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Chockpisit Channuntapipat, Margaret Sedgley, and Graham Collins

Leaf explants were taken from mature leaves of two almond [Prunus dulcis (Miller) D.A. Webb] cultivars, Ne Plus Ultra and Nonpareil selection 15-1, and maintained in vitro to grow shoot tips. Shoot tips were grown also from a pre-existing in vitro culture of an almond-peach rootstock, P. dulcis `Titan' × P. persica `Nemaguard'. The shoot tips were harvested, cryopreserved, and tested for survival after 3 days and then at intervals of 3 months up to two years. The mean survival was 80% for `Ne Plus Ultra', 54% for `Nonpareil', and 78% for the hybrid rootstock, and there were no significant differences in survival between 3 days and 24 months. The effects of in vitro culture and cryopreservation on DNA integrity were examined by both RAPD-PCR, and restriction enzyme digestion followed by RAPD-PCR, using DNA from the original trees from which the explants were derived, from leaves regrown from cultures that had undergone several passages of in vitro culture, and from leaves regrown from cryopreserved shoot tips. No detectable differences were found between the DNA fingerprints of each DNA sample using RAPD-PCR with seven different 10-mer primers. However, differences were detected when the DNA was first digested with the isoschizomeric pairs, Hpa II/Msp I and Bsp 143 I/Mbo I and then subjected to RAPD-PCR with six different 10-mer primers. Changes in the structure and methylation of DNA were found that were probably related to the process of in vitro culture, and in addition, methylation changes were detected that were probably associated with the cryopreservation process. These changes did not appear to be caused by the vitrification solution used before immersion of shoot tips in liquid nitrogen. While cryopreservation appears to be an ideal method for the long-term storage of almond germplasm, the significance of the alterations to both methylation and structure of DNA needs to monitored in regenerated plants, especially as they relate to agronomic performance when the regenerants become reproductively mature.

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Reynato P. Umali, Nanako Kameya, and Ikuo Nakamura

The banana (Musa sp., AAA) genome is continuously expanding due to the high frequency of somaclonal variation. Because of this increasing diversity, numerical and morphological methods of taxonomic and phylogenetic identification of banana cultivars became laborious, difficult, and often the subject of disagreements. The aim of this study, therefore, is to develop molecular tools for DNA fingerprinting that can discriminate Musa, AAA Cavendish subgroup cultivars. In this paper, we showed that the plastid-subtype identity (PS-ID) sequence of the noncoding region between rpl16 and rpl14 genes of plastid DNA was highly conserved except for single-base substitution and deletion. These differences separated the clones into three groups (G1, G2, and G3) and suggested that clones within groups are closely related maternally. Using arbitrary primer A13, we later identified negative RAPD markers A133.0 and A131.3 specifically for S4 (selection from Giant Cavendish subgroup, AAA) and S11 (`Morado' from `Red' and `Green Red' subgroup, AAA), respectively. Fragments corresponding to the missing bands were sequenced and used as templates to design new primers with overlapping sequences. Two of these primers, Ba3.0A and Ba1.3A, successfully generated positive markers consistently amplified as Ba3.0A0.8 and Ba1.3A0.6 for S4 and S11, respectively. It is proposed that the method just described can be a better alternative over screening more arbitrary primers in generating positive markers in cases when negative ones were already identified. Results of PS-ID subtype analysis likewise suggested potential use in identifying wild maternal progenitor in polyploid bananas.

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Darush Struss, Riaz Ahmad, Stephen M. Southwick, and Manuela Boritzki

Simple sequence repeats (SSRs) and amplified fragment-length polymorphisms (AFLPs) were used to evaluate sweet cherry (Prunus avium L.) cultivars using quality DNA extracted from fruit flesh and leaves. SSR markers were developed from a phage library using genomic DNA of the sweet cherry cultivar Valerij Tschkalov. Microsatellite containing clones were sequenced and 15 specific PCR primers were selected for identification of cultivars in sweet cherry and for cross-species amplification in Prunus. In total, 48 alleles were detected by 15 SSR primer pairs, with an average of 3.2 putative alleles per primer combination. The number of putative alleles ranged from one to five in the tested cherry cultivars. Forty polymorphic fragments were scored in the tested cherry cultivars by 15 SSRs. All sweet cherry cultivars were identified by SSRs from their unique fingerprints. We also demonstrated that the technique of using DNA from fruit flesh for analysis can be used to maintain product purity in the market place by comparing DNA fingerprints from 12 samples of `Bing' fruit collected from different grocery stores in the United States to that of a standard `Bing' cultivar. Results indicated that, with one exception, all `Bing'samples were similar to the standard. Amplification of more than 80% of the sweet cherry primer pairs in plum (P. salicina), apricot (P. armeniaca) and peach (P. persica L.) showed a congeneric relationship within Prunus species. A total of 63 (21%) polymorphic fragments were recorded in 15 sweet cherry cultivars using four EcoRI-MseI AFLP primer combinations. AFLP markers generated unique fingerprints for all sweet cherry cultivars. SSRs and AFLP polymorphic fragments were used to calculate a similarity matrix and to perform UPGMA cluster analysis. Most of the cultivars were grouped according to their pedigree. The SSR and AFLP molecular markers can be used for the grouping and identification of sweet cherry cultivars as a complement to pomological studies. The new SSRs developed here could be used in cherry as well as in other Prunus species for linkage mapping, evolutionary and taxonomic study.

