Genetic diversity and relationships among Pistacia species

African Journal of Biotechnology, 2010

Iran has a rich and diverse pistachio germplasm and thereby, the diversity and number of Iranian pistachio cultivars is unique in the world. In this study, 31 pistachio cultivars and genotypes were characterized by random amplified polymorphic DNA (RAPD), inter sequence repeat (ISSR) and simple sequence repeat (SSR) markers. The general dendrogram constructed using the combined data of the three sets of molecular markers was to some extent similar to those obtained separately with each marker. The overall principle coordinate analysis (PCA) based on genetic similarity matrices showed that the first three eigenvectors accounted for 28.46% of the total molecular variation. Therefore, the PCA results confirmed the results of cluster analysis .In SSR population analysis, the four primers produced 11 alleles among 31 pistachio genotypes with an average value of 2.75 alleles. 100% polymorphism was observed at all of these loci. The low average polymorphic information content value of 0.4374 indicated the presence of high genetic similarity among genotypes and entails development of additional polymorphic SSR primers for effective characterization of Iranian pistachio cultivars/genotypes. According to the effective multiplex ratio and assay efficiency index, it was shown that RAPD markers were the most powerful to differentiate the genotypes followed by ISSR and SSR markers, respectively.

المجلة الفلسطينية للتكنولوجيا والعلوم التطبيقية, 2022

It was clearly observed that the performance of the commercial pistachio genotypes was confusing within each variety according to the accredited substantial criteria of international descriptors. Therefore, the current work aimed to assess the genetic variation among 10 genotypes and cultivars, including 4 Ashouri, 2 Batouri, Ajami, Beid alhamam, and Ras alkharof across fifteen ISSR primers in Sweida Research Center 2019-2020. All of the used primers were polymorphic, which revealed a total of 148 bands, 141 of them were polymorphic (95.27%). The number of bands ranged from 6 to 15, with an average of 9.87 bands for each locus. Genetic similarity among all studied genotypes and cultivars ranged from 0.31 to 0.73. Depending on the UPGMA algorithm and the Dice equation, the cluster analysis divided the studied material into three main clusters. The first and second clusters comprised the following white genotypes: White Batouri, Batouri cultivar, Grahi, Beid alhamam, and Ras Alkharof that are analogous in many morphological characters, and the third cluster contained all other genotypes and cultivars: Ajami, White Ashouri, Ashouri cultivar, Ashouri Abureha, and Ashouri Mawardi. The current results demonstrated the efficiency of the ISSR technique by revealing the genetic variation among P. vera genotypes and cultivars and separating all of them into standing apart clusters according to their resembling appearance.

2018

Background: Start Codon Targeted (SCoT) and Inter-Simple Sequence Repeat (ISSR) markers were used to appraise genetic diversity existed in 20 samples of four Iranian pistachio (Pistacia vera L.) cultivars and relative efficiencies of the marker systems were compared. Materials and Methods: 20 and 15 primers were used in SCoT and ISSR markers, respectively. Effective Multiplex Ratio (EMR), Marker Index (MI), Resolving Power (RP) and Polymorphic Information Content (PIC) of the primers were assessed for the two marker systems. Cluster analysis for molecular data was performed. Principal Coordinate Analysis (PCoA) was done too. Results: The most of the parameters examined were found to be more suitable in ISSR system. The most remarkable result of the current research is that cluster analysis on SCoT and ISSR data clearly discriminated the cultivars in terms of their genetic characterizations. There was a high similarity between dendrogram derived from ISSR marker and dendrogram derived from both markers, in spite of some observed differences. Conclusions: It is shown in the current research that there is remarkable genetic diversity among evaluated samples. SCoT and ISSR analysis produces adequate polymorphisms for DNA fingerprinting. This research reports the first application of the SCoT marker in characterization of Iranian pistachio cultivars.

Tree Genetics & Genomes, 2009

Knowledge of pistachio genetic diversity is necessary for the formulation of appropriate management strategies for the conservation of these species. We analysed amplified fragment length polymorphisms in a total of 216 pistachio accessions, which included seven populations from three wild species (Pistacia vera, Pistacia khinjuk and Pistacia atlantica subsp. kurdica) and most of the important cultivars from Iran, together with some foreign cultivars. High levels of genetic diversity were detected within the Iranian cultivars, and they showed a clear separation from foreign cultivars, as revealed by unweighted pair group method with arithmetic averaging and supported by analysis of molecular variance. The lowest amount of polymorphism was observed in P. atlantica subsp. kurdica, which showed the lowest number of total bands as compared to the other species. This revealed strong genetic erosion of P. atlantica subsp. kurdica, which reflected a severe decline in habitat and over-exploitation. Based on these findings, strategies are proposed for the genetic conservation and management of pistachio species and cultivars.

