Retrotransposon Marker Systems as a Tool to Analyze Molecular Diversity of Mediterranean Pistacia Species

Kirdok, E.; Çiftçi, Yelda Özden

doi:10.17957/ijab/15.0132

Cited by 9 publications

(7 citation statements)

References 30 publications

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“…Shahi-Gharahlar et al (2011) reported that wild and cultivated genotypes are rich resources of genes for breeding programs. The results are in agreement with the reports published earlier (Ghaemmaghami et al 2013;Kırdök & Çiftçi 2016). According to Xie et al (2010), high, medium, and low loci polymorphism is appointed as PIC > 0.5; 0.5 > PIC > 0.25; and PIC < 0.25, respectively.…”

Section: Discussionsupporting

confidence: 92%

Assessment of Genetic Relationships among Cultivated and Wild Pistachios (Pistacia vera L.) using Molecular Markers

Pourian

Bakhshi

Aalami

et al. 2019

Journal of Horticultural Research

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Iran is one of the main diversity centers and origins of pistachios in the world. Pistachio cultivation spread first within the ancient Persian Empire and then moved gradually westward. Knowledge of the genetic relationships among wild and cultivated varieties of pistachio is important for the efficient utilization of the available germplasm resources. Three molecular marker strategies, namely, inter-simple sequence repeat (ISSR), inter-retrotransposon amplified polymorphism (IRAP), and retrotransposon microsatellite amplified polymorphism (REMAP), were used to study the genetic relationships among 35 pistachio accessions including 15 wild-type genotypes of Pistacia vera and 20 important cultivars from Iran. According to the results, high levels of polymorphism were observed for all three marker systems. REMAP and IRAP techniques had the higher mean values of genetic relationships parameters than ISSR technique. The results from this study showed that the 5′LTR2, Sukkula, Sukkula + UBC855, and 5′LTR2 + UBC811 primers were the most informative and could be used to evaluate the genetic relationships of pistachios accessions. Cluster analysis using the unweighted pair group method with arithmetic mean (UPGMA) properly separated the accessions and divided them into four main groups. The presence of most cultivated genotypes in a group indicates genetic erosion of cultivated pistachio in Iran. Wild-type genotypes of P. vera are located in different clusters indicating the high diversity of the genotypes. The results provide useful genetic information about wild pistachios in northeastern of Iran and indicate that the use of wild pistachios in breeding programs could be useful for generating new genotypes with interesting characters.

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Section: Discussionsupporting

confidence: 92%

Assessment of Genetic Relationships among Cultivated and Wild Pistachios (Pistacia vera L.) using Molecular Markers

Pourian

Bakhshi

Aalami

et al. 2019

Journal of Horticultural Research

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“…The results of Kılınç et al (2014) and Koç et al (2014) on P. lentiscus based on IRAP and AFLP techniques were supported with the findings of amplification data obtained in our present study in relation to the LTR2 region. Kırdök & Çiftçi (2016) used iPBS, REMAP and IRAP techniques of retrotransposon markers for genetic diversity analysis of Pistacia genus. They found high genetic similarity between P. vera -P. khinjuk, P. atlantica -P. mutica and P. terebinthus -P. palaestina and it was reported that the IRAP technique of retrotransposon-based DNA markers for 7 Mediterranean Pistacia species (total 35 samples) could be used in molecular characterization and molecular breeding trials (Kırdök & Çiftçi 2016).…”

Section: Discussionmentioning

confidence: 99%

“…Kırdök & Çiftçi (2016) used iPBS, REMAP and IRAP techniques of retrotransposon markers for genetic diversity analysis of Pistacia genus. They found high genetic similarity between P. vera -P. khinjuk, P. atlantica -P. mutica and P. terebinthus -P. palaestina and it was reported that the IRAP technique of retrotransposon-based DNA markers for 7 Mediterranean Pistacia species (total 35 samples) could be used in molecular characterization and molecular breeding trials (Kırdök & Çiftçi 2016). In addition, retrotransposon marker systems have also been used in taxonomic studies of the Persian species of the genus Pistacia (P. vera, P. khinjuk, P. atlantica) (Ghaemmaghami et al 2013).…”

Section: Discussionmentioning

confidence: 99%

“…In terms of genetic similarity, the nearest sample to LCHIA genotype was L26A (C1, Güvercinlik village / Bodrum, 3m) and the furthest sample was L33A (C2, sea edge, Göcek / Fethiye, 62m), showing that species locations along seaside or in the lower parts of the mountains were not effective for genetic similarity. (Kırdök & Çiftçi 2016). In addition, retrotransposon marker systems have also been used in taxonomic studies of the Persian species of the genus Pistacia (P. vera, P. khinjuk, P. atlantica) (Ghaemmaghami et al 2013).…”

Section: Discussionmentioning

confidence: 99%

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INTRASPECIFIC VARIATIONS STUDIED BY ISSR AND IRAP MARKERS IN MASTIC TREE (Pistacia lentiscus L.) FROM TURKEY

