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RETRACTED ARTICLE: Potential Start Codon Targeted (SCoT) and Inter-retrotransposon Amplified Polymorphism (IRAP) Markers for Evaluation of Genetic Diversity and Conservation of Wild Pistacia Species Population

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This article was retracted on 10 November 2017

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Abstract

Wild pistachio species is important species in forests regions Iran and provide protection wind and soil erosion. Even though cultivation and utilization of Pistacia are fully exploited, the evolutionary history of the Pistacia genus and the relationships among the species and accessions is still not well understood. Two molecular marker strategies, SCoT and IRAP markers were analyzed for assessment of 50 accessions of this species accumulated from diverse geographical areas of Iran. A thorough of 115 bands were amplified using eight IRAP primers, of which 104 (90.4 %) have been polymorphic, and 246 polymorphic bands (68.7 %) had been located in 358 bands amplified by way of forty-four SCoT primers. Average PIC for IRAP and SCoT markers became 0.32 and 0.48, respectively. This is exposed that SCoT markers have been extra informative than IRAP for the assessment of variety among pistachio accessions. Primarily based on the two extraordinary molecular markers, cluster evaluation revealed that the 50 accessions taken for the evaluation may be divided into three distinct clusters. Those results recommend that the performance of SCoT and IRAP markers was highly the equal in fingerprinting of accessions. The results affirmed a low genetic differentiation among populations, indicating the opportunity of gene drift most of the studied populations. These findings might render striking information in breeding management strategies for genetic conservation and cultivar improvement.

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  • 10 November 2017

    “This article has been retracted by the Publisher in agreement with the Editor-in-Chief, because it contains portions of writings on the same topic already published and without sufficient attribution to these earlier works being given. The principal authors of the paper acknowledged that text from background sources was mistakenly used in this article without proper reference to the original source. Upon investigation carried out according to the Committee on Publication Ethics guidelines, it has been found that the authors have duplicated or rephrased parts from other articles of which the main sources.

References

  • Alavi-Kia S, Mohammadi S, Aharizad A, Moghaddam M (2008) Analysis of genetic diversity and phylogenetic relationships in Crocus genus of Iran using inter-retrotransposon amplified polymorphism. Biotechnol Biotechnol Equip 22:795–800

    Article  CAS  Google Scholar 

  • Alikhani L, Rahmani MS, Shabanian N, Badakhshan H, Khadivi-Khub A (2014) Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers. Gene 552:176–183

    Article  CAS  PubMed  Google Scholar 

  • Amirmoradi B, Talebi R, Karami E (2012) Comparison of genetic variation and differentiation among annual Cicer species using start codon targeted (SCoT) polymorphism, DAMD-PCR, and ISSR markers. Plant Syst Evol 298:1679–1688

    Article  CAS  Google Scholar 

  • Bhattacharyya P, Kumaria S, Kumar S, Tandon P (2013) Start codon targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species. Gene 529:21–26

    Article  CAS  PubMed  Google Scholar 

  • Biswas MK, Xu Q, Deng XX (2014) Utility of RAPD, ISSR, IRAP and REMAP markers for the genetic analysis of Citrus spp. Sci Hortic 124:254–261

    Article  Google Scholar 

  • Bohonak AJ (2002) IBD (isolation by distance): a program for analyses of isolation by distance. J Hered 93:153–154

    Article  CAS  PubMed  Google Scholar 

  • Cabo S, Ferreira L, Carvalho A, Martins-Lopes P, Martín A, Lima-Brito JE (2014) Potential of start codon targeted (SCoT) markers for DNA fingerprinting of newly synthesized tritordeums and their respective parents. J Appl Genet 55:307–312

    Article  CAS  PubMed  Google Scholar 

  • Chen L, Zhao L, Bai Y, Hu R, Si J (2009) Genetic relationship analysis of different provenances of Leonurus japonicus by ISSR marker. Zhongguo Zhong Yao Za Zhi 34:1343–1345

    CAS  PubMed  Google Scholar 

  • Collard BCY, Mackill DJ (2009) Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Biol Rep 27:86–93

    Article  CAS  Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  • Esmail-pour A (2001) Distribution, use and conservation of pistachio in Iran. In: Padulosi S, Hadj-Hassan A (eds) In towards a comprehensive documentation and use of Pistacia genetic diversity in central and West Asia, North Africa and Europe. Report of the IPGRI workshop, 14–17 Dec 1998, Ibrid, Jordan. IPGRI, Rome

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Not 7:574–578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • FAO (2006) FAOSTAT database

  • Gorji AM, Poczai P, Polgar Z, Taller J (2011) Efficiency of arbitrarily amplified dominant markers (SCoT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato. Am J Potato Res 88:226–237

    Article  Google Scholar 

  • He XH, Li YR, Guo YZ, Tang ZP, Li RB (2005) Genetic analysis of 23 mango cultivar collection in Guangxi province revealed by ISSR. Mol Plant Breed 3:829–834