2017

Pistachio (Pistacia vera L.) is an interesting crop for arid areas, well adapted to marginal lands and to drought conditions. Little attention has been directed towards the evaluation of the Pistacia vera L. genetic resources in Tunisia. Therefore, the genetic diversity of twenty ecotypes of pistachio collected from the south of Tunisia was analyzed using leaves morphological parameters. Morphological analysis helped to highlight a fairly high level of diversity and estimate phylogenetic relationships. In addition, the principal component analysis and UPGMA (Unweighted Pair Group Method with Arithmetic Average) tree allowed difference among several ecotypes over the entire samples studied. This variability of leaves traits between varieties which were cultivated in a relatively homogeneous environment may be attributed to different genetic architectures developed. This can be a consequence of adaptation to varied environmental conditions exiting in the distributional area of Pistaci...

DOAJ (DOAJ: Directory of Open Access Journals), 2017

Genetic study of pistachio, especially male genotypes due to the effects of pollen on nut quality and quantity and next generation characterizations, helps to improve its management and breeding program. In the present study, the genetic diversity among 20 male and 36 female pistachio genotypes was investigated using ISSR marker. In total, 178 DNA fragments were proliferated using 12 primers out of which 169 fragments were polymorphic. The average polymorphism information content (PIC) varied from 16% to 35%. Pistachio genotypes were classified into five main categories by cluster analysis. The highest similarity was among the 'Poostkhormayee'and 'Momtaz' cultivars (78%) and the lowest genetic similarity was among 'Ravar3' and 'Ghazvini' with K40 genotype (25%). K38 male genotype had the lowest genetic similarity with female cultivars. Thus, it can be introduced as appropriate pollinizer for other studied cultivars. The results of analysis of molecular variance showed that variability among male and female populations (8%) was lower than the variation within the populations (92%). Based on achieved results, ISSR marker recognized as a powerful tool to study the genetic variation among male and female pistachio genotypes.

2017

Genetic diversity of Pistacia vera sampled in three traditional areas was studied. The sequences variation of the chloroplastic gene: trnL (UAA) trnF (GAA) intergenic spacer, among fifteen pistachio varieties, was performed. The obtained analyses revealed 9 different haplotypes and three geographic groups. The cytoplasmic diversity of the NJ tree seems to be structured with a biogeography repartition of the variability. The overall estimate of genetic divergence (FST) revealed significant genetic differentiation between all population pairs. Nm value was high between Sidi-Bouzid and Gafsa’s populations indicated high connectivity between them, exchange of varieties by human, wind dispersal of pollen and seeds by insects may be the reasons for these observations. On another hand, Nm values were very low among ElGuetar and the others populations. The surrounding geography of El-Guetar, such as Gafsa Mountains, makes it an isolated population. Finally and overall, Tunisian pistachio se...

African Journal of Biotechnology, 2012

Pistacia vera L. is a widely represented plant in Algerian semi-arid regions. It is potentially used to restore degraded ecosystems. Genetic relationships among the cultivars was assessed by using six inter simple sequence repeat (ISSR) primers. During the ISSR screening in this study, good amplification products were obtained from primers based on guanine-adenine (GA), cytosine-adenine (CA) and guanine-adenine-adenine (GAA) repeats. Primers based on cytosine-tyrosine (CT) and CAA repeats produced few large separate bands, so these primers were not selected for the final analysis (eliminated for the final analysis). This study shows that ISSR-PCR analysis is quick, reliable and produces sufficient polymorphisms for large-scale DNA fingerprinting purposes. The total of 111 bands of which 60 were polymorphic, (with 54.04%) was amplified by the six primers, an average of seven bands per primer. The total number of amplified fragments was between five to ten and the number of polymorphic fragments ranged from four to seven. The range of genetic similarity was from 0/84 to 1 and the constructed unweighted pair group method with arithmetic averages (UPGMA), dendrogram classified the tested genotypes into two main clusters. This study shows that there was low genetic diversity among the tested cultivars and the ISSR-PCR analysis produced sufficient polymorphisms for large-scale DNA fingerprinting. This study reports the first application of the ISSR technique in characterization of Algerian pistachio cultivars original from Syria.

