Molecular Genetic Characterization of the Turkish National Green Plum (Prunus cerasifera Ehrh.) Collection

Year 2021, Volume: 31 Issue: 1, 61 - 73, 15.06.2021

Gülsüm Çakır Tülin Taşcıoğlu Andaç Çavdar Sami Doğanlar Amy Frary Anne Frary

https://doi.org/10.18615/anadolu.950008

Cited By: 3

Abstract

Plum is an important fruit worldwide and has high nutritional value. Prunus cerasifera Ehrh., a type of European plum species, is very popular in Turkey and is usually eaten at the green, unripe stage. In this work for the first time, the genetic diversity and population structure of the 66 accessions housed in the Turkish National P. cerasifera collection were investigated using molecular markers. A total of 47 Sequence-Related Amplified Polymorphism (SRAP) primer pairs were used and found to be highly polymorphic with 98% of the 495 amplified alleles providing polymorphism. Average diversity of the accessions was 0.39 as determined using the dice coefficient and was similar to P. cerasifera germplasm from France, Iran and Belarus but higher than that from China. This difference was expected as Turkey, Iran and Belarus are within the geographical origin of this species which was distributed to Europe during ancient times. The genetic relationships among accessions of the germplasm collection were assessed using unweighted neighbor joining dendrogram and population structure analyses. The dendrogram and population structure results were strongly correlated as both methods clustered the material into two main groups with a much smaller third admixed group. The analysis also indicated that Can and Papaz types, despite their morphological differences are not genetically distinct and provides information about genetic relationships that can be used in future plum breeding.

Keywords

Plum, Prunus cerasifera Ehrh., SRAP, national collection, fruit genetics, green plum diversity

Türk Ulusal Yeşil Erik (Prunus cerasifera Ehrh.) Koleksiyonunun Moleküler Genetik Karakterizasyonu

Abstract

Erik, dünya çapında önemli bir meyvedir ve yüksek besin değerine sahiptir. Bir tür Avrupa eriği türü olan Prunus
cerasifera Ehrh., Türkiye'de çok popülerdir ve genellikle yeşil, olgunlaşmamış dönemde yenilmektedir. İlk kez bu çalışmada, Türk Ulusal P. cerasifera koleksiyonunda yer alan 66 genotipin genetik çeşitliliği ve popülasyon yapısı moleküler markörler kullanılarak araştırılmıştır. Toplam 47 Sekansla İlişkili Amplifiye Polimorfizm (SRAP) primer çifti kullanılmıştır ve polimorfizm sağlayan 495 adet çoğaltılmış allelin % 98'inin oldukça polimorfik olduğu bulunmuştur. Genotiplerin ortalama çeşitliliği, dice katsayısı kullanılarak, 0,39 olarak belirlenmiştir ve elde edilen bu değer Fransa, İran ve Beyaz Rusya'dan P. cerasifera germplazmlarıyla yapılan çalışmalarla benzer, ancak Çin'de yapılan çalışmadan daha yüksek bulunmuştur. Antik çağlardan beri Avrupa'ya dağılan türlerin coğrafi orijinleri içersinde Türkiye, İran ve Beyaz Rusya olduğu için bu fark beklenen bir durumdur. Germplazm koleksiyonunu oluşturan genotipler arasındaki genetik ilişkiler, ağırlıksız komşu birleştirme dendrogramı ve popülasyon yapısı analizleri kullanılarak değerlendirilmiştir. Dendrogram ve popülasyon yapısı sonuçları, her iki yöntem de materyali iki ana gruba ve çok daha küçük bir üçüncü, karıştırılmış grupla ayırdığı için güçlü bir şekilde ilişkilendirilmiştir. Ayrıca, analizler, Can ve Papaz erik tiplerinin morfolojik farklılıklarına rağmen genetik olarak farklı olmadıklarını ve gelecekteki erik ıslahında kullanılabilecek genetik ilişkiler hakkında bilgi verdiğini göstermiştir. 

