Ercan VELİOĞLU, Burcu UZAN EKEN, Emrah KIRDÖK, Yelda ÖZDEN ÇİFTÇİ

Assessment of genetic variation of natural populations of wild cherry (Prunus avium L.) via SSR markers

Wild cherry (Prunus avium L, syn. Cerasus avium L. Moench.) is a widely spread forest tree that has ecological and economical importance. However, the genetic diversity of this species is threatened for many reasons. Therefore, a breeding and conservation program should be established in order to minimise the loss of genetic diversity. In this study, we aimed to understand the genetic structure of 440 individual wild cherries sampled from 22 different populations in Turkey using 10 SSR molecular markers. With the molecular variance analysis, we found that the genetic diversity within the population is approximately 88.5% and the genetic diversity among the populations is approximately 9.8%. Thus, wild cherry genetic diversity within populations is high whereas it is moderate between tested populations (FST values 0.02-0.16). Phylogeny, principal component, and genetic STRUCTURE analysis showed that populations are divided according to their geographical locations. Moreover, Veliköy and Kemerköprü populations that are located at higher altitudes, Macara population which is the closest sample to Europe, and the Tota population that is sampled from the Mediterranean Region; were found genetically different from the others. Hence, we suggest in-situ conservation to Veliköy, Kemerköprü, Macara, and Tota populations. Our results will contribute to in-situ and ex-situ conservation and breeding programmes to conserve genetic resources of the wild cherries in Turkey