International Journal of Nuts and Related Sciences, 2012

The aim of this research was to study 33 Pistachio accessions and determine their genetic relationships. Thirty-one morphological characters (17 quantitative and 14 qualitative) together with Randomly Amplified Polymorphic DNA (RAPD) marker data were used for this purpose. Factor analysis was used to determine the effective characteristics and the number of main factors which determined seven main factors. Grouping of pistachio accessions by these factors was performed by Ward's method. Among 77 random decamer primers tested, 12 showed good amplification and polymorphism, and a total of 130 markers were produced that 118 were polymorphism. Grouping by morphological characteristics was compared with the results from RAPD analysis which did not produce a significant correlation.

2021

Pistachio (Pistacia vera L.) is the only cultivated species in Pistacia genus and one of the most important nut crop in terms of production. Pistachio cultivars have signi cant level of variation in their phenotypic appearance and productivity. Understanding the genetic diversity between pistachio cultivars could facilitate breeding programs. Simple sequence repeat (SSR) markers are powerful tools in genetic diversity and germplasm collection studies. However, published information about the characterization of large scale pistachio cultivar germplasm with adequate number of SSR markers is limited. In this study, sixty-six pistachio cultivars and genotypes originated from six different countries were characterized and ngerprinted by 74 genomic and 18 genic SSR markers. SSR analysis identi ed 576 alleles for all 66 cultivars and genotypes. The number of alleles per locus ranged from 2 to 20 (CUPOhBa1592) alleles with a mean value of six alleles per locus. The polymorphism information content (PIC) values ranged from 0.07 (CUPVEST2939) to 0.87 (CUPSiOh2460) with a mean PIC value of 0.58. The pistachio cultivars and genotypes were divided into ve clusters according to Structure and UPGMA (Unweighted Pair Group Method with Arithmetic Average) analysis. Total of 61 cultivar speci c alleles were detected in 34 cultivars, among them three primers (CUPOhBa1592, CUPBaPa1606 and CUPOhBa2127) produced more than four cultivar-speci c loci therefore very promising for cultivar identi cation, ngerprinting and breeding studies in pistachio.

2012

Pistacia vera L. is a widely represented tree in Algerian semi-arid regions. It is potentially usable to restore degraded ecosystems. Genetic relationship among the 10 variety was assessed by using six inter simple sequence repeat (ISSR) primers. During the ISSR screening, good amplification products were obtained from primers based on guanine-adenine (GA), cytosine-adenine (CA) and GAA repeats. But primers based on cytosine-thyrosine (CT), and CAA repeats produced few large separate bands, so these primers were not selected for the final analysis. The total of 111 bands of which 60 (54.04 %) were polymorphic was amplified by the six primers, with an average of seven bands per primer. The total number of amplified fragments was between five to ten, and the number of polymorphic fragments ranged from four to seven. The range of genetic similarity was from 0.84 to 1 and the constructed unweighted pair group method with arithmetic averages (UPGMA), dendrogram classified the tested geno...

Plant Systematics and Evolution, 2011

Pistachio is economically important in Iran. Selection of suitable rootstocks, resistant to unfavorable and soil conditions and diseases, is important for increasing yield and the acreage of this crop. It is essential to identify the genetic relationships among Pistacia species for the breeding of pistachio rootstocks. The goal of this study was to determine the genetic relationship among Pistacia species (P. vera L., P. khinjuk Stocks., P. eurycarpa Yalt., P. atlantica subsp. atlantica Zoh., P. atlantica subsp. mutica Fish et C.A. Mey and P. atlantica subsp. cabulica Stocks.) with potential in the breeding of rootstocks using the selective amplification of microsatellite polymorphic loci (SAMPL) technique. Six primer combinations produced a total of 182 bands, with an average of 30.33 bands per primer pair, of which 128 were polymorphic. Three branches were obtained, the first containing P. vera, and the second containing P. khinjuk, P. eurycarpa, P. atlantica and subspecies mutica and cabulica, with numerous leaflets clustered in the third branch. UPGMA analysis separated P. atlantica subspecies from P. eurycarpa.