Keywords

Erik, Prunus cerasifera Ehrh., SRAP, ulusal koleksiyon, meyve genetiği, yeşil

References

• Abuzayed, M., N. El-Dabba, A. Frary, and S. Doganlar. 2017. GDdom: An online tool for calculation of dominant marker gene diversity. Biochemical Genetics 55(2): 155-157.
• Almada, R., M. J. Arismendi, P. Pimentel, P. Rojas, P. Hinrichsen, M. Pinto, B. Sagredo. 2013. Class 1 non-symbiotic and class 3 truncated hemoglobin-like genes are differentially expressed in stone fruit rootstocks (Prunus L.) with different degrees of tolerance to root hypoxia. Tree Genet. Genomes 9, 1051–1063.
• Amador, M. L., S., Sancho, B., Bielsa, J., Gomez-Aparisi, and M. J., Rubio-Cabetas. 2012. Physiological and biochemical parameters controlling waterlogging stress tolerance in Prunus before and after drainage. Physiol. Plant. 144, 357–368.
• Anonymous. 2012. Erik Yetiştiriciliği. pp: 3-27. In: Sert Çekirdekli Meyve Yetiştiriciliği-2, 62BHY146. Ankara.
• Anonymous. 2019a. Food and Agriculture Organization of the United Nations (FAOSTAT). http://www.fao.org/faostat/en/#home [Accessed 21.12.2019].
• Anonymous. 2019b. USDA. The PLANTS Database. Available online: http://plants.usda.gov. [Accessed 10.12.2019]. National Plant Data Team, Greensboro, NC 27401-4901 USA.
• Anonymous. 2019c. TUİK. Bitkisel üretim istatistikleri. Konularına Göre İstatistikler (in Turkish). https://biruni.tuik.gov.tr/medas/?kn=92&locale =tr. TS30685.
• Asif, M. 2011. The role of fruits, vegetables, and spices in diabetes. International Journal of Nutrition, Pharmacology, Neurological Diseases, 1(1), 27. doi: 10.4103/2231-0738.77527.
• Ayanoğlu, H., S. Bayazit, G. Inan, M. Bakır, A. E. Akpınar, K. Kazan, and A. Ergün. 2007. AFLP analysis of genetic diversity in Turkish green plum accessions (Prunus cerasifera L.) adapted to the Mediterranean region. Scientia Horticulturae 114(4): 263-267.
• Birwal, P., G. Deshmukh, S.P. Saurabh and S. Pragati. 2017. Plums: a brief introduction. Journal of Food, Nutrition and Population Health 1(1).
• Bolat, I., B. E. Ak, I. Acar and A. Ikinci. 2017. Plum culture in Turkey. pp. 15-18 In III EUFRIN Plum and Prune Working Group Meeting on Present Constraints of Plum Growing in Europe 1175. doi: 10.17660/ActaHortic.2017.1175.4.
• Cobianchi, D., and R. Watkins. 1984. Descriptor list for plum and allied species (Prunus). IBPGR.
• Domingo, R., A. Pérez-Pastor, and M. C. Ruiz-Sánchez. 2002. Physiological responses of apricot plants grafted on two different rootstocks to flooding conditions. J. Plant Physiol. 159: 725–732. doi: 10.1078/0176-1617-0670.
• Doyle, J. J. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin - Botanical Society of America 19: 11-15. Earl, D. A. 2012. Structure Harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conservation Genetics Resources 4(2): 359-361. doi: https://doi.org/10.1007/s12686-011-9548-7
• Erbil, Y. and M. Öztürk. 2000. Erik Raporu. Yalova, Turkey: Bitkisel Üretim Özel İhtisas Komisyonu Meyvecilik Alt Komisyonu Raporu (in Turkish). ISBN 975 – 19 – 2915-6. Ercisli, S. 2004. A short review of the fruit germplasm resources of Turkey. Genetic Resources and Crop Evolution 51(4): 419-435. https://doi.org/10.1023/ B:GRES.0000023458.60138.79.
• Ercisli, S., A. Esitken, E. Orhan and O. Ozdemir. 2006. Rootstocks used for temperate fruit trees in Turkey: an overview. Sodininkyste ir Darzininkyste 25 (3): 27-33.
• Faust, M., and D. Surányi. 1999. Origin and dissemination of plums. Hort. Rev 23: 179-231. ISBN 0-471-25445-2.
• Heiges, S. B. 1897. Report of the Pomologist for 1895. US Government Printing Office. SB 354 H45 1895.
• Horvath, A., H. Christmann, and F. Laigret. 2008. Genetic diversity and relationships among Prunus cerasifera (cherry plum) clones. Botany 86.11: 1311-1318. doi: https://doi.org/10.1139/B08-097
• Iacona, C., L. Pistelli, M. Cirilli, L. Gatti, R. Mancinelli, M. N. Ripa, and, R. Muleo. 2019. Day-length is involved in flooding tolerance response in wild type and variant genotypes of rootstock Prunus cerasifera L. Frontiers in Plant Science, 10, 546. doi: https://doi.org/ 10.3389/fpls.2019.00546.
