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1.
Bol. latinoam. Caribe plantas med. aromát ; 23(4): 608-635, jul. 2024. tab, ilus, graf, mapas
Article in English | LILACS | ID: biblio-1538071

ABSTRACT

Chile has two certified origin olive products: Extra-Virgin Olive Oil (EVOO) from Huasco valley and the Azapa variety table olive from the Azapa valley. However, efficient methodologies are needed to determine the varieties and raw materials involved in the end products. In this study, we assessed the size of alleles from ten microsatellites in 20 EVOOs and in leaves and fruits of 16 olive varieties cultivated in Chile to authenticate their origins. The identification of varieties relied on specific allele sizes derived from microsatellites markers UDO99-011 and DCA18-M found in leaves and fruit mesocarp. While most Chilean single-variety EVOOs matched the variety declared on the label, inconsistencies were observed in single-variety EVOOs containing multiple varieties. Our findings confirm that microsatellites serve as a valuable as diagnostic tools for ensuring the quality control of Geographical Indication certification for Azapa olives and EVOO with Designation of Origin from Huasco.


Chile cuenta con dos productos de oliva de origen certificado: El aceite de oliva virgen extra (AOVE) del valle del Huasco y la aceituna de mesa de la variedad Azapa del valle de Azapa. Sin embargo, se necesitan metodologías eficientes para determinar las variedades y materias primas involucradas en los productos finales. En este estudio, evaluamos el tamaño de los alelos de diez microsatélites en 20 AOVEs y en hojas y frutos de 16 variedades de aceituna cultivadas en Chile para autentificar sus orígenes. La identificación de las variedades se basó en los tamaños alélicos específicos derivados de los marcadores microsatélites UDO99-011 y DCA18-M encontrados en las hojas y el mesocarpio de los frutos. Aunque la mayoría de los AOVEs chilenos monovarietales coincidían con la variedad declarada en la etiqueta, se observaron incoherencias en los AOVEs monovarietales que contenían múltiples variedades. Nuestros hallazgos confirman que los microsatélites sirven como valiosas herramientas de diagnóstico para asegurar el control de calidad de la certificación de Indicación Geográfica para aceitunas de Azapa y AOVE con Denominación de Origen de Huasco.


Subject(s)
Plant Extracts/genetics , Microsatellite Repeats , Olea/genetics , Olive Oil/chemistry , Geography , Chile
2.
Sci. agric ; 79(3): e20200308, 2022. tab, graf, mapas
Article in English | VETINDEX | ID: biblio-1290197

ABSTRACT

Olive is one of the most important crops in the Mediterranean Basin, because of the olive oil economic value and its role in characterization of the rural landscape. The strong influence of climatic changes on the modern agriculture and the availability of a large source of genetic variability pose as crucial future challenges. Therefore, safeguarding olive genetic resources becomes fundamental, not only in cultivated forms in ex situ collections, but also in terms of wild trees in their natural habitat. In this study, 174 samples of oleaster collected in different parts of Algeria were analyzed by 16 nuclear Simple Sequence Repeats (SSRs). The analysis showed a huge genetic variability in the oleaster, and the STRUCTURE and Principal Coordinate Analyses (PCoA) highlighted clusterization of genotypes according to their geographic origin and bioclimatic conditions. Genotypes adapted to harsh climatic conditions were identified, which could be useful to enrich the panel of olive genotypes for breeding purposes and preserve genetic diversity of this species from erosion risks.(AU)


Subject(s)
Genetic Variation/genetics , Olea/genetics , Plant Dispersal/genetics , Biodiversity , Algeria
3.
Mol Biol Rep ; 47(6): 4345-4355, 2020 Jun.
Article in English | MEDLINE | ID: mdl-32468255

