Browsing by Author "Tangu, Nesrin Aktepe"

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Assessment of genetic relationship among male and female fig genotypes using simple sequence repeat (SSR) markers
(Univ Agr Sci & Veterinary Med Cluj-Napoca, 2017-04-05) Tangu, Nesrin Aktepe; Durgut, Erdem; Ercişli, Sezai; Teoman, Sevin; İpek, Bayram; Ertürk, Ümran; Barut, Erdoğan; İpek, Ahmet; Uludağ Üniversitesi/Ziraat Fakültesi/Bahçe Bitkileri Bölümü.; 0000-0003-1469-6777; AAE-4675-2019; AAH-3233-2021; AAG-7343-2021; AAE-6913-2019; AAH-2551-2021; 57194462289; 16031208900; 7801661220; 26657823900; 6603912487
Fig (Ficus carica L.) is a traditional crop in Turkey and widely cultivated around the Mediterranean areas. The gynodioecious fig species is present in two sexual forms, i.e. the domesticated fig (female tree) and the caprifig (male tree). Caprifigs are crucial for high quality fig production and breeding while, the studies on assessment of genetic relationship among caprifigs is limited. The aim of this study was to determine genetic diversity among 45 caprifigs and 2 female figs collected from four provinces in Marmara and Aegean Sea Regions of Turkey using simple sequence repeat (SSR) markers. In this work, 24 SSR markers were tested, one was monomorphic and the remaining markers amplified 82 alleles. The number of polymorphic alleles per SSR marker ranged from 2 to 7. The observed heterozygosity (Ho) differed from 0.18 to 0.76 and expected heterozygosity (He) ranged between 0.24 and 0.81. The polymorphism information content (PIC) varied from 0.42 to 0.98. A UPGMA analysis based on Dice similarity matrix clustered fig genotypes into two main groups and similarly, STRUCTURE analysis placed fig genotypes into two different gene pools (K=2). Fig genotypes collected from the same region were not clustered together in a group indicating that the fig genotypes did not cluster on the basis of their collection sites. Our results demonstrated that caprifigs and female figs are not genetically distinct and they clustered together in a group. All fig genotypes had distinct SSR marker profiles suggesting that there were no synonyms or homonyms. These results revealed a high genetic variation among fig genotypes and 23 SSR markers were enough to discriminate all fig genotypes analysed in this study demonstrating that SSR marker system is suitable for genetic analysis in figs.
SNP discovery by GBS in olive and the construction of a high-density genetic linkage map
(Springer, 2016-06) Tangu, Nesrin Aktepe; Öz, Ayşe Tülin; İpek, Ahmet; Yılmaz, Kübra; Sıkıcı, Pelin; Bayraktar, Murat; İpek, Meryem; Gülen, Hatice; Uludağ Üniversitesi/Ziraat Fakültesi/Bahçe Bitkileri Bölümü.; Uludağ Üniversitesi/Fen-Edebiyat Fakültesi/Moleküler Biyoloji ve Genetik Bölümü.; 0000-0001-7586-3108; AAH-3233-2021; AFW-5375-2022; 6603912487; 57194530243; 57140804800; 57140106700; 16031208900; 6603211102
Genetic linkage maps are valuable tools for genetic, genomic, and crop breeding studies. Several genetic linkage maps were constructed for the olive (Olea europaea L.) genome, mainly using amplified fragment length polymorphisms (AFLPs) and simple sequence repeat (SSR) markers. However, AFLPs and SSR markers were not enough to develop a high-density olive linkage map. Genotyping-by-sequencing (GBS), a recently developed single-nucleotide polymorphism (SNP) identification methodology based on next-generation sequencing (NGS) technologies, has been demonstrated to be useful for the identification of a high number of SNP markers and the construction of high-density genetic linkage maps. In the present study, we identified a total of 10,941 SNPs from a cross between the olive cultivars 'Gemlik' and 'Edincik Su' using GBS and de novo SNP discovery implemented in the computer program "Stacks." A high-density genetic linkage map for the olive genome was constructed using 121 cross-pollinated full-sib F1 progeny and 5643 markers (21 SSRs, 203 AFLPs, and 5736 SNPs). This linkage map was composed of 25 linkage groups, covering 3049 cM of the olive genome, and the mean distance between the flanking markers was 0.53 cM. To the best of our knowledge, this map is the most saturated genetic linkage map in olive to date. We demonstrated that GBS is a valuable tool for the identification of thousands of SNPs for the construction of a saturated genetic linkage map in olive. The high-density genetic map developed in this study is a useful tool for locating quantitative trait loci and other economically important traits in the olive genome.
SSR analysis demonstrates that olive production in the southern Marmara Region in Turkey uses a single genotype
(Funpec-Editora, 2009) Öz, Ayşe Tülin; Tangu, Nesrin Aktepe; İpek, Ahmet; Barut, Erdoğan; Gülen, Hatice; İpek, Meryem; Uludağ Üniversitesi/Ziraat Fakültesi/Bahçe Bitkileri Bölümü.; AAE-6913-2019; AAH-3233-2021; 6603912487; 26657823900; 6603211102; 16031208900
The southern Marmara region in Turkey was surveyed to determine the olive cultivars that are used for olive production. Genetic diversity analysis using simple sequence repeat (SSR) markers indicated that the cultivar Gemlik is the major olive cultivar grown in this region, while other olive cultivars are grown only for use as pollinators of Gemlik or for growers' own exotic consumption. Although the quality of Gemlik is widely accepted in Turkey, its tendency toward alternate bearing is a major drawback. Twenty-four genotypes were selected within the cultivar Gemlik because of their tolerance to alternate bearing. These selected genotypes have the same SSR alleles as Gemlik, making them good candidates for developing a Gemlik olive with reduced alternate bearing. About 8% of samples did not share the same SSR alleles with Gemlik, though these genotypes were identified as Gemlik by the growers. Some other standard cultivars that are grown in other regions of Turkey were mistakenly called Gemlik in this region, probably due to the popularity of this cultivar in the southern Marmara region. In conclusion, as indicated by SSR analysis, Gemlik has become the standard cultivar in this region; future research should be focused on techniques to improve the production and quality of table olives and olive oil from this cultivar.
Transcriptome-based SNP discovery by GBS and the construction of a genetic map for olive
(Springer, 2017-02-07) Ercişli, Sezai; Tangu, Nesrin Aktepe; İpek, Ahmet; İpek, Meryem; Uludağ Üniversitesi/Ziraat Fakültesi/Bahçe Bitkileri Bölümü.; AAH-3233-2021; 6603912487; 16031208900
Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique. An analysis was done for 125 olive DNA samples (123 DNA samples from a cross-pollinated F-1 mapping population, and two samples from parents). From 45 to 66% of Illumina reads from GBS analysis were aligned to the olive transcriptome. A total of 22,033 transcriptome-based SNP markers were identified, and 3384 of these were mapped in the olive genome. The genetic linkage map constructed in this study consists of 1 cleaved amplified polymorphic sequence (CAPS), 19 SSR, and 3384 transcriptome-based SNP markers. The map covers 3340.8 cM of the olive genome in 23 linkage groups, with the length of the linkage groups ranging from 55.6 to 248.7 cM. Average map distance between flanking markers was 0.98 cM. This genetic linkage map is a saturated genetic map and will be a useful tool for the localization of quantitative trait loci (QTLs) and gene(s) of interest and for the identification of candidate genes for economically important traits.