Serttaş¹,

Özcan²

2018

Trakya University Journal of Natural Sciences

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In this study, intra-specific variations in naturally growing and cultivated mastic tree (Pistacia lentiscus L.) samples obtained from western parts of Turkey were examined using ISSR and IRAP marker techniques. Samples from Crete and Chios were also included in the study. Morphological measurements of some leaf characteristics of the samples were performed and the measured data was evaluated statistically with a Pearson Correlation analysis to reveal the correlations between character pairs. ISSR primers produced 81 bands between 161-1884bp with 96.3% polymorphism and IRAP primers produced 72 bands between 124-2027bp with 91.67% polymorphism. Polymorphism information content (PIC) values were 0.458 and 0.418 for ISSR and IRAP, respectively. Genetic similarity matrix was examined with Jaccard's coefficient. Maximum similarity was found between the Cretan samples (LG2 and LG3) with the ISSR analysis (0.933) and between L25A (C1, Bodrum) and L29A (C1, Milas) with the IRAP analysis (0.593). Unweighted pair group method with arithmetic mean (UPGMA) dendrogram was divided into 12 and 4 groups by ISSR and IRAP methods, respectively. Specimens were segregated on 3 main different clusters by the Principal Component Analysis (PCA) based on the combined marker systems. The results showed that P. lentiscus has very high ratios of intraspecific variation. The present work is an original study in terms of large sampling including wild genotypes, cultivated specimen, Chios and Cretan varieties, use of ISSR and IRAP combination, determination of relations between culture and wild genotypes and the use of Bagy-1 retrotransposons in intraspecific polymorphism. This study may be considered as a reference study for studies on gene pools of P. lentiscus and phylogenetic relationships within the species and may contribute to species concept and agricultural breeding programs.Özet: Bu çalışmada, ISSR ve IRAP markör teknikleri kullanılarak Türkiye'nin batı kesiminde doğal olarak yetişen ve kültürü yapılan sakız ağacı (Pistacia lentiscus L.) örneklerindeki tür içi varyasyon analizi yapılmıştır. Girit ve Sakız Adası örnekleri de çalışmaya dahil edilmiştir. Bazı yaprak özelliklerinin morfolojik ölçümleri gerçekleştirilmiş ve aralarındaki korelasyon Pearson Korelasyon analizi ile belirlenmiştir. ISSR primerleri 161-1884bç arasında %96,3 polimorfizm ile 81 bant üretmiştir. IRAP primerleri ise 124-2027bç arasında %91,67 polimorfizm ile 72 bant üretmiştir. Polimorfizm bilgi içeriği (PIC) değerleri 0,458 (ISSR) ve 0,418 (IRAP) arasında bulunmuştur. Genetik benzerlik matriksleri Jaccard katsayısıyla oluşturulmuştur. ISSR sonuçlarında en yüksek benzerlik Girit örnekleri (LG2 ve LG3) arasında (0,933) ve IRAP sonuçlarında ise L25A (C1, Bodrum) ve L29A (C1, Milas) arasında bulunmuştur. UPGMA yöntemiyle kurulan dendrogramlarda sırasıyla ISSR için 12 grup ve IRAP için 4 grup ayrılmıştır. Her iki markör sistemi için ortak kurulan temel bileşen analizi (PCA) grafiğinde 3 farklı küme oluşmuştur. Sonuçlar göstermiştir ki, P. lentiscus yüksek oranlarda tü...

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“…At present, no study has been done on P. vera to select salinity tolerant trait using FMs. Molecular marker studies on pistachio are often focused on genetic relationships and diversity, as well as sex determination by using different markers such as Simple Sequence Repeat (SSR) 19 – 21 , Amplified Fragment Length Polymorphism (AFLP) 22 , 23 , Inter-Simple Sequence Repeats (ISSR) 24 – 27 , Randomly Amplified Polymorphic DNA (RAPD) 28 – 30 , Retrotransposon Microsatellite Amplified Polymorphism (REMAP) 31 , Selective Amplification of Microsatellite Polymorphic Loci (SAMPL) 32 and Single Nucleotide Polymorphism (SNP) 33 .…”

Section: Introductionmentioning

confidence: 99%

Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio

Jannesar

Seyedi

Botanga

2021

Sci Rep

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We developed novel miRNA-based markers based on salt responsive miRNA sequences to detect polymorphisms in miRNA sequences and locations. The validation of 76 combined miRNA + miRNA and miRNA + ISSR markers in the three extreme pistachio populations led to the identification of three selected markers that could link salt tolerance phenotype to genotype and divided pistachio genotypes and Pistacia species into three clusters. This novel functional marker system, in addition to more efficient performance, has higher polymorphisms than previous miRNA-based marker systems. The functional importance of the target gene of five miRNAs in the structure of the three selected markers in regulation of different genes such as ECA2, ALA10, PFK, PHT1;4, PTR3, KUP2, GRAS, TCP, bHLH, PHD finger, PLATZ and genes involved in developmental, signaling and biosynthetic processes shows that the polymorphism associated with these selected miRNAs can make a significant phenotypic difference between salt sensitive and tolerant pistachio genotypes. The sequencing results of selected bands showed the presence of conserved miRNAs in the structure of the mitochondrial genome. Further notable findings of this study are that the sequences of PCR products of two selected markers were annotated as Gypsy and Copia retrotransposable elements. The transposition of retrotransposons with related miRNAs by increasing the number of miRNA copies and changing their location between nuclear and organellar genomes can affect the regulatory activity of these molecules. These findings show the crucial role of retrotransposon-derived miRNAs as mobile epigenetic regulators between intracellular genomes in regulating salt stress responses as well as creating new and tolerant phenotypes for adaptation to environmental conditions.

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Retrotransposon Marker Systems as a Tool to Analyze Molecular Diversity of Mediterranean Pistacia Species

Cited by 9 publications

References 30 publications

Assessment of Genetic Relationships among Cultivated and Wild Pistachios (Pistacia vera L.) using Molecular Markers

Assessment of Genetic Relationships among Cultivated and Wild Pistachios (Pistacia vera L.) using Molecular Markers

INTRASPECIFIC VARIATIONS STUDIED BY ISSR AND IRAP MARKERS IN MASTIC TREE (Pistacia lentiscus L.) FROM TURKEY

Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio

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