ABSTRACT

Stearoyl-ACP desaturases (SADs) and fatty acid desaturases (FADs) play a critical role in plant lipid metabolism and also affect oil fatty acid composition introducing double bonds into the hydrocarbon chains to produce unsaturated fatty acids. In the present study, the genomic sequences of three SAD and three FAD candidate genes were characterized in olive and their expression was evaluated in different plant tissues. OeSAD genes corresponded to olive SAD1 and SAD2 and to a newly identified OeSAD4, sharing the conserved protein structure with other plant species. On the other hand, the full-length genomic sequences of two microsomal OeFAD genes (FAD2-1 and FAD2-2) and the plastidial FAD6, were released. When the level of expression was tested on different tissues of cv. Leccino, OeSAD1 and OeSAD2 were mainly expressed in the fruits, while OeFAD genes showed the lowest expression in this tissue. The mRNA profiling of all genes was directly studied in fruits of Leccino and Coratina cultivars during fruit development. In both genotypes, the expression level of OeSAD1 and OeSAD2 had the highest value during and after the pit-hardening period, when oil accumulation in fruit mesocarp is intensively increasing. Furthermore, the expression level of both OeFAD2 genes, which were the main candidates for oleic acid desaturation, were almost negligible during fruit ripening. These results have made possible to define candidate genes of the machinery regulation of fatty acid composition in olive oil, providing information on their sequence, gene structure and chromosomal location.


Subject(s)
Fatty Acid Desaturases/genetics , Mixed Function Oxygenases/genetics , Olea/genetics , Fatty Acids/analysis , Fatty Acids, Unsaturated , Fruit/genetics , Gene Expression Profiling/methods , Gene Expression Regulation, Plant/genetics , Genes, Plant/genetics , Olea/metabolism , Oleic Acid , Plant Growth Regulators/genetics , Plant Growth Regulators/metabolism , Plant Proteins/genetics
4.
Sci Rep ; 9(1): 16968, 2019 11 18.
Article in English | MEDLINE | ID: mdl-31740728

ABSTRACT

Olive is a long-living perennial species with a wide geographical distribution, showing a large genetic and phenotypic variation in its growing area. There is an urgent need to uncover how olive phenotypic traits and plasticity can change regardless of the genetic background. A two-year study was conducted, based on the analysis of fruit and oil traits of 113 cultivars from five germplasm collections established in Mediterranean Basin countries and Argentina. Fruit and oil traits plasticity, broad-sense heritability and genotype by environment interaction were estimated. From variance and heritability analyses, it was shown that fruit fresh weight was mainly under genetic control, whereas oleic/(palmitic + linoleic) acids ratio was regulated by the environment and genotype by environment interaction had the major effect on oil content. Among the studied cultivars, different level of stability was observed, which allowed ranking the cultivars based on their plasticity for oil traits. High thermal amplitude, the difference of low and high year values of temperature, negatively affected the oil content and the oleic acid percentage. Information derived from this work will help to direct the selection of cultivars with the highest global fitness averaged over the environments rather than the highest fitness in each environment separately.


Subject(s)
Olea/physiology , Olive Oil/chemistry , Argentina , Fatty Acids/analysis , Fruit/chemistry , Fruit/physiology , Genotype , Linoleic Acids/analysis , Mediterranean Region , Multifactorial Inheritance , Olea/chemistry , Olea/genetics , Olive Oil/analysis , Palmitic Acid/analysis , Temperature
5.
Sci. agric ; 74(3): 215-225, mai./jun. 2017. tab, ilus, graf
Article in English | VETINDEX | ID: biblio-1497638

ABSTRACT

The olive (Olea europaea L.) is a leading oil crop in the Mediterranean area. Limited information on the inheritance of agronomic significant traits hinders progress in olive breeding programs, which encourages the development of markers linked to the traits. In this study, we report on the development of 46 olive simple sequence repeat (SSR) markers, obtained from 577,025 expressed sequence tags (ESTs) in developing olive fruits generated in the framework of the Slovenian national olive transcriptome project. Sequences were de novo assembled into 98,924 unigenes, which were then used as a source for microsatellites searching. We identified 923 unigenes that contained 984 SSRs among which dinucleotide SSRs (36 %) were the most abundant, followed by tri- (33 %) and hexa- (21 %) nucleotides. Microsatellite repeat motif GA (37 %) was the most common among dinucleotides, while microsatellite repeat motif GAA was the most abundant trinucleotide SSR motif (16 %). Gene ontology annotations could be assigned to 27 % of the unigenes. A hundred and ten expressed sequence tag-derived-simple sequence repeats (EST-SSRs) with annotated genes were selected for primer designing and finally, 46 (42 %) polymorphic EST-SSRs were successfully amplified and used to validate genetic diversity among 24 olive varieties. The average number of alleles per locus, observed heterozygosity, expected heterozygosity, and polymorphic information content were 4.5, 0.649, 0.604 and 0.539, respectively. Twenty-seven EST-SSRs showed good diversity properties and were recommended for further olive genome investigation.