PDF

___

Adamack AT, Gruber B (2014). PopGenReport: simplifying basic population genetic analyses in R. Methods in Ecology and Evolution 5 (4):384–387. doi: 10.1111/2041-210X.12158
Agarwal M, Shrivastava N, Padh H (2008). Advances in molecular marker techniques and their application in plant sciences. Plant Cell Reports 27:617-631. doi:10.1007/s00299-008-0507-z
Arumuganathan K, Earle ED (1991). Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter 9:208-219. doi: 10.1007/BF02672016
Avramidou E, Ganopoulos IV, Aravanopoulos FA (2010). DNA fingerprinting of elite Greek wild cherry (Prunus avium L.) genotypes using microsatellite markers. Forestry 83:1–7. doi: 10.1093/forestry/cpq035
Breitbach N, Laube I, Steffan-Dewenter I, Bohning-Gaese K (2010). Bird diversity and seed dispersal along a human land-use gradient: high seed removal in structurally simple farmland. Oecologia 162:965–976. doi: 10.1007/s00442-009-1547-y
Brookfield JF (1996). A simple new method for estimating null allele frequency from heterozygote deficiency. Molecular Ecology 5 (3):453–455. doi:10.1046/j.1365-294X.1996.00098.x
Chapuis M, Lecoq M, Michalakis Y, Loiseau A, Sword GA et al. (2008). Do outbreaks affect genetic population structure? A worldwide survey in Locusta migratoria, a pest plagues by microsatellite null alleles. Molecular Ecology 17:640–653. doi: 10.1111/j.1365-294X.2008.03869.x
Clarke JB, Tobutt KR (2003). Development and characterization of polymorphic microsatellites from Prunus avium ‘Napoleon’. Molecular Ecology Notes 3 (4):578–580. doi: 10.1046/j.1471- 8286.2003.00517.x
Conkle MT, Schiller G, Grunwald C (1988). Electrophoretic analysis of diversity and phylogeny of Pinus brutia and closely related taxa. Systematic Botany 13 (3):411-424. doi: 10.2307/2419301
Ercisli S (2004). A short review of the fruit germplasm resources of Turkey. Genetic Resources and Crop Evolution 51 (4):419–435. doi: 10.1023/B:GRES.0000023458.60138.79
Ercisli S, Agar G, Yildirim N, Duralija B, Vokurka A et al. (2011). Genetic diversity in wild sweet cherries (Prunus avium) in Turkey revealed by SSR markers. Genetics and Molecular Research 10:1211–1219. doi: 10.4238/vol10-2gmr1196
Esen D, Yildiz O, Cicek E, Kulac S, Kutsal C (2006). Effects of different pretreatments on the germination of different wild cherry (Prunus avium L.) seeds Sources. Pakistan Journal of Botany 38 (3):735-743.
Evanno G, Regnaut S, Goudet J (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14:2611–2620. doi: 10.1111/j.1365-294X.2005.02553.x
Excoffier L, Laval G, Schneider S (2005). Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1:47–50. doi: 10.1177/117693430500100003
Fernandez-Cruz J, Fernandez-Lopez J, Miranda-Fontaina ME, Diaz R, Toval G (2014). Molecular characterization of Spanish Prunus avium plus trees. Forest Systems 23 (1):120-128. doi: 10.5424/fs/2014231-04580
Frascaria N, Santi F, Gouyon PH (1993). Genetic differentiation within and among populations of chestnut (Castanea sativa Mill.) and wild cherry (Prunus avium L.). Heredity 70:634-641. doi: 10.1038/hdy.1993.91
Ganopoulos I, Aravanopoulos FA, Argiriou A, Kalivas A, Tsaftaris A (2011). Is the genetic diversity of small scattered forest tree populations at the southern limits of their range more prone to stochastic events? A wild cherry case study by microsatellitebased markers. Tree Genetics and Genomes 7:1299–1313. doi: 10.1007/s11295-011-0414-2
Goudet J (2005). HIERFSTAT, a package for R to compute and test hierarchical F-statistics. Molecular Ecology Notes 5 (1):184– 186. doi: 10.1111/j.1471-8286.2004.00828.x
Guarino C, Santoro S, De Simone L, Cipriani G (2009). Prunus avium: nuclear DNA study in wild populations and sweet cherry cultivars. Genome 52:320–337. doi: 10.1139/G09-007
Hamrick JL (1989). Isozymes and the analysis of genetic structure in plant populations. In: Soltis DE, Soltis PS, Dudley TR (editors). Isozymes in plant biology, 1st ed. Discorides, Portland, USA pp. 87-105. doi: 10.1007/978-94-009-1840-5_5
Hartl DL, Clark AG (2007). Principles of population genetics. In: 4th edn. Sinauer and Associates, Sunderland MA, USA. doi: 10.1093/jhered/esm035
Işık F, Kaya Z (1995). Toroslarda güney–kuzey doğrultusunda örneklenen kızılçam populasyonlarında genetik çeşitliliğin yapısı. Batı Akdeniz Ormancılık Araştırma Enstitüsü Dergisi 1: 20-54 (in Turkish).
Jarni K, De Cuyper B, Brus R (2012). Genetic variability of wild cherry (Prunus avium L.) seed stands in Slovenia as revealed by nuclear microsatellite loci. PLoS One 7 (7):1-8. doi: 10.1371/ journal.pone.0041231
Jiang GL (2013). Molecular markers and marker-assisted breeding in Plants. In: Andersen SB (editors). Plant Breeding from Laboratories to Fields, 1st ed. InTech, Croatia pp. 45–83. doi: 10.5772/52583
Jombart T (2008). Adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics 24 (11):1403–1405. doi: 10.1093/bioinformatics/btn129
Jombart T, Devillard S, Balloux F, Falush D, Stephens M et al. (2010). Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics 11 (1):94. doi: 10.1186/1471-2156-11-94
Kamvar ZN, Tabima JF, Grünwald NJ (2014). Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2,e281. doi: 10.7717/ peerj.281
Keenan K, Mcginnity P, Cross TF, Crozier WW, Prodöhl PA (2013). DiveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors. Methods in Ecology and Evolution 4 (8):782–788. doi: 10.1111/2041-210X.12067
Khadivi-Khub A, Zamani Z, Fattahi R, Wunsch A (2014). Genetic variation in wild Prunus L. subgen. Cerasus germplasm from Iran characterized by nuclear and chloroplast SSR markers. Trees 28:471–485. doi: 10.1007/s00468-013-0964-z
Ledig FT (1998). Genetic diversity in tree species: with special reference to conservation in Turkey and the eastern Mediterranean. In: Zencirci N, Kaya Z, Anikster Y, Adams WT (editors). The proceedings of international symposium on insitu conservation of plant genetic diversity, 1st edn. Central Research Institute for Field Crops, Ankara, Turkey, pp. 231– 248.
