Genetic diversity of some wild almonds and related Prunus species revealed by SSR and EST-SSR molecular markers

Rahemi, Alireza; Fatahi, R.; Ebadi, A.; Taghavi, Toktam; Hassani, D.; Gradziel, Thomas M.; Folta, Kevin M.; Chaparro, José X.

doi:10.1007/s00606-011-0536-x

Cited by 45 publications

(30 citation statements)

References 40 publications

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“…The average PIC value of EST-SSR loci (0.66) was lower than that of genomic SSR loci (0.80). The present results fit well with previous studies that suggested that EST-SSRs were less polymorphic than their genomic counterparts in other almond genotypes (Rahemi et al 2012) and other species (Tahan et al 2009). However, they are in contrast with results of Xie et al (2006), reporting that genomic and EST-SSR primers amplified similar numbers of alleles.…”

Section: Polymorphism Analysis Of the Ssr Markerssupporting

confidence: 93%

“…These studies established the value of SSR markers for distinguishing different genetic lineages and detected an extensive gene pool available to almond genetic improvement. Promising Iranian almond genotypes, wild almonds, and related Prunus species were also characterized by SSR and EST-SSR markers (Zeinalabedini et al 2012;Rahemi et al 2012). Nuclear DNA markers showed that Moroccan genotypes were genetically different from the tested commercial cultivars and therefore formed a separate genetic pool (El Hamzaoui et al 2013).…”

Section: Introductionmentioning

confidence: 99%

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Genetic variability is preserved among strongly differentiated and geographically diverse almond germplasm: an assessment by simple sequence repeat markers

Halász

Kodad

Galiba

et al. 2019

Tree Genetics & Genomes

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Eighty-six almond accessions of diverse geographic origin, ranging from Central Asia to the USA, were genotyped in 15 simple sequence repeat (SSR) loci to compare genetic diversity parameters, characterize genetic differentiation, and examine factors responsible for the maintenance of genetic diversity and population structure in almond. The mean allele number was 18.86 alleles per locus. All but one primer demonstrated polymorphic information content higher than 0.7. Almond genotypes clustered according to their pedigree and geographic origin. STRUCTURE analysis determined nine genetically distinct subgroups within the studied genotypes including the Kyrgyz, Akdamar, Bademli, Hungarian, Monor, Italian, Moroccan, and Californian accessions and wild species and an admixed group. An AMOVA analysis confirmed that considerable genetic variation occurred within populations (71.30%), and genetic variation among populations was also significant (28.70%). The mean values of the fixation index (F ST ) varied between 0.38 and 0.55, indicating marked genetic differentiation among the populations. The among-population genetic differentiation based on allele sizes (R ST ) was significantly higher than that based on allele identities (F ST ) between the most groups, suggesting that stepwise mutations have also contributed to genetic differentiation. A Mantel test and a neighbor-joining tree showed no significant correlation between the geographic distance and the genetic distance (Rxy = 0.173, P = 0.226) and indicated that geographic distance among the assessed populations has little influence on their genetic differentiation (Rxy = 0.248, P = 0.194). Our data show drift, mutations, and massive gene exchange between several wild species and cultivated P. dulcis as crucial components of genetic differentiation. Slight losses of genetic diversity are attributable to geographic isolation, human selection and not to the relatively recent occurrence of self-compatibility. There was no indication of a major decrease in genetic variability in almond germplasm from Asia to Europe. The present results reveal that almond domestication avoided the occurrence of a genetic bottleneck although its risk is present in many subpopulations.

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Section: Polymorphism Analysis Of the Ssr Markerssupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Genetic variability is preserved among strongly differentiated and geographically diverse almond germplasm: an assessment by simple sequence repeat markers

Halász

Kodad

Galiba

et al. 2019

Tree Genetics & Genomes

View full text Add to dashboard Cite

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“…After pre-screening, 35 primer (Genscript, Nanjing, Jiangsu, China) pairs were chosen that gave distinct, reproducible, and polymorphic amplification products at one or more loci in beach plums. A set of 11 SSR primer pairs were selected on the basis of previous reports of different Prunus species (Rahemi 2012), including BPPCT004, BPPCT007, BPPCT028, BPPCT032, BPPCT039, CPPCT026, CPPCT039, and UDP98-409 as representatives of peaches (Aranza and Dirlewanger 2002, Cipriani 1999, and CPDCT025, CPDCT027, and CPDCT042 for almonds (Table 2). Eleven pairs of primers marked in italics were the effective primers used in this study.…”

Section: Primer Designmentioning

confidence: 99%

Analysis of the genetic diversity of beach plums by simple sequence repeat markers