Subject(s)
Expressed Sequence Tags , Genome, Plant/genetics , Genetic Markers/genetics , Olea/genetics , Microsatellite Repeats/genetics , Repetitive Sequences, Nucleic Acid , Genetic Variation
6.
Sci. agric. ; 74(3): 215-225, mai./jun. 2017. tab, ilus, graf
Article in English | VETINDEX | ID: vti-686519

ABSTRACT

The olive (Olea europaea L.) is a leading oil crop in the Mediterranean area. Limited information on the inheritance of agronomic significant traits hinders progress in olive breeding programs, which encourages the development of markers linked to the traits. In this study, we report on the development of 46 olive simple sequence repeat (SSR) markers, obtained from 577,025 expressed sequence tags (ESTs) in developing olive fruits generated in the framework of the Slovenian national olive transcriptome project. Sequences were de novo assembled into 98,924 unigenes, which were then used as a source for microsatellites searching. We identified 923 unigenes that contained 984 SSRs among which dinucleotide SSRs (36 %) were the most abundant, followed by tri- (33 %) and hexa- (21 %) nucleotides. Microsatellite repeat motif GA (37 %) was the most common among dinucleotides, while microsatellite repeat motif GAA was the most abundant trinucleotide SSR motif (16 %). Gene ontology annotations could be assigned to 27 % of the unigenes. A hundred and ten expressed sequence tag-derived-simple sequence repeats (EST-SSRs) with annotated genes were selected for primer designing and finally, 46 (42 %) polymorphic EST-SSRs were successfully amplified and used to validate genetic diversity among 24 olive varieties. The average number of alleles per locus, observed heterozygosity, expected heterozygosity, and polymorphic information content were 4.5, 0.649, 0.604 and 0.539, respectively. Twenty-seven EST-SSRs showed good diversity properties and were recommended for further olive genome investigation.(AU)


Subject(s)
Genetic Markers/genetics , Olea/genetics , Expressed Sequence Tags , Genome, Plant/genetics , Genetic Variation , Repetitive Sequences, Nucleic Acid , Microsatellite Repeats/genetics
7.
Genet Mol Res ; 14(2): 5958-69, 2015 Jun 01.
Article in English | MEDLINE | ID: mdl-26125795

ABSTRACT

The olive tree is an iconic tree of the Mediterranean, and is used extensively to produce high-quality olive oil. Although the China olive industry has just begun to be valued, there were also existed mislabeling and synonyms in introduced cultivars. The aim of this study was to analyze genetic similarities among olive cultivars in China using SSR and ISSR techniques. Thirty-two samples were collected from Xichang. Five of these cultivars were issued from a Chinese breeding program. Genomic DNA samples were extracted from young leaves and PCR was used to generate SSR and ISSR markers. A total of 107 polymorphic bands were detected on thirteen SSR loci, with an average of eight alleles per locus. The observed heterozygosity ranged from 0.785 (DCA03) to 0.990 (GAPU47), and the expected heterozygosity varied between 0.782 (DCA03) and 0.940 (GAPU103A). The discrimination power ranged from 0.57 to 0.83, while the polymorphism information content values ranged from 0.768 (DCA03) to 0.934 (GAPU103A). Nine ISSR primers generated 85 reproducible bands of which 78 (91.8%) were polymorphic. Based on our data, genetic similarity between cultivars ranged from 0.57 to 0.83. Cluster analysis revealed that 32 cultivars were clustered into six groups, which supports similar morphology such as use, oil content and fruit weight but not similar geographical origins. Our data also allow the identification of unknown cultivars and cases of synonyms.