Physiology and Molecular Biology of Plants, 2019

Pistachio trees (Pistacia vera L.) have been cultivated in Tunisia for decades and the plantation was extended mostly in the center of the country contributing to the economic growth of marginalized areas. Herein we used conserved DNA derived polymorphism (CDDP) technique, which target specifically conserved sequences of plant functional genes, to assess the genetic diversity and construct genetic relationships among 65 Tunisian pistachio trees. A set of nine primers were used and 157 CDDP markers were revealed with an average of 17.44 showing a high degree of polymorphism (99.37%). The average of polymorphism information content of CDDP markers was of 0.86, which indicates the efficiency of CDDP primers in the estimation of genetic diversity between pistachios. UPGMA dendrogram and the principal component analysis showed four clusters of analyzed pistachios trees. Our results showed that the genetic structure depends on: (1) the gene exchanges between groups, (2) the geographical origin and (3) the sex of the tree. The same result was revealed by the Bayesian analysis implemented in STRUCTURE at K = 4, in which the pistachio genotypes of El Guettar, Kasserine and Sfax were assigned with more than 80% of probability. Our results prove polymorphism and efficiency of CDDP markers in the characterization and genetic diversity analysis of P. vera L. genotypes to define conservation strategy.

Acta horticulturae, 2011

This study addresses the phylogenetic relationship between Pistacia species by amplified fragment length polymorphism (AFLP). A total of 44 accessions belonging to P. vera, P. eurycarpa, P. khinjuk, all subspecies of P. atlantica (atlantica, mutica, kurdica and cabulica), three unknown genotypes and three accessions proposed to be hybrids from P. eurycarpa × P. atlantica was the plant material used in this study. The accessions were from Iran, Turkey, USA and Syria. Six AFLP primer combinations produced a total of 475 fragments, with an average of 79.16 fragments per primer pair, of which, 336 bands were polymorphic. Unweighted pair group method based on arithmetic average (UPGMA) analysis was performed on jaccards similarity cofficient matrix and also average similarity of each species. According to the results, two main clusters were developed and P. vera, P. eurycarpa, P. atlantica (subsp. atlantica, kurdica, mutica, cabulica) and the hybrid genotypes were located in the first main cluster. P. khinjuk accessions from Iran and USA localized in second main cluster. The hybrid accessions located between eurycarpa and atlantica species and their hybrid nature between these to species was confirmed. One of the unknown accession clustered with the hybrid ones and the two other were grouped closely with P. khinjuk. According to this study, the closest species to P. vera was Eurycarpa group, followed by P. atlantica. UPGMA analysis separated P. atlantica subsp. mutica and cabulica from P. atlantica and P. eurycarpa. Subspecies mutica and cabulica were two closest genotypes, hence P. atlantica subsp. mutica could be classified as a distinct species as P. mutica and the cabulica as a subspecies of P. mutica. This study revealed that P. eurycarpa is a synonym for P. atlantica subsp. kurdica and should be considered distinct from P. atlantica, however P. atlantica showed a closer genetic similarity to P. eurycarpa than the other species.

Journal of the American Society For Horticultural Science, 2003

ADDITIONAL INDEX WORDS. SSR, DNA fingerprinting, genetic markers, product purity ABSTRACT. A genomic DNA library enriched for dinucleotide (CT)n and (CA)n and trinucleotide (CTT)n microsatellite motifs has been developed from 'Kerman pistachio (Pistacia vera L.). The enrichment method based on magnetic or biotin capture of repetitive sequences from restricted genomic DNA revealed an abundance of simple sequence repeats (SSRs) in the pistachio genome which were used for marker development. After an enrichment protocol, about 64% of the clones contained (CT)n repeats while 59% contained (CA)n for CT and CA enriched libraries, respectively. In the (CT)n enriched library, compound sequences were 45% while for (CA)n it was 13.5%. In both dinucleotide enriched libraries, about 80% of the clones having microsatellites have a repeat length in the range of 10 to 30 units. A library enriched for trinucleotide (CTT)n contained <19% of the clones with (CTT)n repeats. Of the clones that contained microsatellites, 62% had sufficient flanking sequence for primer design. An initial set of 25 pairs of primers was designed, out of which 14 pairs amplified cleanly and produced an easily interpretable PCR product in the commercially important American, Iranian, Turkish, and Syrian pistachio cultivars. The efficient DNA extraction method developed for pistachio kernels and shells (roasted and nonroasted) yielded DNA of sufficient quality to use PCR to create DNA fingerprints. In total, 46 alleles were identified by 14 primer pairs and a dendrogram was constructed on the basis of that information. The SSR markers distinguished most of the tested cultivars from their unique DNA fingerprint. An UPGMA cluster analysis placed most of the Iranian samples in one group while the Syrian samples were the most diverse and did not constitute a single distinct group. The maximum number of cultivar specific markers were found in 'Kerman (4), the current industry standard in the United States, and the Syrian cultivar Jalab (5). The technique of using extracted DNA from pistachio kernal or shell coupled with the appropriate marker system developed here, can be used for analyses and measurement of trueness to type.