Browsing by Author "Simon, Philipp W."

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Association of reversible inactivation of the maize transposable element Ds with tissue-specific processing of the 35S : TPase transcript in carrot (Daucus carota L.)
(Taylor & Francis, 2006-09) Simon, Philipp W.; İpek, Meryem; İpek, Ahmet; Uludağ Üniversitesi/Ziraat Fakültesi/Ziraat Fakültesi Bahçe Bitkileri Bölümü.; AAH-3233-2021; 6603912485
An Ac/Ds-based two-element transposon tagging system has been introduced into carrot. F-1 progeny containing both the 35S-Ac-transposase gene (35S:TPase) and the Ds element were derived from crosses between 35S:TPase- and Ds-bearing parents. While excision of Ds was not detected in any F-1 plants carrying both 35S:TPase and the Ds element, calli initiated from these F-1 plants had the Ds element excised, indicating Ds transposition. Reverse transcriptase-PCR analysis revealed that the 35S:TPase gene was expressed in both F-1 plants and calli, and that introns 1, 2, and 3 were spliced correctly. Although intron 4 was also spliced correctly in calli, incorrectly spliced intron 4 was detected in F-1 plants. Sequence analysis of incorrectly spliced reverse transcriptase-PCR products demonstrated the presence of a cryptic intron donor site within intron 4 of the 35S:TPase transcript. This probably competed with the proposed intron donor site during maturation of the major 35S:TPase transcript. These results suggested that the major transcript of 35S:TPase was incorrectly processed and, consequently, that the Ds element was reversibly inactivated in the somatic tissues of carrot plants, whereas this inactive Ds element was remobilised during tissue culture, where the 35S:TPase transcript was spliced correctly. These observations point to an important role for tissue-specific 35S:TPase transcript processing for successful transposition of Ds in carrot. Therefore, successful processing of the 35S:TPase transcript in carrot callus may indicate strategies to increase Ac transposition in other tissues.
Characterization of an unusual cytoplasmic chimera detected in bolting garlic clones
(American Society of Horticultural Science, 2007-07-02) İpek, Meryem; Senalik, Douglas; Simon, Philipp W.; İpek, Ahmet; Uludağ Üniversitesi/Ziraat Fakültesi/Bahçe Bitkileri Bölümü.; 6603912487
Production of a visible flower stalk, or bolting, has been used as a major trait to categorize garlic (Allium sativum L.) clones. Analysis of mitochondrial genome variation with polymerase chain reaction (PCR) revealed differences between bolting and nonbolting clones of garlic. Screening 333 garlic accessions from diverse geographic origins revealed a 1403-bp mitochondrial DNA marker associated with bolting that the authors call "Bolt Marker" (BltM). Bolt Marker did not amplify in any of the 131 nonbolting clones, whereas amplification of this marker was observed in 127 of 130 (97.7%) garlic clones that bolted completely in Wisconsin. Seventy-two garlic clones bolted incompletely (clones in which some but not all of the plants bolted), and this marker was not amplified in 69 (95.8%) of these clones. Because of the significant association of BltM with bolting, this PCR-based marker can be used to discriminate complete-bolting garlic clones reliably from nonbolting and incomplete-bolting ones. Sequence characterization of this marker revealed that BltM is a chimera involving both mitochondrial and chloroplast DNA. The DNA sequences including and flanking both the 5' and 3' ends of this marker are consistent with an approximate to 4.8-kbp chloroplast DNA fragment having been inserted into the mitochondrial genome downstream from the mitochondrial cox3 gene. Sequence alignment of the chloroplast genes in this chimeric region with the homologous sequences in GenBank indicate the presence of deletions, insertions, and single nucleotide polymorphisms in the coding sequences, resulting in putative, incomplete open reading frames or frame shift mutations. Hence, the authors speculate that this insertion may have occurred long ago in the evolution of garlic.