Subject(s)
Microsatellite Repeats/genetics , Olea/genetics , Phylogeny , Polymorphism, Genetic , China , DNA Fingerprinting , Genotype
8.
Genet Mol Res ; 14(1): 2241-52, 2015 Mar 27.
Article in English | MEDLINE | ID: mdl-25867371

ABSTRACT

The purpose of this research was to characterize an olive core collection using some agronomic characters and simple sequence repeat (SSR) markers and to determine SSR markers associated with the content of fatty acids in olive oil. SSR marker analysis demonstrated the presence of a high amount of genetic variation between the olive cultivars analyzed. A UPGMA dendrogram demonstrated that olive cultivars did not cluster on the basis of their geographic origin. Fatty acid components of olive oil in these cultivars were determined. The results also showed that there was a great amount of variation between the olive cultivars in terms of fatty acid composition. For example, oleic acid content ranged from 57.76 to 76.9% with standard deviation of 5.10%. Significant correlations between fatty acids of olive oil were observed. For instance, a very high negative correlation (-0.812) between oleic and linoleic acids was detected. A structured association analysis between the content of fatty acids in olive oil and SSR markers was performed. STRUCTURE analysis assigned olive cultivars to two gene pools (K = 2). Assignment of olive cultivars to these gene pools was not based on geographical origin. Association between fatty acid traits and SSR markers was evaluated using the general linear model of TASSEL. Significant associations were determined between five SSR markers and stearic, oleic, linoleic, and linolenic acids of olive oil. Very high associations (P < 0.001) between ssrOeUA-DCA14 and stearic acid and between GAPU71B and oleic acid indicated that these markers could be used for marker-assisted selection in olive.


Subject(s)
Fatty Acids/metabolism , Genetic Variation , Microsatellite Repeats/genetics , Olea/genetics , Olea/metabolism , Olive Oil/metabolism , Alleles , Cluster Analysis , Gene Frequency , Genotype , Olea/classification , Olive Oil/chemistry , Phenotype , Polymorphism, Genetic , Species Specificity
9.
Genet Mol Res ; 14(1): 2762-74, 2015 Mar 31.
Article in English | MEDLINE | ID: mdl-25867425

ABSTRACT

The purpose of this study was to characterize olive core collection with amplified fragment length polymorphism (AFLP) markers and fruit traits and to determine AFLP markers significantly associated with these fruit characters in olive. A total of 168 polymorphic AFLP markers generated by five primer combinations and nine fruit traits were used to characterize relationships between 18 olive cultivars. Although all olive cultivars were discriminated from each other by either AFLP markers (<0.75 similarity level) or fruit traits, clustering based on the AFLP markers and fruit traits was not significantly correlated (r = 0.13). Partial clustering of olive cultivars by AFLP markers according to their geographical origin was observed. Associations of AFLP markers with fruits were determined using a multiple-regression analysis with stepwise addition of AFLP markers. Significant associations between eight AFLP markers and fruit traits were identified. While five AFLP markers demonstrated significant negative correlation with fruit and stone weight, width and length and total polyphenols (P < 0.05), three AFLP markers displayed significant positive correlation with α-tocopherol and γ-tocopherol (P < 0.01). This is the first report on the association of molecular markers with fruit traits in olive. Molecular markers associated with morphological and agronomic traits could be utilized for the breeding of olive cultivars. However, the association power of these markers needs to be confirmed in larger populations, and highly correlated markers should then be converted to PCR-based DNA markers such as sequence-characterized amplified region markers for better utilization.


Subject(s)
Amplified Fragment Length Polymorphism Analysis/methods , Fruit/genetics , Genetic Markers/genetics , Olea/genetics , Cluster Analysis , DNA, Plant/genetics , Fruit/metabolism , Olea/classification , Olea/metabolism , Polymorphism, Genetic , Regression Analysis , alpha-Tocopherol/metabolism , gamma-Tocopherol/metabolism
10.
Sci. agric ; 71(1): 52-57, Jan-Fev. 2014. graf, tab
Article in English | VETINDEX | ID: biblio-1497385

