Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Article Thrips parazitoiti Ceranisus (Hymenoptera: Eulophidae) cinsinin morfolojik yapı ve 28S D2 rDNA temelinde Türkiye’deki güncel taksonomik durumları(Türkiye Entomoloji Derneği, 2010) Doğanlar, Oğuzhan; Doğanlar, Mikdat; Frary, AnneÇalışma ile Mayıs 2006 ile Mayıs 2007 tarihleri arasında Güneydoğu Anadolu Bölgesi ve Akdeniz Bölgesi’nin doğusunda bulunan Ceranisus (Hymenoptera: Eulophidae) cinsi ve benzer diğer cinslerin genetik analizleri yapılarak, bu verilerin diğer thrips parazitoitlerinin morfolojik yapılarıyla mukayese edilip, türlerin kesin teşhislerinin yapılması amaçlanmıştır. Bu kapsamda, Hatay, Gaziantep, Adıyaman ve Şanlıurfa’da 38 farklı noktada örnekleme yapılmış ve 20 örnekleme noktasında toplam 143 adet (30 erkek; 113 dişi) Ceranisus cinsine giren tür toplanmıştır. Populasyon morfolojik özelliklerine göre 13 farklı gruba ayrılmıştır. Bu türlerin filogenetik ilişkileri DNA dizileri kullanılarak verilmiştir. Toplam 15 tür 28S D2 ribosomal DNA bölgesi kullanılarak analiz edilmiştir. Analiz sonucunda morfolojik olarak ayrılan 13 farklı tür grubundan 3 tanesinin genetik olarak farklı olduğu görülmüştür. Diğer türlerden ise 4 adetinin C. nr. lepidotus grubu oluşturdukları, 5 adet C. nr. bozovaensis’in ise kendi aralarında 2 farklı grup oluşturdukları belirlenmiştir. Sonuç olarak 3 adet yeni Ceranisus türü, bunun haricinde 3 adet farklı türü oluşturabilecek popülasyon genetik olarak belirlenmiştir.Article Citation - WoS: 20Citation - Scopus: 24Newly Developed Ssr Markers Reveal Genetic Diversity and Geographical Clustering in Spinach (spinacia Oleracea)(Springer Verlag, 2017) Göl, Şurhan; Göktay, Mehmet; Allmer, Jens; Doğanlar, Sami; Frary, AnneSpinach is a popular leafy green vegetable due to its nutritional composition. It contains high concentrations of vitamins A, E, C, and K, and folic acid. Development of genetic markers for spinach is important for diversity and breeding studies. In this work, Next Generation Sequencing (NGS) technology was used to develop genomic simple sequence repeat (SSR) markers. After cleaning and contig assembly, the sequence encompassed 2.5% of the 980 Mb spinach genome. The contigs were mined for SSRs. A total of 3852 SSRs were detected. Of these, 100 primer pairs were tested and 85% were found to yield clear, reproducible amplicons. These 85 markers were then applied to 48 spinach accessions from worldwide origins, resulting in 389 alleles with 89% polymorphism. The average gene diversity (GD) value of the markers (based on a GD calculation that ranges from 0 to 0.5) was 0.25. Our results demonstrated that the newly developed SSR markers are suitable for assessing genetic diversity and population structure of spinach germplasm. The markers also revealed clustering of the accessions based on geographical origin with clear separation of Far Eastern accessions which had the overall highest genetic diversity when compared with accessions from Persia, Turkey, Europe, and the USA. Thus, the SSR markers have good potential to provide valuable information for spinach breeding and germplasm management. Also they will be helpful for genome mapping and core collection establishment.Article Citation - WoS: 33Citation - Scopus: 44Relationship Between Geographical Origin, Seed Size and Genetic Diversity in Faba Bean (vicia Faba L.) as Revealed by Ssr Markers(Springer Verlag, 2017) Göl, Şurhan; Doğanlar, Sami; Frary, AnneFaba bean (Vicia faba L.) is an important legume species because of its high protein and starch content. Broad bean can be grown in different climatic conditions and is an ideal rotation crop because of the nitrogen fixing bacteria in its roots. In this work, 255 faba bean germplasm accessions were characterized using 32 SSR primers which yielded 302 polymorphic fragments. According to the results, faba bean individuals were divided into two main groups based on the neighbor-joining algorithm (r = 0.91) with some clustering based on geographical origin as well as seed size. Population structure was also determined and agreed with the dendrogram analysis in splitting the accessions into two subpopulations. Analysis of molecular variance (AMOVA) revealed high levels of within population genetic variation. Genetic similarity and geographical proximity were related with separation of European accessions from African and Asian ones. Interestingly, there was no significant difference between landrace (38%) and cultivar (40%) diversity indicating that genetic variability has not yet been lost due to breeding. A total of 44 genetically well-characterized faba bean individuals were selected for a core collection to be further examined for yield and nutritional traits.Article Citation - WoS: 30Citation - Scopus: 34Gddom: an Online Tool for Calculation of Dominant Marker Gene Diversity(Springer Verlag, 2017) Abuzayed, Mazen; El-Dabba, Nourhan; Frary, Anne; Doğanlar, SamiGene diversity (GD), also called polymorphism information content, is a commonly used measure of molecular marker