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Öğe Characterization of an unusual cytoplasmic chimera detected in bolting garlic clones(Amer Soc Horticultural Science, 2007) Ipek, Meryem; Ipek, Ahmet; Senalik, Douglas; Simon, Philipp W.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.Öğe Genetic characterization of Allium tuncelianum(Elsevier, 2008) Ipek, Meryem; Ipek, Ahmet; Simon, Philipp W.Allium tuncelianum (Kollman) Ozhatay, Matthew & Siraneci is a native species to the Eastern Anatolia. Its plant architecture resembles garlic (Allium sativum L.) and it has mild garlic odor and flavor. Because of these similarities between two species, A. tuncelianum has been locally called garlic. In addition, both A. tuncelianum and garlic has 16 chromosomes in their diploid genomes. Recently, A. tuncelianum has been suggested as the wild progenitor species of garlic. In this study, amplified fragment length polymorphisms (AFLP) markers and nucleotide sequence analysis of the internal transcribed spacer region (ITS) were used to assess genetic and phylogenetic relationships among A. tuncelianum, garlic and some other Allium species. AFLP analysis demonstrated that A. tuncelianum and garlic are genetically distinct and they are likely different species. Phylogenetic analyses based on the nucleotide sequence of ITS suggested that A. tuncelianum and garlic are distinct species and placed A. tuncelianum, garlic, Allium ampeloprasum and Allium scorodoprasum into the same clade in the neighbor joining dendrogram and in the consensus tree of parsimony analysis. However, A. tuncelianum was phylogenetically less related to garlic than either A. ampeloprasum or A. scorodoprasum, suggesting that A. tuncelianum may not be the immediate wild ancestor species of garlic. Further studies to generate hybrid progeny between A. tuncelianum and garlic (if possible) could provide more information on the homology between the chromosomes of A. tuncelianum and garlic and genetic relationships between these two species. (C) 2007 Elsevier B.V. All rights reserved.Öğe Molecular characterization of Kastamonu garlic: An economically important garlic clone in Turkey(Elsevier Science Bv, 2008) Ipek, Meryem; Ipek, Ahmet; Simon, Philipp W.Turkey is one of the major garlic producing country in the World and the significant amount of Turkey's production has been made using a garlic variety called Kastamonu garlic. Therefore, the purpose of this study was to assess genetic relationship of Kastamonu garlic with 20 previously characterized garlic clones collected from different regions of the world using AFLP and locus specific DNA markers. One putative Kastamonu garlic genotype was obtained from Taskopru district of Kastamonu province while another putative Kastamonu garlic genotype was collected from a local farmers' market in Bursa province and called as Kast-Taskopru and Kast-Bursa in this study, respectively. In the UPGMA dendrogram developed by using 120 AFLP markers, Kast-Taskopru was clustered closely over 97% similarity with other non-bolting garlic clones, P1493112, P1493118 and P1383824. This cluster was also supported by bootstrap analysis with 100% bootstrap value. All clones in this cluster also shared same alleles of gene specific DNA markers. However, Kast-Bursa shared 100% polymorphic AFLP markers and gene specific markers with a different garlic clone, P1497951 in another distinct cluster of UPGMA dendrogram and this clustering has also bootstrap value of 100%. These results suggest that Kastamonu garlic is not unique and garlic production in Turkey has been made using several garlic clones, even though most of this production has been sold as Kastamonu garlic due to its high popularity. Therefore, a standard Kastamonu garlic genotype needs to be determined by fingerprinting all available garlic clones cultivated in Kastamonu province and other regions of Turkey. (C) 2007 Elsevier B.V. All rights reserved.Öğe QTL mapping for fatty acid composition in olive oil using a high-density genetic map based on SNP markers(Tubitak Scientific & Technological Research Council Turkey, 2024) Kaya, Ali Can; Ipek, Meryem; Ipek, Ahmet; Gundogdu, Mehmet Ali; Tangu, Nesrin Aktepe; Duran, Sevin Teoman; Seker, MuratOlive ( Olea europaea L.) is an evergreen tree species that grows naturally in regions with Mediterranean climates. Its oil and fruits are commercially valuable. Olive oil contains high levels of omega-9 (oleic acid). Because the high percentage of oleic acid makes olive oil deterioration-resistant, the development of olive varieties containing high oleic acid is one of the major goals of olive breeding programs. Therefore, this study aimed to determine quantitative trait loci (QTL) affecting the fatty acid composition of olive oil. Thus, early selection of olive genotypes with a high oleic acid content can be possible. For the determination of QTLs affecting the fatty acid composition of olive oil, a high-density genetic map was developed using a segregating olive F1 population with 121 progeny and single- nucleotide polymorphism (SNP) markers based on genotyping by sequencing (GBS). The 2892.14 cM genetic map was composed of 3254 SNP markers on 23 chromosomes, with an average distance of 0.93 cM. For QTL analysis, the fatty acid composition of the segregating olive F1 population was determined using gas chromatography in two different years. A total of 31 QTLs were discovered in the first year and 29 in the second year. Common QTLs associated with fatty acid composition in both years have been found on chromosome 1, chromosome 2, and chromosome 10. For oleic acid, 11 QTLs were discovered in the first year and 12 QTLs in the second year. With these results, the QTLs linked to fatty acid synthesis in olive oil can be used as genetic resources for marker-assisted selection (MAS) in olive breeding studies.Öğe Sequence homology of polymorphic AFLP markers in garlic (Allium sativum L.)(2006) Ipek, Meryem; Ipek, Ahmet; Simon, Philipp W.Linkage mapping and genetic diversity studies with DNA markers in plant species assume that comigrating bands are identical, or at least that they have homologous sequences. To test this assumption in a plant with a large genome, sequence identities of 7 polymorphic amplified fragment length polymorphism (AFLP) markers of garlic, previously used to estimate similarity in genetic diversity studies, were characterized. Among 37 diverse garlic clones, 87 bands from these 7 polymorphisms were excised, amplicons were cloned, and 2 to 6 colonies were sequenced from each band, to yield a total of 191 DNA amplicons. Of these 87 bands, 83 bands (95.4%) contained AFLP amplicons that were identical or highly homologous to the typical marker of that band; only 4 bands contained amplicons with little homology to the same-sized amplicons of other garlic clones. Of these 83 bands, 64 (73.6%) contained only highly homologous amplicons (>90% sequence identity), whereas 19 (21.8%) contained both homologous and nonhomologous amplicons, with sequence identities less than 60%. Of the 37 nonhomologous amplicons identified, 25 (67.5%) differed in length from other amplicons in the band. Sequence conservation of AFLP amplicons followed patterns similar to phylogenetic relationships among garlic clones, making them useful for developing simple PCR-based markers in genetic mapping and diversity assessment. © 2006 NRC.