ABSTRACT

Olive (Olea europaea L.) shows alternate bearing, with unreliable cropping patterns and inconsistent fruit size and quality every year. In many countries, thinning with naphthaleneacetic acid (NAA) is used to minimise alternate bearing behavior in olives. However, in Italy, growers are reluctant to employ this practice and no detailed knowledge is available for specific cultivars. We evaluated the effects of spraying NAA on various dates on the productive and vegetative characteristics of the main Italian table olive cultivar'Nocellara del Belice'. Trunk cross-sectional area, fruit set, fruit drop, fruit size, pit size, yield per tree, crop density and flesh to pit ratio were analysed. The NAA treatment applied on the earliest of the dates selected increased fruit weight and flesh to pit ratio, by reducing crop density and enhancing the leaf to fruit ratio, without reducing yield. Two distinct negative relationships were found between fruit weight and crop density during "on" and "off" years, but a unique relationship between pit weight vs. crop density in both years, suggested that the pit is the strongest sink. Fruit size and quality of'Nocellara del Belice' can be enhanced by NAA application, thereby increasing economic returns in the "on" year.


Subject(s)
Olea/anatomy & histology , Olea/genetics , Food Quality , Italy , Naphthaleneacetic Acids
11.
Sci. Agric. ; 71(1): 52-57, Jan-Fev. 2014. graf, tab
Article in English | VETINDEX | ID: vti-27134

ABSTRACT

Olive (Olea europaea L.) shows alternate bearing, with unreliable cropping patterns and inconsistent fruit size and quality every year. In many countries, thinning with naphthaleneacetic acid (NAA) is used to minimise alternate bearing behavior in olives. However, in Italy, growers are reluctant to employ this practice and no detailed knowledge is available for specific cultivars. We evaluated the effects of spraying NAA on various dates on the productive and vegetative characteristics of the main Italian table olive cultivar'Nocellara del Belice'. Trunk cross-sectional area, fruit set, fruit drop, fruit size, pit size, yield per tree, crop density and flesh to pit ratio were analysed. The NAA treatment applied on the earliest of the dates selected increased fruit weight and flesh to pit ratio, by reducing crop density and enhancing the leaf to fruit ratio, without reducing yield. Two distinct negative relationships were found between fruit weight and crop density during "on" and "off" years, but a unique relationship between pit weight vs. crop density in both years, suggested that the pit is the strongest sink. Fruit size and quality of'Nocellara del Belice' can be enhanced by NAA application, thereby increasing economic returns in the "on" year.(AU)


Subject(s)
Olea/anatomy & histology , Olea/genetics , Food Quality , Naphthaleneacetic Acids , Italy
12.
Genet Mol Res ; 11(3): 2401-11, 2012 Aug 16.
Article in English | MEDLINE | ID: mdl-22614458

ABSTRACT

A total of 91 wild olive accessions and 31 olive cultivars growing in the Extremadura region of central-western Spain were analyzed using morphological traits and RAPD markers. We focused on three main and 16 minor Spanish olive cultivars that are recognized as native or local to the Extremadura region. The five arbitrary 10-mer primers tested on the olive cultivars gave 67 polymorphic bands, representing 91% of the total amplification products. The number of bands per primer ranged from 9 to 18, whereas the number of polymorphic bands ranged from 8 to 17. All the cultivars could be identified by a combination of three primers (OPF-6, OPA-8, and OPK-16); four cultivar-specific markers were detected. The minor local "Jariego" and "Tempranillo" cultivars showed the most distal similarities. The resulting dendrogram, using the unweighted pair-group method with arithmetic mean clustering algorithm, depicted the pattern of relationships between the local Extremadura cultivars and the cultivars from geographically connected regions. This analysis showed a correlation between most of the minor local cultivars and the geographical origin; there was no apparent clustering according to morphological traits or fruit use of olive cultivars when these parameters were used as analysis criteria.