polymorphism. Calculation of GD for dominant markers such as AFLP, RAPD, and multilocus SSRs is valuable for researchers. To meet this need, we developed a free online computer program, GDdom, which provides easy, quick, and accurate calculation of dominant marker GD with a commonly used formula. Results are presented in tabular form for quick interpretation. © 2016, Springer Science+Business Media New York.Article Citation - WoS: 6Citation - Scopus: 5Development of Genomic Simple Sequence Repeat Markers in Faba Bean by Next-Generation Sequencing(Springer Verlag, 2017) Abuzayed, Mazen A.; Göktay, Mehmet; Allmer, Jens; Doğanlar, Sami; Frary, AnneFaba bean (Vicia faba L.) is an important food legume crop with a huge genome. Development of genetic markers for faba bean is important to study diversity and for molecular breeding. In this study, we used Next Generation Sequencing (NGS) technology for the development of genomic simple sequence repeat (SSR) markers. A total of 14,027,500 sequence reads were obtained comprising 4,208 Mb. From these reads, 56,063 contigs were assembled (16,367 Mb) and 2138 SSRs were identified. Mono and dinucleotides were the most abundant, accounting for 57.5 % and 20.9 % of all SSR repeats, respectively. A total of 430 primer pairs were designed from contigs larger than 350 nucleotides and 50 primers pairs were tested for validation of SSR locus amplification. Nearly all (96 %) of the markers were found to produce clear amplicons and to be reproducible. Thirty-nine SSR markers were then applied to 46 faba bean accessions from worldwide origins, resulting in 161 alleles with 87.5 % polymorphism, and an average of 4.1 alleles per marker. Gene diversity (GD) of the markers ranged from 0 to 0.48 with an average of 0.27. Testing of the markers showed that they were useful in determining genetic relationships and population structure in faba bean accessions.Article Citation - WoS: 3Citation - Scopus: 3Genetic relationships among Eurasian Puccinellia distans genotypes(Elsevier Ltd., 2015) Bar, Cantuğ; Doğanlar, Sami; Frary, AnnePuccinellia distans (Jacq.) Parl. is a common grass species found throughout the world. It can grow in arid and saline environments as well as under toxic boron concentrations. In this work we performed sequence related amplified polymorphism (SRAP) marker analysis on 20 wild P. distans genotypes to understand the genetic relationships among different genotypes and subspecies. We tested 119 SRAP primer pairs and found that 43 were polymorphic. The molecular data were then analyzed to determine the genetic relationships and population structure of the genotypes. We were able to trace the origin of genotypes that were carried to distant locations or gathered for research purposes. We also found that geographical distance between genotypes was not an important determinant of genetic relationships as even distantly located Puccinellia genotypes were closely related. As P. distans is known to be tolerant to salinity stress and toxic mineral concentrations, the findings of this work can be used as a starting point for selection of genotypes that should be tested under such conditions.Article Citation - WoS: 6Citation - Scopus: 8Molecular Genetic Diversity in the Turkish National Melon Collection and Selection of a Preliminary Core Set(American Society for Horticultural Science, 2013) Frary, Anne; Şığva, Hasan Özgür; Tan, Ayfer; Taşkın, Tuncer; İnal, Abdullah; Mutlu, Sevgi; Haytaoğlu, Mehmet; Doğanlar, SamiTurkey is a secondary center of diversity for melon (Cucumis melo) and is home to a variety of regional morphotypes. This diversity is housed in a national germplasm repository with more than 500 accessions. Molecular genetic variability of 209 melon genotypes from 115 accessions of this collection was characterized using amplified fragment length polymorphisms (AFLPs). Ten AFLP primer combinations yielded 279 reproducible fragments, which were used for dendrogram and principal coordinate analyses. These analyses showed two major clusters of Turkish melons: one group contained highly similar genotypes (maximum Dice dissimilarity coefficient of 0.18), whereas the other group was genetically more diverse (maximum dissimilarity 0.41). Although average dissimilarity was low (0.13), a broad range of genetic diversity was observed in the collection. A marker allele richness strategy was used to select a core set of 20 genotypes representing the allelic diversity of the AFLP data. The core set had double the average diversity (0.26) of the entire set and represented the major morphotypes present in the collection. Molecular genetic diversity of the core set was further validated using simple sequence repeat marker data (116 polymorphic fragments), which confirmed that the selected core set retained high levels of molecular genetic diversity.Article Citation - WoS: 25Citation - Scopus: 25Application of Est-Ssrs To Examine Genetic Diversity in Eggplant and Its Close Relatives(TUBITAK, 2011) Tümbilen, Yeliz; Frary, Anne; Daunay, Marie