Development and validation of new SSR markers from expressed regions in the garlic genome
(Univ Sao Paulo, 2015-01) Sahin, Nihan; Simon, Philipp W.; Ipek, Meryem; Ipek, Ahmet; Cansev, Asuman; Uludağ Üniversitesi/Ziraat Fakültesi/Bahçe Bitkileri Bölümü.; 0000-0002-0609-3442; 0000-0002-9136-3186; 0000-0002-3353-846X; AAH-3233-2021; AAK-4655-2021; AAH-4255-2019; 16031208900; 6603912487; 26326677200
Only a limited number of simple sequence repeat (SSR) markers is available for the genome of garlic (Allium sativum L.) despite the fact that SSR markers have become one of the most preferred DNA marker systems. To develop new SSR markers for the garlic genome, garlic expressed sequence tags (ESTs) at the publicly available GarlicEST database were screened for SSR motifs and a total of 132 SSR motifs were identified. Primer pairs were designed for 50 SSR motifs and 24 of these primer pairs were selected as SSR markers based on their consistent amplification patterns and polymorphisms. In addition, two SSR markers were developed from the sequences of garlic cDNA-AFLP fragments. The use of 26 EST-SSR markers for the assessment of genetic relationship was tested using 31 garlic genotypes. Twenty six EST-SSR markers amplified 130 polymorphic DNA fragments and the number of polymorphic alleles per SSR marker ranged from 2 to 13 with an average of 5 alleles. Observed heterozygosity and polymorphism information content (PIC) of the SSR markers were between 0.23 and 0.88, and 0.20 and 0.87, respectively. Twenty one out of the 31 garlic genotypes were analyzed in a previous study using AFLP markers and the garlic genotypes clustered together with AFLP markers were also grouped together with EST-SSR markers demonstrating high concordance between AFLP and EST-SSR marker systems and possible immediate application of EST-SSR markers for fingerprinting of garlic clones. EST-SSR markers could be used in genetic studies such as genetic mapping, association mapping, genetic diversity and comparison of the genomes of Allium species.
Development of EST based SSR markers for garlic genome
(Int Soc Horticultural Science, 2012) Simon, Philipp W.; Wako, T.; İpek, Meryem; İpek, Ahmet; Cansev, Asuman; Şeniz, Vedat; Uludağ Üniversitesi/Ziraat Fakültesi/Bahçe Bitkileri Bölümü.; 0000-0002-3353-846X; AAH-3233-2021; AAH-4255-2019; 16031208900; 6603912487; 26326677200; 13604787100
Although it is time consuming and expensive to develop SSR markers, they have some advantages such as co-dominancy, reproducibility and high amount of polymorphic alleles as a PCR based marker system. For genetic and molecular studies in garlic, generally RAPD and AFLP markers have been utilized. However, development and use of SSR markers have been limited to few studies. In order to develop detailed genetic map and genetic studies, co-dominant marker systems like SSRs and SNPs are necessary in garlic. The purpose of this study was the development of SSR markers from expressed sequence tags (ESTs) derived from the genome of garlic. The SSR motifs in EST sequences were screened and it was revealed that SSR motifs are abundant in garlic ESTs. So far six SSR markers have been developed. EST based SSR markers could be used to map genes to garlic genetic maps directly and assessment of genetic diversity for the expressed regions of the garlic genome.