Subject(s)
Ecotype , Olea/anatomy & histology , Olea/genetics , Quantitative Trait, Heritable , Random Amplified Polymorphic DNA Technique/methods , Genetic Markers , Genotype , Phylogeny , Polymorphism, Genetic , Spain
13.
Genet Mol Res ; 11(2): 918-32, 2012 Apr 10.
Article in English | MEDLINE | ID: mdl-22576919

ABSTRACT

Seventy-seven olive accessions corresponding to 25 cultivars from the Extremadura region of Spain were studied using four microsatellite or SSR markers in order to fingerprint them, and evaluate genetic similarity and relationships between local and introduced olive cultivars. The number of alleles per locus ranged from 4 to 8, with a mean of 6.25 alleles per primer pair (a total of 25 alleles). The observed heterozygosity ranged from 0.58 to 0.95, while the expected heterozygosity varied between 0.68 and 0.83. The polymorphism information content values ranged from 0.63 to 0.79. The mean polymorphism information content value of 0.70 for the SSR loci provided sufficient discriminating ability to evaluate the genetic diversity among the cultivars. The SSR data allowed unequivocal identification of all the cultivars; a combination of three SSR markers was sufficient to discriminate all 25 olive cultivars. A dendrogram was prepared, using the unweighted pair-group method with arithmetic mean clustering algorithm; it depicted the pattern of relationships between the cultivars. Most of the local cultivars grouped according to their geographic origin. No clear clustering trends were observed when the morphological traits of fruit endocarps or fruit use of cultivars were employed as analysis criteria. We conclude that there is a high level of variability among local olive cultivars from the Extremadura region at both the morphological and molecular levels; these data should be useful for identifying and distinguishing local germplasm.


Subject(s)
Genetic Markers , Microsatellite Repeats/genetics , Olea/genetics , Alleles , Base Sequence , DNA, Plant/genetics , Heterozygote , Polymorphism, Genetic , Spain
14.
Genet Mol Res ; 11(1): 556-71, 2012 Mar 08.
Article in English | MEDLINE | ID: mdl-22535391

ABSTRACT

Olive trees have been grown since the beginning of civilization, and the consumption of olives and olive products is increasing worldwide, due to their health benefits and organoleptic qualities. To meet the growing market for olives, commercial cultivation of this species is expanding from traditional areas to new regions. Although the Brazilian olive industry has just begun to be established, breeding programs are already developing cultivars that are more adapted to local conditions. We used 12 microsatellite markers to evaluate 60 olive accessions, including several cultivars that were developed in Brazil. The analyses identified 72 distinct alleles; the largest number of alleles per locus were at the markers GAPU 101 and GAPU 71B, which contained 10 and 9 alleles, respectively. The largest allelic diversity and polymorphic information contents were also found at the GAPU 101 and GAPU 71B markers, with values of 0.8399/0.8203 and 0.8117/0.7863, respectively. Additionally, the 12 microsatellite markers generated a cumulative identity probability of 1.51 x 10(-10), indicating a high level of accuracy of accession identification. The set of markers that we used allowed the identification of 52 of the 60 olive genotypes, in addition to the recognition of several varietal synonyms. The components of a two-dimensional principal coordinate analysis explained 48.6% of the total genetic variation. The results obtained from the microsatellite markers showed a substantial degree of genetic diversity in the olive tree accessions used in Brazil.


Subject(s)
Genetic Variation , Microsatellite Repeats , Olea/genetics , Alleles , Brazil , Cluster Analysis , Genotype , Olea/classification , Phylogeny
15.
Genet Mol Res ; 11(1): 707-16, 2012 Mar 19.
Article in English | MEDLINE | ID: mdl-22535406

