (Prunus avium L.). Theor. Appl. Genet., 105: 127-138.
10. Downey, S. L. and Iezzoni, A. F. 2000. Polymorphic DNA Markers in Black Cherry (Prunus serotina) are Identified Using Sequences from Sweet Cherry, Peach, and Sour Cherry. J. Am. Soc. Hortic. Sci., 125: 76-80.
11. El Hamzaoui, A., Oukabli, A., Charafi, J. and Moumni, M. 2013. Moroccan Almond Is a Distinct Gene Pool as Revealed by SSR. Sci. Hortic., 15: 37-44.
12. Esquinas-Alcázar, J. 2005. Protecting Crop Genetic Diversity for Food Security: Political, Ethical and Technical Challenges. Nat. Rev. Genet., 6: 946-953.
13. FAO. 2001. International Treaty for Plant Genetic Resources for Food and Agriculture. http://www.planttreaty.org/content/texts-treaty-official-versions.
14. Font i Forcada, C., Oraguzie, N., Igartua. E., Moreno, M. A. and Gogorcena, Y. 2013. Population Structure and Marker–Trait Associations for Pomological Traits in Peach and Nectarine Cultivars. Tree Genet. Genom., 9: 331-349.
15. García -Muñoz, S., Lacombe, T., de Andres, M. T., Gaforio, L., M-Organero, G., Laucou, V., This, P. and Cabello, F. 2012. Grape Varieties (Vitis vinifera L.) from the Balearic Islands: Genetic Characterization and Relationship with Iberian Peninsula and Mediterranean Basin. Genet. Resour. Crop. Ev., 59: 589-605.
16. Gharbi, O., Wünsch, A. and Rodrigo, J. 2014. Characterization of Accessions of 'Reine Claude Verte' Plum Using Prunus SRR and Phenotypic Traits. Sci. Hortic., 169: 57-65.
17. Gouta, H., Ksia, E., Buhner-Zaharieva, T., Mliki, A. and Gogorcena, Y. 2012. Development of an SSR-Based Identification key for Tunisian Local Almonds. Sci. Agr., 69: 108-113.
18. Gouta, H., Ksia, E., Buhner, T., Moreno, M.A., Zarrouk, M., Mliki, A. and Gogorcena, Y. 2010. Assessment of Genetic Diversity and Relatedness among Tunisian Almond Germplasm Using SSR Markers. Hereditas, 147: 283–292.
19. Halász, J., Hegedűs, A., György, Z., Pállinger, E. and Tóth, M. 2011. S-Genotyping of Old Apple Cultivars from the Carpathian Basin: Methodological, Breeding and Evolutionary Aspects. Tree Genet. Genom., 7: 1135–1145.
20. Hegedus, A., Szabo, Z., Nyeki, J., Halasz, J. and Pedryc, A. 2006. Molecular Analysis of S-Haplotypes in Peach, a Self-Compatible Prunus Species. J. Amer. Soc. Hort. Sci., 131: 738-743.
21. Herrero, J. 1964. Cartography of Stone Fruits and Pome Fruits. =Cartografía de Frutales de Hueso y Pepita. Edn: CSIC - Estación Experimental de Aula Dei, Zaragoza, Spain, 5 Volumes. (in Spanish)
22. Kazija, D. H., Jelacic, T., Vujevic, P., Milinović, B., Čiček, D., Biško, A., Pejić, I., Šimon, S., Žulj Mihaljević, M., Pecina, M., Nikolić, D., Grahić, J., Drkenda, P. and Gaši, F. 2014. Plum Germplasm in Croatia and Neighboring Countries Assessed by Microsatellites and DUS Descriptors. Tree. Genet. Genom., 10: 761-778.
23. Kloosterman, A. D., Budowle, B. and Daselaar, P. 1993. PCR-Amplification and Detection of the Human D1S80 VNTR Locus: Amplification Conditions, Population-Genetics and Application in Forensic Analysis. Int. J. Legal Med., 105: 257-264.
24. Lamia, K., Hedia, B., Jean-Marc, A. and Neila, T. F. 2010. Comparative Analysis of Genetic Diversity in Tunisian Apricot Germplasm Using AFLP and SSR Markers. Sci. Hortic., 127: 54-63.
25. Laquidain, M. J., Urrestarazu, J., Crespo, S., Santesteban, L. G., Miranda, C. and Royo, J. B. 2011. Genetic Identity of Apples, Pears and European Plums from Valderejo Natural Park, Alava, Spain. Acta Hortic., 918: 631-638.
26. Lee, S. and Wen, J. 2001. A Phylogenetic Analysis of Prunus and the Amygdaloideae (Rosaceae) Using ITS Sequences of Nuclear Ribosomal DNA. Am. J. Bot., 88: 150-160.
27. Makovics-Zsohar, N., Toth, M., Suranyi, D., Kovacs, S., Hegedus, A. and Halasz, J. 2017. Simple Sequence Repeat Markers Reveal Hungarian Plum (Prunus domestica L.) Germplasm as a Valuable Gene Resource. Hortsci., 52(12): 1655-1660.
28. Martín, C., Herrero, M. and Hormaza, J. I. 2011. Molecular Characterization of Apricot Germplasm from an Old Stone Collection. Plos One, 6: e23979.