Mohan M, Nair S, Bhagwat A, Krishna MY, Bhatia CR et al (1997). Genome mapping, molecular markers and marker-assisted selection in crop plants. Molecular Breeding 3:87-103. doi: 10.1023/A:1009651919792
Mohanty A, Marti NJP, Aguinagalde I (2001). Chloroplast DNA study in wild populations and some cultivars of Prunus avium L. Theoretical and Applied Genetics 103:112–117. doi: 10.1007/ s001220000532
Mondini L, Noorani A, Pagnotta MA (2009). Assessing plant genetic diversity by molecular tools. Diversity 1 (1):19–35. doi: 10.3390/d1010019
Nei M (1973). Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America 70:3321–3. doi: 10.1073/pnas.70.12.3321
Nei M (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583– 590.
Oksanen J, Guillaume F, Kindt R, Legendre P, Minchin P et al. (2012). Vegan: Community ecology package. R Package Version 2.0-2. Software http://CRAN.R-project.org/package=vegan.
Panda S, Martin JP, Aguinagalde I, Mohanty A (2003). Chloroplast DNA variation in cultivated and wild Prunus avium L.: a comparative study. Plant Breeding 122:92–94. doi: 10.1046/j.1439-0523.2003.00768.x
Paradis E (2010). PEGAS: an R package for population genetics with an integrated-modular approach BT - Bioinformatics. Bioinformatics 26 (3):419–420. doi: 10.1093/bioinformatics/ btp696
Paradis E, Claude J, Strimmer K (2004). APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20 (2):289–290. doi: 10.1093/bioinformatics/btg412
Parveen S, Shahzad A, Yadav V (2016). Molecular markers and their application in plant biotechnology. In: Shahzad A, Sharma S, Siddiqui SA (editors). Biotechnological strategies for the conservation of medicinal and ornamental climbers, 1 st ed. Springer Inter Publishing, Cham (ZG) Switzerland, pp. 506.
Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155.
R Core Team (2020). R: A language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria. Website: https://www.R-project.org/.
Rogatis A, De Ferrazzini D, Ducci F, Guerri S, Carnevale S et al. (2012). Genetic variation in Italian wild cherry (Prunus avium L.) as characterized by nSSR markers. Forestry 86:391–400. doi: 10.1093/forestry/cpt009
Russell K (2003). Technical Guidelines for genetic conservation and use for wild cherry (Prunus avium), EUFORGEN, International Plant Genetic Resources Institute Rome Italy 1–6 [online]. Website: http://www.euforgen.org/fileadmin/templates/ euforgen.org/upload/Publications/Technical_guidelines/859_ Technical_guidelines_for_genetic_conservation_and_use_ for_Wild_cherry__Prunus_avium_.pdf. [accessed 15 Aug 2021].
Saatçioğlu F (1971). Orman ağacı tohumları. İstanbul Üniversitesi Orman Fakültesi Yayınları 173:1649 (in Turkish).
Santi F, Muranty H, Dufour J, Paques LE (1998). Genetic parameters and selection in a multisite wild cherry clonal test. Silvae Genetica 47 (2-3):61-67.
Savill PS (1991). The silviculture of trees used in British forestry. 1 st ed. C.A.B. International, Wallingford, UK. Schueler S, Tusch A, Schuster M, Ziegenhagen B (2003). Characterization of microsatellites in wild and sweet cherry (Prunus avium L.) markers for individual identification and reproductive processes. Genome 46:95-102. doi: 10.1139/g02- 107
Slatkin M, Barton NH (1989). A comparison of three indirect methods for estimating average levels of gene flow. Evolution; International Journal of Organic Evolution 43 (7):1349–1368. doi: 10.1111/j.1558-5646.1989.tb02587.x
Sokal RR, Michener CD (1958). A statistical method for evaluating systematic relationships, University of Kansas Science Bulletin 38:1409–1438.
Tanceva-Crmaric O, Stambuk S, Satovic Z, Kajba D (2011). Genotypic diversity of wild cherry (Prunus avium L.) In the part of its natural distribution in Croatia. Sumarski List 135:543-555. doi: 10.5424/fs/2014231-04580
Temel F (2018). Leaf size variation in natural wild cherry (Prunus avium) populations in Turkey. International Journal of Agriculture and Biology 20:9 pp 2005-2011.
Türkoglu Z, Bilgener S, Ercisli S, Yildirim N (2012). Simple sequence repeat (SSR) analysis for assessment of genetic variability in wild cherry germplasm. Journal of Applied Botany and Food Quality 85:229-233.
Unsal SG, Ozden-Ciftci Y, Uzan-Eken B, Velioglu E, Di Marco G et al. (2019). Intraspecific discrimination study of wild cherry populations from North-Western Turkey by DNA barcoding approach. Tree Genetics and Genomes 15:16. doi: 10.1007/ s11295-019-1323-z
Wei RP (1995). Predicting genetic diversity and optimizing selection in breeding programmes. Dissertation, Sweedish University of Agricultural Sciences.
Weir BS, Cockerham CC (1984). Estimating F-statistics for the analysis of population structure. Evolution 38 (6):1358–1370.
Weiser F (1996). Ergebnisse einer 33 jährigen Einzelbaum – Nachkommenschaftsprüfung nach freiem Abblühen von Vogelkirsche, Prunus avium L. var. avium. Silvae Genetica 45:260–266 (in German with an abstract in English).
Welk E, De Rigo D, Caudullo G (2016). Prunus avium in Europe: distribution, habitat, usage and threats. In: San-Miguel-Ayanz J, de Rigo D, Caudullo G, Houston Durrant T, Mauri A (editors) European Atlas of Forest Tree Species, 1st ed. Luxembourg, pp. e01491d.
Vaughan SP, Cottrell JE, Moodley DJ, Connolly T, Russell K (2007). Clonal structure and recruitment in British wild cherry (Prunus avium L.). Forest Ecology and Management 242:419–430. doi: 10.1016/j.foreco.2007.01.059
Vaughan SP, Russell K (2004). Characterization of novel microsatellites and development of multiplex PCR for large-scale population studies in wild cherry, Prunus avium. Molecular Ecology Notes 4:429–431. doi: 10.1111/j.1471-8286.2004.00673.x
Velioğlu E, Alan M, Atmaca C, Taştan Y, Uzan-Eken B (2020). Türkiye’deki Prunus avium L. popülasyonlarında bazı kantitatif özellikler için genetik parametrelerin tahmini. Ormancılık Araştırma Dergisi 7 (2):01 (in Turkish). doi: 10.17568/ ogmoad.740178
Yaman B (2003). Yabani kiraz (Cerasus avium (L.) Moench). Gazi Üniversitesi Orman Fakültesi Dergisi 3 (1):1303-2399 (in Turkish).