ABSTRACT

Wild olive (O. europaea ssp cuspidata) plants grow in various regions of Iran and are expected to have considerable genetic diversity due to adaptation to the various environmental conditions. We examined the genetic diversity of four populations of wild olive growing in Hormozgan Province located in southern Iran by using 30 RAPDs and 10 ISSR markers. The mean value of polymorphism for RAPD loci was 73.71%, while the value for ISSR loci was 81.74%. The Keshar population had the highest value of intra-population polymorphism for both RAPD and ISSR loci (66.86 and 62.71%, respectively), while the Tudar population had the lowest values (20.35 and 28.81%, respectively). Similarly, the highest and lowest number of effective alleles, Shannon index and Nei's genetic diversity were also found for these two populations. The highest value of H(pop)/H(sp) within population genetic diversity for RAPD and ISSR loci was found for the Keshar population (H(pop) = 0.85 and H(sp) = 0.90). OPA04-750, OPA13-650 and OPA02-350 RAPD bands were specific for Tudar, Bondon and Keshar populations, respectively, while no specific ISSR bands were observed. Analysis of molecular variance as well as the pairwise F(ST) test showed significant differences for RAPD and ISSR markers among the populations. The NJ and UPGMA trees also separated the wild olive populations from each other, indicating their genetic distinctness. UPGMA clustering of the four wild olive populations placed the Tudar population far from the other populations; Keshar and Bokhoon population samples revealed more similarity and were grouped together. We conclude that there is high genetic diversity among O. europaea ssp cuspidata populations located in southern Iran. We also found RAPD and ISSR markers to be useful molecular tools to discriminate and evaluate genetic variations in wild olive trees.


Subject(s)
Genetic Variation , Olea/genetics , Iran , Microsatellite Repeats , Olea/classification , Phylogeny , Phylogeography , Random Amplified Polymorphic DNA Technique
16.
Genet Mol Res ; 9(4): 2248-53, 2010 Nov 16.
Article in English | MEDLINE | ID: mdl-21086261

ABSTRACT

Five different similarity coefficients (Jaccard, Sorensen-Dice, simple matching, Rogers and Tanimoto, and Russel and Rao) were evaluated and 10 wild olives analyzed with RAPD markers. The influence of the similarity coefficients on wild olives clustering was investigated. Forty-five primers were used on samples from 10 wild olives (Wild 1 and 2 obtained from Mugla province; Wild 3, 4, 5, 6, 7, and 8 from Manisa province and Wild 9 and 10 from Izmir province of Turkey). The similarity matrices obtained from RAPD markers were compared by the Mantel test. Cluster analysis was made with UPGMA dendrograms, and the consensus fork indexes between all pairs of dendrograms were calculated. The Jaccard and Sorensen-Dice coefficients gave the same results, due to the fact that both exclude negative co-occurrences. The dendrograms using the simple matching and Rogers and Tanimoto coefficients were similar; Wild 4 (Akhisar, Manisa) and Wild 9 (Bornova, Izmir) olives had the closest genetic similarities. This occurred because these coefficients include negative co-occurrences. The Russel and Rao coefficients produced different results, because they include negative co-occurrences in the denominator. We concluded that the coefficients that do not include negative co-occurrences are more efficient for studies of wild olives clustering based on RAPD markers.


Subject(s)
Genetic Markers , Olea/genetics , Random Amplified Polymorphic DNA Technique , Cluster Analysis
17.
Genet Mol Res ; 9(3): 1865-76, 2010 Sep 21.
Article in English | MEDLINE | ID: mdl-20882482

ABSTRACT

Olea europaea is one of the oldest species of domesticated trees. We used microsatellite markers for fingerprinting and for evaluation of genetic similarity and structure of 26 Greek olive cultivars, which cover most of the olive cultivation regions of Greece, including previously undescribed denominations from northern Greece. Eighty-one alleles were revealed with six SSR loci that were selected as most informative of 10 SSR primers that were initially investigated. The number of alleles per locus varied from 7 to 20 (mean, 13.5). Heterozygosity ranged from 0.240 at locus DCA-3 to 0.826 at locus UDO99-9, with a mean value of 0.600. Analysis of 104 trees representing 26 denominations (four trees per denomination) revealed 26 distinct SSR profiles, indicating 26 olive cultivars; no intracultivar variability was observed. Genetic and geographic distances were not significantly correlated, based on the Mantel test. These SSR loci allowed unequivocal identification of all the cultivars and will be useful for future breeding and olive germplasm management efforts.