Wang

Zhang

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The purpose of this study was to measure the genetic diversity of wild beach plum and cultivated species, and to determine the species relationships using SSRs markers. An analysis of genetic diversity from ten beach plum germplasms was carried out using 11 simple sequence repeat (SSR) primers selected from 35 primers to generate distinct PCR products. From this plant material, 44 allele variations were detected, with 3-5 alleles identified from each primer. The analysis showed that the genetic similarity coefficient varied from 0.721 ± 0.155 to 0.848 ± 0.136 within each of the ten beach plum germplasms and changed within the range of 0.551 ± 0.084 to 0.695 ± 0.073 between any two pairs of germplasms. According to the genetic dissimilarity coefficient matrix, a cluster analysis of SSRs using the unweighted pair group mean average method in the NTSYSpc 2.10 software revealed that the ten germplasms could be divided into two groups at the dissimilarity coefficient of 0.606. Class I included 77.8, 12.5, 30, and 33.3% of MM, MI, NY, and CM, respectively. Class II contains the remaining 9 beach plum germplasms. The markers generated by 11 SSR primers proved very effective in distinguishing the beach plum germplasm resources. It was clear that the geographical distribution did not correspond 9693-9702 (2015) with the genetic relationships among the different beach plum strains. This result will be of value to beach plum breeding programs.

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“…Total genomic DNA was extracted from dried leaves using CTAB protocol (Doyle and Doyle 1987) with some modification (Ortega et al 2005;Rahemi et al 2012b). DNA quantity and quality were determined by spectrophotometry and agarose gel electrophoresis.…”

Section: Dna Extractionmentioning

confidence: 99%

Phylogenetic relationships among the first and second introns of selectedPrunus S-RNase genes

et al. 2015

Self Cite

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Phylogenetic relationships among the first and second introns of selected Prunus S-RNase genes. Can. J. Plant Sci. 95: 1145Á 1154. To identify and evaluate self-incompatible alleles in almonds and related germplasm, DNA from 15 Prunus species was amplified using two degenerate consensus primer pairs flanking first and second S-locus introns (PaConsI-FD'EMPc1ConsRD and EM-Pc2ConsFD'EM-Pc3ConsRD). Twenty-eight amplified PCR products were analyzed by automated sequencer capillary electrophoresis. Sequenced fragments were aligned against available Prunus S-locus sequences in the National Center for Biotechnology Information and S-alleles identities were determined. The phylogenetic relationships between S-alleles in the germplasm studied were determined by the homology between their sequences and dendrograms were obtained for each primer pair. The Maximum Likelihood (homology) ranged from 84 to 100%. Most sequences were similar to cultivated almond (Prunus dulcis) or to the European wild almond (P. webbii). Twenty-six alleles for the first and the second introns were registered in the database in the GenBank. Two sequences of the first and second introns, which were taken from Prunus nairica and had similarity in GenBank, were registered in the database under a common sequence of the first and second intron. Analysis of phylogenetic relationships (dendrograms) among S-alleles from wild almond species as well as S-alleles cluster relations showed most pairs of alleles well supported by bootstrap. Key words: Germplasm diversity, self-incompatibility, S-allele, PrunusRahemi, A., Gradziel T.M., Chaparro J.X., Folta, K.M., Taghavi, T., Fatahi, R., Ebadi, A. et Hassani, D. 2015. Liens phyloge´ne´tiques entre le premier et le deuxie`me intron des ge`nes de la S-RNase de certaines espe`ces du genre Prunus. Can. J. Plant Sci. 95: 1145Á1154. Les auteurs ont amplifie´l'ADN de 15 espe`ces du genre Prunus pour identifier puis e´valuer les alle`les auto-incompatibles dans l'amande et le mate´riel ge´ne´tique connexe. À cette fin, ils ont utilise´deux paires d'amorces consensuelles de´ge´ne´re´es, situe´es de part et d'autre du premier et du deuxie`me intron du locus-S (PaConsI-FD'EMPc1ConsRD et EM-Pc2ConsFD'EM-Pc3ConsRD). Vingt-huit produits amplifie´s de la PCR ont e´te´analyse´s par e´lectrophore`se capillaire a`se´quenc¸age automatique. Les fragments se´quence´s ont e´te´compare´s aux se´quences du locus-S du genre Prunus disponibles au National Center for Biotechnology Information et les alle`les ont e´te´identifie´s. Les liens phyloge´ne´tiques entre les alle`les-S du mate´riel ge´ne´tique a`l'e´tude ont e´te´e´tablis par homologie entre les se´quences, et les auteurs ont obtenu les dendrogrammes de chaque paire d'amorces. La fourchette de probabilite´maximale (homologie) varie de 84 a`100 pour cent. La plupart des se´quences ressemblent a`celles de l'amandier cultive´(Prunus dulcis) ou de l'amandier sauvage d'Europe (P. webbii). Vingt-six alle`les du premier et du deuxie`me intron ont e´te´enregistre´s dans la base de donne...

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Genetic diversity of some wild almonds and related Prunus species revealed by SSR and EST-SSR molecular markers

Cited by 45 publications

References 40 publications

Genetic variability is preserved among strongly differentiated and geographically diverse almond germplasm: an assessment by simple sequence repeat markers

Genetic variability is preserved among strongly differentiated and geographically diverse almond germplasm: an assessment by simple sequence repeat markers

Analysis of the genetic diversity of beach plums by simple sequence repeat markers

Phylogenetic relationships among the first and second introns of selectedPrunus S-RNase genes

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