29. Martínez-Gómez, P., Arulsekar, S., Potter, D. and Gradziel, T. M. 2003. An Extended Interspecific Gene Pool Available to Peach and Almond Breeding as Characterized Using Simple Sequence Repeat (SSR) Markers. Euphytica, 131: 313–322.
30. Mnejja, M., García -Mas, J., Audergon, J. M. and Arús, P. 2010. Prunus Microsatellite Marker Transferability across Rosaceous Crops. Tree Genet. Genom., 6: 689-700.
31. Mnejja, M., Garcia-Mas, J., Howad, W. and Arús, P. 2005. Development and Transportability across Prunus Species of 42 Polymorphic Almond Microsatellites. Mol. Ecol. Notes, 5: 531–535.
32. Mnejja, M., García -Mas, J., Howad, W., Badenes, M. L. and Arús, P. 2004. Simple-Sequence Repeat (SSR) Markers of Japanese Plum (Prunus salicina Lindl.) Are Highly Polymorphic and Transferable to Peach and Almond. Mol. Ecol. Notes, 4: 163-166.
33. Nei, M. 1973. Analysis of Gene Diversity in Subdivided Populations. Proc. Natl. Acad. Sci. USA, 70: 3321-3323
34. Nei, M. and Li, W. H. 1979. Mathematical-Model for Studying Genetic-Variation in Terms of Restriction Endonucleases. Proc. Natl. Acad. Sci. USA, 76: 5269-5273.
35. Öz, M. H., Vurgun, H., Bakir, M., Buyuk, I., Yuksel, C., Unlu, H. M., Cukadar, K., Karadogan, B., Kose, O. and Ergul A. 2013. Molecular Analysis of East Anatolian Traditional Plum and Cherry Accessions Using SSR Markers. Genet. Mol. Res., 12: 5310-5320.
36. Pérez -Romero, L. F., Suárez, M. P., Dapena, E. and Rallo, P. 2015. Molecular and Morphological Characterization of Local Apple Cultivars in Southern Spain. Genet. Mol. Res., 14: 1487-1501.
37. Pina, A., Urrestarazu, J. and Errea, P. 2014. Analysis of the Genetic Diversity of Local Apple Cultivars from Mountainous Areas from Aragon (Northeastern Spain). Sci. Hortic., 174: 1-9.
38. Rallo, P., López, C., Suárez, M. P., Morales-Sillero, A.M., Casanova, L., Jiménez, R., Sánchez, A. and Guzmán, J. R. 2011. Molecular Characterization of Prunus Accessions of Traditional Cultivars Prospected in Western Andalusia, Spain. Acta Hortic., 918: 685-688.
39. Rakonjac, V., Mratinic, E., Jovkovic, R. and Fotiric Akšic, M. 2014. Analysis of Morphological Variability in Wild Cherry (Prunus avium l.) Genetic Resources from Central Serbia. J. Agr. Sci. Tech., 16: 151-162.
40. Rehder, A. 1940. Manual of Cultivated Trees and Shrubs Hardy in North America. 2nd Edition, Macmillan, New York, USA, 996 PP.
41. Sehic, J., Nybom, H., Hjeltnes, S. H. and Gasi, F. 2015. Genetic Diversity and Structure of Nordic Plum Germplasm Preserved Ex Situ and On-Farm. Sci. Hortic., 190: 195-202.
42. Testolin, R., Marrazzo, T. and Cipriani, G. 2000. Cross-Species Amplification of Microsatellite Markers Isolated from Peach by Means of Heterologous Primer Pairs. Acta Hortic., 538: 511-516.
43. Trujillo, I., Ojeda, M. A., Urdiroz, N. M., Potter, D., Barranco, D., Rallo, L. and Diez, C. M. 2014. Identification of the Worldwide Olive Germplasm Bank of Cordoba (Spain) Using SSR and Morphological Markers. Tree Genet. Genom., 10: 141-155.
44. Vaughan, S. P. and Russell, K. 2004. Characterization of Novel Microsatellites and Development of Multiplex PCR for Large-Scale Population Studies in Wild Cherry, Prunus avium. Mol. Ecol. Notes, 4: 429-431.
45. Vilanova, S., Soriano, J. M., Lalli, D. A., Romero, C., Abbott, A. G., Llacer, G. and Badenes, M. L. 2006. Development of SSR Markers Located in the G1 Linkage Group of Apricot (Prunus armeniaca L.) Using a Bacterial Artificial Chromosome Library. Mol. Ecol. Notes, 6: 789-791.
46. Wünsch, A. 2009. Cross-Transferable Polymorphic SSR loci in Prunus Species. Sci. Hortic., 120: 348-352.
47. Wünsch, A., Carrera, M. and Hormaza, J. I. 2006. Molecular Characterization of Local Spanish Peach Prunus persica (L.) Batsch Germplasm. Genet. Resour. Crop Ev., 53: 925-932.
48. Wünsch, A. and Hormaza, J. I. 2004. Molecular Evaluation of Genetic Diversity and S-Allele Composition of Local Spanish Sweet Cherry (Prunus avium L.) Cultivars. Genet. Resour. Crop Ev., 51: 635-641.
Journal of Agricultural Science and Technology
Volume 21, Issue 4
July and August 2019
Pages 943-955