Subject(s)
Microsatellite Repeats/genetics , Olea/classification , Olea/genetics , DNA Fingerprinting/methods , Greece , Phylogeny , Polymerase Chain Reaction
18.
Genet Mol Res ; 9(3): 1550-6, 2010 Aug 10.
Article in English | MEDLINE | ID: mdl-20714997

ABSTRACT

We examined genetic relationships among wild and cultivated olives, which is a very important crop in the economy of the Aegean region. We used RAPD analysis to evaluate relationships among and within 22 olive subspecies from Manisa, Mugla and Izmir provinces in Turkey. Twelve of the subspecies were wild and 10 were cultivated olives. Fifty-two primers were used (OP-Q 1-20, OP-I 1-20, OP-F 14-15-16-17, and OP-K 1-8) and 49 polymorphic bands were selected and used for analysis. The dendrogram based on unweighted pair-group cluster analysis using the Sorensen-Dice coefficient of similarity index indicated two major groups, dividing wild olives from cultivated olives. The patterns of genetic relationships among and within the different olives were analyzed by means of analysis of molecular variance. We found significant differences between wild and cultivated olives (Phi(st) = 0.1507; P < 0.001). In order to determine the genetic relationship among wild and cultivated olives, principal coordinate analysis was used to examine the variation among subspecies. The wild and cultivated olives formed two main groups, one on the right side and the other on the left side of the principal coordinates graph, respectively. This was compatible with the results we obtained from analysis of molecular variance.


Subject(s)
Olea/genetics , Random Amplified Polymorphic DNA Technique/methods , Cluster Analysis , Olea/classification , Phylogeny
19.
Genet Mol Res ; 9(2): 884-90, 2010 May 11.
Article in English | MEDLINE | ID: mdl-20467981

ABSTRACT

The RAPD technique was used for determining genetic differences between 12 wild-olive varieties grown in the Aegean provinces of Izmir, Mugla, and Manisa in Turkey. Wild olives obtained from the same provinces were included in the same plot. Twenty of 25 operon primers (OP-I 4, OP-I 14, OP-I 15, OP-I 16, OP-I 17, OP-Q1, OP-Q2, OP-Q3, OP-Q4, OP-Q11, OP-Q12, OP-Q13, OP-Q14, OP-Q15, OP-Q16, OP-Q17, OP-Q18, OP-Q19, OP-Q20, OP-F1, OP-F2, OP-F3, OP-F6, OP-F7, OP-F8) yielded bands. The differences between the varieties were determined based on their genetic similarities, using principal coordinate analysis; genetic distances were determined using neighbor-joining analysis. The varieties wild 7 and wild 12 had the lowest genetic similarity (0.97, Jaccard similarity index); they also had the greatest genetic distance between them (0.3606, Nei's genetic distance). It was concluded that the RAPD technique is adequate for the evaluation of genetic relationships among wild olives. Principal coordinate analysis and neighbor-joining analysis gave results that support the use of this type of analysis to help understand the genetic background of olives and for further genetic studies.


Subject(s)
Olea/genetics , Algorithms , Genes, Plant , Models, Genetic , Models, Statistical , Operon , Phylogeny , Principal Component Analysis , Random Amplified Polymorphic DNA Technique , Sequence Alignment , Species Specificity , Turkey
20.
Genet Mol Res ; 9(2): 966-72, 2010 May 25.
Article in English | MEDLINE | ID: mdl-20506083

ABSTRACT

Genetic similarities and distances between wild-type olives in Turkey were studied using an RAPD-PCR assay. Seven wild olive tree samples were collected from villages in Manisa and Izmir provinces. Genomic DNA was extracted from young leaves and the RAPD-PCR assay was used to generate RAPD markers. Sixty-five random primers obtained from Operon Technologies were tested for the assay (OP-A 1-20, OP-I 1-20, OP-Q 1-20, and OP-J 1-5). Thirty-two of these primers yielded 115 highly polymorphic bands. The mean number of usable bands per primer for all the samples was 3.59. The genetic distance values ranged from 0.1498 to 0.6845, and genetic similarity values varied from 0.8609 to 0.5043. We found that the closest samples based on their genetic distance and similarity values were from Harlak and Sabancilar; the most distant samples were from Bornova and Bademli.


Subject(s)
Olea/genetics , Random Amplified Polymorphic DNA Technique/methods , DNA Primers/genetics , Genes, Plant , Genetic Markers/genetics , Genetic Variation , Genotype , Models, Genetic , Phenotype , Phylogeny , Turkey
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