Detection of in silico SSR Markers Specific to Uzun and Kırmızı Cultivars in Pistachio
Keywords:Pistachio, Cultivar-Specific, SSRs, Prevention of confusion , Farmers
In the current paper, it was aimed to detect the SSR markers that can be used in the prevention of confusion that may occur in breeding or nurseries, and directly genetically separating Uzun and Kırmızı pistachio cultivars from other commercial cultivars. A total of genotypes of 16 Pistacia vera species, one P. atlantica, one P. eurycarpa and two P. terebinthus species were obtained from the farmer's orchard in Nizip district of Gaziantep province for genetic characterization. Genetic diversity and clustering analyzes were performed with UPGMA (Unweighted Pair Group Method with Arithmetic Average) and STRUCTURE 2.3.4 programs using the scored SSR loci. Genetic relationship and population structure of genotypes were defined using common and distinct polymorphic PCR fragments. Cultivar-specific markers to be used in identifying and distinguishing the genetic structure of Uzun and Kırmızı cultivars were carried out in the current research. CUPOhBa2127 marker has the highest allele number (Na=10). In addition, 11 out of 25 SSR markers were explained as cultivar-specific SSRs that can distinguish Uzun and Kırmızı cultivars. These markers can be used directly by breeders and geneticists without any preliminary screnning of the markers. A quite serious providence will be achieved in the cost and time that will occur with the preliminary analysis, and thus, the confusion that may occur in large scale orchard establishments or nurseries will be reduced to pretty low levels with DNA analysis.
Ahmad R, Ferguson L, Southwick S. M. 2003. Identification of pistachio (Pistacia vera L.) nuts with microsatellite markers. Journal of the American Society for Horticultural Science, 128(6): 898-903.
Ahmad R, Ferguson L, Southwick SM. 2005. Molecular marker analyses of pistachio rootstocks by simple sequence repeats and sequence-related amplified polymorphisms. The Journal of Horticultural Science and Biotechnology, 80(3): 382-386.
Arabnezhad H, Bahar M, Pour AT. 2011. Evaluation of genetic relationships among Iranian pistachios using microsatellite markers developed from Pistacia khinjuk Stocks. Scientia horticulturae, 128(3): 249-254.
Ashkenazi V, Chani E, Lavi U, Levy D, Hillel J, Veilleux RE. 2001. Development of microsatellite markers in potato and their use in phylogenetic and fingerprinting analyses. Genome, 44(1): 50-62.
Baghizadeh A, Noroozi S, Javaran MJ. 2010. Study on genetic diversity of some Iranian Pistachio (Pistacia vera L.) cultivars using random amplified polymorphic DNA (RAPD), inter sequence repeat (ISSR) and simple sequence repeat (SSR) markers: A comparative study. African Journal of Biotechnology, 9(45): 7632-7640.
Caruso T, Iannini C, Barone E, Marra FP, Sottile F, Greco CI, Laghezali M. 1997. Genetic and phenotypic diversity in pistachio (P. vera L.) germplasm collected in Mediterranean countries. In II International Symposium on Pistachios and Almonds 470 (pp. 168-180).
Dollo L, Hormaza JI, Polito VS. 1995. RAPD Polymorphisms Among Pistachio (Pistacia vera L.) Cultivars.
Doyle JJ. 1987. A rapid isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull., 19: 11-15.
Fan L, Zhang MY, Liu QZ, Li LT, Song Y, Wang LF, Wu J. 2013. Transferability of newly developed pear SSR markers to other Rosaceae species. Plant Molecular Biology Reporter, 31(6): 1271-1282.
Güney M, Kafkas S, Koc A, Aras S, Keles H, Karci H. 2019. Characterization of quince (Cydonia oblonga Mill.) accessions by simple sequence repeat markers. Turkish Journal of Agriculture and Forestry, 43(1): 69-79.
Güney M, Kafkas S, Keles H, Aras S, Ercişli S. 2018. Characterization of hawthorn (Crataegus spp.) genotypes by SSR markers. Physiology and molecular biology of plants, 24(6): 1221-1230.
Hasanbegovic J, Hadziabulic S, Kurtovic M, Gasi F, Lazovic B, Dorbic B, Skender A. 2021. Genetic characterization of almond (Prunus amygdalus L) using microsatellite markersin the area of Adriatic Sea. Turkish Journal of Agriculture and Forestry, 45(6): 797-806.
Hormaza JI. 2002. Molecular characterization and similarity relationships among apricot (Prunus armeniaca L.) genotypes using simple sequence repeats. Theoretical and Applied Genetics, 104(2): 321-328.
Hormaza JI, Dollo L, Polito VS. 1994. Determination of relatedness and geographical movements ofPistacia vera (Pistachio; Anacardiaceae) germplasm by RAPD analysis. Economic Botany, 48(4): 349-358.
Kafkas S. 2006. Phylogenetic analysis of the genus Pistacia by AFLP markers. Plant Systematics and Evolution, 262(1): 113-124.
Kafkas S. 2006b. Phylogeny, Evolution and Biodiversity in the Genus Pistacia (Anacardiaceae). (A.K. SHARMA and A. SHARMA, Editor). Plant Genome, Biodiversity and Evolution. Volume 1, part C, Phanerogams (Angiosperm Dicotyledons), Science Publishers, Enfield(NH), Jersey, Plymouth, USA, pp 526-557.