    CAS  Google Scholar 

  • Horvath A, Christmann H, Laigret F (2008) Genetic diversity and relationships among Prunus cerasifera (cherry plum) clones. Botany 86:1311–1318

    Article  CAS  Google Scholar 

  • IPGRI (1998) Descriptors for Pistacia spp (excluding P. vera L.). International Plant Genetic Resources Institute, Rome

    Google Scholar 

  • Iranjo P, Nabati Ahmadi D, Sorkheh K, Rajabi Memeari H, Ercisli S (2015) Genetic diversity and phylogenetic relationships between and within wild Pistacia species populations and implications for its conservation. J For Res. doi:10.1007/s11676-015-0098-9

    Google Scholar 

  • Joshi CP, Zhou H, Huang X, Chiang VL (1997) Context sequences of translation initiation codon in plants. Plant Mol Biol 35:993–1001

    Article  CAS  PubMed  Google Scholar 

  • Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98:704–711

    Article  CAS  Google Scholar 

  • Karimi HR, Hajizadeh M, Abadi H, Maleki Kohbanani A (2012) Genetic diversity of Pistacia khinjuk Stocks. using RAPD markers and leaf morphological characters. Plant Syst Evol 298:963–968

  • Karimi HR, Kafkas S (2011) Genetic relationships among Pistacia species studied by SAMPL markers. Plant Syst Evol 297:207–212

  • Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479–532

    Article  CAS  PubMed  Google Scholar 

  • Landry BS, Li RQ, Cheung WY, Granger RL (1994) Phylogeny analysis of 25 apple rootstocks using RAPD markers and tactical gene tagging. Theor Appl Genet 89:847–852

    CAS  PubMed  Google Scholar 

  • Luo C, He XH, Chen H, Ou SJ, Gao MP (2010) Analysis of diversity and relationships among mango cultivars using start codon targeted (SCoT) markers. Biochem Syst Ecol 38:1176–1184

    Article  CAS  Google Scholar 

  • Luo C, He XH, Chen H, Ou SJ, Gao MP, Brown JS, Tondo CT, Schnell RJ (2011) Genetic diversity of mango cultivars estimated using SCoT and ISSR markers. Biochem Syst Ecol 39:676–684

    Article  CAS  Google Scholar 

  • Mantel N (1967) The detection of disease clustering and generalized regression approach. Cancer Res 27:209–220

    CAS  PubMed  Google Scholar 

  • Milbourne D, Meyer R, Bradshaw JE, Baird E, Bonar N, Provan J, Powell W, Waugh R (1997) Comparison of PCR-based marker system for the analysis of genetic relationships in cultivated potato. Mol Breed 3:127–136

    Article  CAS  Google Scholar 

  • Milligan BG, Leebens-Mack J, Strand AE (1994) Conservation genetics: beyond the maintenance of marker diversity. Mol Ecol 12:844–855

    Google Scholar 

  • Mulpuri S, Muddanuru T, Francis G (2013) Start codon targeted (SCoT) polymorphism in toxic and non-toxic accessions of Jatropha curcas L. and development of a codominant SCAR marker. Plant Sci 207:117–127

    Article  CAS  PubMed  Google Scholar 

  • Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pazouki L, Mardi M, Shanjani PS, Hagidimitriou M, Pirseyedi SM, Naghavi MR, Avanzato D, Vendramin E, Kafkas S, Ghareyazie B, Ghaffari MR, Nekoui SMK (2010) Genetic diversity and relationships among Pistacia species and cultivars. Conserv Genet 11:311–318

    Article  Google Scholar 

  • Peakall R, Smouse PE (2006) GenAlEx 6: genetic analysis in excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  • Poczai P, Varga I, Laos M, Cseh A, Bell N, Valkonen J, Hyvönen J (2013) Advances in plant gene-targeted and functional markers: a review. Plant Meth 9:6

    Article  CAS  Google Scholar 

  • Powell W, Morgante M, Andre C, Mm Hanafey, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Razavi S (2006) Pistachio production, Iran vs. the World. Acta Hortic 726:689–694

    Article  Google Scholar 

  • Rohlf FJ (1993) NTSYS-PC. Numerical Taxonomy and Multivariate Analysis System Version 1.80. Exeter Software, Setauket, New York

    Google Scholar 

  • Sawant SV, Singh PK, Gupta SK, Madnala R, Tuli R (1999) Conserved nucleotide sequences in highly expressed genes in plants. J Genet 78:123–131

    Article  CAS  Google Scholar 

  • Schneider S, Roessli D, Excoffier L (2000) Arlequin: a software for population genetics data analysis version 2.000. Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva, Switzerland

    Google Scholar 

  • Shanjani PS, Mardi M, Pazouki L, Hagidimitriou M, Avanzato D, Pirseyedi SM, Ghaffari MR, Khayam Nekoui SM (2009) Analysis of the molecular variation between and within cultivated and wild Pistacia species using AFLPs. Tree Genet Genomes 5:447–458

    Article  Google Scholar 

  • Shimada T, Hayama H, Haji T, Yamaguchi M, Yoshida M (1999) Genetic diversity of plums characterized by random amplified polymorphic DNA (RAPD) analysis. Euphytica 109:143–147