• Ingram, C. 1948. Ornamental Cherries. Publisher, Country Life.Lecouls, A. C., M. J. Rubio-Cabetas,, J. C. Minot, R.Voisin, A.Bonnet, G.Salesses,, E. Dirlewanger and D. Esmenjaud. 1999. RAPD and SCAR markers linked to the Ma1 root-knot nematode resistance gene in Myrobalan plum (Prunus cerasifera Ehr.). Theoretical and Applied Genetics, 99(1-2), 328-335. DOI: https://doi.org/10.1007/s001220051240.
• Lecouls, A. C., V. Bergougnoux, M. J. Rubio-Cabetas, N. Bosselut, R. Voisin, J.-L. Poessel, M. Faurobert, A. Bonnet, G. Salesses, E. Dirlewanger and, D. Esmenjaud. 2004. Marker-assisted selection for the wide-spectrum resistance to root-knot nematodes conferred by the Ma gene from Myrobalan plum (Prunus cerasifera) in interspecific Prunus material. Molecular Breeding, 13(2), 113-124. DOI: 10.1023/B:MOLB.0000018758.56413.cf.
• Li, G. and C. F. Quiros. 2001. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theoretical and Applied Genetics 103(2-3): 455-461. doi: https://doi.org/ 10.1007/s001220100570.
• Lin, Z. X., D. He, X. L. Zhang, Y. Nie, X. Guo, C. Feng, J. McD. Stewart. 2005. Linkage map construction and mapping QTL for cotton fibre quality using SRAP, SSR and RAPD. Plant Breeding 124(2): 180-187. doi: https:// doi.org/10.1111/j.1439-0523.2004.01039.x.
• Miloševi´c T., and N. Miloševi´c. 2018. Plum (Prunus spp.) Breeding. pp: 178-228. In: J. M. Al-Khayri, S.M. Jain, and D.V. Johnson (Eds). Advances in Plant Breeding Strategies: Fruits Vol:3. Springer. doi: https:// doi.org/10.1007/978-3-319-91944-7_5.
• Nasri, A., E. Baklouti, A. B. Romdhane, M. Maalej, H. M. Schumacher, N. Drira, and L. Fki. 2019. Large-scale propagation of Myrobolan (Prunus cerasifera) in RITA® bioreactors and ISSR-based assessment of genetic conformity. Scientia Horticulturae, 245, 144-153. doi: https://doi.org/10.1016/j.scienta.2018.10.016.
• Peakall, R. O. D., and Peter E. Smouse. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6.1: 288-295. doi: https://doi.org/10.1111/j. 1471-8286.2005.01155.x.
• Perrier, X. and J. P. Jacquemoud-Collet. 2006. DARwin software. Available online: http://darwin.cirad.fr/ darwin.
• Pritchard, J. K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155(2): 945-959. PMID: 10835412; PMCID: PMC1461096.
• Rubio-Cabetas, M. J., C. Pons, B. Bielsa, M. L. Amador, C. Marti, and A. Granell. 2018. Preformed and induced mechanisms underlie the differential responses of Prunus rootstock to hypoxia. J. Plant Physiol. 228, 134–149. doi: 10.1016/j.jplph.2018.06.004.
• Slavin, J. L., and B. Lloyd. 2012. Health benefits of fruits and vegetables. Advances in Nutrition, 3(4), 506-516. doi: https://doi.org/10.3945/an.112.002154. The Plant List (2013). Version 1.1. http://www.theplantlist.org/ (accessed 1st January, 2020).
• Urbanovich, O. Y., P. V. Kuzmitskaya and A. V. Kilchevsky. 2017. Identification and genetic diversity of plum cultivars grown in Belarus. Russian Journal of Genetics 53(7): 775-784. doi: https://doi.org/10.1134/ S1022795417070134.
• Walkowiak-Tomczak, D., J. Reguła and G. Łysiak. 2008. Physico-chemical properties and antioxidant activity of selected plum cultivars fruit. Acta Scientiarum Polonorum Technologia Alimentaria 7(4): 15-22. ISSN: 1644-0730.
• Wöhrmann, T., D. Guicking, K. Khoshbakht and K. Weising. 2011. Genetic variability in wild populations of Prunus divaricata Ledeb. in northern Iran evaluated by EST-SSR and genomic SSR marker analysis. Genetic Resources and Crop Evolution 58(8): 1157-1167. ISSN : 0925-9864.
• Zhao, Y., Y. Li, Y. Liu and Y.F. Yang. 2015. Genetic diversity of wild Prunus cerasifera Ehrhart (wild cherry plum) in China revealed by simple-sequence repeat markers. Gene Conserve 14(56). doi: 10.4238/2015.July.28.7.
• Zhebentyayeva, T., V. Shankar, R. Scorza, A. Callahan, M. Ravelonandro, S. Castro, T. Dejong, C. A. Saski and C. Dardick. 2019. Genetic characterization of worldwide Prunus domestica (plum) germplasm using sequence-based genotyping. Horticulture Research, 6(1), 1-13. doi: https://doi.org/10.1038/s41438-018-0090-6
• Zubair, S.J., A.M. Ali and J.M. Jubrael. 2016. Genetic variation assessment of some Prunus species using SRAP markers. Science Journal of University of Zakho 4(2): 173-176. doi: 10.25271/2016.4.2.77.