Kafkas S. 2019. Advances in breeding of pistachio. Chapter. Burleigh Dodds Science Publishing Limited. Doi.10.19103/AS.2018.0042.17
Kafkas S, Ozkan H, Ak BE, Acar I, Atli HS, Koyuncu S. 2006. Detecting DNA polymorphism and genetic diversity in a wide pistachio germplasm: Comparison of AFLP, ISSR, and RAPD markers. Journal of the American Society for Horticultural Science, 131(4): 522-529.
Kafkas S, Perl-Treves R, Kaska N. 2000. Unusual Pistacia atlantica Desf.(Anacardiaceae) monoecious sex type in the Yunt Mountains of the Manisa Province of Turkey. Israel Journal of Plant Sciences, 48(4): 277-280.
Karcı H, Paizila A, Güney M, Zhaanbaev M, Kafkas S. 2022. Revealing genetic diversity and population structure in Pistachio (Pistacia vera L.) by SSR markers. Genetic Resources and Crop Evolution, 1-13.
Karcι H, Paizila A, Topçu H, Ilikçioğlu E, Kafkas S. 2020. Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L. Frontiers in genetics, 11: 1021.
Kashaninejad M, Tabil LG. 2011. Pistachio (Pistacia vera L.). In Postharvest biology and technology of tropical and subtropical fruits (pp. 218-247e). Woodhead Publishing.
Khadivi A. 2018. Assessment of genetic variability in pistachio (Pistacia vera L.) with nuclear SSR molecular markers. Erwerbs-Obstbau, 60(4): 289-294.
Khodaeiaminjan M, Kafkas S, Motalebipour EZ, Coban N. 2018. In silico polymorphic novel SSR marker development and the first SSR-based genetic linkage map in pistachio. Tree Genetics & Genomes, 14(4): 1-14.
Kolahi-Zonoozi SH, Mardi M, Zeinalabedini M, Pirseyedi SM, Mahmoodi P, Tabatabaei I, Ahmadi K. 2014. Development of 12 new SSR markers for genetic diversity and structure analysis in pistachio (Pistacia vera L.). The Journal of Horticultural Science and Biotechnology, 89(6): 707-711.
Lui K. 2005. PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics, 21: 2128-2129.
Mažeikienė I, Šikšnianienė JB, Baniulis D, Gelvonauskienė D, Frercks B, Starkus A, Stanys V. 2019. SSR analysis based on molecular characterisation of apple germplasm in Lithuania. Zemdirbyste-Agriculture, 106(2): 159-166.
Melaku G, Zhang S, Haileselassie T. 2018. Comparative evaluation of rice SSR markers on different Oryza species. J Rice Res Dev, 1(1): 38-48.
Orman E, Ateş D, Özkuru E, Hepaksoy S, Kafkas S, Tanyolac MB. 2020. Association mapping of several nut characters in walnut (Juglans regia L.). Turkish Journal of Agriculture and Forestry, 44(2): 208-227.
Pan YB. 2006. Highly polymorphic microsatellite DNA markers for sugarcane germplasm evaluation and variety identity testing. Sugar Tech, 8(4): 246-256.
Pazouki L, Mardi M, Shanjani PS, Hagidimitriou M, Pirseyedi SM, Naghavi MR, Khayam Nekoui SM. 2010. Genetic diversity and relationships among Pistacia species and cultivars. Conservation genetics, 11(1): 311-318.
Peakall, R, Smouse, PE. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular ecology notes, 6(1): 288-295.
Potts SM, Han Y, Khan MA, Kushad MM, Rayburn AL, Korban SS. 2012. Genetic diversity and characterization of a core collection of Malus germplasm using simple sequence repeats (SSRs). Plant Molecular Biology Reporter, 30(4): 827-837.
Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155(2): 945-959.
S Kumar, G Stecher, M Li, C Knyaz, K Tamura. 2018. MEGA, X. molecular evolutionary genetics analysis across computing platforms; Molecular Biology and Evolution, 35(1): 1547-1549.
Schuelke M. 2000. An economic method for the fluorescent labeling of PCR fragments. Nature biotechnology, 18(2): 233-234.
Topcu H, Kafkas S, Dogan A, Akcay ME, Ercisli S. 2015. Genetic relatedness among quince (Cydonia oblonga Miller) accessions from Turkey using amplified fragment length polymorphisms. Journal of Applied Botany and Food Quality, 88(1).
Tunalıoglu R, Taskaya B. 2003 Antepfıstıgı Tarımsal Ekonomi Araştırma Enstitüsü T.E.A.E Bakıs. 5(2): 1-4.
Vendramin E, Dettori MT, Verde I, Micali S, Giovinazzi J, Mardi M, Quarta R. 2007. Molecular characterization of Pistacia genus by microsatellite markers. In I Balkan Symposium on Fruit Growing 825 (pp. 55-62).
Zaloğlu S, Kafkas S, Doğan Y, Güney M. 2015. Development and characterization of SSR markers from pistachio (Pistacia vera L.) and their transferability to eight Pistacia species. Scientia Horticulturae, 189: 94-103.
Ziya Motalebipour E, Kafkas S, Khodaeiaminjan M, Çoban N, Gözel H. 2016. Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: development of novel SSR markers and genetic diversity in Pistacia species. BMC genomics, 17(1): 1-14.
Zohary M. 1952. A monographical study of the genus Pistacia. Palestine Journal of Botany (Jerusalem Series), 5(4): 187-228
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