Differentially expressed genes in leaf, meristematic and flower tissues of garlic
(Int Soc Horticultural Science, 2012) Senalik, Douglas A.; Simon, Philipp W.; Wako, T.; İpek, Meryem S.; İpek, Ahmet; Aydoğan, Çiğdem; Uludağ Üniversitesi/Ziraat Fakültesi/Bahçe Bitkileri Bölümü.; 0000-0003-4884-5304; AAH-3233-2021; AAG-6532-2020; 16031208900; 6603912487; 55481474200
Differential gene expression analysis has been investigated to reveal important genes in many plant species. Identification of genes controlling metabolic pathways in garlic could contribute to the understanding of garlic genetic. In this study, transcript (mRNA) profile of differentially expressed genes was determined in leaf, meristematic and flower tissues of three genetically divers garlic clones at different developmental stages using cDNA-AFLP approach. In total, 352 differentially expressed transcript-derived fragments (TDFs) were evaluated from 20 primer combinations. While seven TDFs fragments expressed only in meristematic tissues, 30 TDFs expressed only in leaf tissues. Twenty seven fragments expressed in both meristematic and leaf tissues with intensity polymorphism and two fragments differentially expressed in flower tissues. BLAST analysis of these tissue specific expressed fragments revealed that some genes have significant similarities with previously determined sequences in the database of NCBI GenBank while some of them are unique to garlic genome. These tissue specific expressed genes can be used to develop tissue specific markers for garlic genome.
Genetic transformation of an Ac/Ds-based transposon tagging system in carrot (Daucus carota L.)
(ISHS, 2006-12) Masson, P.; Simon, Philipp W.; İpek, Ahmet; Bursa Uludağ Üniversitesi/Ziraat Fakültesi/Bahçe Bitkileri Bölümü.; 6603912487
Maize transposable elements, Activator (Ac) and Dissociation (Ds) have been transformed into several heterologous plant species and they have been successfully used to tag and clone genes in Arabidopsis, flax, petunia, tobacco, and tomato. To investigate the possibility of transposon tagging for subsequent cloning of carrot genes, carrot calli were transformed with a modified maize transposable element Activator-transposase (Ac-TPase) and Ds using an Agrobacterium-mediated transformation method. Ds excision was observed in the tissue culture-regenerated plants carrying both Ac-TPase and Ds. Analysis of Ds footprints in six plants demonstrated the occurrence of small deletions at the donor site. Reinsertion of Ds into new chromosomal sites was detected in the transgenic plants analysed and the analysis of sequences flanking Ds at the insertion sites using TAIL-PCR demonstrated that 37.5% of Ds insertions were into gene regions in the carrot genome. Although previous studies suggested that the autonomous Ac element may not be a suitable transposon for insertional mutagenesis in carrot, our results deduced that the Ac/Ds based two-element transposon tagging system can be another tool to mutagenise the carrot genome for the purpose of cloning carrot genes.
Testing the utility of matK and ITS DNA regions for discrimination of Allium species
(Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, 2013-11-27) Simon, Philipp W.; İpek, Meryem S.; İpek, Ahmet; Uludağ Üniversitesi/Ziraat Fakültesi/Bahçe Bitkileri Bölümü.; AAH-3233-2021; 16031208900; 6603912487
Molecular phylogenetic analysis of the genus Allium L. has been mainly based on the nucleotide sequences of the ITS region. In 2009, matK and rbcL were accepted as a 2-locus DNA barcode to classify plant species by the Consortium for the Barcode of Life Plant Working Group. The matK region was chosen as a DNA barcode because of its effective species discrimination power, high quality sequence recovery, and easy experimental procedures. Integration of matK sequences into Allium phylogeny could improve phylogenetic reconstruction of this genus. This study was carried out to test the utility of nucleotide sequences of matK for discrimination of Allium species and to compare topologies of the phylogenetic trees based on matK and ITS analyses. Topologies of the phylogenetic trees based on ITS and matK analyses were very similar but a few accessions were placed into distant phylogenetic groups. Neither ITS nor matK analyses were able to discriminate some closely related Allium species alone. However, we do not suggest the use of a concatenated data approach to increase resolving power of ITS and matK because of the presence of the paralogous sequences and different types of cytoplasm in different accessions of a species. Therefore, we can suggest use of the matK region as an additional tool for phylogenetic analysis in Allium because characterization of the nucleotide sequences of matK region was easier to recover and more cost-effective than those of the ITS region.