    Article  CAS  Google Scholar 

  • Shimamura M, Yasue H, Ohshima K, Abe H, Kato H, Kishiro T, Goto M, Munechika I, Okada N (1997) Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature 388:666–670

    Article  CAS  PubMed  Google Scholar 

  • Sneller CH, Miles JW, Hoyt JM (1997) Agronomic performance of soybean plant introductions and their genetic similarity to elite lines. Crop Sci 37:1595–1600

    Article  Google Scholar 

  • Soorni A, Nazeri V, Fattahi R, Khadivi-Khub A (2013) DNA fingerprinting of Leonurus cardiaca L. germplasm in Iran using amplified fragment length polymorphism and interretrotransposon amplified polymorphism. Biochem Syst Ecol 50:438–447

    Article  CAS  Google Scholar 

  • Talebi M, Kazemi M, Ebrahim Sayed-Tabatabaei B (2012) Molecular diversity and phylogenetic relationships of Pistacia vera, Pistacia atlantica subsp. mutica and Pistacia khinjuk using SRAP. Biochem Syst Ecolo 44:179–185

    Article  CAS  Google Scholar 

  • Techen N, Crockett S, Khan I, Scheffler B (2004) Authentication of medicinal plants using molecular biology techniques to compliment conventional methods. Curr Med Chem 11:1391–1401

    Article  CAS  PubMed  Google Scholar 

  • Voytas DF, Cummings MP, Konieczny AK, Ausubel FM, Rodermel SR (1992) Copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA 89:7124–7128

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Waugh R, Mc Lean K, Flavell AJ, Pearce SR, Kumar A, Thomas BBT, Powell W (1997) Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet 253:687–694

    Article  CAS  PubMed  Google Scholar 

  • Xiong FQ, Tang RH, Chen ZL, Pan LH, Zhuang WJ (2009) SCoT: a novel gene targeted marker technique based on the translation start codon. Mol Plant Breed 7:635–638

    CAS  Google Scholar 

  • Xiong F, Zhong R, Han Z, Jiang J, He L, Zhuang W, Tang R (2011) Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes. Mol Biol Rep 38:3487–3494

  • Yeh FC, Yang RC, Boyle T (1999) POPGENE. Microsoft Windows-based Freeware for Population Genetic Analysis. Release 1.31. University of Alberta, Edmonton

    Google Scholar 

  • Yu Q, Sheng XX, Sheng YF, Chen JH, Shi CG, Wang ZA (2009) AFLP analysis of genetic diversity of Leonurus japonicus germplasm resources. Zhongcaoyao 40:1296–1299

    CAS  Google Scholar 

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Acknowledgments

This study was supported by Shahid Chamran University of Ahwaz, Iran. We thank the Iranian pistachio research institute, Rafsanjan, Iran. The authors would like appreciative much appreciated from Heman Ebrahimi for arrangement of the pictures in the site of www.banehpedia.com with let authorization to utilize.

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Correspondence to Karim Sorkheh.

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The authors declare that they have no competing of interests.

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All authors have contributed equally to this work.

This article has been retracted by the Publisher in agreement with the Editor-in-Chief, because it contains portions of writings on the same topic already published and without sufficient attribution to these earlier works being given. The principal authors of the paper acknowledged that text from background sources was mistakenly used in this article without proper reference to the original source. Upon investigation carried out according to the Committee on Publication Ethics guidelines, it has been found that the authors have duplicated or rephrased parts from other articles of which the main sources are the following:

Alikhani L, Rahmani MS, Shabanian N, Badakhshan H, Khadivi-Khub A (2014) Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers. Gene 552:176-183

Iranjo P, Nabati Ahmadi D, Sorkheh K, Rajabi Memeari H, Ercisli S (2016) Genetic diversity and phylogenetic relationships between and within wild Pistacia species populations and implications for its conservation. J For Res 27: 685-697

Shanjani PS, Mardi M, Pazouki L, Hagidimitriou M, Avanzato D, Pirseyedi SM, Ghaffari MR, Khayam Nekoui SM (2009) Analysis of the molecular variation between and within cultivated and wild Pistacia species using AFLPs. Tree Genet Genomes 5:447-458

Luo C, He XH, Chen H, Ou SJ, Gao MP (2010) Analysis of diversity and relationships among mango cultivars using start codon targeted (SCoT) markers. Biochem Syst Ecol 38:1176-1184

In a commitment to scientific integrity we decided to retract the article.

A correction to this article is available online at https://doi.org/10.1007/s10528-017-9830-9.

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Sorkheh, K., Amirbakhtiar, N. & Ercisli, S. RETRACTED ARTICLE: Potential Start Codon Targeted (SCoT) and Inter-retrotransposon Amplified Polymorphism (IRAP) Markers for Evaluation of Genetic Diversity and Conservation of Wild Pistacia Species Population. Biochem Genet 54, 368–387 (2016). https://doi.org/10.1007/s10528-016-9725-1

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