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L.S. Boiteux, M.E.N. Fonseca, and P.W. Simon

Seven plant genomic DNA purification protocols were evaluated for genetic fingerprinting analysis using six tissues obtained from inbred carrot (Daucus carota L.) lines. Evaluations included 1) DNA yield, 2) DNA purity, 3) DNA cleavage with HindIII, 4) DNA integrity, and 5) DNA suitability for amplification in a random amplified polymorphic DNA (RAPD) system. Significant differences were observed among tissues and purification methods for the total amount of DNA. An extraction method using CTAB buffer + organic solvents gave the best results in DNA yield, purity, and HindIII cleavage when compared with the other six nonorganic extraction methods. Of the tissues examined, flowers yielded the most DNA (average value = 115 ng of DNA/mg of fresh tissue); followed by seeds (54 ng·mg-1), fresh leaves (48 ng·mg-1), lyophilized leaves (40 ng·mg-1), calli (22 ng·mg-1), and tap roots (4 ng·mg-1). For most of the preparations, the DNA showed no traces of degradation. However, DNA preparations were not consistently accessible to HindIII cleavage in all tissue-extraction method combinations. Uncut DNA was observed chiefly in extractions from flowers and fresh leaves suggesting a tissue-specific adverse effect on restriction endonuclease activity. Differences in RAPD band (amplicon) intensity and number were observed across tissues and DNA extraction methods using identical PCR conditions for RAPD. Callus was the best type of tissue for RAPD-based fingerprinting yielding a consistently higher number of more intense amplicons when compared to the other tissues. In flowers and seeds, only DNA obtained with the CTAB extraction method could be amplified. Polymorphisms deviating from genetic expectations were mainly observed in root and fresh leaf DNA, indicating that some RAPD markers may not present satisfactory levels of reproducibility. Judicious and uniform selection of DNA purification method as well as tissue source for DNA extraction are, therefore, important considerations for reliable RAPD-based DNA fingerprinting analysis in carrot. In addition, our studies allowed the identification of a better combination of procedures for use in routine manipulations of carrot DNA such as RFLP-RAPD-based cultivar fingerprinting, molecular mapping, screening of transgenic plants, construction of genomic libraries, and gene cloning.

Open access

Iqrar Ahmad Khan, Ahmad Sattar Khan, Ishtiaq Ahmad Rajwana, Asif Ali Khan, Muhammad Abubakkar Azmat, and Syed Ali Raza

extracted from the young tender leaves of nine mango genotypes by using modified cetyltrimethylammonium bromide method ( Azmat et al., 2012 ). The extracted DNA was subjected to DNA fingerprinting by using 120 simple sequence repeat/inter-simple sequence

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Naomi R. Smith, Robert N. Trigiano, Mark T. Windham, Kurt H. Lamour, Ledare S. Finley, Xinwang Wang, and Timothy A. Rinehart

molecular markers can be used in patent applications and subsequently for protection of the patented cultivars against infringement ( Saunders et al., 2001 ; Weising et al., 1995 ). Currently, one of the most popular DNA fingerprinting techniques is

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Samuel G. Obae, Mark H. Brand, and Richard C. Kaitany

cultivars. AFLP is one of the techniques that could be used to develop molecular markers to identify and differentiate B. thunbergii cultivars. AFLP is a DNA fingerprinting assay that combines restriction enzyme digestion and polymerase chain reaction (PCR

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Salih Kafkas, Mustafa Özgen, Yıldız Doğan, Burcu Özcan, Sezai Ercişli, and Sedat Serçe

, percentage of polymorphic bands, resolving power, and polymorphism information content in the DNA fingerprinting of mulberry accessions from three Morus species sampled across Turkey. When we attempted to characterize Turkish mulberry accessions

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Margaret T. Mmbaga, and Roger J. Sauvé,

. Bleeker, M. Reijans, M. vander Lee, T. Jornes, M. Frijters, A. Pot, J. Peleman, J. Kuiper, M. Zabeau, M. 1995 AFLP: A new technique for DNA fingerprinting Nucl. Acids Res. 23

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Yuan Huang, Xue-qin Wang, Chun-yan Yang, and Chun-lin Long

new technique for DNA fingerprinting Nucleic Acids Res. 23 4407 4414 Zane, L. Bargelloni, L. Patarnello, T. 2002 Strategies for microsatellite isolation: A review Mol. Ecol. 11 1 16