Christine; Doğanlar, SamiWithin the genus Solanum, the term 'eggplant' encompasses several cultivated species that are used for food and, to a lesser extent, for medicine. Th e use of one common name to describe more than one species and the existence of many related wild species have led to taxonomic confusion which, in turn, have complicated analyses of evolutionary relationships and genetic diversity within this groups of species. A further challenge for eggplant research is that, despite the fact that the use of molecular markers for phylogenetic studies is well-established, very few studies have described the development of new markers for eggplant. In our work, genic microsatellite (SSR) markers were identified from an expressed sequence tag library of S. melongena and used for analysis of 47 accessions of eggplant and closely related species. Th e markers had very good polymorphism in the 18 species tested including 8 S. melongena accessions. Moreover, genetic analysis performed with these markers showed concordance with previous research and knowledge of eggplant domestication. Th ese markers are expected to be a valuable resource for studies of genetic relationships, fingerprinting, and gene mapping in eggplant.Article Citation - WoS: 34Citation - Scopus: 45Fine Mapping of Quantitative Trait Loci for Improved Fruit Characteristics From Lycopersicon Chmielewskii Chromosome 1(National Research Council of Canada, 2003) Frary, Anne; Doğanlar, Sami; Frampton, Anna; Fulton, Theresa M.; Uhlig, John W.; Yates, Heather E.; Tanksley, Steven D.The near-isogenic line (NIL) TA1150 contains a 56-cM introgression from Lycopersicon chmielewskii chromosome 1 and has several interesting phenotypic characteristics including fruit with orange color, high levels of soluble solids, thick pericarp, small stem scars, and good firmness. A set of overlapping recombinant lines (subNILs) was developed and field tested to fine map the quantitative trait loci (QTL) controlling these traits. The results indicated that the solids, pericarp thickness, and firmness QTL are distinct from the color locus. Several of the QTL mapped in this study, including the soluble-solids QTL, probably correspond to QTL mapped in other wild species of tomato. However, analysis of a set of TA523 subNILs containing complementary introgressions from Lycopesicon hirsutum chromosome 1 suggests that this wild species may contain a different locus for improved soluble solids. Thus, it might be possible to combine the L. chmielewskii and L. hirsutum alleles for these loci in a single line with the potential for extremely highly soluble solids. The TA1150 subNIL TA1688 contains the smallest introgression of the solids locus (approximately 19 cM), as well as the pericarp thickness and firmness QTL, with a yield that was equivalent to two of the three control lines. Isolation of recombinant subNILs from TA1688 should break the linkage between orange color and high solids and provide a small introgressed segment for marker-assisted breeding and genetic improvement of processing tomato.Article Citation - WoS: 76Citation - Scopus: 86Mapping Quantitative Trait Loci in Inbred Backcross Lines of Lycopersicon Pimpinellifolium (la1589)(National Research Council of Canada, 2002) Doğanlar, Sami; Frary, Anne; Ku, Hsin-mei; Tanksley, Steven D.Although tomato has been the subject of extensive quantitative trait loci (QTLs) mapping experiments, most of this work has been conducted on transient populations (e.g., F2 or backcross) and few homozygous, permanent mapping populations are available. To help remedy this situation, we have developed a set of inbred backcross lines (IBLs) from the interspecific cross between Lycopersicon esculentum cv. E6203 and L. pimpinellifolium (LA1589). A total of 170 BC2F1 plants were selfed for five generations to create a set of homozygous BC2F6 lines by single-seed descent. These lines were then genotyped for 127 marker loci covering the entire tomato genome. These IBLs were evaluated for 22 quantitative traits. In all, 71 significant QTLs were identified, 15% (11/71) of which mapped to the same chromosomal positions as QTLs identified in earlier studies using the same cross. For 48% (34/71) of the detected QTLs, the wild allele was associated with improved agronomic performance. A number of new QTLs were identified including several of significant agronomic importance for tomato production: fruit shape, firmness, fruit color, scar size, seed and flower number, leaf curliness, plant growth, fertility, and flowering time. To improve the utility of the IBL population, a subset of 100 lines giving the most uniform genome coverage and map resolution was selected using a randomized greedy algorithm as implemented in the software package MapPop (http://www.bio.unc.edu/faculty/vision/lab/ mappop/). The map, phenotypic data, and seeds for the IBL population are publicly available (http://soldb.cit.cornell.edu) and will provide tomato geneticists and breeders with a genetic resource for mapping, gene discovery, and breeding.